4 results on '"Ozcan, Emrah"'
Search Results
2. Comparison of Three Methods for Estimating Volume of the Uterine Layers in Healthy Women: A Stereological Study
- Author
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Karaca-Saygili, Omur, Taskin, Mine Islimye, Keyik, Bahar Yanik, Sackes, Mesut, Ozcan, Emrah, and Kus, Ilter
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Volume ,Planimetry ,Uterus ,Volumen ,Cavalieri ,Útero ,Planimetría ,MRI ,IRM - Abstract
SUMMARY: Aim of this study is to measure the volume of the uterine layers in healthy women according to the menstrual cycle phases and to test the agreement between three methods. The study was performed with 28 healthy women. Participants were divided into three groups as follicular (n=7), luteal (n=10) and postmenopausal phase (n=11). We used the point-counting and planimetry method in MR images and the ellipsoid methods in images obtained by transvaginal ultrasonography. Spearman correlation analysis showed significant negative correlations between the volumes of uterine layers and age (p
- Published
- 2018
3. Dynamic co-culture metabolic models reveal the fermentation dynamics, metabolic capacities and interplays of cheese starter cultures
- Author
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Merve Seven, Emrah Özcan, Burcu Şirin, Emrah Nikerel, Bas Teusink, Ebru Toksoy Oner, Tunahan Çakır, Ozcan, Emrah, Seven, Merve, Sirin, Burcu, Cakir, Tunahan, Nikerel, Emrah, Teusink, Bas, Toksoy Oner, Ebru, Systems Bioinformatics, and AIMMS
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0106 biological sciences ,0301 basic medicine ,LEUCONOSTOC ,Bioengineering ,LACTIC-ACID BACTERIA ,01 natural sciences ,Applied Microbiology and Biotechnology ,Models, Biological ,Article ,Systems Biotechnology ,03 medical and health sciences ,chemistry.chemical_compound ,ARTICLES ,Starter ,Cheese ,Lactobacillales ,FOOD FERMENTATIONS ,010608 biotechnology ,Food science ,LACTOCOCCUS-LACTIS ,DIACETYL PRODUCTION ,FLAVOR FORMATION ,Organism ,genome-scale metabolic network ,biology ,Lactococcus lactis ,co-culture metabolic modelling ,starter cultures ,food and beverages ,co‐culture metabolic modelling ,biology.organism_classification ,genome‐scale metabolic network ,STREPTOCOCCUS-THERMOPHILUS ,Coculture Techniques ,Lactic acid ,lactic acid bacteria ,030104 developmental biology ,chemistry ,Leuconostoc mesenteroides ,GROWTH ,Fermentation ,Flux (metabolism) ,REQUIREMENTS ,Bacteria ,FLUX BALANCE ANALYSIS ,Biotechnology - Abstract
In this study, we have investigated the cheese starter culture as a microbial community through a question: can the metabolic behaviour of a co‐culture be explained by the characterized individual organism that constituted the co‐culture? To address this question, the dairy‐origin lactic acid bacteria Lactococcus lactis subsp. cremoris, Lactococcus lactis subsp. lactis, Streptococcus thermophilus and Leuconostoc mesenteroides, commonly used in cheese starter cultures, were grown in pure and four different co‐cultures. We used a dynamic metabolic modelling approach based on the integration of the genome‐scale metabolic networks of the involved organisms to simulate the co‐cultures. The strain‐specific kinetic parameters of dynamic models were estimated using the pure culture experiments and they were subsequently applied to co‐culture models. Biomass, carbon source, lactic acid and most of the amino acid concentration profiles simulated by the co‐culture models fit closely to the experimental results and the co‐culture models explained the mechanisms behind the dynamic microbial abundance. We then applied the co‐culture models to estimate further information on the co‐cultures that could not be obtained by the experimental method used. This includes estimation of the profile of various metabolites in the co‐culture medium such as flavour compounds produced and the individual organism level metabolic exchange flux profiles, which revealed the potential metabolic interactions between organisms in the co‐cultures., Co‐cultures of lactic acid bacteria were investigated using dynamic genome‐scale metabolic modelling techniques. Özcan and co‐workers estimated the metabolic capacity, microbial abundance, potential of flavour compounds production and metabolic interactions of the co‐cultures using the features of individual organisms that constituted the co‐cultures.
- Published
- 2021
- Full Text
- View/download PDF
4. A genome-scale metabolic network of the aroma bacterium Leuconostoc mesenteroides subsp. cremoris
- Author
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Emrah Nikerel, Emrah Özcan, Ebru Toksoy Oner, Bas Teusink, S. Selvin Selvi, Tunahan Çakır, Özcan, E., Selvi, S.S., Nikerel, E., Teusink, B., Toksoy Öner, E., Çakır, T., Yeditepe Üniversitesi, Ozcan, Emrah, Selvi, S. Selvin, Nikerel, Emrah, Teusink, Bas, Oner, Ebru Toksoy, Cakir, Tunahan, Systems Bioinformatics, and AIMMS
- Subjects
MECHANISM ,Flux balance analysis ,Leuconostoc mesenteroides ,Applied Microbiology and Biotechnology ,CITRATE ,chemistry.chemical_compound ,LACTOBACILLUS-PLANTARUM ,Adenosine Triphosphate ,Cheese ,Lactic acid bacteria ,Food science ,Citrates ,Heterolactic fermentation ,Flavor ,0303 health sciences ,biology ,Acetoin ,food and beverages ,General Medicine ,Aerobiosis ,GROWTH ,Oxidation-Reduction ,Metabolic Networks and Pathways ,Biotechnology ,Phosphoketolase ,LACTIC-ACID BACTERIA ,Leuconostoc mesenteroides subsp ,GLUCOSE-6-PHOSPHATE-DEHYDROGENASE ,03 medical and health sciences ,Genome-scale metabolic model ,LACTOCOCCUS-LACTIS ,STARTER CULTURES ,PHYSIOLOGY ,030304 developmental biology ,030306 microbiology ,biology.organism_classification ,Diacetyl ,Carbon ,Leuconostoc mesenteroides subsp. cremoris ,chemistry ,cremoris ,Genes, Bacterial ,Fermentation ,Odorants ,Food Microbiology ,Flavor metabolism ,Bacteria ,Genome, Bacterial - Abstract
Leuconostoc mesenteroides subsp. cremoris is an obligate heterolactic fermentative lactic acid bacterium that is mostly used in industrial dairy fermentations. The phosphoketolase pathway (PKP) is a unique feature of the obligate heterolactic fermentation, which leads to the production of lactate, ethanol, and/or acetate, and the final product profile of PKP highly depends on the energetics and redox state of the organism. Another characteristic of the L. mesenteroides subsp. cremoris is the production of aroma compounds in dairy fermentation, such as in cheese production, through the utilization of citrate. Considering its importance in dairy fermentation, a detailed metabolic characterization of the organism is necessary for its more efficient use in the industry. To this aim, a genome-scale metabolic model of dairy-origin L. mesenteroides subsp. cremoris ATCC 19254 (iLM.c559) was reconstructed to explain the energetics and redox state mechanisms of the organism in full detail. The model includes 559 genes governing 1088 reactions between 1129 metabolites, and the reactions cover citrate utilization and citrate-related flavor metabolism. The model was validated by simulating co-metabolism of glucose and citrate and comparing the in silico results to our experimental results. Model simulations further showed that, in co-metabolism of citrate and glucose, no flavor compounds were produced when citrate could stimulate the formation of biomass. Significant amounts of flavor metabolites (e.g., diacetyl and acetoin) were only produced when citrate could not enhance growth, which suggests that flavor formation only occurs under carbon and ATP excess. The effects of aerobic conditions and different carbon sources on product profiles and growth were also investigated using the reconstructed model. The analyses provided further insights for the growth stimulation and flavor formation mechanisms of the organism. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature. FEN-C-DRP-091116-0498 2214-A Türkiye Bilimsel ve Teknolojik Araştirma Kurumu Funding information This work received financial support from The Scientific and Technological Research Council of Turkey through TUBITAK 2214-A program and the Marmara University Scientific Research Project Fund through Project No: FEN-C-DRP-091116-0498.
- Published
- 2019
- Full Text
- View/download PDF
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