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Publication Open Access Acute inhibition of centriolar satellite function and positioning reveals their functions at the primary cilium(Public Library of Science, 2020) Department of Molecular Biology and Genetics; Karalar, Elif Nur Fırat; Faculty Member; Department of Molecular Biology and Genetics; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/A; 206349Centriolar satellites are dynamic, membraneless granules composed of over 200 proteins. They store, modify, and traffic centrosome and primary cilium proteins, and help to regulate both the biogenesis and some functions of centrosomes and cilium. In most cell types, satellites cluster around the perinuclear centrosome, but their integrity and cellular distribution are dynamically remodeled in response to different stimuli, such as cell cycle cues. Dissecting the specific and temporal functions and mechanisms of satellites and how these are influenced by their cellular positioning and dynamics has been challenging using genetic approaches, particularly in ciliated and proliferating cells. To address this, we developed a chemical-based trafficking assay to rapidly and efficiently redistribute satellites to either the cell periphery or center, and fuse them into stable clusters in a temporally controlled way. Induced satellite clustering at either the periphery or center resulted in antagonistic changes in the pericentrosomal levels of a subset of proteins, revealing a direct and selective role for their positioning in protein targeting and sequestration. Systematic analysis of the interactome of peripheral satellite clusters revealed enrichment of proteins implicated in cilium biogenesis and mitosis. Importantly, induction of peripheral satellite targeting in ciliated cells revealed a function for satellites not just for efficient cilium assembly but also in the maintenance of steady-state cilia and in cilia disassembly by regulating the structural integrity of the ciliary axoneme. Finally, perturbing satellite distribution and dynamics inhibited their mitotic dissolution, and mitotic progression was perturbed only in cells with centrosomal satellite clustering. Collectively, our results for the first time showed a direct link between satellite functions and their pericentrosomal clustering, suggested new mechanisms underlying satellite functions during cilium assembly, and provided a new tool for probing temporal satellite functions in different contextsPublication Open Access Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions(Wiley, 2017) Department of Chemical and Biological Engineering; Hacısüleyman, Aysima; Erman, Burak; Faculty Member; Department of Chemical and Biological Engineering; College of Engineering; N/A; 179997A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink-source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence.Publication Open Access Coagulation measurement from whole blood using vibrating optical fiber in a disposable cartridge(Society of Photo-optical Instrumentation Engineers (SPIE), 2017) Çivitci, Fehmi; Barış, İbrahim; Yaralıoğlu, Göksenin; Department of Electrical and Electronics Engineering; Yaras, Yusuf Samet; Gündüz, Ali Bars; Sağlam, Gökhan; Ölçer, Selim; Ürey, Hakan; Other; Faculty Member; Department of Electrical and Electronics Engineering; College of Engineering; N/A; N/A; N/A; N/A; 8579In clinics, blood coagulation time measurements are performed using mechanical measurements with blood plasma. Such measurements are challenging to do in a lab-on-a-chip (LoC) system using a small volume of whole blood. Existing LoC systems use indirect measurement principles employing optical or electrochemical methods. We developed an LoC system using mechanical measurements with a small volume of whole blood without requiring sample preparation. The measurement is performed in a microfluidic channel where two fibers are placed inline with a small gap in between. The first fiber operates near its mechanical resonance using remote magnetic actuation and immersed in the sample. The second fiber is a pick-up fiber acting as an optical sensor. The microfluidic channel is engineered innovatively such that the blood does not block the gap between the vibrating fiber and the pick-up fiber, resulting in high signal-to-noise ratio optical output. The control plasma test results matched well with the plasma manufacturer's datasheet. Activated-partial-thromboplastin-time tests were successfully performed also with human whole blood samples, and the method is proven to be effective. Simplicity of the cartridge design and cost of readily available materials enable a low-cost point-of-care device for blood coagulation measurements.Publication Open Access Combined metabolic activators therapy ameliorates liver fat in nonalcoholic fatty liver disease patients(EMBO Press, 2021) Altay, O.; Arif, M.; Li, X.; Yang, H.; Fredolini, C.; Kim, W.; Schwenk, J.M.; Zhang, C.; Shoaie, S.; Nielsen, J.; Uhlen, M.; Boren, J.; Mardinoğlu, A.; Zeybel, Müjdat; Ural, Dilek; Gönenli, Mehmet Gökhan; Akyıldız, Murat; Kurtoğlu, Burçin Sağlam; Faculty Member; Faculty Member; Teaching Faculty; Faculty Member; School of Medicine; Koç University Hospital; 214694; 1057; 350445; 123080; N/ANonalcoholic fatty liver disease (NAFLD) refers to excess fat accumulation in the liver. In animal experiments and human kinetic study, we found that administration of combined metabolic activators (CMAs) promotes the oxidation of fat, attenuates the resulting oxidative stress, activates mitochondria, and eventually removes excess fat from the liver. Here, we tested the safety and efficacy of CMA in NAFLD patients in a placebo-controlled 10-week study. We found that CMA significantly decreased hepatic steatosis and levels of aspartate aminotransferase, alanine aminotransferase, uric acid, and creatinine, whereas found no differences on these variables in the placebo group after adjustment for weight loss. By integrating clinical data with plasma metabolomics and inflammatory proteomics as well as oral and gut metagenomic data, we revealed the underlying molecular mechanisms associated with the reduced hepatic fat and inflammation in NAFLD patients and identified the key players involved in the host-microbiome interactions. In conclusion, we showed that CMA can be used to develop a pharmacological treatment strategy in NAFLD patients.Publication Open Access Correspondence: importance of the validated serum biochemistry and hemogram parameters for rapid diagnosis and to prevent false negative results during COVID-19 pandemic(Wiley, 2020) Ulusu, Nuriye Nuray; Aydemir, Duygu; Faculty Member; PhD Student; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); School of Medicine; 6807; N/ACOVID-19 threatens millions of lives, especially elderly population and people with chronic diseases including diabetes, hypertension, cancer, and cardiovascular diseases. Rapid and effective diagnoses are vital for the isolation of infected people and starting treatment immediately to stop the spread of COVID-19 virus. Bioinformatics techniques such as artificial intelligence should be used for collecting the hemogram and serum biochemistry data of all COVID-19- infected people worldwide, even they do not show severe symptoms. These data may help find a biomarker that can be used in combination with the CT results for rapid and accurate diagnosis of COVID-19.Publication Open Access Effects of the endocrine disrupting chemical, DEHP, on the mitochondrial metabolism of the detoxification organs(Wiley, 2019) N/A; N/A; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Health Sciences; School of MedicinePublication Open Access Evaluation of the performance of sysmex XN-3100 automated hematology analyzer regarding the sysmex XE-2100 and microscopic examination(De Gruyter, 2021) Palaoğlu, Kerim Erhan; İncir, Said; Faculty Member; Koç University HospitalObjectives: we performed a verification study of the Sysmex XN-3100 hematology analyzer in comparison with the XE-2100 according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI) and the International Council for Standardization in Hematology (ICSH). Materials and methods: blood samples and quality control materials were used for precision. For comparison, we used the current XE-2100 as the comparative method and analyzed 540 blood samples. The Passing-Bablok and Bland-Altman tests were performed according to the CLSI EP09-A3 and a carryover study was performed according to the CLSI H26-A2 guidelines. The flagging performance of the two analyzers was compared, using two experienced laboratory technicians as the reference method. Results: the Sysmex XN-3100 demonstrated high levels of precision for most parameters. For the comparison analysis, all parameters, except for MCHC, monocytes and basophils were within the systematic error limits of desirable biological variability criterion (SeDBV). The carryover was less than 0.4% for all parameters. The flagging performance of the XN-3100 was satisfactory and the overall efficiency was high. Conclusions: the XN-3100 not only showed a strong correlation and agreement with the XE-2100 but also displayed a comparable analytical sensitivity, and increased specificity, which may result in an improved turnaround time and throughpu.Publication Open Access Impact of the butylparaben on the glutathione-dependent enzyme metabolism(Wiley, 2019) Öztaşçı, Burcu; Barlas, Nurhayat; N/A; Aydemir, Duygu; Ulusu, Nuriye Nuray; PhD Student; Faculty Member; School of Medicine; N/A; 6807Publication Open Access Machine learning helps identify CHRONO as a circadian clock component(Public Library of Science, 2014) Anafi, Ron C.; Lee, Yoo; Sato, Trey K.; Venkataraman, Anand; Ramanathan, Chidambaram; Hughes, Michael E.; Baggs, Julie E.; Growe, Jacqueline; Liu, Andrew C.; Kim, Junhyong; Hogenesch, John B.; Kavaklı, İbrahim Halil; Faculty Member; College of Engineering; 40319Over the last decades, researchers have characterized a set of ‘‘clock genes’’ that drive daily rhythms in physiology and behavior. This arduous work has yielded results with far-reaching consequences in metabolic, psychiatric, and neoplastic disorders. Recent attempts to expand our understanding of circadian regulation have moved beyond the mutagenesis screens that identified the first clock components, employing higher throughput genomic and proteomic techniques. In order to further accelerate clock gene discovery, we utilized a computer-assisted approach to identify and prioritize candidate clock components. We used a simple form of probabilistic machine learning to integrate biologically relevant, genome-scale data and ranked genes on their similarity to known clock components. We then used a secondary experimental screen to characterize the top candidates. We found that several physically interact with known clock components in a mammalian two-hybrid screen and modulate in vitro cellular rhythms in an immortalized mouse fibroblast line (NIH 3T3). One candidate, Gene Model 129, interacts with BMAL1 and functionally represses the key driver of molecular rhythms, the BMAL1/CLOCK transcriptional complex. Given these results, we have renamed the gene CHRONO (computationally highlighted repressor of the network oscillator). Bi-molecular fluorescence complementation and co-immunoprecipitation demonstrate that CHRONO represses by abrogating the binding of BMAL1 to its transcriptional co-activator CBP. Most importantly, CHRONO knockout mice display a prolonged free-running circadian period similar to, or more drastic than, six other clock components. We conclude that CHRONO is a functional clock component providing a new layer of control on circadian molecular dynamics.Publication Open Access Pancreas-specific activation of mTOR and loss of p53 induce tumors reminiscent of acinar cell carcinoma(BioMed Central, 2016) Kong, Bo; Cheng Tao; Qian, Chengjia; Wu, Weiwei; Steiger, Katja; Cao, Jing; Schlitter, Anna Melissa; Regel, Ivonne; Raulefs, Susanne; Friess, Helmut; Esposito, Irene; Kleeff, Joerg; Michalski, Christoph W.; N/A; Erkan, Murat Mert; Faculty Member; School of Medicine; 214689Background: Pancreatic acinar cell carcinoma (ACC) is a rare tumor entity with an unfavorable prognosis. Recent whole-exome sequencing identified p53 mutations in a subset of human ACC. Activation of the mammalian target of rapamycin (mTOR) pathway is associated with various pancreatic neoplasms. We thus aimed at analyzing whether activation of mTOR with a concomitant loss of p53 may initiate ACC. Methods: We generated transgenic mouse models in which mTOR was hyperactivated through pancreas-specific, homozygous tuberous sclerosis 1 (Tsc1) deficiency, with or without deletion of p53 (Tsc1(-/-) and Tsc1(-/-); p53(-/-)). Activity of mTOR signaling was investigated using mouse tissues and isolated murine cell lines. Human ACC specimens were used to corroborate the findings from the transgenic mouse models. Results: Hyperactive mTOR signaling in Tsc1(-/-) mice was not oncogenic but rather induced a near-complete loss of the pancreatic acinar compartment. Acinar cells were lost as a result of apoptosis which was associated with p53 activation. Concomitantly, ductal cells were enriched. Ablation of p53 in Tsc1-deficient mice prevented acinar cell death but promoted formation of acinar cells with severe nuclear abnormalities. One out of seven Tsc1(-/-); p53(-/-) animals developed pancreatic tumors showing a distinctive tumor morphology, reminiscent of human ACC. Hyperactive mTOR signaling was also detected in a subset of human ACC. Conclusion: Hyperactive mTOR signaling combined with loss of p53 in mice induces tumors similar to human ACC.