Recombinant α and β Subunits of M.AquI Constitute an Active DNA Methyltransferase

Pinarbasi, Hatice,Pinarbasi, Ergun,Hornby, David 생화학분자생물학회 2002 Journal of biochemistry and molecular biology Vol.35 No.3

AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from S-adenosyl-L-methionine to the C5 position of the outermost deoxycytidine base in the DNA sequence 5'CYCGRG3'. M.AquI is encoded by two overlapping ORFs (termed $\alpha$ and $\beta$) instead of the single ORF that is customary for Class II methyltransferase genes. The structural organization of the M.AquI protein sequence is quite similar to that of other bacterial C5-DNA methyltransferases. Ten conserved motifs are also present in the correct order, but only on two polypeptides. We separately subcloned the genes that encode the $\alpha$ and $\beta$ subunits of M.AquI into expression vectors. The overexpressed His-fusion $\alpha$ and $\beta$ subunits of the enzyme were purified to homogeneity in a single step by Nickel-chelate affinity chromatography. The purified recombinant proteins were assayed for biological activity by an in vitro DNA tritium transfer assay. The $\alpha$ and $\beta$ subunits of M.AquI alone have no DNA methyltransferase activity, but when both subunits are included in the assay, an active enzyme that catalyses the transfer of the methyl group from S-adenosyl-L-methionine to DNA is reconstituted. We also showed that the $\beta$ subunit alone contains all of the information that is required to generate recognition of specific DNA duplexes in the absence of the $\alpha$ subunit.

RecombinantαandβSubunits of M.AquI Constitute an Active DNA Methyltransferase

Pinarbasi, Hatice,Pinarbasi, Ergun,Hornby, David 한국생화학분자생물학회 2002 BMB Reports Vol.35 No.3

AquI DNA methyltransferase, M.AquI, catalyses the transfer of a methyl group from S-adenosyl-L-methionine to the C5 position of the outermost deoxycytidine base in the DNA sequence 5’CYCGRG3’. M.AquI is encoded by two overlapping ORFs (termed α and β) instead of the single ORF that is customary for Class II methyltransferase genes. The structural organization of the M.AquI protein sequence is quite similar to that of other bacterial C5-DNA methyltransferases. Ten conserved motifs are also present in the correct order, but only on two polypeptides. We separately subcloned the genes that encode the α and β subunits of M.AquI into expression vectors. The overexpressed His-fusion α and β subunits of the enzyme were purified to homogeneity in a single step by Nickel-chelate affinity chromatography. The purified recombinant proteins were assayed for biological activity by an in vitro DNA tritium transfer assay. The α and β subunits of M.AquI alone have no DNA methyltransferase activity, but when both subunits are included in the assay, an active enzyme that catalyses the transfer of the methyl group from S-adenosyl-Lmethionine to DNA is reconstituted. We also showed that the β subunit alone contains all of the information that is required to generate recognition of specific DNA duplexes in the absence of the α subunit.

Experimental study on partially-reinforced steel RHS compression members

Pinarbasi, Seval Techno-Press 2017 Structural Engineering and Mechanics, An Int'l Jou Vol.63 No.3

This paper presents an experimental study on the behavior of axially-loaded steel RHS (rectangular hollow section) compression members that are partially reinforced along their lengths with welded steel plates. 28 slender column tests were carried out to investigate the effects of the slenderness ratio of the unreinforced member and the ratio of the reinforced length of the member to its entire length. In addition to the slender column tests, 14 stub-column tests were conducted to determine the basic mechanical properties of the test specimens under uniform compression. Test results show that both the compressive strength and stiffness of an RHS member can be increased significantly compared to its unreinforced counterpart even when only the central quarter of the member is reinforced. Based on the limited test data, it can be concluded that partial reinforcement is, in general, more effective in members with larger slenderness ratios. A simple design expression is also proposed to predict the compressive strength of RHS columns partially reinforced along their length with welded steel plates by modifying the provisions of AISC 360-10 to account for the partial reinforcement.

Compression of hollow-circular fiber-reinforced rubber bearings

Pinarbasi, Seval,Okay, Fuad Techno-Press 2011 Structural Engineering and Mechanics, An Int'l Jou Vol.38 No.3

Earlier studies on hollow-circular rubber bearings, all of which are conducted for steel-reinforced bearings, indicate that the hole presence not only decreases the compression modulus of the bearing but also increases the maximum shear strain developing in the bearing due to compression, both of which are basic design parameters also for fiber-reinforced rubber bearings. This paper presents analytical solutions to the compression problem of hollow-circular fiber-reinforced rubber bearings. The problem is handled using the most-recent formulation of the "pressure method". The analytical solutions are, then, used to investigate the effects of reinforcement flexibility and hole presence on bearing's compression modulus and maximum shear strain in the bearing in view of four key parameters: (i) reinforcement extensibility, (ii) hole size, (iii) bearing's shape factor and (iv) rubber compressibility. It is shown that the compression stiffness of a hollow-circular fiber-reinforced bearing may decrease considerably as reinforcement flexibility and/or hole size increases particularly if the shape factor of the bearing is high and rubber compressibility is not negligible. Numerical studies also show that the existence of even a very small hole can increase the maximum shear strain in the bearing significantly, which has to be considered in the design of such annular bearings.

Compression of hollow-circular fiber-reinforced rubber bearings

Seval Pinarbasi,Fuad Okay 국제구조공학회 2011 Structural Engineering and Mechanics, An Int'l Jou Vol.38 No.3

Earlier studies on hollow-circular rubber bearings, all of which are conducted for steelreinforced bearings, indicate that the hole presence not only decreases the compression modulus of the bearing but also increases the maximum shear strain developing in the bearing due to compression, both of which are basic design parameters also for fiber-reinforced rubber bearings. This paper presents analytical solutions to the compression problem of hollow-circular fiber-reinforced rubber bearings. The problem is handled using the most-recent formulation of the “pressure method”. The analytical solutions are, then, used to investigate the effects of reinforcement flexibility and hole presence on bearing’s compression modulus and maximum shear strain in the bearing in view of four key parameters: (i) reinforcement extensibility, (ii) hole size, (iii) bearing’s shape factor and (iv) rubber compressibility. It is shown that the compression stiffness of a hollow-circular fiber-reinforced bearing may decrease considerably as reinforcement flexibility and/or hole size increases particularly if the shape factor of the bearing is high and rubber compressibility is not negligible. Numerical studies also show that the existence of even a very small hole can increase the maximum shear strain in the bearing significantly, which has to be considered in the design of such annular bearings.

Experimental study on partially-reinforced steel RHS compression members

Seval Pinarbasi 국제구조공학회 2017 Structural Engineering and Mechanics, An Int'l Jou Vol.63 No.3

This paper presents an experimental study on the behavior of axially-loaded steel RHS (rectangular hollow section) compression members that are partially reinforced along their lengths with welded steel plates. 28 slender column tests were carried out to investigate the effects of the slenderness ratio of the unreinforced member and the ratio of the reinforced length of the member to its entire length. In addition to the slender column tests, 14 stub-column tests were conducted to determine the basic mechanical properties of the test specimens under uniform compression. Test results show that both the compressive strength and stiffness of an RHS member can be increased significantly compared to its unreinforced counterpart even when only the central quarter of the member is reinforced. Based on the limited test data, it can be concluded that partial reinforcement is, in general, more effective in members with larger slenderness ratios. A simple design expression is also proposed to predict the compressive strength of RHS columns partially reinforced along their length with welded steel plates by modifying the provisions of AISC 360-10 to account for the partial reinforcement.

Analysis of fiber-reinforced elastomeric isolators under pure "warping"

Seval Pinarbasi,Yalcin Mengi 국제구조공학회 2017 Structural Engineering and Mechanics, An Int'l Jou Vol.61 No.1

As a relatively new type of multi-layered rubber-based seismic isolators, fiber-reinforced elastomeric isolators (FREIs) are composed of several thin rubber layers reinforced with flexible fiber sheets. Limited analytical studies in literature have pointed out that "warping" (distortion) of reinforcing sheets has significant influence on buckling behavior of FREIs. However, none of these studies, to the best knowledge of authors, has investigated their warping behavior, thoroughly. This study aims to investigate, in detail, the warping behavior of strip-shaped FREIs by deriving advanced analytical solutions without utilizing the commonly used “pressure”, incompressibility, inextensibility and the "linear axial displacement variation through the thickness" assumptions. Studies show that the warping behavior of FREIs mainly depends on the (i) aspect ratio (shape factor) of the interior elastomer layers, (ii) Poisson’s ratio of the elastomer and (iii) extensibility of the fiber sheets. The basic assumptions of the "pressure" method as well as the commonly used incompressibility assumption are valid only for isolators with relatively large shape factors, strictly incompressible elastomeric material and nearly inextensible fiber reinforcement.

Durability of Sustained Virologic Response in Chronic Hepatitis C

( Ahmet Uyanikoglu ),( Sabahattin Kaymakoglu ),( Ahmet Danalioglu ),( Filiz Akyuz ),( Fatih Ermis ),( Binnur Pinarbasi ),( Kadir Demir ),( Fatih Besisik ),( Yilmaz Cakaloglu ) 대한소화기학회 2013 Gut and Liver Vol.7 No.4

Background/Aims: The aim of this study is to investigate the rate of sustained virologic response (SVR) in chronic hepatitis C patients receiving antiviral treatment. Methods: The files of patients with chronic hepatitis C treated with interferon±ribavirin between 1995 and 2009 were reviewed retrospectively. Six months after the end of treatment, patients with negative hepatitis C virus (HCV)-RNA (<50 IU/mL, as determined by the polymerase chain reaction method) were enrolled in the study. Results: The mean age of 196 patients (89 males) was 46.13±11.10 years (range, 17 to 73 years). In biopsies, the mean stage was 1.50±0.94; histological activity index was 7.18±2.43. In total, 139 patients received pegylated interferon (IFN) +ribavirin, 21 patients received classical IFN+ribavirin, and 36 patients received IFN alone. The HCV genotypes of 138 patients were checked: 77.5% were genotype 1b, and 22.5% were other genotypes. After achievement of SVR, the median follow-up period was 33.5 months (range, 6 to 112 months), and in this period relapse was only detected in two patients (1.02%) at 18 and 48 months after treatment. Conclusions: In total, 98.9% of patients with SVR in chronic hepatitis C demonstrated truly durable responses over the long-term follow-up period of 3 years; relapsed patients had intermittent or low-grade viremia. (Gut Liver 2013; 7:458-461)

CYP1A1, GSTM1, and GSTT1 polymorphisms, smoking, and lung cancer risk in a pooled analysis among Asian populations.

Lee, Kyoung-Mu,Kang, Daehee,Clapper, Margie L,Ingelman-Sundberg, Magnus,Ono-Kihara, Masko,Kiyohara, Chikako,Min, Shen,Lan, Qing,Le Marchand, Loic,Lin, Pinpin,Lung, Maria Li,Pinarbasi, Hatice,Pisani, P American Association for Cancer Research 2008 Cancer Epidemiology, Biomarkers & Prevention Vol.17 No.5

<P>To evaluate the roles of CYP1A1 polymorphisms [Ile 462Val and T 6235C (MspI)] and deletion of GSTM1 and GSTT1 in lung cancer development in Asian populations, a pooled analysis was conducted on 13 existing studies included in Genetic Susceptibility to Environmental Carcinogenesis database. This pooled analysis included 1,971 cases and 2,130 controls. Lung cancer risk was estimated as odds ratios (OR) and 95% confidence intervals (95% CI) using unconditional logistic regression model adjusting for age, sex, and pack-year. The CYP1A1 6235C variant was associated with squamous cell lung cancer (TC versus TT: OR, 1.42; 95% CI, 0.96-2.09; CC versus TT: OR, 1.97; 95% CI, 1.26-3.07; P trend = 0.003). In haplotype analysis, 462Val-6235T and Ile-C haplotypes were associated with lung cancer risk with reference to the Ile-T haplotype (OR, 3.41; 95% CI, 1.78-6.53 and OR, 1.39; 95% CI, 1.12-1.71, respectively). The GSTM1-null genotype increased squamous cell lung cancer risk (OR, 1.36; 95% CI, 1.05-1.77). When the interaction was evaluated with smoking, increasing trend of lung cancer risk as pack-year increased was stronger among those with the CYP1A1 6235 TC/CC genotype compared with those with TT genotype (P interaction = 0.001) and with the GSTM1-null genotype compared with the present type (Pinteraction = 0.08, when no genotype effect with no exposure was assumed). These results suggest that genetic polymorphisms in CYP1A1 and GSTM1 are associated with lung cancer risk in Asian populations. However, further investigation is warranted considering the relatively small sample size when subgroup analyses were done and the lack of environmental exposure data other than smoking.</P>