Development of a non-immunological system for the study of the cellular localization of BRCA1 gene product in living cells

Ankara : The Department of Molecular Biology and Genetics and The Institute of Engineering and Science of Bilkent Univ., 1997.Thesis (Master's) -- Bilkent University, 1997.Includes bibliographical references leaves 64-71.BRCAl, is a familial breast and ovarian cancer susceptibility gene that has been cloned and shown to be either lost or mutated in families with breast and ovarian cancer. BRCAl, has been postulated to encode a tumor suppressor, a protein that acts as a negative regulator of tumor growth. To explore the biolo^cal function of BRCAl, several studies have been performed for the identification of cellular localization of BRCAl gene product. Results obtained from these immunofluorescent/ immunohistochemical studies generated two opposing views, cytoplasmic localization versus nuclear localization. Here, we describe a non-immunological system employing the Eukaiyotic Green fluorescent Protein (EGFP) tag for the study of the cellular localization of BRCAl gene product in living cells. Proteins carrying the green fluorescent protein (GFP) of Aequorea victoria provide a powerful system to analyze protein expression and targeting in living cells. Fusion proteins containing the GFP tag are therefore valuable tools to analyze nuclear trafficking in living cells. Here, we reporte the use of a mutant GFP, namely Eukaryotic Green Fluorescent Protein (EGFP), as a marker for the protein import into mammalian nuclei. We have analyzed the behavior of a protein domain of the BRCAl, that contains five putative nuclear localization signals (NLSs), in vivo using a chimera constructed from this polypeptide and the EGFP. This in vivo studies showed that EGFP was distributed uniformly throughout the cytoplasm and the nucleus. When EGFP was fused to NLSs containing domain of the BRCAl protein, fluorescent was predominantly detected in the nucleus, showing that these potential NLSs consensus sequences may destínate the full-lengh BRCAl producy into the nucleus of mammalian cell. This study has also shown that EGFP can be used as a potential fluorescent tag for visualization of gene expression and cellular protein localization in living cells.Çağatay, TolgaM.S

Tek Nokta Enjeksiyonlu Buji ile Ateşlemeli Bir Motorda Motor Devri ve Yükünün Motor Titreşimleri ve Gürültüye Etkisinin Deneysel İncelenmesi

Titreşim ve gürültü gerek günlük hayatta gerekse enerji üretim ve dönüşüm sistemlerinde istenmeyen etkilerdir. Bu çalışmada, motorun temel işletme parametrelerinden olan motor devri ve yükünün buji ile ateşlemeli bir motorda gürültü ve titreşime etkisi ele alınmıştır. Çalışma deneysel olarak iki aşamada gerçekleştirilmiştir. İlk olarak yüksüz motor şartlarında farklı motor devirlerinde deneyler yapılmıştır. İkinci aşamada sabit motor devrinde (1750 rpm) motor farklı yüklerde çalıştırılmıştır. Bu deney 2500 rpm motor devrinde de tekrarlanmıştır. Yapılan deneylerde elde edilen sonuçlar hem motor devrinin hem de motor yükünün titreşim ve gürültüyü arttırdığı görülmüştür

Effects of ethylenediaminetetraacetic acid and sodium hypochlorite on the bond strength of bonding agents to pulp chamber lateral walls

AbstractBackground/purposeThe purposes of this in vitro study were to determine the microtensile bond strengths of four different dentin adhesive materials placed in pulp chamber walls, and to test the effects of 5% sodium hypochlorite (NaOCl) and 17% ethylenediaminetetraacetic acid (EDTA) pretreatments on resin dentin bond strengths.Materials and methodsRecently extracted human third molars were selected. The teeth were divided into four groups. Specimens in each group were treated as follows: irrigated with distilled water; irrigated with EDTA for 5 minutes; irrigated with sodium hypochlorite for 5 minutes; and irrigated with EDTA for 5 minutes followed by NaOCl for 5 minutes. Treated specimens were dried, bonded with a total-etching adhesive, two self-etching adhesives, or a one-bottle self-etching adhesive system. After the bonding procedure and composite restoration, teeth were sectioned, and 15 dentin sticks were obtained. Microtensile testing was performed, and scanning electron micrographs were taken of each irrigated group.ResultsIn the control group, the one-bottle self-etching adhesive system showed statistically higher bond strength values. EDTA irrigation did not affect the bond strength except for the total-etching adhesive. NaOCl significantly reduced the bond strengths of all adhesives. The EDTA and NaOCl combination did not show a statistically significant reduction in bond strengths of the adhesives to pulpal dentin.ConclusionThere was a reduction in bond strengths of all adhesive systems used to test pulp chamber lateral walls after endodontic irrigation solutions were used

Architecture-Dependent Noise Discriminates Functionally Analogous Differentiation Circuits

Gene regulatory circuits with different architectures (patterns of regulatory interactions) can generate similar dynamics. This raises the question of why a particular circuit architecture is selected to implement a given cellular process. To investigate this problem, we compared the Bacillus subtilis circuit that regulates differentiation into the competence state to an engineered circuit with an alternative architecture (SynEx) in silico and in vivo. Time-lapse microscopy measurements showed that SynEx cells generated competence dynamics similar to native cells and reconstituted the physiology of differentiation. However, architectural differences between the circuits altered the dynamic distribution of stochastic fluctuations (noise) during circuit operation. This distinction in noise causes functional differences between the circuits by selectively controlling the timing of competence episodes and response of the system to various DNA concentrations. These results reveal a tradeoff between temporal precision and physiological response range that is controlled by distinct noise characteristics of alternative circuit architectures

Impact of SARS-CoV-2 ORF6 and its variant polymorphisms on host responses and viral pathogenesis

: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes several proteins that inhibit host interferon responses. Among these, ORF6 antagonizes interferon signaling by disrupting nucleocytoplasmic trafficking through interactions with the nuclear pore complex components Nup98-Rae1. However, the roles and contributions of ORF6 during physiological infection remain unexplored. We assessed the role of ORF6 during infection using recombinant viruses carrying a deletion or loss-of-function (LoF) mutation in ORF6. ORF6 plays key roles in interferon antagonism and viral pathogenesis by interfering with nuclear import and specifically the translocation of IRF and STAT transcription factors. Additionally, ORF6 inhibits cellular mRNA export, resulting in the remodeling of the host cell proteome, and regulates viral protein expression. Interestingly, the ORF6:D61L mutation that emerged in the Omicron BA.2 and BA.4 variants exhibits reduced interactions with Nup98-Rae1 and consequently impairs immune evasion. Our findings highlight the role of ORF6 in antagonizing innate immunity and emphasize the importance of studying the immune evasion strategies of SARS-CoV-2

p53 mutations as a source of aberrant Beta-catenin accumulation in cancer cells

Cataloged from PDF version of article.β-catenin is involved in both cell-cell interactions and wnt pathway-dependent cell fate determination through its interactions with E-cadherin and TCF/LEF transcription factors, respectively. Cytoplasmic/nuclear levels of β-catenin are important in regulated transcriptional activation of TCF/LEF target genes. Normally, these levels are kept low by proteosomal degradation of â-catenin through Axin1- and APC-dependent phosphorylation by CKI and GSK-3β. Deregulation of β-catenin degradation results in its aberrant accumulation, often leading to cancer. Accordingly, aberrant accumulation of β-catenin is onberved at high frequency in many cancers. This accumulation correlates with either mutational activation of CTNNB1 (β-catenin) or mutational inactivation of APC and Axin1 genes in some tumors. However, there are many tumors that display β-catenin accumulation in the absence of a mutation in these genes. Thus, there must be additional sources for aberrant β-catenin accumulation in cancer cells. Here, we provide experimental evidence that wild-type β-catenin accumulates in hepatocellular carcinoma (HCC) cells in association with mutational inactivation of p53 gene. We also show that worldwide p53 and β-catenin mutation rates are inversely correlated in HCC. These data suggest that inactivation of p53 is an important cause of aberrant accumulation of β−catenin in cancer cells.Çağatay, TolgaPh.D

CFAR processing with switching exponential smoothers for nonhomogeneous environments

Conventional constant false alarm rate (CFAR) methods use a fixed number of cells to estimate the background variance. For homogeneous environments, it is desirable to increase the number of cells, at the cost of increased computation and memory requirements, in order to improve the estimation performance. For nonhomogeneous environments, it is desirable to use less number of cells in order to reduce the number of false alarms around the clutter edges. In this work, we present a solution with two exponential smoothers (first order IIR filters) having different time-constants to leverage the conflicting requirements of homogeneous and nonhomogeneous environments. The system is designed to use the filter having the large time-constant in homogeneous environments and to promptly switch to the filter having the small time constant once a clutter edge is encountered. The main advantages of proposed Switching IIR CFAR method are computational simplicity, small memory requirement (in comparison to windowing based methods) and its good performance in homogeneous environments (due to the large time-constant smoother) and rapid adaptation to clutter edges (due to the small time-constant smoother)

İçten Yanmalı Motorlu Bir Taşıtta Titreşim ve Gürültünün Deneysel Olarak Belirlenmesi

İçten yanmalı motora sahip bir taşıtın sürüş karakteristiğini etkileyen temel parametreler motor devri ve motor yüküdür. Sürücü temelde taşıt hızı ayarlar ve bu ayar için temel kontrol noktası gaz pedalıdır. Gaz pedalına basma miktarı, taşıtın karşılaştığı dirençlere ve vites kademesine bağlıdır. Bu çalışmanın amacı taşıtın temel sürüş parametrelerindeki değişimin titreşim ve gürültüye etkisini deneysel olarak incelemektir. Bu amaçla düz yol koşullarında ve belirli bir vites kademesinde (5. vites) taşıt hızına bağlı olarak titreşim ve gürültü ölçümleri gerçekleştirilmiştir. Taşıt hızına bağlı olarak toplam ortalama titreşim yaklaşık 3 kat, gürültü ise 9,4 dB(A) artmıştır. Ayrıca 50 km/h ve 90 km/h taşıt hızlarında elde edilen veriler 4. vites kademesiyle karşılaştırılmıştır. 5. vitesteki ölçüm sonuçları ile karşılaştırıldığında toplam ortalama titreşim 4. vites kademesinde 50 km/h taşıt hızında %18 ve 90 km/h taşıt hızında %43,4 artış göstermiştir. Gürültü ölçüm sonuçları karşılaştırıldığında ise; her iki vites kademesi arasında dikkate değer bir fark görülmemiştir

Investigation of the mechanical properties of high strength concrete

Bu çalışmada yüksek dayanımlı betonların mekanik özellikleri incelenmiştir. Farklı oranlarda silis dumanı, su/çimento oranları ve süperakışkanlaştırıcı ile sabit çimento, agrega miktarı ve çökme ile laboratuarda silindir, küp ve kiriş deney betonları üretilmiş, sertleşmiş beton üzerinde birtakım deneyler yapılarak; değişik yaşlardaki beton basınç ve çekme dayanımları tespit edilmiştir. Belirtilen tüm şartlar için kullanılacak bir agrega gradasyonu başlangıçta belirlenmiştir. Bu doğrultuda, zaman basınç dayanımı ilişkisi, zaman çekme dayanımı ilişkisi, farklı silis dumanı / bağlayıcı malzeme oranlarına göre farklı yaşlarda basınç ve çekme dayanımı ilişkisi incelenmiş tüm bu faktörlerin basınç ve çekme dayanımı üzerindeki etkileri gözlenmiştir. Silis dumanı / bağlayıcı malzeme oyanının beton basınç dayanımı için önemli olduğu, belirli bir orana kadar kullanılan silis dumanının basınç dayanımının arttığı, fakat belirli bir miktardan sonra silis dumanı miktarındaki artışın basınç dayanımını azalttığı ve silis dumanı / bağlayıcı malzeme oranının çekme dayanımına etkisinin oldukça düşük bir oranda kaldığı tespit edilmiştir.In this study, the mechanical properties of high strength concrete is investigated. Different ratios of silica fume and superplasticezer with constant cementetious material amount, aggregate amount and slump are used for this study. Cylinder, cube and beam samples are cast to find the compressive and tensile strength of concrete. First the gradation of aggregate is determined and then the samples are casted. Relationships between time — compressive strength, time — tensile strength, compressive strength - tensile strength, silica fume - cementetious material are investigated. The effects of them on the concrete are observed. It is observed that the silica fume / cementatious material ratio affects the compressive strength of concrete, up to a definity ratio, the compressive strength increases but over this ratio it decreases and that the silica fume / cementatious material ratio affects the tensile strength lower