Browsing by Author "Akgül, Bünyamin"
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Aggregatibacter actinomycetemcomitans GroEL Protein Promotes Conversion of Human CD4+ T Cells into IFNγ IL10 Producing Tbet+ Th1 Cells
Saygılı, Tahsin; Akıncılar, Semih Can; Akgül, Bünyamin; Nalbant Aldanmaz, Ayten (Public Library of Science, 2012-11)One of the heat shock family protein (Hsp) expressing bacteria is the gram negative, periodontal pathogen Aggregatibacter actinomycetemcomitans (Aa). A. actinomycetemcomitans' Hsp is a 64-kDa GroEL-protein, which has been ... -
Analysis of temporal and spatial expression of drosophila embryonic small RNAs by deep-sequencing method
Coşacak, Mehmet İlyas (Izmir Institute of Technology, 2012)The world of small RNAs is expanding and new types of small RNAs are being identified. By using deep-sequencing techniques in addition to most abundant small RNAs; miRNA and siRNA, piRNA and tRFs were further characterized ... -
Cloning of polysome-associated small RNAs in Drosophila melanogaster embryos
Yiğit, Hatice (Izmir Institute of Technology, 2009)Genome-encoded regulatory small RNAs are classified into 3 groups; microRNAs (miRNAs), endogeneous small interfering RNAs (endo siRNAs) and piwi interacting RNAs (piRNAs). miRNAs, 17-21 nucleotide in size, are involved in ... -
Deep sequencing reveals two Jurkat subpopulations with distinct miRNA profiles during camptothecin-induced apoptosis
Erdoğan, İpek; Coşacak, Mehmet İlyas; Nalbant, Ayten; Akgül, Bünyamin (TUBITAK, 2018)MicroRNAs (miRNAs) are small noncoding RNAs of about 19-25 nt that regulate gene expression posttranscriptionally under various cellular conditions, including apoptosis. The miRNAs involved in modulation of apoptotic events ... -
Differentially expressed tRNA-derived small RNAs co-sediment primarily with non-polysomal fractions in Drosophila
Göktaş, Çağdaş; Yiğit, Hatice; Coşacak, Mehmet İlyas; Akgül, Bünyamin (MDPI, 2017-11)Recent studies point to the existence of poorly characterized small regulatory RNAs generated from mRNAs, rRNAs and tRNAs. To explore the subcellular location of tRNA-derived small RNAs, 0–1 and 7–8 h Drosophila embryos ... -
Evidence for a stabilizer element in the untranslated regions of Drosophila glutathione S-transferase D1 mRNA
Akgül, Bünyamin; Tu, Chen-Pei D. (American Society for Biochemistry and Molecular Biology, 2002-09)The neighboring genes gstD1 and gstD21 share 70% sequence identity, gstD1 encodes a 1,1,1-trichloro-2,2-bis-(P-chlorophenyl)ethane dehydrochlorinase; gstD21, a ligandin. Both of their mRNAs are inducible by pentobarbital ... -
Garlic accelerates red blood cell turnover and splenic erythropoietic gene expression in mice: Evidence for erythropoietin-independent erythropoiesis
Akgül, Bünyamin; Lin, Kai-Wei; Yang, Hui-Mei Ou; Chen, Yen-Hui; Lu, Tzu-Huan; Chen, Chien-Hsiun; Kikuchi, Tateki; Chen, Yuan-Tsong; Tu, Chen-Pei D. (Public Library of Science, 2010)Garlic (Allium sativum) has been valued in many cultures both for its health effects and as a culinary flavor enhancer. Garlic's chemical complexity is widely thought to be the source of its many health benefits, which ... -
Gene reporter assay to validate microRNA targets in drosophila S2 cells
Akgül, Bünyamin; Göktaş, Çağdaş (Humana Press, 2014)Bioinformatics programs have helped tremendously in identifying the targets of microRNAs, which are small noncoding RNAs that regulate gene expression posttranscriptionally. However, the partial complementarity between ... -
Genomic profiling of microRNAs regulating translation in drosophila melanogaster embryos
Tüncel, Özge (Izmir Institute of Technology, 2008)Among the small RNAs, microRNAs are a particular class of 21 to 23 nucleotide RNAs that negatively regulate translation and play a pivotal role in posttranscriptional gene expression. microRNAs are found in many phyla that ... -
Identification of complexes that interact with tRNA-derived small RNAs by gene expression methods
Öztürk, Saniye Elvan (Izmir Institute of Technology, 2013)tRNA is a vital molecule of life and has been a focus of biochemical research since long. New aspects of tRNA biology have been drawn to light recently. Accumulating data indicates that tRNA has many diverse biological ... -
Identification of long non-coding RNAs that regulate apoptosis in human
Ahmadov, Ulvi (Izmir Institute of Technology, 2015-12)Apoptosis is essential for cellular homeostasis and normal development. Aberrant apoptosis (too much or too less) is associated with many important diseases such as autoimmune diseases and cancer. Studies have led to the ... -
Identification of microRNAs involved in camptothecin-induced apoptosis in Jurkat T cell line
Erdoğan, İpek (Izmir Institute of Technology, 2008)MicroRNAs which are non-coding RNAs 19-25 nt in length regulate gene expression at post-transcriptional and translational stages. Although it is known that they play a role in critical processes such as development and ... -
Indentification of circular ribonucleic acids differentially expressed in apoptotic HeLa cells
Yaylak, Bilge (Izmir Institute of Technology, 2018-07)Apoptosis is a mechanism of programmed cell death that is essential for survival, homeostatis and development. Various protein coding genes and non-coding RNAs were reported as apoptosis regulators. However, the potential ... -
Investigation of the functions of candidate miRNAs in camptothecin-induced apoptosis in human cells
Demir, Şeyda (Izmir Institute of Technology, 2012)MicroRNAs are non-coding 19-25nt long, small RNAs that regulate expression of about 30% of human genes by inhibiting mRNA translation or inducing its degradation. MicroRNAs play important role in cell growth, differentiation, ... -
Investigation of tRNA-derived small RNAs in drosophila melangaster
Göktaş, Çağdaş (Izmir Institute of Technology, 2011)Types of small RNAs considered as crucial players of regulation of gene expression increase gradually in number. Improvements in cloning and sequencing strategies and technologies resulted in identification of tRNA derived ... -
Master regulators of posttranscriptional gene expression are subject to regulation
Hamid, Syed Muhammad; Akgül, Bünyamin (Springer, 2014)MicroRNAs (miRNAs) are small noncoding RNAs of 17-25 nt in length that control gene expression posttranscriptionally. As master regulators of posttranscriptional gene expression, miRNAs themselves are subject to tight ... -
Molecular characterization of the GTF2A-1 antisense long non-coding RNA
Yarımçam, Murat Caner (Izmir Institute of Technology, 2017-12)One of the essential events in cell regulation and normal development of an organism is apoptosis. The dysregulation of apoptosis is associated with diseases such as cancer. Apoptosis induction can kill cancer cells ... -
mRNA decay analysis in Drosophila melanogaster: Drug-induced changes in glutathione S-transferase D21 mRNA stability
Akgül, Bünyamin; Tu, Chen-Pei D. (Elsevier, 2008)We have established an in vivo system to investigate mechanisms by which pentobarbital (PB), a psychoactive drug with a sedative effect, changes the rate of decay of gstD21 mRNA (encoding a Drosophila glutathione S-transferase). ... -
Pentobarbital-mediated Regulation of Alternative Polyadenylation in Drosophila Glutathione S-Transferase D21 mRNAs
Akgül, Bünyamin; Tu, Chen-Pei D. (American Society for Biochemistry and Molecular Biolog, 2004-02)Two nearly identical, gstD21(L) and gstD21(S) mRNAs whose polyadenylation sites differ by 19 nucleotides, are transcribed from the intronless glutathione S-transferase D21 gene in Drosophila. Both mRNAs are intrinsically ... -
Re-arrangements in the cytoplasmic distribution of small RNAs following the maternal-to-zygotic transition in Drosophila embryos
Coşacak, Mehmet İlyas; Yiğit, Hatice; Kızıl, Çağhan; Akgül, Bünyamin (MDPI, 2018-02)Small ribonucleic acids (RNAs) are known to regulate gene expression during early development. However, the dynamics of interaction between small RNAs and polysomes during this process is largely unknown. To investigate ...
