Welcome to the Koç University Institutional Academic Repository
The Koç University Institutional Academic Repository (KUHub Research) is a state-of-the-art academic repository that consolidates all academic outputs—such as articles, conference proceedings, theses, research data, and more—produced by the university since its establishment in 1993.
KUHub Research adheres to the principles of Open Access and FAIR (Findable, Accessible, Interoperable, Reusable), providing access to the bibliographic records, research data, and full texts of research outputs. Equipped with innovative features such as Author Profile pages and enhanced tools, KUHub Research aims to enhance the visibility of researchers both nationally and internationally. KUHub Research aims to preserve and maintain Koç University's valuable academic legacy for future generations while also serving the needs of today’s researchers.
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Recent Submissions
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2028-01-01) Chretien, Anaïs; Ertem Kuzucu, Fatma Betul; Summers, Jacob; Wranik, Maximilian; 0000-0001-8480-1443; 0000-0002-2144-989x; 0000-0003-3113-0353; 0000-0002-2482-0164
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Mechanisms of fast CO2 fixation reaction by enoyl-CoA carboxylases/reductase
(European Synchrotron Radiation Facility, 2027-01-01) Summers, Jacob; Sanctis, Daniele; Vlahakis, Niko; Knight, Victoria; Ertem Kuzucu, Fatma Betul; Chretien, Anaïs; Nurizzo, Didier; 0000-0003-3113-0353; 0000-0003-0391-8290; 0000-0002-5092-0265; 0000-0002-2144-989x; 0000-0001-8480-1443; 0000-0002-7367-5098
Carbon dioxide (CO2) is an atmospheric greenhouse gas that feeds all life, plays a critical role in global warming, and could constitute an inexpensive carbon source for future sustainable industries. While synthetic chemistry lacks suitable catalysts to functionalize carbon dioxide in mild reaction conditions, autotrophs do it constantly, and thus there is increasing interest in exploiting the CO2-fixation mechanisms offered by nature. In this exchange proposal, we propose fast time-resolved structural-dynamics studies of one of the fastest CO2-fixation enzymes, enoyl-CoA carboxylase/reductase (ECR), using ambient temperature serial X-ray crystallography on Beamline ID29, ESRF, which achieves 10μs resolution. This study will reveal details of the enzyme subunit coupling as well as the enzyme-substrate interactions to correlate the structural and functional states of the enzyme during fixation and pave the way for faster biomolecule productions using engineered C-cycling enzymes.
Effect of late-onset on multiple sclerosis phenotype and outcome: evidence from a multi-national registry
(Springer Science and Business Media LLC, 2026-02-01) Altıntaş, Ayşe; Souissi, Amira; Patti, Francesco; Spelman, Tim; Chisari, Clara; Gargouri, Amina; John, Nevin; Kermode, Allan G.; Kalincik, Tomas; Butzkueven, Helmut; Sajedi, Seyed Aidin; Lechner-Scott, Jeannette; Roos, Izanne; Laureys, Guy; Taylor, Bruce; Alroughani, Raed; Khoury, Samia J.; Macdonell, Richard; Weinstock-Guttman, Bianca; Havrdova, Eva Kubala; Maimone, Davide; Reddel, Stephen; Fabis-Pedrini, Marzena; Willekens, Barbara; Moghadasi, Abdorreza Naser; Lalive, Patrice; Lugaresi, Alessandra; Ozakbas, Serkan; Solaro, Claudio; Cárdenas-Robledo, Simón; Shaygannejad, Vahid; Etemadifar, Masoud; Boz, Cavit; Eichau, Sara; Tomassini, Valentina; Terzi, Murat; Prat, Alexandre; Habek, Mario; Blanco, Yolanda; Gerlach, Oliver; Turkoglu, Recai; Buzzard, Katherine; Skibina, Olga; Soysal, Aysun; van der Walt, Anneke; Hughes, Stella; van Pesch, Vincent; Foschi, Matteo; Surcinelli, Andrea; Prevost, Julie; Ramo-Tello, Cristina; McGuigan, Chris; Sa, Maria Jose; Kuhle, Jens; Spitaleri, Daniele; Singhal, Bhim; Ampapa, Radek; de Gans, Koen; Petersen, Thor; Simu, Mihaela; Lapointe, Emmanuelle; Sanchez-Menoyo, Jose Luis; Gray, Orla; Garber, Justin; Aguera-Morales, Eduardo; Gross-Paju, Katrin; Castillo-Triviño, Tamara; Al-Asmi, Abdullah; Grigoriadis, Nikolaos; Inshasi, Jihad; Al-Harbi, Talal; Hardy, Todd A.; Ramanathan, Sudarshini; Cambron, Melissa; Shuey, Neil; sempere, Angel Perez; Csepany, Tunde; Treviño-Frenk, Irene; Rozsa, Csilla; Cauchi, Marija; Karabudak, Rana; Mrabet, Saloua; Gouider, Riadh; School of Medicine; KUTTAM (Koç University Research Center for Translational Medicine); Yes; SCHOOL OF MEDICINE; Research Center
Multiple Sclerosis (MS) severity is influenced by several factors. Understanding the impact of age at disease onset may help to better characterize clinical and disease features across age groups. This study aimed to characterize the clinical features and disability outcomes of late-onset MS (LOMS) and very late-onset MS (vLOMS), compared to adult-onset MS (AOMS).We conducted an observational study using data from the MSBase registry and categorized patients based on age at MS onset: AOMS (18-39 years), transition onset (40-49 years), LOMS (50-59 years), and vLOMS (≥ 60 years). Disease progression was assessed using the 24 week confirmed disability progression, EDSS4 and 6 milestones, conversion to secondary progressive MS(SPMS), and the first progression independent of relapse activity (PIRA) event. Cox proportional hazard regression models were used to determine unadjusted hazard ratios(HR), and propensity score inverse probability of treatment weighting(PS-IPTW) balanced covariate distributions.Among 81,236 patients, 5.2% had LOMS and 1% had vLOMS. Primary progressive MS was more frequent in LOMS and vLOMS (21.7 and 24%, respectively). Patients with LOMS and vLOMS had a significantly increased risk of 24 week confirmed disability progression (HR:LOMS = 1.39, vLOMS = 1.80), EDSS 4 (HR:LOMS = 2.14, vLOMS = 2.95), EDSS 6 (HR:LOMS = 2.33, vLOMS = 6.33), SPMS (HR:LOMS = 1.62, vLOMS = 2.38), and first PIRA event (HR:LOMS = 2.12, vLOMS = 2.93).LOMS and vLOMS exhibited a more progressive disease onset and higher disability milestones compared with AOMS.
Incidental and symptomatic pulmonary thromboembolism: clinical features and prognostic comparison
(Springer Science and Business Media LLC, 2026-01-27) Karataş, Ferhan; Dikensoy, Öner; Coşkun Doğan; KUH (Koç University Hospital); KUH (KOÇ UNIVERSITY HOSPITAL)
Background Incidental pulmonary thromboembolism (iPTE) is increasingly being detected owing to the widespread use of computed tomography; however, its clinical significance and prognostic impact compared with symptomatic pulmonary thromboembolism (sPTE) remains controversial. Materials and Methods This retrospective observational study included adult patients with acute pulmonary embolism confirmed using CT pulmonary angiography between January 2022 and January 2025. Patients were classified as having iPTE or sPTE based on the clinical presentation and indications for imaging. Demographic characteristics, comorbidities, clinical findings, laboratory parameters, imaging features, and outcomes were compared between groups. Survival was assessed using Kaplan–Meier analysis, and predictors of mortality were evaluated using Cox regression analysis. Results A total of 306 patients were included, of whom 42 (13.7%) had iPTE and 264 (86.3%) had sPTE. Patients with iPTE had a higher prevalence of malignancy and comorbidities, but showed lower heart rate, higher oxygen saturation, lower cardiac biomarker levels, and less right ventricular dysfunction. Radiologically, iPTE was associated with a less extensive embolic burden and fewer parenchymal complications. The median survival did not differ significantly between the iPTE and sPTE groups (log-rank, p = 0.346). In multivariate analysis, malignancy (hazard ratio [HR] 3.07, p < 0.001) and elevated troponin T (HR 2.70, p = 0.002) were independent predictors of mortality, whereas iPTE status was not. Conclusion Despite a lower hemodynamic and radiological burden, incidental pulmonary thromboembolism was associated with survival comparable to that of symptomatic cases. Mortality was primarily driven by underlying malignancy and myocardial injury rather than by embolism presentation. Trial registration Not applicable (retrospective observational study).
Disentangling subspecies delimitation in Heldreichia bupleurifolia Boiss. (Brassicaceae) through genomic and quantitative morphological approaches
(Elsevier, 2026) Sağlam, İsmail Kudret; Ilgın Deniz Can; Emrullah Yılmaz; Kurtuluş Özgişi; Hakan Gür; Barış Özüdoğru; Department of Molecular Biology and Genetics; Yes; College of Sciences
Heldreichia bupleurifolia Boiss., the only species in its genus, is distributed across the Taurus and Anatolian Diagonal Mountains in Türkiye and presents considerable taxonomic challenges. The species is currently divided into five subspecies and one variety and has long posed challenges for infraspecific classification due to overlapping morphological traits and unresolved phylogenetic relationships. To address these issues and clarify the boundaries of the described subspecies and their evolutionary history, this study integrates comprehensive morphometric analyses of 502 individuals from 36 populations, as well as SNP- and locus-based genomic analyses from RAD-seq data of 136 individuals from 20 populations. While morphometric assessments showed significant differentiation in foliar and fruit traits, especially between western and eastern populations, genomic analyses identified distinct genetic clusters corresponding to geographic regions. High levels of genetic admixture and morphological plasticity were seen in the Central Taurus populations, indicating either historical hybridization or the preservation of ancestral polymorphisms. In accordance with morphological and admixture analyses, coalescent-based subspecies delimitation supported a three-subspecies model, resulting in revised taxonomic classifications that included new combinations. To further contextualize these results within an evolutionary perspective, we adopted the speciation continuum framework, interpreting morphological, genetic, and reproductive differentiation as components of a continuous process of divergence. These results emphasize the drawbacks of using morphology alone for taxonomy and the value of integrative methods for determining subspecies boundaries in areas with complex topography.