Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum w... more Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum wheat (Triticum durum Desf.) is widely used in human diets but has the potential to accumulate Cd. It also has a high level of genetic diversity, which may be exploited to develop cultivars with low Cd content. We aimed to perform marker-assisted selection and validate previously identified Cd markers in durum wheat germplasm for use in the investigation of accessions that accumulate low grain Cd content. We assessed 130 durum wheat accessions phenotypically and using three different molecular markers. Grain Cd contents of the studied germplasm varied 4.91-fold (26.2–128.7 μg/kg) with an average of 58.2 μg/kg. Landraces showed lower average values of grain Cd content than cultivars. Three molecular markers (usw47, Cad-5B and KASP marker Cad-5B) were used to differentiate high and low Cd accumulating lines. Results showed high correlation and successfully classified the accessions to the expected high or low Cd level; 87 accessions showed the low Cd alleles, and 43 accessions the high Cd alleles, except for five accessions with the usw47 marker that showed heterozygous status. A significant correlation coefficient (r = 0.944*) was observed among the three molecular markers. Based on molecular markers, 96.2% of the accessions were classified accurately. The KASP assay was highly effective in successfully separating low from high Cd content accessions and could be used as a molecular tool in durum wheat breeding programs, with less cost and time, targeting reduced grain Cd levels. The results of this study will allow durum wheat breeders to accelerate their progress to select suitable genotypes with the desired alleles.
TEZ6397Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2007.Kaynakça (s.51-55) var.x, 56 s. ... more TEZ6397Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2007.Kaynakça (s.51-55) var.x, 56 s. : res. ; 29 cm.Retinal guanylate cyclases, retGC-1 and retGC-2, are a subclass of the membrane dependent guanylate cyclase family. Synthesize cGMP, the intracelular second messenger of phototransduction, they play a crucial role in photoreceptor physiology. In recent work, it is intended to investigate the effect of adenine nucleotides and all-trans retinal on the retinal guanylate cyclase activity. Crosslinking experiments indicate, protein phosphorylation might be essential for physiological activity of cyclases.Retinal guanilat siklazlar, retGC-1 ve retGC-2, membrana bağlı guanilat siklaz ailesinin bir alt kolunu oluştururlar. Fototransdüksiyonunun intraselüler mesajcısı olan cGMP'yi sentezledikleri için fotoreseptör fizyolojisinde önemli rol oynarlar. Bu çalışmada, adenin nükleotidlerinin retinal guanilat siklazların fizyolojisine etkilerinin incelenmesi amaçlanmıştır. Çapraz bağ...
<p>a) Verification of the transfer of RsAqpZ into <i>Rhodobacter sphaeroides 17023<... more <p>a) Verification of the transfer of RsAqpZ into <i>Rhodobacter sphaeroides 17023</i> by colony PCR using primers directed to <i>pRKPLHT7</i> vector backbone. Lanes 1: negative control, 2: positive control (<i>E. coli</i> cloning vector), 3–9: <i>Rhodobacter</i> exconjugants (expected band 864 bp), L: NEB 100 bp ladder; b) SDS-PAGE of RsAqpZ overexpressed and purified from <i>Rhodobacter</i>. M:Marker, P:Pellet, FT: Flow-through, W3∶3rd Wash fraction, E1: First Elution from IMAC column, E2: Second elution; c) Western-blot image of the gel in part b); RsAqpZ in monomeric and tetrameric form were detected by anti-His antibody.</p
<p>ABA55 polymersomes embedded with EcAqpZ and RsAqpZ-mBanana were prepared using film rehy... more <p>ABA55 polymersomes embedded with EcAqpZ and RsAqpZ-mBanana were prepared using film rehydration method and dialyzed for insertion of the proteins in polymer. Unilamellar polymersomes with a low polydispersity (PDI <0.25) were obtained using consecutive extrusions through 400 nm and 200 nm track-etched filters and were then used to measure water permeability by stopped-flow light scattering. EcAqpZ and RsAqpZ-mBanana remained active in ABA55 polymer vesicles. RsAqpZ-mBanana showed higher water permeability in part due to higher incorporation efficiency.</p
<p>a) Phylogeny analysis of RsAqpZ indicates that it is an orthodox aquaporin with a close ... more <p>a) Phylogeny analysis of RsAqpZ indicates that it is an orthodox aquaporin with a close relationship to <i>E.coli</i> AqpZ, as well as the archeal aquaporin, AqpM. Evolutionary relationship of RsAqpZ to other aquaporins was evaluated by the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Saitou1" target="_blank">[24]</a>. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (2000 replicates) is shown next to the branches <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Felsenstein1" target="_blank">[44]</a>. The evolutionary distances were computed using the Equal Input method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Tajima1" target="_blank">[45]</a> and are in the units of the number of amino acid substitutions per site. The analysis involved 10 amino acid sequences. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA5 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-TamuraK1" target="_blank">[25]</a>. b) Multiple sequence alignment of aquaporin sequences. Amino acid sequence alignment was performed using Clustal Ω <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Goujon1" target="_blank">[23]</a> with the mRNA translation sequences retrieved from Genbank. RsAqpZ had signature residues Phe-39, His-173 and Arg-188 representing the orthodox aquaporins. Val-182 is a unique residue in the selectivity filter of RsAqpZ, which has significantly higher hydrophobicity, compared to the equivalent Thr-183 of EcAqpZ and Cys-189 of AQP1. Similar small hydrophobic residues were also found in AQY1 from <i>Pichia pastoris</i> (Ala-220) and human AQP4 (Ala-209), which might contribute to relatively higher water permeability in these aquaporins due to reduced interaction between water molecules and the amino acid residue in the selectivity filter.</p
<p>mBanana fluorescent protein was expressed as a C-terminal fusion partner along with RsAq... more <p>mBanana fluorescent protein was expressed as a C-terminal fusion partner along with RsAqpZ. The water permeability did not show a significant change, which enabled assessment of the protein properties at the single molecule level.</p
<p>mBanana fusion of RsAqpZ was expressed and purified from <i>R. sphaeroides</i&g... more <p>mBanana fusion of RsAqpZ was expressed and purified from <i>R. sphaeroides</i> and reconstituted in PC/PS vesicles at varying protein to lipid ratios. The number of RsAqpZ tetramers per liposome was evaluated by FCS, a) Normalized autocorrelation curves of mBanana species, mBanana fluorescent protein, RsAqpZ-mBanana protein tetramer and phospholipid vesicles embedded with RsAqpZ tetramer has significantly different diffusion times across the confocal volume, which can be inferred by the lag time required to reach the half of the value of the autocorrelation factor, τ<sub>G(0)</sub>/<sub>2</sub>. b) Autocorrelation curves for RsAqpZ-mBanana proteoliposomes before and after resolubilization in detergent 2.5% OG. A relatively high correlation coefficient for liposomes indicates a low number of particles in the confocal volume (N<sub>lip</sub>). For RsAqpZ-mBanana liposomes at PLR of 0.02, when detergent is added the diffusion time of the particles across the confocal volume decreased more than 18 times and the number of particles increased more than 10 times (N<sub>prot</sub>), implying effective resolubilization of RsAqpZ-mBanana. The autocorrelation curves were fit to a 3D diffusion equation (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830.e003" target="_blank">Equation 3</a>) to obtain the concentration of the particles in the confocal volume. The stoichiometry of RsAqpZ tetramers per liposome (N<sub>RsAqpZ</sub>) was calculated taking the ratio of N<sub>prot</sub> over N<sub>lip</sub>. c) Reconstitution efficiency of RsAqpZ-mBanana in phospholipid vesicles. The stoichiometry of RsAqpZ per liposome obtained from FCS was compared to the theoretically maximum value for each protein to lipid ratio (PLR) to evaluate the efficiency of reconstitution (details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830.s008" target="_blank">File S1</a>).</p
Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future, 2013
The objective of this study to investigate the role of antioxidant enzymes against toxic reactive... more The objective of this study to investigate the role of antioxidant enzymes against toxic reactive oxygen species in human Hydatid disease (HD). This study took place in the Faculty of Medicine, University of Cukurova, Balcali Hospital in Adana, Turkey, from March 2004 to October 2005. The study was conducted on patients with cyctic echinococcosis (CE) before the surgical treatment and compared with healthy controls. Cyctic echinococcosis was determined by ELISA and western blotting method in serum samples. We assayed catalase (CAT) and superoxide dismutase activities (SOD) measured of 28 subjects and matched in 45 healthy controls. CAT and SOD activities of the patients and control group were found as 15.18 × 104 ± 3.25 ± 104 lU/mg Hb, 2.40 ± 0.27 U/mL and 17.84 × 104 ± 2.61 × 104 IU/mg Hb, 3.63 ± 0.41 U/mL, respectively. Present results showed that there was a significant decrease in CAT (p &lt; 0.05) and SOD (p &lt; 0.001) activities of patients group as compared with that of the controls. There is an increase in oxidative stress in cystic echinococcosis. Despite this stress, the antioxidant system is deficient and adequate, in patients with cystic echinococcosis could be a defense system promotes the regulation and expression of these enzymes
Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum w... more Cadmium (Cd) is a non-essential heavy metal having toxic effects on all living organisms. Durum wheat (Triticum durum Desf.) is widely used in human diets but has the potential to accumulate Cd. It also has a high level of genetic diversity, which may be exploited to develop cultivars with low Cd content. We aimed to perform marker-assisted selection and validate previously identified Cd markers in durum wheat germplasm for use in the investigation of accessions that accumulate low grain Cd content. We assessed 130 durum wheat accessions phenotypically and using three different molecular markers. Grain Cd contents of the studied germplasm varied 4.91-fold (26.2–128.7 μg/kg) with an average of 58.2 μg/kg. Landraces showed lower average values of grain Cd content than cultivars. Three molecular markers (usw47, Cad-5B and KASP marker Cad-5B) were used to differentiate high and low Cd accumulating lines. Results showed high correlation and successfully classified the accessions to the expected high or low Cd level; 87 accessions showed the low Cd alleles, and 43 accessions the high Cd alleles, except for five accessions with the usw47 marker that showed heterozygous status. A significant correlation coefficient (r = 0.944*) was observed among the three molecular markers. Based on molecular markers, 96.2% of the accessions were classified accurately. The KASP assay was highly effective in successfully separating low from high Cd content accessions and could be used as a molecular tool in durum wheat breeding programs, with less cost and time, targeting reduced grain Cd levels. The results of this study will allow durum wheat breeders to accelerate their progress to select suitable genotypes with the desired alleles.
TEZ6397Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2007.Kaynakça (s.51-55) var.x, 56 s. ... more TEZ6397Tez (Yüksek Lisans) -- Çukurova Üniversitesi, Adana, 2007.Kaynakça (s.51-55) var.x, 56 s. : res. ; 29 cm.Retinal guanylate cyclases, retGC-1 and retGC-2, are a subclass of the membrane dependent guanylate cyclase family. Synthesize cGMP, the intracelular second messenger of phototransduction, they play a crucial role in photoreceptor physiology. In recent work, it is intended to investigate the effect of adenine nucleotides and all-trans retinal on the retinal guanylate cyclase activity. Crosslinking experiments indicate, protein phosphorylation might be essential for physiological activity of cyclases.Retinal guanilat siklazlar, retGC-1 ve retGC-2, membrana bağlı guanilat siklaz ailesinin bir alt kolunu oluştururlar. Fototransdüksiyonunun intraselüler mesajcısı olan cGMP'yi sentezledikleri için fotoreseptör fizyolojisinde önemli rol oynarlar. Bu çalışmada, adenin nükleotidlerinin retinal guanilat siklazların fizyolojisine etkilerinin incelenmesi amaçlanmıştır. Çapraz bağ...
<p>a) Verification of the transfer of RsAqpZ into <i>Rhodobacter sphaeroides 17023<... more <p>a) Verification of the transfer of RsAqpZ into <i>Rhodobacter sphaeroides 17023</i> by colony PCR using primers directed to <i>pRKPLHT7</i> vector backbone. Lanes 1: negative control, 2: positive control (<i>E. coli</i> cloning vector), 3–9: <i>Rhodobacter</i> exconjugants (expected band 864 bp), L: NEB 100 bp ladder; b) SDS-PAGE of RsAqpZ overexpressed and purified from <i>Rhodobacter</i>. M:Marker, P:Pellet, FT: Flow-through, W3∶3rd Wash fraction, E1: First Elution from IMAC column, E2: Second elution; c) Western-blot image of the gel in part b); RsAqpZ in monomeric and tetrameric form were detected by anti-His antibody.</p
<p>ABA55 polymersomes embedded with EcAqpZ and RsAqpZ-mBanana were prepared using film rehy... more <p>ABA55 polymersomes embedded with EcAqpZ and RsAqpZ-mBanana were prepared using film rehydration method and dialyzed for insertion of the proteins in polymer. Unilamellar polymersomes with a low polydispersity (PDI <0.25) were obtained using consecutive extrusions through 400 nm and 200 nm track-etched filters and were then used to measure water permeability by stopped-flow light scattering. EcAqpZ and RsAqpZ-mBanana remained active in ABA55 polymer vesicles. RsAqpZ-mBanana showed higher water permeability in part due to higher incorporation efficiency.</p
<p>a) Phylogeny analysis of RsAqpZ indicates that it is an orthodox aquaporin with a close ... more <p>a) Phylogeny analysis of RsAqpZ indicates that it is an orthodox aquaporin with a close relationship to <i>E.coli</i> AqpZ, as well as the archeal aquaporin, AqpM. Evolutionary relationship of RsAqpZ to other aquaporins was evaluated by the Neighbor-Joining method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Saitou1" target="_blank">[24]</a>. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (2000 replicates) is shown next to the branches <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Felsenstein1" target="_blank">[44]</a>. The evolutionary distances were computed using the Equal Input method <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Tajima1" target="_blank">[45]</a> and are in the units of the number of amino acid substitutions per site. The analysis involved 10 amino acid sequences. All ambiguous positions were removed for each sequence pair. Evolutionary analyses were conducted in MEGA5 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-TamuraK1" target="_blank">[25]</a>. b) Multiple sequence alignment of aquaporin sequences. Amino acid sequence alignment was performed using Clustal Ω <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830-Goujon1" target="_blank">[23]</a> with the mRNA translation sequences retrieved from Genbank. RsAqpZ had signature residues Phe-39, His-173 and Arg-188 representing the orthodox aquaporins. Val-182 is a unique residue in the selectivity filter of RsAqpZ, which has significantly higher hydrophobicity, compared to the equivalent Thr-183 of EcAqpZ and Cys-189 of AQP1. Similar small hydrophobic residues were also found in AQY1 from <i>Pichia pastoris</i> (Ala-220) and human AQP4 (Ala-209), which might contribute to relatively higher water permeability in these aquaporins due to reduced interaction between water molecules and the amino acid residue in the selectivity filter.</p
<p>mBanana fluorescent protein was expressed as a C-terminal fusion partner along with RsAq... more <p>mBanana fluorescent protein was expressed as a C-terminal fusion partner along with RsAqpZ. The water permeability did not show a significant change, which enabled assessment of the protein properties at the single molecule level.</p
<p>mBanana fusion of RsAqpZ was expressed and purified from <i>R. sphaeroides</i&g... more <p>mBanana fusion of RsAqpZ was expressed and purified from <i>R. sphaeroides</i> and reconstituted in PC/PS vesicles at varying protein to lipid ratios. The number of RsAqpZ tetramers per liposome was evaluated by FCS, a) Normalized autocorrelation curves of mBanana species, mBanana fluorescent protein, RsAqpZ-mBanana protein tetramer and phospholipid vesicles embedded with RsAqpZ tetramer has significantly different diffusion times across the confocal volume, which can be inferred by the lag time required to reach the half of the value of the autocorrelation factor, τ<sub>G(0)</sub>/<sub>2</sub>. b) Autocorrelation curves for RsAqpZ-mBanana proteoliposomes before and after resolubilization in detergent 2.5% OG. A relatively high correlation coefficient for liposomes indicates a low number of particles in the confocal volume (N<sub>lip</sub>). For RsAqpZ-mBanana liposomes at PLR of 0.02, when detergent is added the diffusion time of the particles across the confocal volume decreased more than 18 times and the number of particles increased more than 10 times (N<sub>prot</sub>), implying effective resolubilization of RsAqpZ-mBanana. The autocorrelation curves were fit to a 3D diffusion equation (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830.e003" target="_blank">Equation 3</a>) to obtain the concentration of the particles in the confocal volume. The stoichiometry of RsAqpZ tetramers per liposome (N<sub>RsAqpZ</sub>) was calculated taking the ratio of N<sub>prot</sub> over N<sub>lip</sub>. c) Reconstitution efficiency of RsAqpZ-mBanana in phospholipid vesicles. The stoichiometry of RsAqpZ per liposome obtained from FCS was compared to the theoretically maximum value for each protein to lipid ratio (PLR) to evaluate the efficiency of reconstitution (details in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086830#pone.0086830.s008" target="_blank">File S1</a>).</p
Food, Pharmaceutical and Bioengineering Division 2013 - Core Programming Area at the 2013 AIChE Annual Meeting: Global Challenges for Engineering a Sustainable Future, 2013
The objective of this study to investigate the role of antioxidant enzymes against toxic reactive... more The objective of this study to investigate the role of antioxidant enzymes against toxic reactive oxygen species in human Hydatid disease (HD). This study took place in the Faculty of Medicine, University of Cukurova, Balcali Hospital in Adana, Turkey, from March 2004 to October 2005. The study was conducted on patients with cyctic echinococcosis (CE) before the surgical treatment and compared with healthy controls. Cyctic echinococcosis was determined by ELISA and western blotting method in serum samples. We assayed catalase (CAT) and superoxide dismutase activities (SOD) measured of 28 subjects and matched in 45 healthy controls. CAT and SOD activities of the patients and control group were found as 15.18 × 104 ± 3.25 ± 104 lU/mg Hb, 2.40 ± 0.27 U/mL and 17.84 × 104 ± 2.61 × 104 IU/mg Hb, 3.63 ± 0.41 U/mL, respectively. Present results showed that there was a significant decrease in CAT (p &lt; 0.05) and SOD (p &lt; 0.001) activities of patients group as compared with that of the controls. There is an increase in oxidative stress in cystic echinococcosis. Despite this stress, the antioxidant system is deficient and adequate, in patients with cystic echinococcosis could be a defense system promotes the regulation and expression of these enzymes
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