Molecular Biology and Genetics / Moleküler Biyoloji ve Genetik
Permanent URI for this collectionhttps://hdl.handle.net/11147/9
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Book Part Citation - Scopus: 5Epitranscriptomics Changes the Play: M6a Rna Modifications in Apoptosis(Springer, 2022) Akçaöz, Azime; Akgül, BünyaminApoptosis is a form of programmed cell death that is essential for cellular and organismal homeostasis. Any irregularities that disturb the balance between apoptosis and cell survival have severe implications, such as improper development or life-threatening diseases. Thus, it is highly critical to maintain a proper rate of apoptosis throughout development. In fact, several complex transcriptional and posttranscriptional mechanisms exist in eukaryotes to critically regulate the rate of apoptotic processes. Recent studies suggest that not only RNA sequences but also their modifications, such as m6A methylation, play a fundamental role in these transcriptional and posttranscriptional processes. A specific set of proteins, called writer, eraser, and reader of m6A marks, modulate the rate of apoptosis by determining the m6A repertoire and the fate of certain transcripts associated with apoptosis. In this Review, we will cover the dynamic m6A RNA modifications and their impact on modulation of apoptosis.Book Part Citation - Scopus: 15Stem Cell Culture Under Simulated Microgravity(Springer, 2020) Anıl İnevi, Müge; Sarıgil, Öykü; Kızılkaya, Melike; Meşe, Gülistan; Tekin, Hüseyin Cumhur; Özçivici, EnginChallenging environment of space causes several pivotal alterations in living systems, especially due to microgravity. The possibility of simulating microgravity by ground-based systems provides research opportunities that may lead to the understanding of in vitro biological effects of microgravity by eliminating the challenges inherent to spaceflight experiments. Stem cells are one of the most prominent cell types, due to their self-renewal and differentiation capabilities. Research on stem cells under simulated microgravity has generated many important findings, enlightening the impact of microgravity on molecular and cellular processes of stem cells with varying potencies. Simulation techniques including clinostat, random positioning machine, rotating wall vessel and magnetic levitation-based systems have improved our knowledge on the effects of microgravity on morphology, migration, proliferation and differentiation of stem cells. Clarification of the mechanisms underlying such changes offers exciting potential for various applications such as identification of putative therapeutic targets to modulate stem cell function and stem cell based regenerative medicine. © Springer Nature Switzerland AG 2020.Book Part Citation - WoS: 10Synteny Among Solanaceae Genomes(Springer, 2016) Frary, Amy; Doğanlar, Sami; Frary, AnneThe Solanaceae was among the first plant families to be analyzed via comparative mapping and thus was a pioneer in the realm of synteny studies. Analyses of chromosome content and organization have employed a range of techniques, including linkage mapping of genes and molecular markers, physical mapping via fluorescence in situ hybridization, and sequencing of relatively small genomic segments as well as the complete sequencing of the tomato genome. Early comparisons in the family involved tomato and its close relative potato and have extended outward to include eggplant, pepper, tobacco, and petunia. Not surprisingly, the degree of synteny among these species is a function of the time since their divergence, with inversion, translocation, and transposition being the chief mechanisms of chromosome rearrangement. The results of this work provide important insight into the modes and tempo of plant genome evolution while serving a practical purpose as well: knowledge of genome synteny and colinearity makes it easier to leverage resources from one species to another in this agronomically important family.Book Part Citation - WoS: 59Citation - Scopus: 68Stem Cell Therapy for Multiple Sclerosis(Springer, 2019) Genç, Bilgesu; Bozan, Hemdem Rodi; Genç, Şermin; Genç, KürşadMultiple sclerosis (MS) is a chronic inflammatory, autoimmune, and neurodegenerative disease of the central nervous system (CNS). It is characterized by demyelination and neuronal loss that is induced by attack of autoreactive T cells to the myelin sheath and endogenous remyelination failure, eventually leading to functional neurological disability. Although recent evidence suggests that MS relapses are induced by environmental and exogenous triggers such as viral infections in a genetic background, its very complex pathogenesis is not completely understood. Therefore, the efficiency of current immunosuppression-based therapies of MS is too low, and emerging disease-modifying immunomodulatory agents such as fingolimod and dimethyl fumarate cannot stop progressive neurodegenerative process. Thus, the cell replacement therapy approach that aims to overcome neuronal cell loss and remyelination failure and to increase endogenous myelin repair capacity is considered as an alternative treatment option. A wide variety of preclinical studies, using experimental autoimmune encephalomyelitis model of MS, have recently shown that grafted cells with different origins including mesenchymal stem cells (MSCs), neural precursor and stem cells, and induced-pluripotent stem cells have the ability to repair CNS lesions and to recover functional neurological deficits. The results of ongoing autologous hematopoietic stem cell therapy studies, with the advantage of peripheral administration to the patients, have suggested that cell replacement therapy is also a feasible option for immunomodulatory treatment of MS. In this chapter, we overview cell sources and applications of the stem cell therapy for treatment of MS. We also discuss challenges including those associated with administration route, immune responses to grafted cells, integration of these cells to existing neural circuits, and risk of tumor growth. Finally, future prospects of stem cell therapy for MS are addressed.Book Part Citation - Scopus: 9Differential Expression of Toxoplasma Gondii Micrornas in Murine and Human Hosts(Springer, 2016) Allmer, Jens; Saçar Demirci, Müşerref Duygu; Bağcı, CanerMicroRNAs are short RNA sequences involved in post-transcriptional gene regulation. MicroRNAs are known for a wide variety of species ranging from bacteria to plants. It has become clear that some cross-kingdom regulation is possible especially between viruses and their hosts. We hypothesized that intracellular parasites, like Toxoplasma gondii, similar to viruses would be able to modulate their host’s gene expression. We were able to show that T. gondii produces many putative pre-miRNAs which are actually transcribed. Furthermore, some of these expressed pre-miRNAs have a striking resemblance to host mature miRNAs. Previous studies indicated that T. gondii infection coincides with increased abundance of some miRNAs. Here we were able to show that many of these miRNAs have close relatives in T. gondii which may not be distinguishable using PCR. Taken together, the similarity to host miRNAs, their confirmed expression, and their upregulation during infection, it suggests that T. gondii actively transfers miRNAs to regulate its host. We conclude, that this type of cross-kingdom regulation may be possible, but that targeted analysis is necessary to consolidate our computational findings. © Springer International Publishing Switzerland 2016. All rights are reserved.Book Part Citation - Scopus: 4Epigenetics of Breast Cancer: Dna Methylome and Global Histone Modifications(Springer, 2016) Meşe, Gülistan; Yalçın Özuysal, ÖzdenBreast cancer, a heterogeneous disease comprised of tumors with different histological characteristics and clinical outcomes, is the leading cause of cancer deaths in women. Heterogeneous nature of the breast cancer demands delicate approaches to diagnose and follow the most appropriate strategy for clinical management. Based on microarray analysis of mRNA expression, four main molecular subtypes were identified: (a) luminal A, (b) luminal B, (c) basal-like, and (d) ERBB2(+). Even though molecular subtypes provided novel insights into our understanding of breast cancer heterogeneity, there is still room for improvement for better diagnostic, prognostic and therapeutic approaches. In this sense, epigenetics, specifically DNA methylation and histone modifications, have emerged as prominent candidates since several epigenetic factors were observed to be recurrently mutated in cancers including breast cancer. Recent advances in the field implicated that DNA methylation profiles and histone modifications are strongly associated with breast tumor subtypes and patient prognosis. Therefore, understanding contributions of epigenetics to breast cancer biology will lead to better diagnostic and prognostic strategies and will enable development of novel therapeutic approaches. © Springer International Publishing Switzerland 2016.