Objective: A cephalosporin C acylase catalyzes hydrolysis of cephalosporin C to 7-aminocephalosporanic acid directly. This work was considered helpful for the further study of the cephalosporin C acylase and also useful for the strain improvement. Methods: Its mutant (G139αS/F58βN/I75βT/I176βV/S471βC) named A12 was cloned into pET28a (+) vector and expressed in E.coli BL21 (DE3). The three dimentional structure of A12 was constructed by the homology modeling and its’ catalytic sites was analyzed by the DOCK software. Results: The mutant A12 was expressed in E.coli BL21 (DE3) with the molecular weight 87kDa containing two subunits of 58kDa α-subunit and 25kDa β-subunit. The activity of A12 was 291 U/L which was lower than that of AcyII (322 U/L) because of the low expression level. The specific activity of A12 was 6.011 U/mg which was higher than that of the AcyII (2.868 U/ mg). Catalytic analysis suggested that A12 had the improved catalytic efficiency (kcat/Km) to convert cephalosporin C to 7-ACA at the beginning of the reaction. These results combined with the model analysis indicated that Phe58β、Ile75β and Ile176β were involved in the catalysis from CPC to 7-ACA. Conclusion: In this work, the gene of cephalosporin C acylase AcyII was synthesized, mutated and expressed successfully in the E.coli BL21 (DE3). The specific activity and the catalytic efficiency of A12 increased 2-fold and 3-fold respectively. Compared with the study of cephalosporin C acylase in N176, this work was considered helpful for the further study of the catalytic mechanism of cephalosporin C acylase and also useful for the strain improvement for the cephalosporin C acylase production.
{"title":"Site-Directed Mutagenesis of Cephalosporin C Acylase and Enzymatic Conversion of Cephalosporin C to 7-Aminocephalosporanic Acid","authors":"Yuanyuan Ren, Yulin Lei, Yushan Zhu","doi":"10.5505/TJB.2014.48569","DOIUrl":"https://doi.org/10.5505/TJB.2014.48569","url":null,"abstract":"Objective: A cephalosporin C acylase catalyzes hydrolysis of cephalosporin C to 7-aminocephalosporanic acid directly. This work was considered helpful for the further study of the cephalosporin C acylase and also useful for the strain improvement. Methods: Its mutant (G139αS/F58βN/I75βT/I176βV/S471βC) named A12 was cloned into pET28a (+) vector and expressed in E.coli BL21 (DE3). The three dimentional structure of A12 was constructed by the homology modeling and its’ catalytic sites was analyzed by the DOCK software. Results: The mutant A12 was expressed in E.coli BL21 (DE3) with the molecular weight 87kDa containing two subunits of 58kDa α-subunit and 25kDa β-subunit. The activity of A12 was 291 U/L which was lower than that of AcyII (322 U/L) because of the low expression level. The specific activity of A12 was 6.011 U/mg which was higher than that of the AcyII (2.868 U/ mg). Catalytic analysis suggested that A12 had the improved catalytic efficiency (kcat/Km) to convert cephalosporin C to 7-ACA at the beginning of the reaction. These results combined with the model analysis indicated that Phe58β、Ile75β and Ile176β were involved in the catalysis from CPC to 7-ACA. Conclusion: In this work, the gene of cephalosporin C acylase AcyII was synthesized, mutated and expressed successfully in the E.coli BL21 (DE3). The specific activity and the catalytic efficiency of A12 increased 2-fold and 3-fold respectively. Compared with the study of cephalosporin C acylase in N176, this work was considered helpful for the further study of the catalytic mechanism of cephalosporin C acylase and also useful for the strain improvement for the cephalosporin C acylase production.","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78130936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D. Gowdhaman, Ganesan Jeyalakshmi, Karuppiah Sugumaran, Nagarajan Sai Subramanian, R. Santhosh, Venkatachalam Ponnusami
Objective: The objective of the present study was to isolate a potential and novel Bacillus strain from paper mill effluent for the production of an industrially important xylanase. Material and Methods: A potent xylanase producing microorganism was isolated from paper mill effluent based on zone of clearance on xylan agar medium. The strain was identified based on 16S rRNA analysis and biochemical characterization. Xylanase produced by the isolated strain was partially purified and characterized for its activity and stability. Results: The xylanase produced by this Bacillus aerophilus KGJ2 was thermophilic, shows higher activity and stability at 70°C. Xylanase had activity peak at pH 4.0 and was very acid stable. Birchwood xylan and beef extract were identified as best suited carbon source and nitrogen source, respectively. Conclusion: The results confirm that Bacillus aerophilus KGJ2 produced a unique acido-
{"title":"Optimization of the xylanase production with the newly isolated Bacillus aerophilus KGJ2","authors":"D. Gowdhaman, Ganesan Jeyalakshmi, Karuppiah Sugumaran, Nagarajan Sai Subramanian, R. Santhosh, Venkatachalam Ponnusami","doi":"10.5505/TJB.2014.92300","DOIUrl":"https://doi.org/10.5505/TJB.2014.92300","url":null,"abstract":"Objective: The objective of the present study was to isolate a potential and novel Bacillus strain from paper mill effluent for the production of an industrially important xylanase. Material and Methods: A potent xylanase producing microorganism was isolated from paper mill effluent based on zone of clearance on xylan agar medium. The strain was identified based on 16S rRNA analysis and biochemical characterization. Xylanase produced by the isolated strain was partially purified and characterized for its activity and stability. Results: The xylanase produced by this Bacillus aerophilus KGJ2 was thermophilic, shows higher activity and stability at 70°C. Xylanase had activity peak at pH 4.0 and was very acid stable. Birchwood xylan and beef extract were identified as best suited carbon source and nitrogen source, respectively. Conclusion: The results confirm that Bacillus aerophilus KGJ2 produced a unique acido-","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76429598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Gedikli, Yeliz Buruk, E. Apohan, A. Çabuk, O. Yesilada, N. Burnak
Objective: The aim of this study was to investigate the laccase production of Trametes versicolor under submerged fermentation condition. Then, dye decolorization by laccase was optimized using Box-Behnken methodology. Methods: The optimal culture conditions for producing high amount of laccase were determined using Taguchi methodology. The experiments were designed with five factors (glucose, yeast extract, CuSO 4 , inoculum size and pH) at three levels with orthogonal array layout of L27 (3 5 ). Then, the optimum conditions for high decolorization activity of Reactive Blue 49 by obtained crude laccase were also investigated using Box-Behnken methodology. Results: The optimum culture conditions for production of high amounts of laccase were detected as 2 g L -1 of glucose, 5 g L -1
目的:研究色曲霉在深层发酵条件下漆酶的产生。然后，采用Box-Behnken法优化漆酶对染料的脱色效果。方法:采用田口法确定高产漆酶的最佳培养条件。试验采用L27(35)正交设计，以葡萄糖、酵母浸膏、cuso4、接种量和pH为5个因素，进行3个水平的试验设计。然后，采用Box-Behnken方法对活性蓝49粗漆酶高脱色活性的最佳条件进行了研究。结果:葡萄糖用量为2 g L -1，葡萄糖用量为5 g L -1，是产生大量漆酶的最佳培养条件
{"title":"Laccase production and dye decolorization by Trametes versicolor: application of Taguchi and Box-Behnken Methodologies","authors":"S. Gedikli, Yeliz Buruk, E. Apohan, A. Çabuk, O. Yesilada, N. Burnak","doi":"10.5505/TJB.2014.62533","DOIUrl":"https://doi.org/10.5505/TJB.2014.62533","url":null,"abstract":"Objective: The aim of this study was to investigate the laccase production of Trametes versicolor under submerged fermentation condition. Then, dye decolorization by laccase was optimized using Box-Behnken methodology. Methods: The optimal culture conditions for producing high amount of laccase were determined using Taguchi methodology. The experiments were designed with five factors (glucose, yeast extract, CuSO 4 , inoculum size and pH) at three levels with orthogonal array layout of L27 (3 5 ). Then, the optimum conditions for high decolorization activity of Reactive Blue 49 by obtained crude laccase were also investigated using Box-Behnken methodology. Results: The optimum culture conditions for production of high amounts of laccase were detected as 2 g L -1 of glucose, 5 g L -1","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88529338","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objective: Quality planning in a laboratory can be defined as designing quality wanted or required for a test. The objective of a suitable choice is to determine the most efficient quality control rules and the number of control measurements. The aim of this study is to evaluate the features of the tools of quality planing while choosing quality control procedure. Methods: In this study, the tools of quality planing used to choose quality control procedure were operated for the data generated by simulation. These tools were created for both clinical decision interval and total analytical error model. EZ Rules 3.0 programme was used to obtain OPSpecs chart and critical error chart for both models. Results: In critical error chart, in clinical decision interval model, N=4, R=1 as control procedures, probability of detecting error is over 90% and probability of refusing wrong is less than 5%, in total analytical error model, probability of error detecting is almost 100%, probability of refusing wrong is less than 5%. Procedures applicable to total analytical error model and clinical decision interval model of OPSspecs model are N=4 and R=1. Conclusion: As a result, the number of control measurements required based on random and systematic error observed in the measurement procedure, and the above mentioned approaches, which facilite selecting control rules are important for quality control evaluations in clinical chemistry laboratories. In addition they are difficult to comment and to obtain without software.
{"title":"The importance of quality planning tools in clinical chemistry laboratory","authors":"L. Tomak","doi":"10.5505/TJB.2015.80488","DOIUrl":"https://doi.org/10.5505/TJB.2015.80488","url":null,"abstract":"Objective: Quality planning in a laboratory can be defined as designing quality wanted or required for a test. The objective of a suitable choice is to determine the most efficient quality control rules and the number of control measurements. The aim of this study is to evaluate the features of the tools of quality planing while choosing quality control procedure. Methods: In this study, the tools of quality planing used to choose quality control procedure were operated for the data generated by simulation. These tools were created for both clinical decision interval and total analytical error model. EZ Rules 3.0 programme was used to obtain OPSpecs chart and critical error chart for both models. Results: In critical error chart, in clinical decision interval model, N=4, R=1 as control procedures, probability of detecting error is over 90% and probability of refusing wrong is less than 5%, in total analytical error model, probability of error detecting is almost 100%, probability of refusing wrong is less than 5%. Procedures applicable to total analytical error model and clinical decision interval model of OPSspecs model are N=4 and R=1. Conclusion: As a result, the number of control measurements required based on random and systematic error observed in the measurement procedure, and the above mentioned approaches, which facilite selecting control rules are important for quality control evaluations in clinical chemistry laboratories. In addition they are difficult to comment and to obtain without software.","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84803599","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
O. Alatas, A. Akalin, G. Çiftçi, G. Yorulmaz, Ipek Ertorun, N. Kebapçı, B. Efe
Objective: Obesity and age related vascular changes coupled with the effect of estrogen with- drawal increases predisposition to atherosclerosis in postmenopausal women. But the func- tions of high density lipoprotein (HDL) were not well established in postmenopausal women. In the present study, we mainly aimed to evaluate the changes in the functions of HDL and aimed to measure, lipid peroxidation, lipid profile and homocysteine levels as a supporting evidence in pre and postmenopausal obese women as a result of estrogen depletion. Material and Methods: This study included 20 premenopausal, 22 postmenopausal 42 obese (BMI>30 kg/m2) and 26 premenopausal non-obese. These twenty six premenopausal women with normal BMI (20
{"title":"Oxidative and inflammatory status and HDL functions of obese pre and post menopausal women","authors":"O. Alatas, A. Akalin, G. Çiftçi, G. Yorulmaz, Ipek Ertorun, N. Kebapçı, B. Efe","doi":"10.5505/TJB.2014.82787","DOIUrl":"https://doi.org/10.5505/TJB.2014.82787","url":null,"abstract":"Objective: Obesity and age related vascular changes coupled with the effect of estrogen with- drawal increases predisposition to atherosclerosis in postmenopausal women. But the func- tions of high density lipoprotein (HDL) were not well established in postmenopausal women. In the present study, we mainly aimed to evaluate the changes in the functions of HDL and aimed to measure, lipid peroxidation, lipid profile and homocysteine levels as a supporting evidence in pre and postmenopausal obese women as a result of estrogen depletion. Material and Methods: This study included 20 premenopausal, 22 postmenopausal 42 obese (BMI>30 kg/m2) and 26 premenopausal non-obese. These twenty six premenopausal women with normal BMI (20<BMI<25 kg/m2) were recruited to serve as the control group. Markers of cardiovascular disease (CVD), namely high sensitive C-reactive protein (hsCRP), homocysteine and lipoprotein(a) (Lp(a)) were measured. Glucose, lipid parameters and Malo- ndialdehyde (MDA), antiinflammatory HDL levels were also measured. Functional proper- ties of HDL were determined by the change in fluorescence intensity resulting from oxida- tion of DCFH (Dichloroflorescein) by LDL in the presence of patient HDL in cell free serum. Results: Lipid profiles were impaired in both pre and postmenopausal obese women. CVD markers and glucose levels increased in post menopausal women. But hsCRP levels were also increased in premenopausal compared to control group. MDA, the product of lipid peroxida- tion was increased in both pre and postmenopausal women. Antiinflammatory characteris- tics of HDL were only impaired in postmenopausal women. Conclusion: Postmenopausal obese women have lost their antiinflammatory HDL functions. This situation can be a significant indicator of endothelial dysfunction and cardiovascular disease in postmenopausal women. But the increase in oxidative stress was observed in all of the obese patients regardless of estrogen withdrawal.","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75815254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The effect of alpha lipoic acid on hydrogen peroxide-induced lipid peroxidation in rat liver homogenates","authors":"S. B. Yapar, S. Eskiocak","doi":"10.5505/TJB.2014.71501","DOIUrl":"https://doi.org/10.5505/TJB.2014.71501","url":null,"abstract":"","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81369379","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aim: HSP90, one of the most important and multifunctional stress proteins in cells, plays important role in cell self-protection and environmental adaptability in crustacean. Our pre- vious study showed that application of imidazole derivative KK-42 can increase survival rate of Penaeus vannumei. In an attempt to research the possible molecular mechanism of KK-42 increasing survival rate in P. vannumei, one HSP90 cDNA sequence from the hepatopancreas was first isolated and then its spatiotemporal expressions were analyzed. Material and Methods: The HSP90 was cloned from the hepatopancreas of P. vannumei using the rapid amplification of cDNAends methods and its sequence was analyzed with biological software. Expression level was determined by real-time PCR. Results: The full-length cDNA contains a 2163 bp open reading frame encoding a predicted protein of 721 amino acids. The P. vannumei HSP90 protein sequence is most closely related to other HSP90 enzymes, the higher mRNA level is detected in hepatopancreas. The hepato- pancreas HSP90 expression is significantly induced by KK-42 and increases more than 69.1 %, even up to 505.5 % and 481.7 % on day 2 and day 3, respectively. Conclusion: The up-regulation of HSP90 expression induced by KK-42 is beneficial to imp- rove adaptability that is likely one of the molecular mechanisms of KK-42 increasing survival
{"title":"A partial genomic characterization and up-regulation of HSP90 by imidazole derivative KK-42 in the shrimp Penaeus vannumei","authors":"X. Xi-chao, W. Wenfeng, Yang Hong, Ning Qianji","doi":"10.5505/TJB.2014.43265","DOIUrl":"https://doi.org/10.5505/TJB.2014.43265","url":null,"abstract":"Aim: HSP90, one of the most important and multifunctional stress proteins in cells, plays important role in cell self-protection and environmental adaptability in crustacean. Our pre- vious study showed that application of imidazole derivative KK-42 can increase survival rate of Penaeus vannumei. In an attempt to research the possible molecular mechanism of KK-42 increasing survival rate in P. vannumei, one HSP90 cDNA sequence from the hepatopancreas was first isolated and then its spatiotemporal expressions were analyzed. Material and Methods: The HSP90 was cloned from the hepatopancreas of P. vannumei using the rapid amplification of cDNAends methods and its sequence was analyzed with biological software. Expression level was determined by real-time PCR. Results: The full-length cDNA contains a 2163 bp open reading frame encoding a predicted protein of 721 amino acids. The P. vannumei HSP90 protein sequence is most closely related to other HSP90 enzymes, the higher mRNA level is detected in hepatopancreas. The hepato- pancreas HSP90 expression is significantly induced by KK-42 and increases more than 69.1 %, even up to 505.5 % and 481.7 % on day 2 and day 3, respectively. Conclusion: The up-regulation of HSP90 expression induced by KK-42 is beneficial to imp- rove adaptability that is likely one of the molecular mechanisms of KK-42 increasing survival","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91181426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Razavi, Z. Nourouzi, Alireza Ghasemiian, A. Ghorbani, Saeedeh Latifi
Objective: The genus Artemisia (Asteraceae) comprises approximately 400 species of commonly perennial and fragrant herbs distributed in the northern temperate region of the world. Artemisia austriaca JACQ. is one of the most common species of the genus distributed from central Europe to Siberia, Turkey, and Iran. In Iran, the plant is indigenous to East Azerbaijan and Ardabil province. In the present study, the essential oil composition of the aerial part of Artemisia austriaca and some allelopathic potential of the oil were studied. Methods: The essential oil of the plant was obtained by hydrodistillation using a clevenger type apparatus. After dehydratation, the essential oil was analyzed by GC and GC-MS. Results: The results showed that the camphor (15.88%), 1,8-cineole (10.75%), camphene (3.53%) and beta-fenchyl alcohol (3.03%) were the main components among 51 constituents characterized in the oil. The plant essential oil showed significant anti-sclerotinia and phytotoxic activity. Conclusion: Our findings indicated that there is a high level similarity between the major compound of essential oil of A. austriaca samples collected from northwest of Iran, Ardabil, and Turkey. Accordingly, the two samples may represent the same chemotype. On the other
{"title":"Chemical composition of the essential oil of Artemisia austriaca JACQ. growing wild in Iran","authors":"S. Razavi, Z. Nourouzi, Alireza Ghasemiian, A. Ghorbani, Saeedeh Latifi","doi":"10.5505/TJB.2014.28199","DOIUrl":"https://doi.org/10.5505/TJB.2014.28199","url":null,"abstract":"Objective: The genus Artemisia (Asteraceae) comprises approximately 400 species of commonly perennial and fragrant herbs distributed in the northern temperate region of the world. Artemisia austriaca JACQ. is one of the most common species of the genus distributed from central Europe to Siberia, Turkey, and Iran. In Iran, the plant is indigenous to East Azerbaijan and Ardabil province. In the present study, the essential oil composition of the aerial part of Artemisia austriaca and some allelopathic potential of the oil were studied. Methods: The essential oil of the plant was obtained by hydrodistillation using a clevenger type apparatus. After dehydratation, the essential oil was analyzed by GC and GC-MS. Results: The results showed that the camphor (15.88%), 1,8-cineole (10.75%), camphene (3.53%) and beta-fenchyl alcohol (3.03%) were the main components among 51 constituents characterized in the oil. The plant essential oil showed significant anti-sclerotinia and phytotoxic activity. Conclusion: Our findings indicated that there is a high level similarity between the major compound of essential oil of A. austriaca samples collected from northwest of Iran, Ardabil, and Turkey. Accordingly, the two samples may represent the same chemotype. On the other","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87549531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Aim: The objectives of this study are, first, to investigate a star network analysis of phylogenetic trees of identified Y. lipolytica strains with or without one out-group, and secondly, to show the redundancy of the out-groups in phylogenetic tree. Material and Methods: In this study we used 22 Yarrowia lipolytica strains which were identified with sequencing of D1/D2 domain of 26S rDNA region, two phylogenetic trees were reconstructed by the neighbor joining method including an out-group or not. The star- like weighted network analysis of these two phylogenetic trees was investigated. Results: The adjacency matrix formalism of our weighted phylogenetic network with the out- group looks like a directed star graph adjacency matrix. The lowest weight is the edge from the central node to Candida sake out-group (0.00008) corresponding to the narrowest edge. However, the edge going from central node to Yarrowia lipolytica TEM YL 19 has a weight of 0.0825 and the thickest structure. Conclusion: Thus network analysis show that phylogenetic relationship between close strain and subspecies can be confirmed and also the out-group in this phylogenetic tree is unnecessary due to the negligible change in the average weighted degree and its some
{"title":"Star network analysis of sequence based identified Yarrowia lipolytica strains","authors":"O. Akpınar, Emir Haliki, F. Uçar, A. H. Uztan","doi":"10.5505/TJB.2014.75768","DOIUrl":"https://doi.org/10.5505/TJB.2014.75768","url":null,"abstract":"Aim: The objectives of this study are, first, to investigate a star network analysis of phylogenetic trees of identified Y. lipolytica strains with or without one out-group, and secondly, to show the redundancy of the out-groups in phylogenetic tree. Material and Methods: In this study we used 22 Yarrowia lipolytica strains which were identified with sequencing of D1/D2 domain of 26S rDNA region, two phylogenetic trees were reconstructed by the neighbor joining method including an out-group or not. The star- like weighted network analysis of these two phylogenetic trees was investigated. Results: The adjacency matrix formalism of our weighted phylogenetic network with the out- group looks like a directed star graph adjacency matrix. The lowest weight is the edge from the central node to Candida sake out-group (0.00008) corresponding to the narrowest edge. However, the edge going from central node to Yarrowia lipolytica TEM YL 19 has a weight of 0.0825 and the thickest structure. Conclusion: Thus network analysis show that phylogenetic relationship between close strain and subspecies can be confirmed and also the out-group in this phylogenetic tree is unnecessary due to the negligible change in the average weighted degree and its some","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82825385","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Objective: V617F mutation of Janus kinase (JAK2) gene is used in the diagnosis of BCR-ABL negative myeloproliferative diseases such as polycytemia vera, essential thrombocythemia and primary myelofibrosis. In this study, we evaluated the frequency of JAK2 V617F mutation in a group of Turkish individuals and its association with whole blood count parameters. Methods: We retrospectively reviewed the records of 201 patients (174 males and 27 females) who were tested for JAK2 V617F mutation from January 2012 to December 2012. JAK2V617F mutation, BCR-ABL mutation, level of white blood cell count (WBC), red blood cell count (RBC), platelet count (PLT), red blood cell distribution width (RDW), hemoglobin (Hb), hematocrit (Hct), level of iron, iron binding capacity and demographic data of patients were also noted. A commercial kit assay for the identification of V617F mutation based on real time-polymerase chain reaction had been used to investigate mutation of the JAK2 gene. Results: 14.9 % of the 201 samples being investigated for JAK2 V617F mutation were positive. Patients who were ordered for JAK2 V617F mutation testing were divided into two groups according to mutation being positive and negative. Age, RDW and PLT levels were significantly higher in mutation positive group (p<0.05). Besides JAK2 V617F mutation, BCR-ABL mutation orders were examined and BCR-ABL mutation reports were also evaluated on subjects. Age, RDW and PLT were significantly higher in JAK2 V617F mutation positive / BCR-ABL mutation negative group (p<0.05). Conclusion: In this study significant differences for age, RDW and platelet count were determined in mutation positive subjects. Findings of this study suggest that JAK2 V617F mutation could cause proliferation of megakaryocytic cells as well as erythroid cells and as a result of disturbance in erythroid maturation process, the proliferation in the erythroid cells could cause an increase in RDW.
{"title":"The Frequency Of JAK2 V617F Gen Mutation And Its Associations With Whole Blood Count Parameters","authors":"Kübranur Ünal, S. Erdogan, F. Yilmaz","doi":"10.5505/TJB.2014.39206","DOIUrl":"https://doi.org/10.5505/TJB.2014.39206","url":null,"abstract":"Objective: V617F mutation of Janus kinase (JAK2) gene is used in the diagnosis of BCR-ABL negative myeloproliferative diseases such as polycytemia vera, essential thrombocythemia and primary myelofibrosis. In this study, we evaluated the frequency of JAK2 V617F mutation in a group of Turkish individuals and its association with whole blood count parameters. Methods: We retrospectively reviewed the records of 201 patients (174 males and 27 females) who were tested for JAK2 V617F mutation from January 2012 to December 2012. JAK2V617F mutation, BCR-ABL mutation, level of white blood cell count (WBC), red blood cell count (RBC), platelet count (PLT), red blood cell distribution width (RDW), hemoglobin (Hb), hematocrit (Hct), level of iron, iron binding capacity and demographic data of patients were also noted. A commercial kit assay for the identification of V617F mutation based on real time-polymerase chain reaction had been used to investigate mutation of the JAK2 gene. Results: 14.9 % of the 201 samples being investigated for JAK2 V617F mutation were positive. Patients who were ordered for JAK2 V617F mutation testing were divided into two groups according to mutation being positive and negative. Age, RDW and PLT levels were significantly higher in mutation positive group (p<0.05). Besides JAK2 V617F mutation, BCR-ABL mutation orders were examined and BCR-ABL mutation reports were also evaluated on subjects. Age, RDW and PLT were significantly higher in JAK2 V617F mutation positive / BCR-ABL mutation negative group (p<0.05). Conclusion: In this study significant differences for age, RDW and platelet count were determined in mutation positive subjects. Findings of this study suggest that JAK2 V617F mutation could cause proliferation of megakaryocytic cells as well as erythroid cells and as a result of disturbance in erythroid maturation process, the proliferation in the erythroid cells could cause an increase in RDW.","PeriodicalId":23355,"journal":{"name":"Turkish Journal of Biochemistry-turk Biyokimya Dergisi","volume":null,"pages":null},"PeriodicalIF":0.7,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81668998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：