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Permanent URI for this collectionhttps://hdl.handle.net/20.500.14288/3
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Item Metadata only The signalling lipid PI3,5P 2 is essential for timely mitotic exit(Royal Society Publishing, 2023) 0000-0003-2570-1367; N/A; N/A; 0000-0002-3470-7421; Department of Molecular Biology and Genetics; N/A; N/A; N/A; Çaydaşı, Ayşe Koca; Bektaş, Şeyma Nur; Bekdaş, Barış; Huda, Mariam; Faculty Member; PhD Student; Master Student; PhD Student; College of Sciences; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; 252978; N/A; N/A; N/ACoordination of mitotic exit with chromosome segregation is key for successful mitosis. Mitotic exit in budding yeast is executed by the mitotic exit network (MEN), which is negatively regulated by the spindle position checkpoint (SPOC). SPOC kinase Kin4 is crucial for SPOC activation in response to spindle positioning defects. Here, we report that the lysosomal signalling lipid phosphatidylinositol-3,5-bisphosphate (PI3,5P 2) has an unanticipated role in the timely execution of mitotic exit. We show that the lack of PI3,5P 2 causes a delay in mitotic exit, whereas elevated levels of PI3,5P 2 accelerates mitotic exit in mitotic exit defective cells. Our data indicate that PI3,5P 2 promotes mitotic exit in part through impairment of Kin4. This process is largely dependent on the known PI3,5P 2 effector protein Atg18. Our work thus uncovers a novel link between PI3,5P 2 and mitotic exit. © 2023 Royal Society Publishing. All rights reserved.Publication Metadata only Navigating centriolar satellites: the role of PCM1 in cellular and organismal processes(WILEY, 2024) Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Begar, Efe; Seyrek, Ece; Karalar, Elif Nur Fırat; Graduate School of Sciences and Engineering; College of SciencesCentriolar satellites are ubiquitous membrane-less organelles that play critical roles in numerous cellular and organismal processes. They were initially discovered through electron microscopy as cytoplasmic granules surrounding centrosomes in vertebrate cells. These structures remained enigmatic until the identification of pericentriolar material 1 protein (PCM1) as their molecular marker, which has enabled their in-depth characterization. Recently, centriolar satellites have come into the spotlight due to their links to developmental and neurodegenerative disorders. This review presents a comprehensive summary of the major advances in centriolar satellite biology, with a focus on studies that investigated their biology associated with the essential scaffolding protein PCM1. We begin by exploring the molecular, cellular, and biochemical properties of centriolar satellites, laying the groundwork for a deeper understanding of their functions and mechanisms at both cellular and organismal levels. We then examine the implications of their dysregulation in various diseases, particularly highlighting their emerging roles in neurodegenerative and developmental disorders, as revealed by organismal models of PCM1. We conclude by discussing the current state of knowledge and posing questions about the adaptable nature of these organelles, thereby setting the stage for future research.Publication Metadata only Proteome analysis of the circadian clock protein PERIOD2(Wiley, 2022) Gül, Hüseyin; Selvi, Saba; Yılmaz, Fatma; Özçelik, Gözde; Olfaz-Aslan, Senanur; Yazan, Şeyma; Tiryaki, Büşra; Gül, Şeref; Öztürk, Nuri; 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; Yurtseven, Ali; Kavaklı, İbrahim Halil; Master Student; Faculty Member; Faculty Member; Graduate School of Sciences and Engineering; College of Engineering; College of Sciences; N/A; 40319; 105301Circadian rhythms are a series of endogenous autonomous 24-h oscillations generated by the circadian clock. At the molecular level, the circadian clock is based on a transcription-translation feedback loop, in which BMAL1 and CLOCK transcription factors of the positive arm activate the expression of CRYPTOCHROME (CRY) and PERIOD (PER) genes of the negative arm as well as the circadian clock-regulated genes. There are three PER proteins, of which PER2 shows the strongest oscillation at both stability and cellular localization level. Protein-protein interactions (PPIs) or interactome of the circadian clock proteins have been investigated using classical methods such as two-dimensional gel electrophoresis, immunoprecipitation-coupled mass spectrometry, and yeast-two hybrid assay where the dynamic and weak interactions are difficult to catch. To identify the interactome of PER2 we have adopted proximity-dependent labeling with biotin and mass spectrometry-based identification of labeled proteins (BioID). In addition to known interactions with such as CRY1 and CRY2, we have identified several new PPIs for PER2 and confirmed some of them using co-immunoprecipitation technique. This study characterizes the PER2 protein interactions in depth, and it also implies that using a fast BioID method with miniTurbo or TurboID coupled to other major circadian clock proteins might uncover other interactors in the clock that have yet to be discovered.Publication Metadata only Running on empty: Does mitochondrial DNA mutation limit replicative lifespan in yeast? Mutations that increase the division rate of cells lacking mitochondrial DNA also extend replicative lifespan in Saccharomyces cerevisiae(Wiley, 2011) Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Dunn, Cory David; Other; College of Sciences; N/AMitochondrial DNA (mtDNA) mutations escalate with increasing age in higher organisms. However, it has so far been difficult to experimentally determine whether mtDNA mutation merely correlates with age or directly limits lifespan. A recent study shows that budding yeast can also lose functional mtDNA late in life. Interestingly, independent studies of replicative lifespan (RLS) and of mtDNA-deficient cells show that the same mutations can increase both RLS and the division rate of yeast lacking the mitochondrial genome. These exciting, parallel findings imply a potential causal relationship between mtDNA mutation and replicative senescence. Furthermore, these results suggest more efficient methods for discovering genes that determine lifespan.Publication 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 Phylo-comparative analyses reveal the dual role of drift and selection in reproductive character displacement(Academic Press Inc Elsevier Science, 2019) Miller, Michael R.; O'Rourke, Sean; Çağlar, Selim S.; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Sağlam, İsmail Kudret; Faculty Member; College of Sciences; 168783When incipient species meet in secondary contact, natural selection can rapidly reduce costly reproductive interactions by directly targeting reproductive traits. This process, called reproductive character displacement (RCD), leaves a characteristic pattern of geographic variation where divergence of traits between species is greater in sympatry than allopatry. However, because other forces can also cause similar patterns, care must be given in separating pattern from process. Here we show how the phylo-comparative method together with genomic data can be used to evaluate evolutionary processes at the population level in closely related species. Using this framework, we WA the role of RCD in speciation of two cricket species endemic to Anatolian mountains by quantifying patterns of character displacement, rates of evolution and adaptive divergence. Our results show differing patterns of character displacement between species for reproductive vs. non-reproductive characters and strong patterns of asymmetric divergence. We demonstrate diversification results from rapid divergence of reproductive traits towards multiple optima under the dual influence of strong drift and selection. These results present the first solid evidence for RCD in Anatolian mountains, quantify the amount of drift and selection necessary for RCD to lead to speciation, and demonstrate the utility of phylo-comparative methods for quantifying evolutionary parameters at the population level.Publication Metadata only Genome-wide excision repair map of cyclobutane pyrimidine dimers in arabidopsis and the roles of csa1 and csa2 proteins in transcription-coupled repair(dagger)(Wiley, 2022) Kaya, Sezgi; Adebali, Ogun; Sancar, Aziz; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Öztaş, Onur; Faculty Member; College of Sciences; 330370Plants depend on light for energy production. However, the UV component in sunlight also inflicts DNA damage, mostly in the form of cyclobutane pyrimidine dimers (CPD) and (6-4) pyrimidine-pyrimidone photoproducts, which are mutagenic and lethal to the plant cells. These lesions are repaired by blue-light-dependent photolyases and the nucleotide excision repair enzymatic systems. Here, we characterize nucleotide excision repair in Arabidopsis thaliana genome-wide and at single nucleotide resolution with special focus on transcription-coupled repair and the role of the CSA1 and CSA2 genes/proteins in dictating the efficiency and the strand preference of repair of transcribed genes. We demonstrate that CSA1 is the dominant protein in coupling repair to transcription with minor contribution from CSA2.Publication Metadata only NEUROD2 transcription factor regulates expression of Id2 gene during neuronal differentiation(Wiley-Blackwell, 2014) N/A; N/A; N/A; Department of Molecular Biology and Genetics; Department of Molecular Biology and Genetics; Güzelsoy, Gizem; Bayam, Efil; Dunn, Gülayşe İnce; Master Student; Researcher; Other; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Sciences; N/A; N/A; N/AN/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/A