Publications without Fulltext
Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
Browse
232 results
Filters
Advanced Search
Filter by
Settings
Search Results
Publication Metadata only 3D printed styrax liquidus (liquidambar orientalis miller)-loaded poly (l-lactic acid)/chitosan based wound dressing material: fabrication, characterization, and biocompatibility results(Elsevier, 2023) Cakmak, Hanife Yuksel; Ege, Hasan; Yilmaz, Senanur; Agturk, Gokhan; Enguven, Gozde; Sarmis, Abdurrahman; Cakmak, Zeren; Gunduz, Oguzhan; Ege, Zeynep Ruya; Yöntem, Fulya Dal; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of MedicineThe medicinal plant of Styrax liquidus (ST) (sweet gum balsam) which extracted from Liquidambar orientalis Mill tree, was loaded into the 3D printed polylactic acid (PLA)/chitosan (CS) based 3D printed scaffolds to investigate its wound healing and closure effect, in this study. The morphological and chemical properties of the ST loaded 3D printed scaffolds with different concentrations (1 %, 2 %, and 3 % wt) were investigated by Scanning Electron Microscopy (SEM) and Fourier Transform Infrared Spectroscopy (FT-IR), respectively. In addition, the me-chanical and thermal properties of the materials were investigated by Tensile test and Differential Scanning Calorimetry (DSC), respectively. The antimicrobial activities of the ST loaded 3D printed scaffolds and their incubation media in the PBS (pH 7.4, at 37 degrees C for 24 h) were investigated on two Gram-positive and two Gram -negative standard pathogenic bacteria with the agar disc diffusion method. The colorimetric MTT assay was used to determine the cell viability of human fibroblast cells (CCD-1072Sk) incubated with free ST, ST loaded, and unloaded 3D printed scaffolds. The 1 % and 2 % (wt) ST loaded PLA/CS/ST 3D printed scaffolds showed an increase in the cell number. Annexin V/PI double stain assay was performed to test whether early or late apoptosis was induced in the PLA/CS/1 % ST and PLA/CS/2 % ST loaded groups and the results were consistent with the MTT assay. Furthermore, a wound healing assay was carried out to investigate the effect of ST loaded 3D printed scaffolds on wound healing in CCD-1072Sk cells. The highest wound closure compared to the control group was observed on cells treated with PLA/CS/1 % ST for 72 h. According to the results, novel biocompatible ST loaded 3D printed scaffolds with antimicrobial effect can be used as wound healing material for potential tissue engineering applications.Publication Metadata only Author correction: combined inhibition of BET family proteins and histone deacetylases as a potential epigenetics-based therapy for pancreatic ductal adenocarcinoma(Nature Research, 2024) Mazur PK, Herner A, Mello SS, Wirth M, Hausmann S, Sánchez-Rivera FJ, Lofgren SM, Kuschma T, Hahn SA, Vangala D, Trajkovic-Arsic M, Gupta A, Heid I, Noël PB, Braren R, Kleeff J, Sipos B, Sayles LC, Heikenwalder M, Heßmann E, Ellenrieder V, Esposito I, Jacks T, Bradner JE, Khatri P, Sweet-Cordero EA, Attardi LD, Schmid RM, Schneider G, Sage J, Siveke JT.; Koç University HospitalIn the originally published version of this article, there were errors in the histological sections depicted in Supplementary Figs. 4 and 10. Specifically: In Supplementary Fig. 4, the image of the Ki67 immunohistochemistry (IHC) for the Gemcitabine+JQ1 group was incorrect In Supplementary Fig. 10, the pSTAT3 image for the IHC for the JQ1 group was incorrect In Supplementary Fig. 10, Ki67 and MYC IHC images for JQ1 and JQ1+SAHA were swapped In Supplementary Fig. 4, the image of the Ki67 immunohistochemistry (IHC) for the Gemcitabine+JQ1 group was incorrect In Supplementary Fig. 10, the pSTAT3 image for the IHC for the JQ1 group was incorrect In Supplementary Fig. 10, Ki67 and MYC IHC images for JQ1 and JQ1+SAHA were swapped The original data were available and these errors have been corrected in the Supplementary Information accompanying this notice. Additionally, the authors wish to clarify that the Sirius Red staining for the control and JQ1 groups were identical in both Supplementary Figs. 4 and 10 because the control mice (JQ1 only or control treatment) were shared between experiments. To avoid confusion, the sections depicting Sirius Red staining for the control and JQ1 groups in Supplementary Fig. 4 were replaced with alternative sections from the same respective samplesPublication Metadata only Characterization and comparison of insulinoma tumor model and pancreatic damage caused by the tumor, and identification of possible markers(Springer Science and Business Media B.V., 2024) Karatug Kacar, Ayse; Aylar, Dilara; Celikten, Mert; Bolkent, Sehnaz; Bulutay, Pınar; School of MedicineInsulinoma is a neuroendocrine tumor. It arises from the uncontrolled proliferation of pancreatic β cells. In this study, we created an insulinoma tumor model in nude mice. INS-1 cells were injected in two different ways, subcutaneously (S.C.) or intraperitoneally (I.P.). Body weight, tumor weight, and size were measured. ELISA kits were used analyze to Glucose, insulin, and CA19-9 levels in serum, pancreas, and tumor tissues. KCNN4, KCNK1, GLUT2, IR, HSP70, HSF1, and HSP90 levels were analyzed by western blotting of membrane and/or cytosolic fractions of tumor and pancreas tissue. Tumor formation occurred in nude mice, but it did not occur in Wistar albino rats. The tumor has neuroendocrine cell morphology. Insulin and CA19-9 levels increased in pancreas tissue. In tumor tissue, KCNN4 levels were higher in both membrane and cytosolic fractions, while KCNK1 levels were lower in the membrane fraction of the S.C. group. HSP70 levels were also lower in the S.C. group. In pancreas tissue, KCNK1 levels were lower in the membrane fraction of the S.C. and I.P. groups. GLUT2 levels increased in both groups according to the control group, while IR levels decreased in the S.C. group compared to the control group. However, HSF1 levels increased in the I.P. group, while HSP90 decreased in the S.C. group in pancreatic tissues. The S.C. group is a more suitable insulinoma tumor model. KCNN4, KCNK1, and HSP70 proteins may be important biomarkers in the diagnosis and treatment of insulinoma.Publication Metadata only Shared proteins and pathways of cardiovascular and cognitive diseases: relation to vascular cognitive impairment(Amer Chemical Soc, 2024) Picon-Pages, Pol; Garcia-Elias, Anna; Tajes, Marta; Munoz, Francisco J.; Oliva, Baldomero; Garcia-Ojalvo, Jordi; Barbu, Eduard; Vicente, Raul; Nattel, Stanley; Ois, Angel; Puig-Pijoan, Albert; Department of Chemical and Biological Engineering;Department of Computer Engineering; Zeylan, Melisa Ece; Şenyüz, Simge; Keskin, Özlem; Gürsoy, Attila; Graduate School of Sciences and Engineering; College of EngineeringOne of the primary goals of systems medicine is the detection of putative proteins and pathways involved in disease progression and pathological phenotypes. Vascular cognitive impairment (VCI) is a heterogeneous condition manifesting as cognitive impairment resulting from vascular factors. The precise mechanisms underlying this relationship remain unclear, which poses challenges for experimental research. Here, we applied computational approaches like systems biology to unveil and select relevant proteins and pathways related to VCI by studying the crosstalk between cardiovascular and cognitive diseases. In addition, we specifically included signals related to oxidative stress, a common etiologic factor tightly linked to aging, a major determinant of VCI. Our results show that pathways associated with oxidative stress are quite relevant, as most of the prioritized vascular cognitive genes and proteins were enriched in these pathways. Our analysis provided a short list of proteins that could be contributing to VCI: DOLK, TSC1, ATP1A1, MAPK14, YWHAZ, CREB3, HSPB1, PRDX6, and LMNA. Moreover, our experimental results suggest a high implication of glycative stress, generating oxidative processes and post-translational protein modifications through advanced glycation end-products (AGEs). We propose that these products interact with their specific receptors (RAGE) and Notch signaling to contribute to the etiology of VCI.Publication Metadata only Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes(WILEY, 2024) Department of Molecular Biology and Genetics; Begar, Efe; Seyrek, Ece; Karalar, Elif Nur Fırat; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of SciencesCentriolar satellites are ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.Publication Metadata only SETD3 regulates endoderm differentiation of mouse embryonic stem cells through canonical Wnt signaling pathway(Wiley, 2024) Alganatay, Ceren; Balbasi, Emre; Sezginmert, Dersu; Cizmecioglu, Nihal Terzi; Department of Chemical and Biological Engineering; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; College of EngineeringWith self-renewal and pluripotency features, embryonic stem cells (ESCs) provide an invaluable tool to investigate early cell fate decisions. Pluripotency exit and lineage commitment depend on precise regulation of gene expression that requires coordination between transcription (TF) and chromatin factors in response to various signaling pathways. SET domain-containing 3 (SETD3 Delta) is a methyltransferase that can modify histones in the nucleus and actin in the cytoplasm. Through an shRNA screen, we previously identified SETD3 as an important factor in the meso/endodermal lineage commitment of mouse ESCs (mESC). In this study, we identified SETD3-dependent transcriptomic changes during endoderm differentiation of mESCs using time-course RNA-seq analysis. We found that SETD3 is involved in the timely activation of the endoderm-related gene network. The canonical Wnt signaling pathway was one of the markedly altered signaling pathways in the absence of SETD3. The assessment of Wnt transcriptional activity revealed a significant reduction in Setd3-deleted (setd3 increment ) mESCs coincident with a decrease in the nuclear pool of the key TF beta-catenin level, though no change was observed in its mRNA or total protein level. Furthermore, a proximity ligation assay (PLA) found an interaction between SETD3 and beta-catenin. We were able to rescue the differentiation defect by stably re-expressing SETD3 or activating the canonical Wnt signaling pathway by changing mESC culture conditions. Our results suggest that alterations in the canonical Wnt pathway activity and subcellular localization of beta-catenin might contribute to the endoderm differentiation defect of setd3 Delta increment mESCs.Publication Metadata only Tracking data highlight the importance of human-induced mortality for large migratory birds at a flyway scale(Elsevier Ltd, 2024) Serratosa, Juan; Oppel, Steffen; Rotics, Shay; Santangeli, Andrea; Butchart, Stuart H.M.; Cano-Alonso, Luis S.; Tellería, Jose Luis; Kemp, Ryno; Nicholas, Aaron; Kalvāns, Aigars; Galarza, Aitor; Franco, Aldina M.A.; Andreotti, Alessandro; Kirschel, Alexander N.G.; Ngari, Alex; Soutullo, Alvaro; Bermejo-Bermejo, Ana; Botha, Andre J.; Ferri, Andrea; Evangelidis, Angelos; Cenerini, Anna; Stamenov, Anton; Hernández-Matías, Antonio; Aradis, Arianna; Grozdanov, Atanas P.; Rodríguez, Beneharo; Cerecedo-Iglesias, Catuxa; Kassara, Christina; Barboutis, Christos; Bracebridge, Claire; García-Ripollés, Clara; Kendall, Corinne J.; Denac, Damijan; Schabo, Dana G.; Barber, David R.; Popov, Dimitar V.; Dobrev, Dobromir D.; Mallia, Egidio; Kmetova-Biro, Elena; Álvarez, Ernesto; Buechley, Evan R.; Bragin, Evgeny A.; Cordischi, Fabrizio; Zengeya, Fadzai M.; Monti, Flavio; Mougeot, Francois; Tate, Gareth; Stoyanov, Georgi; Dell'Omo, Giacomo; Lucia, Giuseppe; Gradev, Gradimir; Ceccolini, Guido; Friedemann, Guilad; Bauer, Hans-Günther; Kolberg, Holger; Peshev, Hristo; Catry, Inês; Øien, Ingar J.; Alanís, Isidoro Carbonell; Literák, Ivan; Pokrovsky, Ivan; Ojaste, Ivar; Østnes, Jan E.; de la Puente, Javier; Real, Joan; Guilherme, João L.; González, José C.; Fernández-García, José M.; Gil, Juan Antonio; Terraube, Julien; Poprach, Karel; Aghababyan, Karen; Klein, Katharina; Bildstein, Keith L.; Wolter, Kerri; Janssens, Kjell; Kittelberger, Kyle D.; Thompson, Lindy J.; AlJahdhami, Mansoor H.; Galán, Manuel; Tobolka, Marcin; Posillico, Mario; Cipollone, Mario; Gschweng, Marion; Strazds, Māris; Boorman, Mark; Zvidzai, Mark; Acácio, Marta; Romero, Marta; Wikelski, Martin; Schmidt, Matthias; Sarà, Maurizio; McGrady, Michael J.; Dagys, Mindaugas; Mackenzie, Monique L.; Al Taq, Muna; Mgumba, Msafiri P.; Virani, Munir Z.; Kassinis, Nicolaos I.; Borgianni, Nicolò; Thie, Nikki; Tsiopelas, Nikos; Anglister, Nili; Farwig, Nina; Sapir, Nir; Kleven, Oddmund; Krone, Oliver; Duriez, Olivier; Spiegel, Orr; Al Nouri, Osama; López-López, Pascual; Byholm, Patrik; Kamath, Pauline L.; Mirski, Paweł; Palatitz, Peter; Serroni, Pietro; Raab, Rainer; Buij, Ralph; Žydelis, Ramūnas; Nathan, Ran; Bowie, Rauri C.K.; Tsiakiris, Rigas; Hatfield, Richard Stratton; Harel, Roi; Kroglund, Rolf T.; Efrat, Ron; Limiñana, Ruben; Javed, Salim; Marinković, Saša P.; Rösner, Sascha; Pekarsky, Sasha; Kapila, Shiv R.; Marin, Simeon A.; Krejčí, Šimon; Giokas, Sinos; Tumanyan, Siranush; Turjeman, Sondra; Krüger, Sonja C.; Ewing, Steven R.; Stoychev, Stoycho; Nikolov, Stoyan C.; Qaneer, Tareq E.; Spatz, Theresa; Hadjikyriakou, Thomas G.; Mueller, Thomas; Katzner, Todd E.; Aarvak, Tomas; Veselovský, Tomáš; Nygård, Torgeir; Mellone, Ugo; Väli, Ülo; Sellis, Urmas; Urios, Vicente; Nemček, Vladimír; Arkumarev, Volen; Getz, Wayne M.; Fiedler, Wolfgang; Van den Bossche, Willem; Lehnardt, Yael; Jones, Victoria R.; Department of Molecular Biology and Genetics; Şekercioğlu, Çağan Hakkı; Department of Molecular Biology and Genetics; College of SciencesHuman-induced direct mortality affects huge numbers of birds each year, threatening hundreds of species worldwide. Tracking technologies can be an important tool to investigate temporal and spatial patterns of bird mortality as well as their drivers. We compiled 1704 mortality records from tracking studies across the African-Eurasian flyway for 45 species, including raptors, storks, and cranes, covering the period from 2003 to 2021. Our results show a higher frequency of human-induced causes of mortality than natural causes across taxonomic groups, geographical areas, and age classes. Moreover, we found that the frequency of human-induced mortality remained stable over the study period. From the human-induced mortality events with a known cause (n = 637), three main causes were identified: electrocution (40.5 %), illegal killing (21.7 %), and poisoning (16.3 %). Additionally, combined energy infrastructure-related mortality (i.e., electrocution, power line collision, and wind-farm collision) represented 49 % of all human-induced mortality events. Using a random forest model, the main predictors of human-induced mortality were found to be taxonomic group, geographic location (latitude and longitude), and human footprint index value at the location of mortality. Despite conservation efforts, human drivers of bird mortality in the African-Eurasian flyway do not appear to have declined over the last 15 years for the studied group of species. Results suggest that stronger conservation actions to address these threats across the flyway can reduce their impacts on species. In particular, projected future development of energy infrastructure is a representative example where application of planning, operation, and mitigation measures can enhance bird conservation. © 2024 The US Geological Survey, The Author(s)Publication Metadata only Effects of alprazolam and haloperidol on thyroglobulin, antithyroglobulin, anti thyroid peroxidase and TSH in Rat(Walter De Gruyter Gmbh, 2018) Samadi, Afshin; Ansari, Mohammad Hassan Khadem; Ulusu, Nuriye Nuray; Faculty Member; School of Medicine; 6807Background: A large number of psychotropic drugs can interfere with the thyroid physiology, function and autoimmunity. Objective: The aim of the present study was to investigate the effects of alprazolam and haloperidol on thyroglobulin, antithyroglobulin (aTg), antithyroid peroxidase, and thyroid stimulating hormone levels on rats. Materials and Methods: First group of adult male Wistar rats was the control, second group received 0.5 mg kg(-1) haloperidol in physiological saline and the third group received 0.5 mg kg(-1) alprazolam, via gastric gavage once daily for 28 days. Plasma levels of all thyroid function tests were measured with chemiluminescent assay. Results: We have investigated a decrease in aTg amounts of control group (5.461 +/- 0.718) compared with drug treated rats with alprazolam (1.433 +/- 0.225) and haloperidol (1.21 +/- 0.228). (P-aTg = 0.00([ALP]), P-aTg = 0.01([HAL])). Although there were not any change in thyroglobulin levels in the haloperidol treated groups (0.9583 +/- 0.014) relative to control group (0.975 +/- 0.015); but in opposition Tg levels decreased significantly in response to alprazolam (0.36 +/- 0.16) compared with the control group (0.975 +/- 0.015), p-values are (P-Tg = 0. 001([ALP])), (P-Tg = 0. 021([HAL])). Conclusion: We found that these two drugs may interfere with the thyroid physiology and metabolism.Publication Metadata only Effects of ligand binding upon flexibility of proteins(Wiley-Blackwell, 2015) Department of Chemical and Biological Engineering; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; 179997Binding of a ligand on a protein changes the flexibility of certain parts of the protein, which directly affects its function. These changes are not the same at each point, some parts become more flexible and some others become stiffer. Here, an equation is derived that gives the stiffness map for proteins. The model is based on correlations of fluctuations of pairs of points in proteins, which may be evaluated at different levels of refinement, ranging from all atom molecular dynamics to general elastic network models, including the simplest case of isotropic Gaussian Network Model. The latter is used, as an example, to evaluate the changes of stiffness upon dimerization of ACK1. Proteins 2015; 83:805-808. (c) 2015 Wiley Periodicals, Inc.Publication Metadata only A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for pi-stacking interactions: dimers of benzene and planar C-6(Springer, 2015) Department of Chemistry; Yurtsever, İsmail Ersin; Faculty Member; Department of Chemistry; College of Sciences; 7129A practical mixed basis set was developed to facilitate accurate calculations of potential energy surfaces for pi-stacking interactions. Correlation consistent basis sets (cc-PVXZ) were augmented by p-type Gaussian functions placed above and below the planes of C-6 moieties. Moller-Plesset (MP2, SCS-MP2) and coupled cluster [CCSD(T)] calculations show that such generated basis sets provide an accurate description of p-stacking systems with favorable computation times compared to the standard augmented basis sets. The addition of these off-center functions eliminates the linear dependence of the augmented basis sets, which is one of the most encountered numerical problems during calculation of the oligomers of polyaromatic hydrocarbons (PAH). In this work, we present a comparative study of the general characteristics of the potential energy surfaces for the parallel stacked and T-shape conformations of benzene and planar C6 clusters, using a combination of cc-PVXZ and our optimized functions. We discuss properties, such as the depth and curvature of the potential functions, short and long distance behavior, and the frictional forces between two model monomers.