Moleküler Biyoloji ve Genetik Bölümühttps://hdl.handle.net/20.500.12418/5032024-03-29T00:29:23Z2024-03-29T00:29:23Zİnfertil Erkeklerin Seminal Plazma Sıvısı ve Spermatozoasında Sisteinden Zengin Salgı Proteini 2 (CRISP2) ve Semenogelin 1 (SEMG1) ile mir-582-5p, mir-27a, mir-21 ve mir-216b Ekspresyonunun AraştırılmasıKALOĞLU, CelalBudak, MahirKorkmaz, Ertan MahirHamutoğlu, Rasimhttps://hdl.handle.net/20.500.12418/151002024-03-08T21:47:34Zİnfertil Erkeklerin Seminal Plazma Sıvısı ve Spermatozoasında Sisteinden Zengin Salgı Proteini 2 (CRISP2) ve Semenogelin 1 (SEMG1) ile mir-582-5p, mir-27a, mir-21 ve mir-216b Ekspresyonunun Araştırılması
KALOĞLU, Celal; Budak, Mahir; Korkmaz, Ertan Mahir; Hamutoğlu, Rasim
Bu çalışmada İnfertil Erkeklerin Seminal Plazma Sıvısı ve Spermatozoasında Sisteinden Zengin Salgı Proteini 2 (CRISP2) ve Semenogelin 1 (SEMG1) ile mir-582-5p, mir-27a, mir-21 ve mir-216b Ekspresyonunu arasındaki ilişki araştırılmıştır.
A novel, conserved and possibly functional motif “WHWGHTW” in mitochondrial transcription across BilateriaAydemir, Merve NurAydemir, Habeş BilalBudak, MahirKızıltepe, BirselÇelebi, MelissaKorkmaz, Ertan MahirBaşıbüyük, Hasan Hüseyinhttps://hdl.handle.net/20.500.12418/150952024-03-08T21:47:31Z2023-01-01T00:00:00ZA novel, conserved and possibly functional motif “WHWGHTW” in mitochondrial transcription across Bilateria
Aydemir, Merve Nur; Aydemir, Habeş Bilal; Budak, Mahir; Kızıltepe, Birsel; Çelebi, Melissa; Korkmaz, Ertan Mahir; Başıbüyük, Hasan Hüseyin
The animal mitogenomes which undergone a reductive evolution has an obvious loss of coding capacity compared to their known closest relatives, but it has not yet been fully investigated why and how the intergenic regions do not encode protein and have no known functions, are stably maintained, replicated, and transmitted by the genome. These relatively small intergenic regions may not be under neutral evolution and they may have functional and/or regulatory roles that have yet to be identified. Here, the distribution pattern, sequence content and location of a novel sequence motif of ‘WWWGHTW’ were bioinformatically investigated and characterised by constructing a sampling mitogenome dataset of 1889 species from 14 phyla representing the clade of Bilateria. This motif is reverse complementary of the previously described DmTTF binding sequence and found in the nd4L- (X) -trnT gene cluster. This cluster commonly exhibits a strand displacement region and an intergenic region among the bilaterian superphylums, particularly in Ecdysozoa. This motif may be accepted as a substrate providing binding sites for the specific interaction with transcription factors because of (i) its reverse complementarity of previously described DmTTF binding sequence, and (ii) the possession of G and T nucleotides in the fourth and sixth positions, (iii) the bias on T and G nucleotides instead of C and A in the degenerated positions. This suggestion is also supported by the presence of a strand displacement region in the nd4L- (X) -trnT gene cluster, particularly in Ecdysozoa consisting of the most rearranged mitogenomes among the bilaterian superphylums.
2023-01-01T00:00:00ZDifferential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcriptsAydemir, Habeş BilalAydemir, Merve NurKorkmaz, Ertan Mahirhttps://hdl.handle.net/20.500.12418/150942024-03-08T21:47:30ZDifferential sense and antisense expression profiles of Syrista parreyssi (Hymenoptera: Cephidae) mitochondrial transcripts
Aydemir, Habeş Bilal; Aydemir, Merve Nur; Korkmaz, Ertan Mahir
The transcription of the mitogenome shows a unique pattern that is both similar to and different from the nuclear and bacterial patterns. Mitochondrial transcription generates five polycistronic units from three promoters in Drosophila melanogaster, and different expression levels of genes were observed in both different and, interestingly, the same polycistronic units in D. melanogaster. This study was conducted to test this phenomenon in the mitogenome of Syrista parreyssi (Hymenoptera: Cephidae). RNA isolation and DNase digestion were performed using only one whole individual, and real-time polymerase chain reaction analyses were performed with complementary DNAs of 11 gene regions using gene-specific primers. It was found that the expression level of each gene exhibited differences from each other, and some genes (e.g., cox genes, and rrnS) were interestingly expressed at significant levels in the corresponding antisense chain. Additionally, the mitogenome of S. parreyssi was found to have the capacity to encode 169 additional peptides from 13 known protein-coding genes, most of which were encoded in antisense transcript units. One of the unique findings was a potential open reading frame sequence that was potentially encoded in the antisense rrnL gene and included a conserved cox3 domain
Trichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profilingÖzkale, EvrimYörük, EmreBudak, MahirKorkmaz, Ertan Mahirhttps://hdl.handle.net/20.500.12418/150932024-03-08T21:47:31ZTrichoderma atroviride suppresses Fusarium graminearum by altering primary and secondary metabolite biosynthesis profiling
Özkale, Evrim; Yörük, Emre; Budak, Mahir; Korkmaz, Ertan Mahir
The use of Trichoderma spp. offers an ecologically friendly tool for the struggle with mycotoxigenic Fusarium spp. Here, the alterations in transcriptome level were investigated in 6-day- old Fusarium graminearum cultures treated with Trichoderma atroviride and nontreated with T. atroviride (FGc), using whole transcriptome sequencing to better understand the associated biological processes. Transcriptome analysis indicated a total of 55 up-regulated genes and 728 down-regulated genes with padj < 0.05. Enrichment analysis revealed that the up-regulated genes were related to fatty acid biosynthesis, AMP-dependent biosynthesis, amino acid recognition/activation processes and secondary metabolite production, whereas down-regulated genes were involved in amino acid synthesis, oxidation–reduction processes, metal ion-binding and metabolic/ catalytic activities. Among the down-regulated genes, the expression of pigmentation-related genes such as aurO, gip1 and aurR2 was remarkable. Similarly, the expression levels of key enzyme-coding genes involved in deoxynivalenol mycotoxin production were significantly decreased in the range of −1.77 and −2.94. For up-regulated genes, nonribosomal peptide synthetase and polyketide synthase genes were notably distinguished from the remaining down-regulated genes as these genes can be involved in biosynthesis of common secondary metabolites. The results clearly emphasize that T. atroviride repressed the biosynthesis of primary metabolites in F. graminearum while simultaneously up-regulating the expression of genes involved in the synthesis of secondary metabolites. This is the first report showing how T. atroviride leads to transcriptome alterations and the findings suggest that T. atroviride could serve as an effective fungus by employing a wide variety of strategies against phytopathogenic fungi.