22 results on '"Tazebay, Uygar H."'
Search Results
2. Coiled-coil domain-containing protein-124 (Ccdc124) is a novel RNA binding factor up-regulated in endometrial, ovarian, and urinary bladder cancers
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Arslan, Özge, primary, Soylu, Neşe Karadağ, additional, Akillilar, Pelin Telkoparan, additional, and Tazebay, Uygar H., additional
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- 2021
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3. Unliganded estrogen receptor-α activates transcription of the mammary gland Na +/I − symporter gene
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Alotaibi, Hani, Yaman, Elif Çankaya, Demirpençe, Ediz, and Tazebay, Uygar H.
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- 2006
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4. The mammary gland iodide transporter is expressed during lactation and in breast cancer
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Tazebay, Uygar H., Wapnir, Irene L., Levy, Orlie, Dohan, Orsolya, Zuckier, Lionel S., Hua Zhao, Qing, Fu Deng, Hou, Amenta, Peter S., Fineberg, Susan, Pestell, Richard G., and Carrasco, Nancy
- Abstract
The sodium/iodide symporter mediates active iodide transport in both healthy and cancerous thyroid tissue. By exploiting this activity, radioiodide has been used for decades with considerable success in the detection and treatment of thyroid cancer. Here we show that a specialized form of the sodium/iodide symporter in the mammary gland mediates active iodide transport in healthy lactating (but not in nonlactating) mammary gland and in mammary tumors. In addition to characterizing the hormonal regulation of the mammary gland sodium/iodide symporter, we demonstrate by scintigraphy that mammary adenocarcinomas in transgenic mice bearing Ras or Neu oncogenes actively accumulate iodide by this symporter in vivo. Moreover, more than 80% of the human breast cancer samples we analyzed by immunohistochemistry expressed the symporter, compared with none of the normal (nonlactating) samples from reductive mammoplasties. These results indicate that the mammary gland sodium/iodide symporter may be an essential breast cancer marker and that radioiodide should be studied as a possible option in the diagnosis and treatment of breast cancer., Author(s): Uygar H. Tazebay [1, 8]; Irene L. Wapnir [5, 8]; Orlie Levy [1, 7]; Orsolya Dohan [1]; Lionel S. Zuckier [2]; Qing Hua Zhao [2]; Hou Fu Deng [2]; [...]
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- 2000
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5. Intronic elements in the Na+/I- symporter gene (NIS) interact with retinoic acid receptors and mediate initiation of transcription
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Alotaibi, Hani, Yaman, Elif, Salvatore, Domenico, Di Dato, Valeria, Telkoparan, Pelin, Di Lauro, Roberto, and Tazebay, Uygar H.
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- 2010
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6. RasGEF1A and RasGEF1B are guanine nucleotide exchange factors that discriminate between Rap GTP-binding proteins and mediate Rap2-specific nucleotide exchange
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Yaman, Elif, Gasper, Raphael, Koerner, Carolin, Wittinghofer, Alfred, and Tazebay, Uygar H.
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- 2009
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7. Coiled-Coil Domain Containing Protein 124 Is a Novel Centrosome and Midbody Protein That Interacts with the Ras-Guanine Nucleotide Exchange Factor 1B and Is Involved in Cytokinesis
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Telkoparan, Pelin, primary, Erkek, Serap, additional, Yaman, Elif, additional, Alotaibi, Hani, additional, Bayık, Defne, additional, and Tazebay, Uygar H., additional
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- 2013
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8. Fiber laser-microscope system for femtosecond photodisruption of biological samples
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Yavaş, Seydi, primary, Erdogan, Mutlu, additional, Gürel, Kutan, additional, Ilday, F. Ömer, additional, Eldeniz, Y. Burak, additional, and Tazebay, Uygar H., additional
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- 2012
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9. Texturing of titanium (Ti6Al4V) medical implant surfaces with MHz-repetition-rate femtosecond and picosecond Yb-doped fiber lasers
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Erdoǧan, Mutlu, primary, Öktem, Bülent, additional, Kalaycıoǧlu, Hamit, additional, Yavaş, Seydi, additional, Mukhopadhyay, Pranab K., additional, Eken, Koray, additional, Özgören, Kıvanç, additional, Aykaç, Yaşar, additional, Tazebay, Uygar H., additional, and Ilday, F. Ömer, additional
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- 2011
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10. The Ability to Generate Senescent Progeny as a Mechanism Underlying Breast Cancer Cell Heterogeneity
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Mumcuoglu, Mine, primary, Bagislar, Sevgi, additional, Yuzugullu, Haluk, additional, Alotaibi, Hani, additional, Senturk, Serif, additional, Telkoparan, Pelin, additional, Gur-Dedeoglu, Bala, additional, Cingoz, Burcu, additional, Bozkurt, Betul, additional, Tazebay, Uygar H., additional, Yulug, Isik G., additional, Akcali, K. Can, additional, and Ozturk, Mehmet, additional
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- 2010
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11. The Comparative Effects of Gene Modulators on Thyroid-Specific Genes and Radioiodine Uptake
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Tuncel, Murat, primary, Aydin, Didem, additional, Yaman, Elif, additional, Tazebay, Uygar H., additional, Güç, Dicle, additional, Doğan, A. Lale, additional, Taşbasan, Burçin, additional, and Uğur, ömer, additional
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- 2007
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12. Unliganded estrogen receptor-α activates transcription of the mammary gland Na+/I− symporter gene
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Alotaibi, Hani, primary, Yaman, Elif Çankaya, additional, Demirpençe, Ediz, additional, and Tazebay, Uygar H., additional
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- 2006
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13. Ras Protein Ailesi: Hücresel İşlevi, Moleküler Kontrolü, Onkogenezdeki Rolü.
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Telkoparan, Pelin and Tazebay, Uygar H.
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PROTEINS , *BIOMOLECULES , *G proteins , *MEMBRANE proteins , *RAS proteins - Abstract
Small GTPases belonging to Ras family of proteins have key roles in regulating nearly every aspect of cell biology, such as cell division, cellular differentiation, vesicular transport and localization of cargo proteins, cell morphology, and gene expression. Depending on the extra- cellular signals, Ras family members oscillate between GTP-bound (active) and GDP-bound (inactive) conformations, and in the active form they interact with downstream effector molecules, leading to conformational changes in those effectors. As a result, extracellular signals trigger cellular responses, by means of initiation of a phosphorylation cascade. Functional cycles of Ras family of proteins include interactions with GTPase Activating Proteins (GAPs), and with Guanine Nucleotide Exchange Factors (GEFs) that regulate these small GTPases. GAP proteins activate intrinsic GTP hydrolysis activities of these small G-proteins, and convert active Ras-GTP to inactive Ras-GTP. On the other hand, GEF proteins interact with inactivated Ras-GDP molecules, and convert those inactivated molecules back to activated Ras-GTP, by triggering dissociation of GDP, and reassociation of Ras with GTP which is found at higher concentrations as compared to GDP in the cell cytoplasm. It is well known that mutations in Ras that block these molecules in GTP-bound forms by impairing GTP hydrolysis activity could trigger an uncontrolled and aberrant cellular proliferation. This type of mutations in Ras genes causing uncontrolled activation of the protein, are found in approximately 30% of human cancers overall, and they indicate the significance of mutations in genes encoding Ras family members in cellular proliferation related to de novo oncogenesis in human. [ABSTRACT FROM AUTHOR]
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- 2011
14. Unliganded estrogen receptor-α activates transcription of the mammary gland Na+/I− symporter gene
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Alotaibi, Hani, Yaman, Elif Çankaya, Demirpençe, Ediz, and Tazebay, Uygar H.
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TRETINOIN , *GENE expression , *ESTROGEN , *MAMMARY glands - Abstract
Abstract: The function of sodium iodide symporter (Na+/I− symporter, or NIS) in mammary epithelial cells is essential for the accumulation of I− in milk; the newborn’s first source of I− for thyroid hormone synthesis. Furthermore, increased mammary gland NIS expression has previously been shown in human breast cancer. Several hormones and factors including all-trans-retinoic acid (tRA) regulate the expression of NIS. In this study, using breast cancer cell lines, we established that tRA-responsive NIS expression is confined to estrogen receptor-α (ERα) positive cells and we investigated the role of ERα in the regulation of NIS expression. We showed that the suppression of endogenous ERα by RNA interference downregulates NIS expression in ERα positive mammary cells. Besides, in an ERα negative cell line, reintroduction of ERα resulted in the expression of NIS in a ligand-independent manner. We also identified a novel estrogen-responsive element in the promoter region of NIS that specifically binds ERα and mediates ERα-dependent activation of transcription. Our results indicate that unliganded ERα (apo-ERα) contributes to the regulation of NIS gene expression. [Copyright &y& Elsevier]
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- 2006
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15. Fiber laser-microscope system for femtosecond photodisruption of biological samples
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Kutan Gürel, Uygar H. Tazebay, Seydi Yavas, Mutlu Erdogan, Y. B. Eldeniz, Fatih Omer Ilday, Yavaş, Seydi, Erdoğan, Mutlu, Gürel, Kutan, İlday, F. Ömer, and Tazebay, Uygar H.
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ocis:(170.7160) Ultrafast technology ,Microscope ,Materials science ,ocis:(170.1020) Ablation of tissue ,Photodisruption ,Acousto-optic modulator ,Cells ,Field programmable gate arrays (FPGA) ,Mu-m ,Femtoseconds ,Ablation ,law.invention ,Fiber lasers ,Realtime imaging ,Biological samples ,Optics ,Mode-locked ,law ,Fiber laser ,Pulse generators ,Ytterbium ,Individual cells ,Tissue ,Sample position ,business.industry ,Arbitrary pulse ,Pulse generator ,Repetition rate ,Biological targets ,Dechirping ,Diffraction limited ,Laser ,Mode-locked fiber lasers ,Atomic and Molecular Physics, and Optics ,Laser-Tissue Interactions ,Ablation process ,Nanosurgery ,Femtosecond ,Grating compressors ,Exposure-time ,business ,Ultrashort pulse ,Ultra-fast ,Yb fiber lasers ,Biotechnology - Abstract
Cataloged from PDF version of article. We report on the development of a ultrafast fiber laser-microscope system for femtosecond photodisruption of biological targets. A mode-locked Yb-fiber laser oscillator generates few-nJ pulses at 32.7 MHz repetition rate, amplified up to similar to 125 nJ at 1030 nm. Following dechirping in a grating compressor, similar to 240 fs-long pulses are delivered to the sample through a diffraction-limited microscope, which allows real-time imaging and control. The laser can generate arbitrary pulse patterns, formed by two acousto-optic modulators (AOM) controlled by a custom-developed field-programmable gate array (FPGA) controller. This capability opens the route to fine optimization of the ablation processes and management of thermal effects. Sample position, exposure time and imaging are all computerized. The capability of the system to perform femtosecond photodisruption is demonstrated through experiments on tissue and individual cells. (c) 2012 Optical Society of America
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- 2012
16. The ability to generate senescent progeny as a mechanism underlying breast cancer cell heterogeneity
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Hani Alotaibi, Betül Bozkurt, Bala Gur-Dedeoglu, Mehmet Ozturk, Mine Mumcuoglu, Isik G. Yulug, Pelin Telkoparan, Uygar H. Tazebay, Burcu Cingoz, Sevgi Bagislar, Haluk Yuzugullu, K. Can Akcali, Serif Senturk, Mumcuoğlu, Mine, Bağışlar, Sevgi, Yüzügüllü, Haluk, Alotaibi, Hani, Şentürk, Şerif, Telkoparan, Pelin, Gür-Dedeoğlu, Bala, Cingöz, Burcu, Tazebay, Uygar H., Yuluğ, Işık G., Akçalı, Kamil Can, and Öztürk, Mehmet
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CD24 antigen ,Pathology ,medicine.medical_specialty ,Cellular differentiation ,Cell ,Blotting, Western ,Cell Biology/Cell Growth and Division ,Estrogen receptor ,lcsh:Medicine ,Breast Neoplasms ,Biology ,Cyclin dependent kinase inhibitor 1 ,Cell Line, Tumor ,Receptors ,medicine ,Cluster Analysis ,Humans ,Progenitor cell ,skin and connective tissue diseases ,lcsh:Science ,Hermes antigen ,Multidisciplinary ,CD24 ,CD44 ,lcsh:R ,Myoepithelial cell ,Cell Biology/Cellular Death and Stress Responses ,Immunohistochemistry ,Tamoxifen ,medicine.anatomical_structure ,Receptors, Estrogen ,Cell culture ,Oncology/Breast Cancer ,Cancer research ,biology.protein ,Female ,lcsh:Q ,Research Article - Abstract
BACKGROUND: Breast cancer is a remarkably heterogeneous disease. Luminal, basal-like, "normal-like", and ERBB2+ subgroups were identified and were shown to have different prognoses. The mechanisms underlying this heterogeneity are poorly understood. In our study, we explored the role of cellular differentiation and senescence as a potential cause of heterogeneity. METHODOLOGY/PRINCIPAL FINDINGS: A panel of breast cancer cell lines, isogenic clones, and breast tumors were used. Based on their ability to generate senescent progeny under low-density clonogenic conditions, we classified breast cancer cell lines as senescent cell progenitor (SCP) and immortal cell progenitor (ICP) subtypes. All SCP cell lines expressed estrogen receptor (ER). Loss of ER expression combined with the accumulation of p21(Cip1) correlated with senescence in these cell lines. p21(Cip1) knockdown, estrogen-mediated ER activation or ectopic ER overexpression protected cells against senescence. In contrast, tamoxifen triggered a robust senescence response. As ER expression has been linked to luminal differentiation, we compared the differentiation status of SCP and ICP cell lines using stem/progenitor, luminal, and myoepithelial markers. The SCP cells produced CD24+ or ER+ luminal-like and ASMA+ myoepithelial-like progeny, in addition to CD44+ stem/progenitor-like cells. In contrast, ICP cell lines acted as differentiation-defective stem/progenitor cells. Some ICP cell lines generated only CD44+/CD24-/ER-/ASMA- progenitor/stem-like cells, and others also produced CD24+/ER- luminal-like, but not ASMA+ myoepithelial-like cells. Furthermore, gene expression profiles clustered SCP cell lines with luminal A and "normal-like" tumors, and ICP cell lines with luminal B and basal-like tumors. The ICP cells displayed higher tumorigenicity in immunodeficient mice. CONCLUSIONS/SIGNIFICANCE: Luminal A and "normal-like" breast cancer cell lines were able to generate luminal-like and myoepithelial-like progeny undergoing senescence arrest. In contrast, luminal B/basal-like cell lines acted as stem/progenitor cells with defective differentiation capacities. Our findings suggest that the malignancy of breast tumors is directly correlated with stem/progenitor phenotypes and poor differentiation potential.
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- 2010
17. Monoclonal antibody production for coiled-coil domain containing-124 (CCDC-124) and its molecular characterization
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Gürbüz, İrem, Tazebay, Uygar Halis, Moleküler Biyoloji ve Genetik Anabilim Dalı, and Tazebay, Uygar H.
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Antibodies--genetics ,Antibodies, Monoclonal ,Gene expression ,Monoclonal antibodies ,Immunoglobulin genes ,QW575.5.A6 G87 2010 ,Biology ,Biyoloji - Abstract
Sarılı-sarmal-bölge-içeren-124 (Coiled-coil domain containing-124; CCDC-124) henüz fonksiyonu belirlenmemiş olan yeni bir gendir. Bu gen ökaryotlar arasında korunmuştur ve genin 223 amino asitten oluşan bir protein kodladığı düşünülmektedir. Geçmişte Tazebay grup projeleri kapsamında yapılan maya ikili hibrid deneyleri, CCDC-124 proteinin RasGEF1B guanine değiştirme faktörü ile etkileşim halinde olduğunu göstermiştir. RasGEF1B'nin ise Rap2'ye özgü bir guanine değiştirme faktörü olduğu araştırmalarda gösterilmiştir. CCDC-124 proteinin hücre içindeki fonksiyonunu ortaya çıkarmak için, Western Blotlama ve hücre içindeki yer taramalarını da içeren çeşitli biyokimyasal deneyler yapılmıştır. Bu deneylerde, CCDC-124 proteininin N-uç bölgesini tanıyan, bir poliklonal antikor kullanılmıştır. Fakat, antikorun poliklonal doğası doğrultusunda, bir çok, spesifik olmayan bağlanma da görülmüştür. Yapılan deneylerde, genin 33 kDa'lık bir proteini kodladığı ve proteinin hücre içinde dağınık, sitoplazmik bir yerleşim izlediği gözlemlenmiştir. Fakat, spesifik olmayan bağlanmalar da göz önüne alındığında, bu sonuçlar kesin değildir. Proteinin daha hassas bir şekilde algılanabilmesi için, CCDC-124 proteinine karşı monoclonal antikorlar üretilmiştir. Bu proje süresince farelere His işaretli CCDC-124 proteini enjekte edilmiştir. Antikorlar hibridoma teknolojisi ile üretilmiş ve daha sonra, bağlanma kapasiteleri doğrultusunda seçilmişlerdir. Proje neticesinde 3 adet hibridoma klonu elde edilmiştir. Bunlar 7F7, 15C11 ve 4B3 klonlarıdır. Üretilen antikorları karakterize etmek amacıyla Western Blotlama deneyleri yapılmış ve antikorların bağlanma özellikleri poliklonal antikor ile karşılaştırılmıştır. 3 antikor içinde, 33 kDa'da, en net sonucu veren 4B3 klonu olmuştur. Üretilen antikorlar, ileride, proteinin hücre içindeki yerinin belirlenmesinde ve bu yerin dışarıdan gelen sinyaller doğrultusunda değişip değişmemesinin araştırılmasında kullanılacaktır. Bu tür deneyler, CCDC-124 proteininin hücre içindeki fonksiyonunun araştırılmasına ışık tutacaktır. Coiled-coil-domain-containing-124 (CCDC-124) is a novel protein of unknown function. The Ccdc-124 gene is highly conserved among eukaryotic species and is predicted to encode a 223 amino acids long protein. Yeast-two-hybrid assays had shown that CCDC-124 interacts with RasGEF1B guanine exchange factor, which was previously identified as a specific guanine exchange factor for Rap2, a member of the Rap subfamily of Ras-like G-proteins. In order to reveal the cellular function of CCDC-124 protein, different biochemical experiments, including Western Blotting and Sub-cellular localization studies were performed. In those experiments, a polyclonal antibody against an N-terminal peptide of CCDC-124 was used. Nevertheless, due to its polyclonal nature this antibody exhibited non-specific binding. Although it was determined that the gene encodes a 33 kDa protein and that the protein has diffused cytoplasmic localization, the results were not precise. In order to detect the protein more accurately, monoclonal antibodies were generated against CCDC-124. Throughout the project, mice were injected with pure His-Tagged CCDC-124 protein. Via hybridoma technology antibodies were generated and selected for their recognition capacities. At the end, 3 positive hybridoma clones were produced: 7F7, 15C11 and 4B3. To characterize the produced monoclonal antibodies, Western Blot experiments were performed and their binding properties were compared to the polyclonal antibody. Among the three monoclones, 4B3 gave the most promising results at 33 kDa, in Western Blotting. The antibodies will be used in the determination of the protein's sub-cellular localization and in the analysis of its response to extracellular signals. These in turn will aid further analyses related to the protein's role within the cell. 73
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- 2010
18. Ras guanin değişim faktörü-1 (RasGEF1) ailesi proteinlerin Rap2 aktivatörleri olarak tanımlanması ve Ccdc-124 ile etkileşiminlerinin belirlenmesi
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Yaman, Elif, Tazebay, Uygar H., Tazebay, Uygar Halis, and Moleküler Biyoloji ve Genetik Anabilim Dalı
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Genetics ,Protein-protein interactions ,Genetik ,QP551.5 .Y36 2009 - Abstract
Ccdc-124 geni bütün ökaryot canlılarda korunmuştur. Ccdc-124 proteininde bilinen protein motiflerine gözlemlenmemiştir. Bu tez kapsamında yapılan çalışmalarda, maya ikili hibrit analizleri sonucunda, guanin nükleotid değişim faktörü olduğu düşünülen RasGEF1B'nin Ccdc-124 ile etkileştiği bulunmuştur. Fonksiyonu ve özelliği bilinmeyen, ancak yüksek oranda korunmuş olan RasGEF1 ailesi proteinlerinin, C-ucunda CDC25-Homoloji Bölgesi, N-ucunda ise RasGEF-N, Ras Değişim Motifi, bölgesi bulunmaktadır. Ccdc-124 ve RasGEF1 ailesi proteinlerinin birbirlerine bağlanması immünopresipitasyon ve GST çöktürme yöntemleri ile de doğrulanmıştır. Saflaştırılmış RasGEF1A, RasGEF1B ve birçok Ras ailesi proteinleri kullanılarak yapılan deneylerde, RasGEF1A ve RasGEF1B proteinlerinin Ras benzeri G poteinlerinden sadece Rap2'ye özgün değiştirici faktör olarak ekileştiği bulunmuştur. Bu proteinler Rap1 ve diğer Ras ailesi proteinlerine etki etmemişlerdir. Diğer yandan, Ccdc-124 proteini, in vitro deneylerde, RasGEF1 ailesinin hiçbir G proteini stimülasyonunu da etkilememiştir. Karşılıklı bölge-yönelimli mutagenez ile RasGEF1 proteinlerinin Rap1 ve Rap2 proteinlerini ayırt edici bölgesi analiz edilmiş ve Rap2'nin switch I bölgesinde yeralan fenilalanin39'un özgüllüğü sağlayan amino asit olduğu bulunmuştur. Rap1 üzerinde bu bölgeye karşılık gelen serin39'un mutasyonu ise RasGEF1B ile stimülasyonunu sağlamaktadır. Bu çalışma sonucunda insan hücrelerinde sadece Rap2'ye özgün bir nükleotid değiştirici faktörün varlığı ilk defa belirlenmiştir. Coiled coil domain-124 gene is highly conserved among eukaryotes and the human counterpart encodes a protein with no domain similarities with any previously characterized eukaryotic proteins. In this study, we aimed to identify biological functions and interaction partners of human Ccdc-124. A yeast-two-hybrid analysis carried in this study has revealed that Ccdc-124 interacts with RasGEF1B which was predicted to be a member of Ras guanine exchange factors. The highly conserved RasGEF1 family of proteins contain C-terminal CDC25-homology domain (CDC25-HD) and an N-terminal RasGEF-N domain (Ras Exchange Motif, REM), and is of unknown function and specificity. In this thesis, the interaction of Ccdc-124 and RasGEF1 family of proteins was also established with co-immunoprecipitation and GST pull down assays. On the other hand, by using purified RasGEF1A and RasGEF1B proteins, as well as a large number of Ras family of G-proteins, we established that RasGEF1A and RasGEF1B function as very specific exchange factors for Rap2, a member of the Rap subfamily of Ras-like G-proteins. They do not act on Rap1 or other members of the Ras subfamily. On the other hand, Ccdc-124 protein did not change the stimulatory effect of RasGEF1 family of proteins on any of the tested G proteins in vitro. Furthermore, using reciprocal site-directed mutagenesis, we analyzed residues that allow RasGEF1 proteins to discriminate between Rap1 and Rap2, and we were able to identify Phe39 in the switch I region of Rap2 as a specificity residue. Mutation of the corresponding Ser39 in Rap1 changed the specificity and allowed the nucleotide exchange of Rap1(S39F) to be stimulated by RasGEF1B. This study describes for the first time GEFs that are uniquely specific for Rap2 among Rap family of G-proteins. 121
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- 2009
19. HANEIN-1, tüm insan dokularında ifadesi görülen korunmuş yeni bir ökaryotik protein
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Erkek, Serap, Tazebay, Uygar Halis, Moleküler Biyoloji ve Genetik Anabilim Dalı, and Tazebay, Uygar H.
- Subjects
Genetic transcription ,Functional analysis ,Proteins--Analysis ,QP551 .E74 2008 ,Eukaryetic cells ,Biology ,Biyoloji - Abstract
HANEIN-1 Na+/I- simporter geninin 3' regulasyon elementleri araştırılırken keşfedilen yeni bir gendir. Bu yeni protein bütün ökaryot canlılarda korunmakla birlikte, bilinen hiçbir proteinle ortak işlevsel bölgelere sahip değildir. Veritabanlarında kıvrım-kıvrım (coiled-coil) bölge içeren-124 hipotetik proteini olarak tanımlanmakta ve 223 amino asit içeren bir protein olduğu tahmin edilmektedir. Bu projededeki amaç HANEIN-1 proteinini çeşitli biyoinformatik ve biyokimyasal analiz yöntemleriyle karakterize etmekti. HANEIN-1 proteinin amino acid dizi benzerliği analizi, bu proteinin memelilerde %75, böcek ve nematodlarda ise % 50 oranında korunduğunu gösterdi. Gen ifade analiz yöntemleri ile HANEIN-1 ifadesinin en fazla iskelet kasında olduğu tespit edildi. Bunun yanı sıra, northern blot analizi ile HANEIN-1 transcript büyüklüğü yaklaşık 1000 bp olarak belirlendi. Western blot tekniği ile protein düzeyinde yapılan çalışmalar, HANEIN-1 geninin 33 kDa büyüklüğünde bir proteini kodladığını ve proteini N-son ucu ve C-son ucu Flag epitopu ile işaretlemenin protein stabilitesini farklı şekilde etkilediğini gösterdi. Laboratuvarımızda yapılan maya ikili-hibrid deneyleriyle, HANEIN-1 proteinin henüz tam olarak karakterize edilmemiş, bir guanin nükleotit değişim faktörü (Guanine Exchange Factor) olan RASGEF1B proteiniyle etkileştiği bulunmuştur. Gen ifade analizleri RASGEF1B ve HANEIN-1 ifade profilleri arasında ters bir bağlantı olduğunu göstermiştir. Son olarak, serin-tarayıcı mutasyon analizleriyle, 194. konumdaki serin mutasyonunun protein stabilitesini önemli ölçüde değiştirdiği saptanmıştır. HANEIN-1 was first identified in a study investigating 3? transcriptional regulatory elements of the Na+/I- symporter gene. The protein is highly conserved among eukaryotes and bears no domain similarities with any known proteins. In databases, it is described as coiled coil containing-124 hypothetical protein and predicted to encode a 223 amino acid-protein. In this project, our aim was to characterize this highly conserved protein by using several bioinformatics and biochemical methodologies. Sequence similarity search analysis showed that it had around 75% identity in mammals, 50% identity with insects and nematodes. Expressional analysis revealed that HANEIN-1 was expressed in all tissues ubiquitously with a remarkable expression status in skeletal muscle. Beside providing information about expression status of HANEIN-1, northern blotting showed that HANEIN-1 transcript size was approximately 1000 bp. Regarding protein level expression, western blotting revealed that HANEIN-1 encoded a 33 kDa protein and protein stability was affected in a different way upon labeling with Flag epitope at N-ter and C-ter. Yeast double hybrid screening performed in our laboratory showed that HANEIN-1 interacted with RASGEF1B, which was a guanine nucleotide exchange factor not fully characterized. Expressional analysis displayed that RASGEF1B expression profile inversely correlated with HANEIN-1. Finally, serine-scanning mutagenesis analysis showed that site-directed mutagenesis of serine at position 194 significantly affected the stability of the protein. 63
- Published
- 2008
20. Ökaryotik canlılarda korunmuş olan Loc115098 geninin işlevsel tanımlandırılması
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Karaköse, Esra, Tazebay, Uygar H., Tazebay, Uygar Halis, and Diğer
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Moleküler Tıp ,Biyokimya ,Molecular Medicine ,Aspergillus ,QK623.A9 K37 2007 ,Biochemistry ,Biology ,Biyoloji - Abstract
ÖZETÖKARYOT K CANLILARDA KORUNMUŞ OLAN LOC115098 GEN N NŞLEVSEL TANIMLANDIRILMASIEsra KaraköseMoleküler Biyoloji ve Genetik Yüksek Lisans DerecesiTez Yöneticisi: Yard. Doç. Dr. Uygar H. TazebayOcak 2007, 76 SayfaLoc115098 ilk kez tarafımızdan bulunmuş bir gendir. lk defa bu genin komşusu olanNIS (Sodyum-Iyot Simporter) geninin anlatımından sorumlu cis kontrol bölgelerininaydınlatılması amacıyla yapılan bir çalışma sırasında bulunmuştur. Bu gen 4 eksondanmeydana gelmektedir. Bioınformatik analizlerden faydalanarak yaptığımız araştırmalarbu genin oldukça ilginç özelliklere sahip olduğunu gösterdi, örneğin proteinin yapısıgenel olarak pozitif yüklü amino asitlerden oluşuyor, çekirdek sinyali taşıyor veökaryotik organizmalarda oldukça korunmuş bir şekilde bulunuyor. Bizim bu çalışmadakiamacımız bu genin işlevini anlamaktı. Bu nedenle öncelikle farklı dokularda bu geninifadesi olduğunu teyid ettik. Sonra bu proteinin hücre içersindeki konumunu anlamak içinçalışmalar yaptık. Sonuçlar, bu proteinin hücre döngüsü kontrolüyle ilgili bir işleve sahipolabileceği hipotezini kurmamızı sağladı. Bunun üzerine çalışmalarımızı sürdürmekamacıyla loc115098 geninin homoloğunu taşıyan daha düşük bir ökaryot olan Aspergillusnidulans'ı seçtik. Bu organizma bizim çalışmalarımız açısından oldukça kullanışlıydıçünkü hem loc115098 geninin çok benzer bir homoloğunu taşıyordu hem de bir modelorganizma olarak genetik araştırmalarda sıklıkla kullanılıyordu. Öncelikle loc115098geninin anlatımını çeşitli hücre döngüsü mutasyonlarına sahip olan A. nidulans ırklarındave doğal (wild type) ırkta karşılaştırmalı olarak inceledik. Bu çalışmanın sonucu bizemutant olan ırkların yaşamalarına müsaade etmeyen sıcaklık derecelerinde loc115098ifadesinin azaldığını gösterdi. Aynı zamanda bu organizma ile de LOC115098 proteininhücre içindeki konumlanışını araştırdık ve sonuç bize bu proteinin çoğunluklasitoplazmada bazen de çekirdeğin etrafını saracak şekilde bulunduğunu gösterdi. AyrıcaDouble-Joint PCR adı verilen oldukça sofistike bir metoddan faydalanarak knock-outçalışmalar yaptık ve ilk elde ettiğimiz sonuçlar bize bu genin, hücrenin yaşamsalolaylarından sorumlu bir işleve sahip olabileceğini gösterdi çünkü bu genin knock-outedildiği durumlarda canlının yaşadığı örneklere hiç rastlamadık. Loc115098 genininişlevini aydınlatmaya dair çalışmalarımız halen devam ediyor. ABSTRACTFUNCTIONAL CHARACTERIZATION OF LOC115098: A NOVEL GENECONSERVED IN EUKARYOTIC GENOMESEsra KaraköseM.Sc. in Molecular Biology and GeneticsSupervisor: Assist Prof. Uygar H. TazebayJanuary 2007, 76 PagesLoc115098 is a newly identified gene in our laboratory. The gene was firstly discoveredin an unrelated study in which the cis-acting regulatory elements of a neighboring geneNIS (Sodium-Iodide Symporter) were investigated. It is composed of 4 exons. Accordingto the computational predictions, it has rather interesting features such as having acomposition of mostly charged amino acids, carrying a nuclear localization signal andbeing well conserved throughout the eukaryotic kingdom. Our aim in this study was tounderstand the function of this new gene. Firstly we confirmed that it is expressed inseveral different tissues, later we conducted a subcellular localization study whose resultsled us to hypothesize that the function of loc115098 could be related to cell cycleregulation. According to our hypothesis we decided to utilize a lower eukaryote carryinga human homologue of loc115098 which we selected to be Aspergillus nidulans. It was avery useful model organism for our study not only because it carries a very similarhomologue of loc115098 but also it is an easily handled organism which is widely usedfor genetic studies. Firstly we compared the expression profile of loc115098 in severalcell cycle mutants of A. nidulans as well as a wild type strain, the results indicated thatthe expression of loc115098 decreases in the restrictive temperature of cell cycle mutantstrains. We also conducted subcellular localization studies in A. nidulans and the resultsindicated that it was mostly cytoplasmic and sometimes perinuclear. Our other aim was toutilize A. nidulans as a model for our knock-out experiments. We designed a knock-outsystem by the help of a sophisticated method called Double-Joint PCR. Our first attemptssupported that the knock-out of loc115098 was likely to cause lethality in the organismand therefore we improved our system to conditionally knock out the gene. Ourpreliminary results indicated that the knock out of loc115098 causes cell death and wesuspect that it could be due to a damage in one of the crucial metabolic events for cellviability such as mitosis. Our attempts to functionally characterize the function ofloc115098 are currently going on. 76
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- 2007
21. Identification of novel genetic elements controlling transcriptional regulation of the human Na(formula)/I(formula) symporter (NIS) gene
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Alotaibi, Hani and Tazebay, Uygar H.
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Genetic transcription ,QH450.2 .A45 2006 ,health care economics and organizations - Abstract
Cataloged from PDF version of article. The function of sodium iodide symporter (NIS) in mammary gland epithelial cells is essential for the accumulation of iodide in mother’s milk, which is the first source of iodide for the synthesis of thyroid hormones in the newborn. In addition to the lactating mammary gland, NIS expression has been also detected in breast tumors. Several hormones and ligands have been implicated in the functional expression of NIS in the mammary gland and breast cancer cell line models but the molecular determinants governing this expression are not yet identified. In this study we aimed to identify cis- and trans-acting elements regulating NIS expression in the breast cancer cell line MCF-7 in response to all-trans-retinoic acid (tRA), and to assess the possible role of 17-β-estradiol (E2) in regulating the expression of NIS. Using comparative bioinformatics, we have identified several regions that were conserved in human, mouse and rat in the sequences flanking and including the NIS gene. By using luciferase reporter assays, we have established that conserved clusters 3 and 4 respond to tRA in MCF-7. We have also shown that putative retinoic acid response elements controlling tRA-induced NIS expression in MCF-7 are located in the first intron of this gene. This tRA-responsive NIS expression was also correlated with the estrogen receptor status of mammary gland cell lines and we investigated roles of ERα in the regulation of NIS expression. We showed that the suppression of endogenous ERα by RNA interference resulted in down-regulation of both basal and tRA-induced NIS expression in MCF-7, furthermore, we have also shown that (E2) is capable of up-regulating NIS expression in MCF-7. In the ERα negative cell line MDA-MB-231, re-introduction of ERα resulted in NIS expression in a ligand independent manner. The role of ERα in the regulation of NIS expression was supported by the identification of an estrogen response element (ERE) in the promoter of NIS, this ERE was conserved in human, mouse and rat. We have also showed that this ERE could respond to E2 stimulation, and that ERα occupies the NIS promoter by binding to this novel element in vivo. These results indicate that E2 and ERα contribute to the regulation of NIS in the breast cancer cell line MCF-7. Alotaibi, Hani Ph.D.
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- 2006
22. Meme dokusunda sodyum iyot taşıyıcı proteinin estradiyol ile regülasyonu
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Gülbağci, Neriman Tuba, Tazebay, Uygar H., Tazebay, Uygar Halis, and Diğer
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Sodium iodine symporter ,WP870 .G85 2002 ,Breast Neoplasms ,ER-α ,Tretinoin ,Estrogens ,Breast ,Breast neoplasms ,NIS ,Estrogen ,RA ,Medical Biology ,Tıbbi Biyoloji - Abstract
ÖZET Meme Dokusunda Sodyum İyot Taşıyıcı Proteinin Estradiyol ile Regülasyonu Neriman Tuba Gülbağcı M.S. Moleküler Biyoloji ve Genetik Danışman: Assist. Prof. H. Uygar Tazebay Ağustos 2002, 64 sayfa Sodyum İyot Taşıyıcısı (NIS) tiroid bezi, meme dokusu, miğde ve tükrük bezlerinde sentezlenen bir hücre zan proteinidir. MS proteininin tiroid bezindeki transkripsiyonel kontrolünde rol alan cis- ve trans-etkin genetik elemanlar daha önce belirlenmiştir. Nevar ki meme dokusunda NIS 'in transkripsiyonunun hangi hormonlar tarafından düzenlendiği belirlenmiş ancak cis- ve trans-etkin elemanlar henüz belirlenmemiştir. Farelerle yapılan in vivo deneylerde elde edilen sonuçlarda östrojenin memede NIS transkripsiyonel düzenlenmesinde indükleyici bir etkisi olduğu gösterilmişti. Bu çalışmada, (ER(+) östrojen reseptörü içeren MCF-7 meme kanser hücrelerinde yapılan araştırmalar, bu hücre hattında NIS transkripsiyonunu artırabilmek için retinoik asitin gerekli olduğunu ancak estradiolun bu artışa etkisi olmadığını göstermiştir. ER(-) MDA-MB-231 meme kanser hücrelerinde ERa nın varlığı ERE elemanları indüklemesine rağmen mgNIS transkripsiyonunu indükleyebilmek için yetersiz kalmıştır. İlginç bir sonuç olarak, çalışmamız ER antagonisti olan tamoksifenin MCF-7 hücrelerinde RA yokluğuna rağmen NIS transkripsiyonunu indüklediğini göstermiştir. Bu sonuç memede NIS regülasyonu ve östrojene dayalı kontrol mekanizmaları arasında bir ilişki olduğuna işaret etmektedir. ER(+) meme kanseri tedavisinde kullanılan etkin bir ilaç olan tamoksifenin bir de NIS genini memede artırması, tamoksifen tedavisine tabi tutulan tümörlerin radyoaktif iyot izotopları kullanılarak da gözlemlenmesini ve kontrol altında tutulmasını sağlayabilmesi açısından oldukça ilginç ve meme kanserinde tedaviye yönelik uygulamaları olabilecek bir sonuçtur. 111 ABSTRACT STUDIES ON ESTRADIOL DEPENDENT TRANSCRIPTIONAL REGULATION OF HUMAN SODIUM IODD3E SYMPORTER GENE IN MAMMARY GLANDS Neriman Tuba Gülbağcı M.S. in Molecular Biology and Genetics Supervisor: Assist. Prof. H. Uygar Tazebay August 2002, 64 pages Sodium Iodide Symporter (NIS) is a transmembrane protein, which is expressed in thyroid, mammary gland (mg), stomach, and salivary gland. NIS' s transcriptional regulation in terms of cis-and trans-acting elements in thyroid gland is widely studied. However, despite identification of NIS and studies on its hormonal regulation in mammary gland, cis-and trans-acting elements controlling the mgNIS gene in this tissue are not identified yet. From in vivo experiments, it was learned that estrogen has an up regulatory effect on mgNIS transcriptional regulation. In this study, it was shown that in vitro, estrogen (even in pharmacological concentrations) was not able to induce mgNIS in estrogen receptor positive (ER(+)) MCF-7 breast carcinoma cells, and it had no additive effect on retinoic acid (RA) in NIS up regulation when it was administered in physiological concentrations. In ER (-) MDA-MB-231 breast cancarcinoma cells, ERa might be insufficient to induce mgNIS transcription inspite of the fact that ERa was able to transactivate ERE elements. Interestingly, our study indicates that tamoxifen antagonist of ER, together with estrogen induces mgNIS transcription in MCF-7 cell lines in the absence of RA. This study clearly shows the presence of a yet unidentified link between mgNIS regulation and estrogen responsive mechanisms. Bearing in mind that tamoxifen is a powerful substance in treatment of ER(+) breast cancers, and that radioactive iodide is used in thyroid cancer diagnosis and treatment. This weak induction of mgNIS expression in response to tamoxifen may also have interesting novel applications in fight against breast cancer...`is,,--'..A `/ Key Words: NIS, Estrogen, ER-a, RA. s^^Si^r.,:& 64
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- 2002
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