Researcher: Barış, İbrahim
Name Variants
Barış, İbrahim
Email Address
Birth Date
37 results
Search Results
Now showing 1 - 10 of 37
Publication Metadata only Functional characterization of Cryptochrome 2 gene SNPs(Springernature, 2024) Gul, Seref; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Parlak, Gizem Çağla; Barış, İbrahim; Kavaklı, İbrahim Halil; Graduate School of Sciences and Engineering; College of SciencesPublication Metadata only Investigation of the possible role of CITED2 transcription factor in the circadian clock mechanism(Springernature, 2024) Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Barış, İbrahim; Çakmak, Çağla; Velioğlu, Başak; Uyanık, Elif; Kavaklı, İbrahim Halil; Graduate School of Sciences and Engineering; College of SciencesPublication Metadata only Functional characterization of CLOCK gene SNPs using in-silico and in-vitro experimental approach(Springernature, 2024) Gul, Seref; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Efendi, Seden Nadire; Kavaklı, İbrahim Halil; Barış, İbrahim; Graduate School of Sciences and Engineering; College of SciencesPublication Metadata only SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay(Elsevier, 2013) Etlik, Ozdal; Koksal, Vedat; Ocak, Zeynep; Baris, Saniye Tugba; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; College of Sciences; 111629Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T. discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.Publication Metadata only Transcriptional regulation of the starch synthases isoforms in the leaf and the stem under long and short photoperiod in lentil(Wiley-Blackwell, 2014) Gercek, Y. C.; Oz, G. Cevahir; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Barış, İbrahim; Kavaklı, İbrahim Halil; Teaching Faculty; Faculty Member; College of Sciences; College of Engineering; 111629; 40319N/APublication Metadata only Isolation and characterization of cDNAs of lentil ADP-glucose pyrophosphorylase(Current Biology Ltd, 2011) Oz, Gul Cevahir; Tulum, Isil; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Kavaklı, İbrahim Halil; Barış, İbrahim; Faculty Member; Teaching Faculty; College of Engineering; College of Sciences; 40319; 111629N/APublication Metadata only Transcriptional regulation of the starch branching enzyme isoforms in the leaf and the stemunder long and short photoperiod in lentil(Wiley-Blackwell, 2014) Boztas, K.; Morgil, H.; Oz, G. Cevahir; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Barış, İbrahim; Kavaklı, İbrahim Halil; Teaching Faculty; Faculty Member; College of Sciences; College of Engineering; 111629; 40319N/APublication Metadata only Identification and characterization of a new class of (6−4) photolyase from Vibrio cholerae(Amer Chemical Soc, 2019) Ozcelik, Gozde; Ozturk, Nuri; N/A; N/A; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Dikbaş, Uğur Meriç; Tardu, Mehmet; Gül, Şeref; Barış, İbrahim; Kavaklı, İbrahim Halil; Master Student; PhD Student; Researcher; Teaching Faculty; Faculty Member; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; College of Engineering; N/A; N/A; N/A; 111629; 40319Light is crucial for many biological activities of most organisms, including vision, resetting of circadian rhythm, photosynthesis, and DNA repair. The cryptochrome/photolyase family (CPF) represents an ancient group of UV-A/blue light sensitive proteins that perform different functions such as DNA repair, circadian photoreception, and transcriptional regulation. The CPF is widely distributed throughout all organisms, including marine prokaryotes. The bacterium Vibrio cholerae was previously shown to have a CPD photolyase that repairs UV-induced thymine dimers and two CRY-DASHs that repair UV-induced single-stranded DNA damage. Here, we characterize a hypothetical gene Vca0809 encoding a new member of CPF in this organism. The spectroscopic analysis of the purified protein indicated that this enzyme possessed a catalytic cofactor, FAD, and photoantenna chromophore 6,7-dimethyl 8-ribityllumazin. With a slot blot-based DNA repair assay, we showed that it possessed (6-4) photolyase activity. Further phylogenetic and computational analyses enabled us to classify this gene as a member of the family of iron-sulfur bacterial cryptochromes and photolyases (FeS-BCP). Therefore, we named this gene Vc(6-4) FeS-BCP.Publication Metadata only Rapid diagnosis of spinal muscular atrophy using tetra-primer ARMS PCR assay: Simultaneous detection of SMN1 and SMN2 deletion(Elsevier, 2010) Etlik, Ozdal; Koksal, Vedat; Arican-Baris, S. Tugba; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Barış, İbrahim; Teaching Faculty; College of Sciences; 111629Spinal muscular atrophy (SMA), the leading genetic cause of death in childhood, is an autosomal recessive neuromuscular disorder characterized by progressive muscle weakness, associated with deletions of the survival motor neuron 1 (SMN1) gene. Approximately 94% of SMA patients carry homologous deletions of SMN1 exon(s) 7 (and 8). Because of the high incidence and severity of the disease, precise detection and quantification of SMN1 and SMN2 gene copy numbers is essential for diagnosis and genetic counseling. We have developed a reliable single-tube tetra-primer PCR assay to simultaneously detect both the SMN1 and SMN2 exon 7 deletion using the advantage of C/T difference at nucleotide position of 840 in exon 7. The assay has been optimized and tested in 48 healthy controls, 20 known patients with SMA, 12 carriers (one SMN1 copy), and 8 amniotic fluids suspected of having SMA for whom we had determined the SMN1/SMN2 deletion by an additional PCR-RFLP method. We have observed complete concordance between methods. Our tetra-primer PCR assay is sensitive, low-cost, and easy to use method for simultaneous detection of both SMN1 and SMN2 deletion, which could be used even in "low-tech" laboratories.Publication Metadata only MEMS biosensor for blood plasma viscosity measurements(Elsevier Science Bv, 2012) N/A; Department of Electrical and Electronics Engineering; Department of Mechanical Engineering; N/A; N/A; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Department of Molecular Biology and Genetics; Department of Chemical and Biological Engineering; Department of Mechanical Engineering; Department of Electrical and Electronics Engineering; Çakmak, Onur; Elbüken, Çağlar; Ermek, Erhan; Bulut, Selma; Kılınç, Yasin; Barış, İbrahim; Kavaklı, İbrahim Halil; Alaca, Burhanettin Erdem; Ürey, Hakan; PhD Student; Researcher; Other; PhD Student; PhD Student; Teaching Faculty; Faculty Member; Faculty Member; Faculty Member; Koç University Surface Science and Technology Center (KUYTAM) / Koç Üniversitesi Yüzey Teknolojileri Araştırmaları Merkezi (KUYTAM); Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; College of Engineering; College of Engineering; College of Engineering; N/A; N/A; N/A; N/A; N/A; 111629; 40319; 115108; 8579N/A