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    Comprehensive Review of Transcriptomics (RNAs) Workflows from Blood Specimens
    (Taylor & Francis Inc, 2022) Husseini, Abbas Ali; Derakhshandeh, Masoud; Tatlisu, Nevruz Berna
    Blood is the most interesting tissue for molecular analysis in a wide range of diseases since it provides accumulative information of the whole body state. Transcriptomic analysis of the blood is one of the most favorable omics approaches for clinical and research purposes. However, blood sample preparation for RNA analyses is highly diverse encompassing specific methodology and application. In this study, we review the common sample preparation maneuvers including RNA handling techniques, sample collection and stabilization, blood cell sorting, extracellular vesicle enrichment, RNA extraction, globin/ribosomal RNA reduction, and RNA concentration and quality assessment. These techniques are the most prevalent procedures of blood sample preparation in RNA transcriptomic analyses. The methodologies, technical challenges of the current approaches, and latest advances in the field are discussed in detail.
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    Development of a fermented ice-cream as influenced by in situ exopolysaccharide production: Rheological, molecular, microstructural and sensory characterization
    (Elsevier Sci Ltd, 2016) Dertli, Enes; Toker, Omer S.; Durak, M. Zeki; Yilmaz, Mustafa T.; Tatlisu, Nevruz Berna; Sagdic, Osman; Cankurt, Hasan
    This study aimed to investigate the role of in situ exopolysaccharide (EPS) production by EPS+ Streptococcus thermophilus strains on physicochemical, rheological, molecular, microstructural and sensory properties of ice cream in order to develop a fermented and consequently functional ice-cream in which no stabilizers would be required in ice-cream production. For this purpose, the effect of EPS producing strains (control, strain 1, strain 2 and mixture) and fermentation conditions (fermentation temperature; 32,37 and 42 degrees C and time; 2,3 and 4 h) on pH, S. thermophilus count, EPS amount, consistency coefficient (K), and apparent viscosity (eta(50)) were investigated and optimized using single and multiple response optimization tools of response surface methodology. Optimization analyses indicated that functional ice-cream should be fermented with strain 1 or strain mixture at 40-42 degrees C for 4 h in order to produce the most viscous ice-cream with maximum EPS content. Optimization analysis results also revealed that strain specific conditions appeared to be more effective factor on in situ EPS production amount, K and 1750 parameters than did fermentation temperature and time. The rheological analysis of the ice-cream produced by EPS+ strains revealed its high viscous and pseudoplastic non-Newtonian fluid behavior, which demonstrates potential of S. thermophilus EPS as thickening and gelling agent in dairy industry. FTIR analysis proved that the EPS in ice-cream corresponded to a typical EPS, as revealed by the presence of carboxyl, hydroxyl and amide groups with additional alpha-glycosidic linkages. SEM studies demonstrated that it had a web-like compact microstructure with pores in ice-cream, revealing its application possibility in dairy products to improve their rheological properties. (C) 2015 Published by Elsevier Ltd.
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    EFFECT OF IN SITU EXOPOLYSACCHARIDE PRODUCTION ON SENSORY PROPERTIES OF TURKISH-TYPE FERMENTED SAUSAGE
    (Yildiz Technical Univ, 2016) Yilmaz, Mustafa Tahsin; Toker, Omer Said; Tatlisu, Nevruz Berna; Arici, Muhammet; Dertli, Enes
    In this study, effect of in situ exopolysaccharide (EPS) production on sensory properties of Turkish-type fermented sausage (sucuk) was determined. Sausage mixes were prepared as four groups: (a) Control group, control sausage samples produced without LAB addition, with natural flora, (b) Strain 1 group, sausage samples produced by using Strain 1 (EPS+ Lactobacillus plantarum 162 R strain), (c) Strain 2 group: sausage samples produced by using Strain 2 (EPS+ Leuconostoc mesenteroides N6) and (d) Mixture group, sausage samples produced by using mixture of Strain 1 and Strain 2. These mixes were fermented at 14, 16 and 18 degrees C for 8, 12 and 16 days. Fermentation conditions remarkably affected the sensory properties of the sausage using different EPS producing EPS. These results of this study demonstrated the importance of in situ EPS production on final sensory properties of sausage.
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    Effects of in situ exopolysaccharide production and fermentation conditions on physicochemical, microbiological, textural and microstructural properties of Turkish-type fermented sausage (sucuk)
    (Elsevier Sci Ltd, 2016) Dertli, Enes; Yilmaz, Mustafa Tahsin; Tatlisu, Nevruz Berna; Toker, Omer Said; Cankurt, Hasan; Sagdic, Osman
    In this work, the role of in situ exopolysaccharide (EPS) production under different fermentation conditions on physicochemical, microbiological, textural and microstructural properties of sucuk was determined. For this purpose, the effect of EPS producing strains (control, strain 1, strain 2 and mixture) and fermentation conditions (fermentation temperature; 14, 16 and 18 C and time; 8, 12 and 16 days) on physicochemical, microbiological, textural and microstructural properties were investigated using response surface methodology. In situ EPS production was observed to remarkably affect these properties while fermentation conditions were also seen to dominantly influence the physicochemical properties of sucuk, revealing that the ripening temperature appeared to be more determinant factor. EPS producing cultures enhanced the textural properties of sucuk which became harder, less adhesive and tougher. The microstructural analysis revealed the formation of web -like structure by in situ EPS production in sucuk mix during fermentation process. This study revealed the importance of in situ EPS production on final technological properties of sucuk. (C) 2016 Elsevier Ltd. All rights reserved.