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Öğe Antimicrobial activity of phytic acid, citric acid, and EDTA with and without propolis against Enterococcus Faecalis and Candida Albicans(Mashhad University of Medical Sciences, 2022) Özata, Merve Yeniçeri; Acer, Ömer; Demirci, Özlem; Çolak, Mehmet; Tartuk, Gizem AkınIntroduction: This study aimed to investigate the antimicrobial efficacy of chelation agents on Enterococcus faecalis (E. faecalis) and Candida albicans (C. albicans) when used alone or in combination with propolis. Methods: One hundred fifty mandibular premolar teeth were selected. Each canal was prepared with Reciproc R25. The roots were then divided into two parts along their long axis (n=300). For E. faecalis and C. albicans, the samples were divided into 16 groups (14 experimental and 2 control) as follows: Group 1A-1B [17% Ethylenediaminetetraacetic acid (EDTA)], Group 2A-2B [10% Citric Acid (CA)], Group 3A-3B [1% phytic acid/inositol hexaphosphate (IP6)], Group 4A-4B (17% EDTA+8 mg/mL propolis), Group 5A-5B (10% CA+8 mg/mL propolis), Group 6A-6B (1% IP6+8mg/mL propolis), Group 7A-7B (8 mg/mL propolis), Control A-B (Dimethyl Sulfoxide). Each tooth was randomly irrigated with 2 mL of one of the group solutions or dispersions for 5 min, and the solutions were examined for the bactericidal effect. Results: For C. albicans, all groups showed less optical density (OD) than the control group (P<0.05). The propolis group and the IP6 group had higher OD values than the CA group (P<0.05). For E. faecalis, on the other hand, significantly lower OD values were observed in the propolis+ CA group, compared to the CA and propolis groups (P<0.05). There was no significant difference between microbial growth among IP6, EDTA, propolis+ CA, propolis+IP6, and propolis+ EDTA groups (P>0.05). Conclusion: CA and IP6 showed promising results in eliminating E. faecalis, one of the collective organisms responsible for failed root canals.Öğe Aroclor 1254’e maruz kalan elastinin yapısında meydana gelen değişikliklerin incelenmesi(Dicle Üniversitesi Fen Bilimleri Enstitüsü, 2020) Demirci, Özlem; Uğurlu, Pelin; Bingölbalı, Nurcan Doğan; Acer, Ömer; Kılınç, ErsinElastin prolin, valin ve glisin aminoasitlerinin yoğun olarak yer aldığı hidrofobik bölge ve alanin aminoasitinin yer aldığı çapraz bağlanma bölgesinden oluşan ve omurgalı canlıların dokularına esneklik ve hareketlilik sağlayan bir protein çeşididir. Elastinde meydana gelecek hasarlar pek çok hastalığa neden olduğundan elastin proteini üzerine çok sayıda araştırma yapılmıştır. Fakat toksik bir maddeye maruz kalan elastinde oluşacak hasarla ilgili çalışmalar literatürde sınırlı sayıdadır. Bu amaçla önemli kalıcı organik kirleticilerden biri olan Aroclor 1254’e maruz kalan elastin proteininin yapısında meydana gelen değişiklikler histopatolojik olarak incelenmiş ve oluşan hasarın konsantrasyona bağlı olduğu tespit edilmiştir.Öğe Bioaccumulation, resistance, removal of U(VI) and Th(IV) and their rffects on antioxidant enzymes on thermophilic anoxybacillus flavithermus ST15(Taylor & Francis, 2021) Acer, Ömer; Kılınç, Ersin; Özdemir, SadinIn this research, a novel heavy metals resistance thermophilic Anoxybacillus flavithermus ST15 was isolated from a hot spring mud sample in Afyonkarahisar (Omer). 16S rRNA analyzing revealed that strain ST15 was 99.7% similar to Anoxybacillus flavithermus subsp. yunnanensis str. E13. We propose that U(VI) and Th(IV) have an effect on A. flavithermus at the cellular level and that this bacteria can be used as a bioindicator. Therefore, the effects of U(VI) and Th(IV) resistance, removal, and bioaccumulation on the antioxidant enzyme systems of thermophilic A. flavithermus have been thoroughly investigated. SOD and CAT activities were observed to be increased by different concentrations of U(VI) and Th(IV). A scanning electron microscope and fourier transform infrared spectroscopy were used to analyze changes in the surface macrostructure and functionality of A. flavithermus following interaction with U(VI) and Th(IV). The highest bioaccumulation efficiency amounts for U(VI) were 102.36 mg/g dried bacteria at 24 h at 12.5 mg/l concentration and 105.7 mg/g dried bacteria at 36 h at 12.5 mg/l concentration was detected for Th(IV). At the 24th h and 12.5 mg/l, the highest U(VI) and Th(IV) cell membrane bioaccumulation capacities of A. flavithermus were calculated as 307.08 and 289.52 mg metal/g wet membrane, respectively. This is the first research to examine U(VI) and Th(IV) resistance, removal, and bioaccumulation in thermophilic A. flavithermus.Öğe Characterization of a thermally stable ?-galactosidase produced by thermophilic anoxybacillus sp. AH1(Bingöl Üniversitesi Fen Bilimleri Enstitüsü, 2021) Acer, Ömer; Bekler, Fatma MatpanThermostable β-galactosidases from thermophilic bacteria have attracted increasing interest to have various advantages in industrial and biotechnological applications. In this study, a highly thermally stable β-galactosidase produced by Anoxybacillus sp. AH1 was purified and characterized. The highest enzyme production was achieved after the bacterium was incubated for 24 hours. The enzyme was purified by precipitation with ammonium sulphate dialysis, gel filtration chromatography using Sephadex G-75. After the purification steps, β-galactosidase was found to be purified 10.2-fold and a yield of 13.9%. The molecular mass of the β-galactosidase was estimated to be 75 kDa by SDS-PAGE. The purified enzyme was highly stable and retained at 71% of the original activity at 60 °C and 53% at 70 oC within 120 minutes. The Km and Vmax values of purified β-galactosidase were calculated as 1.249 mM and 0.5 μmol minutes-1 , respectively. Ca2+, Zn2+, and Mg2+ significantly activated β-galactosidase activity, whereas enzyme activity was inhibited significantly by Cu+2 as well as by the metal ion chelators1,10- phenanthroline (phen) and ethylenediaminetetraacetic acid (EDTA). The Purified β-galactosidase activity was increased by PMSF (phenylmethylsulfonyl fluoride), PCMB (pchloromercuribenzoic acid), DTT (dithiothreitol), and β-ME (β-mercaptoethanol) at 2 mM, but inhibited completely by NEM (N-ethylmaleimide) at 1 mM.Öğe Cloning, purification and characterization of a thermostable β- galactosidase from Bacillus licheniformis strain KG9(Cellular and Molecular Biology Association, 2015) Bekler, Fatma Matpan; Stougaard, Peter; Güven, Kemal; Güven, Reyhan Gül; Acer, ÖmerA thermo- and alkalitolerant Bacillus licheniformis KG9 isolated from Taslidere hot water spring in Batman/Turkey was found to produce a thermostable ?-galactosidase. Phylogenetic analysis showed that the 16S rRNA gene from B. licheniformis strain KG9 was 99.9% identical to that of the genome sequenced B. licheniformis strain DSM 13. Analysis of the B. licheniformis DSM 13 genomic sequence revealed four putative ?-galactosidase genes. PCR primers based on the genome sequence of strain DSM 13 were used to isolate the corresponding ?-galactosidase genes from B. licheniformis strain KG9. The calculated molecular weights of the ?-galactosidases I, II, III, and IV using sequencing data were 30, 79, 74, and 79 kDa, respectively. The genes were inserted into an expression vector and recombinant ?-galactosidase was produced in Escherichia coli. Of the four ?-galactosidase genes identified in strain KG9, three of them were expressed as active, intracellular enzymes in E. coli. One of the recombinant enzymes, ?-galactosidase III, was purified and characterized. Optimal temperature and pH was determined to be at 60 °C and pH 6.0, respectively. Km was determined to be 1.3 mM and 13.3 mM with oNPG (ortho-nitrophenyl-?-D-galactopyranoside) and lactose as substrates, respectively, and Vmax was measured to 1.96 ?mol/min and 1.55 ?mol/min with oNPG and lactose, respectively.Öğe A highly inducible ?-galactosidase from enterobacter sp(Serbian Chemical Society, 2020) Shaikhan, Bestoon Ahmed; Güven, Kemal; Bekler, Fatma Matpan; Acer, Ömer; Güven, Reyhan GülEnterobacter sp. 3TP2A isolated from a petroleum station was found to produce a novel, highly inducible mesophilic intracellular β-galactosidase in the presence of lactose up to 76.5 U mg-1. The enzyme was purified to 17.3-fold after gel permeation chromatography with a yield of approximately 11 %. The optimum pH and temperature values of the purified enzyme were found to be 8.0-9.0 and 35 °C, respectively. The molecular weight of the enzyme was approx. 60 kDa with a single band by both SDS-PAGE and native-PAGE, and estimated by gel filtration chromatography. The enzyme was inhibited by Zn2+ and EDTA, while Cu2+ had strong inhibitory effect even at low concentrations. Activation by Mg2+ and inhibition by EDTA show that the enzyme is metal-dependent or a metalloenzyme. The enzyme was slightly activated by 2-mercaptoethanol, while slightly inhibited by iodoacetamide. On the other hand, PCMB inhibited the enzymatic activity to a great extent, whereas it was completely inhibited by N-ethylmaleimide. The Vmax and Km values were calculated as 0.701 μmol min-1 and 0.104 mM, respectively. The results indicated that the β-galactosidase Enterobacter sp. 3TP2A might well be a good candidate for use in biotechnology, particularly in the area of environment and health.Öğe Petrolle kirletilmiş topraklardan petrolü parçalayan bakterilerin izolasyonu ve karakterizasyonu(2015) Acer, ÖmerMutajenik, karsinojenik ve güçlü immünotoksik olan petrol bileşiklerinin toprağa ve yeraltı sularına kontrolsüz bir şekilde salınımı insan ve hayvan sağlığı için ciddi bir tehdit oluşturmaktadır. Kapsamlı petrol arama, işleme, depolama ve taşıma faaliyetleri, yeterince önlem alınmadığı vakit sık sık çevre kirliliğine yol açarak ekosistemin biyotik ve abiyotik bileşenleri için yıkıcı hasarlara yol açmaktadır. Petrolle kirlenmiş sistemlerin remediasyonu ya fiziko-kimyasal ya da biyolojik yöntemlerle başarılmaktadır. Petrolle kirlenmiş toprakların biyodegradasyonu etkili, ekonomik ve çok yönlü olarak kurulmuştur. Bu çalışmanın amacı, petrolle kirlenmiş topraklardan petrolü parçalayan bakteri izolasyonu ve karakterizasyonunu gerçekleştirmektir. Diyarbakır ve Batman'daki petrol sahalarında bulunan petrolle kirlenmiş topraklardan sırasıyla Acinetobacter, Cronobacter ve Stenotrophomanas cinslerine ait beş bakteri türü izole edilmiştir. Bakterilerin morfolojik, fizyolojik, biyokimyasal ve kemotaksonomik özelliklerine bakılmıştır. Sırasıyla ST5, GC2, BT1A, BT1B ve 2TP1A şeklinde etiketlendirilen bakterilerin 16S rRNA gen dizi analizine göre Acinetobacter calcoaceticus ve Acinetobacter pittii, Acinetobacter lwofii, Acinetobacter baumannii, Cronobacter malonaticus ve Stenotrophomonas maltophilia türlerine yakın oldukları belirlenmiştir. Hemen hemen tüm bakteri türlerinin gelişmek için ham petrolü karbon ve enerji kaynağı olarak kullandıkları bulunmuştur. Bakterilerin alifatik hidrokarbonlardan, sadece uzun zincirli n-alkanlarda (tridekan, pentadekan, hegzadekan) ürediği görülmüştür. Kısa zincirli n-alkanlarda (heptan) üreme kaydedilmemiştir. Test edilen uzun zincirli alkanlar arasında, genel olarak en çok tercih edilen hekzadekan olmuştur. GC-MS analizi, BT1A, ST5, 2TP1A ve GC2'nin 7 günlük inkübasyon ile ham petrolde bulunan n-alkanları sırasıyla yaklaşık olarak %83, %41, %41 ve %6 oranlarında degrade ettiklerini göstermiştir. Sonuç olarak bu çalışma, izole edilen bakterilerin petrolle kirlenmiş bölgelerde hidrokarbon biyodegradasyonunda etkili bir şekilde kullanılabileceklerini göstermektedir. Anahtar Kelimeler: Bakteri izolasyonu ve karakterizasyonu, petrolü parçalayan bakteriler, 16S rRNA dizi analizi, GC-MSÖğe Preconcentrations of Zn(II) and Hg(II) in environmental and food samples by SPE on B. licheniformis loaded amberlite XAD-4(Springernature, 2022) Özdemir, Sadin; Kılınç, Ersin; Acer, Ömer; Soylak, MustafaIn this work, the separations and preconcentrations of Zn(II) and Hg(II) ions on Bacillus lichenifoemis loaded onto Amberlite XAD-4 resin by solid-phase extraction has been performed. The biosorbent was characterized by using FT-IR, SEM, and EDX. pH, sample flow rate, eluent type and concentration, amount of B. licheniformis and XAD-4 resin, sample volume, and possible interfering ions effect were investigated in details as experimental variables in the SPE procedure. Limit of detection values for Zn(II) and Hg(II) were detected as 0.03 and 0.06 ng-mL(-1), respectively. 0.2-15 ng-mL(-1) linear range values were achieved for Zn(II) and Hg(II), respectively. Relative standard deviation values were found to be lower than 5%. For validation of the procedure, the certified standard reference materials (CWW-TM-D, EU-L-2, NCS ZC73O14, NCS ZC73350) were analyzed. The concentrations of Zn(II) and Hg( II) in water and food samples were measured by ICP-OES. Consequently, it can be inferred that the immobilized B. licheniformis microcolumn has ideal selectivity for Zn(II) and Hg(II) biosorption.Öğe Production and purification of novel thermostable alkaline protease from Anoxybacillus sp. KP1(Cellular and Molecular Biology Association, 2015) Bekler, Fatma Matpan; Acer, Ömer; Güven, KemalIn this study, an extracellular novel alkaline protease (EC 3.4.21-24, 99) from a thermophilic and aerobic strain of Anoxybacillus sp. KP1 has been studied. Maximum protease activity was obtained at 50 °C at pH 9.0 after 24 hours of incubation. Among the carbon and nitrogen sources used; the optimum protease production was with soluble starch, maltose, urea and casamino acid. The enzyme was purified by ammonium sulphate precipitation and Sephadex G-75 gel chromatography. Molecular weight of purified enzyme was determined as 106 kDa by SDS-PAGE. Purified protease was stable at 50-60 °C and at pH 9.0 for 1 h. The enzyme activity was increased in the presence of Ca2+, Cu2+, Tween 80 and Triton X-100, however the enzyme activity was inhibited in the presence of Hg2+, ethylene diamine tetra acetic acid (EDTA) and H2O2. Proteolytic activity was completely inhibited by phenyl methyl sulfonyl fluoride (PMSF). The enzyme seems to be a serine alkaline protease. In the presence of detergents, the protease was clearly stable and residual activity was between 73-82%.Öğe Production, purification and characterisation of thermostable metallo-protease from newly isolated bacillus sp KG5(Foundation for Enviromental Protection and Research, 2015) Ahmetoğlu, Nazenin; Bekler, Fatma Matpan; Acer, Ömer; Güven, Reyhan Gül; Güven, KemalBackground: Due to the importance of microbial proteases in biotechnological applications, a number of microorganisms are being explored. The production, purification and characterisation of extracellular metallo-proteases by producing Bacillus sp. KG5 was studied. Material and Methods: Bacterial strain KG5 was isolated from Kös (Bingöl) hot spring. The strain KG5 was identified by morphological, physiological, biochemical and 16S rRNA gene sequencing. The effects of various parameters on protease production, such as time, temperature, pH, carbon and nitrogen sources and CaCl2were studied. The enzyme was purified by ammonium sulphate precipitation and Sephadex G-75 gel permeation chromatography. Molecular weight was calculated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymographic analysis. The effects of some metal ions, chelators and inhibitors on enzyme activity were determined. Results: The optimum temperature, pH and incubation period for protease production were 40-45°C, 7.0 and 24 h, respectively. It was determined that the best nitrogen sources were yeast extract and urea, while the best carbon sources were lactose and galactose. However, glucose as a source of carbon was found to inhibit the production of the enzyme. The maximum enzyme production was increased in the presence of CaCl2. The molecular weight of purified enzyme was found to be approximately 48 kDa. It was found that the enzyme was fully stable in the presence of 2 mM CaCl2 at 50°C after 120 min. Purified protease was significantly activated by Ca2+ and Mg2+, while it was greatly inhibited by Cu2+, Zn2+, Hg2+ and SDS as well as by the metal ion chelators ethylenediaminetetraacetic (EDTA) and 1,10-phenanthroline. Phenylmethylsulfonyl fluoride (PMSF) had a little effect on the enzyme. Conclusions: Our findings suggest the potential of this isolate for protease production and that this enzyme may be suitable for biotechnological applications.Öğe Purification and characterization of polyphenol oxidase from purslane(Sociedade Brasileira de Ciencia e Tecnologia de Alimentos, SBCTA, 2017) Güven, Reyhan Gül; Güven, Kemal; Bekler, Fatma Matpan; Acer, Ömer; Alkan, Hüseyin; Doğru, MehmetThe polyphenol oxidase (PPO) is an enzyme that is responsible for the enzymatic browning of fruits and vegetables. This is generally undesired process and need to be prevented in food technology. PPO from purslane was purified, characterised and the kinetic parameters for three substrates namely, catechol, L-Dopa and 4-methylcatechol were determined. The optimum pH and temperature values were found to be pH 7.0 and 50 °C, respectively using the catechol as substrate. The apparent molecular weight of the PPO from purslane was determined as high as 163 kDa by partially denaturing SDS-PAGE. Moreover, the inhibition kinetics of the purified PPO were determined, using both synthetic and natural inhibitors. Among inhibitors tested, ascorbic acid was the most effective inhibitor with the lowest Ki value of 0.36 mM. This is the first study on the purification and characterisation of PPO from purslane (Portulaca oleracea) that may provide new insight into how to overcome the enzymatic browning.Öğe Purification and characterization of thermostable and detergent-stable α-amylase from Anoxybacillus sp. AH1(University of Zagreb, 2016) Acer, Ömer; Bekler, Fatma Matpan; Pirinççioğlu, Hemşe; Güven, Reyhan Gül; Güven, KemalA thermostable and detergent-stable ?-amylase from a newly isolated Anoxybacillus sp. AH1 was purified and characterized. Maximum enzyme production (1874.8 U/mL) was obtained at 24 h of incubation. The amylase was purified by using Sephadex G-75 gel filtration, after which an 18-fold increase in specific activity and a yield of 9 % were achieved. The molecular mass of the purified enzyme was estimated at 85 kDa by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE). The optimum pH and temperature values of the enzyme were 7.0 and 60 °C, respectively. The enzyme was highly stable in the presence of 30 % glycerol, retaining 85 % of its original activity at 60 °C within 120 min. Km and vmax values were 0.102 ?mol and 0.929 ?mol/min, respectively, using Lineweaver- Burk plot. The enzyme activity was increased by various detergents, but it was significantly inhibited in the presence of urea. Mg2+ and Ca2+ also significantly activated ?-amylase, while Zn2+, Cu2+ and metal ion chelators ethylenediaminetetraacetic acid (EDTA) and 1,10-phenanthroline (phen) greatly inhibited the enzyme activity. ?-Amylase activity was enhanced by ?-mercaptoethanol (?-ME) and dithiothreitol (DTT) to a great extent, but inhibited by p-chloromercuribenzoic acid (PCMB). Iodoacetamide (IAA) and N-ethylmaleimide (NEM) had a slight, whereas phenylmethylsulfonyl fluoride (PMSF) had a strong inhibitory effect on the amylase activity.Öğe Termofilik Anoxybacillus sp. AH1'de α-amilaz enzimi üzerine çalışmalar(2016) Acer, Ömer; Güven, KemalBu çalışmada Dargeçit (Mardin) sıcak su kaplıcalarından izole edilen termofilik Anoxybacillus sp. AH1'de biyoteknolojik öneme sahip olan ? -amilaz enziminin bazı özelliklerinin araştırılması amaçlanmıştır. Anoxybacillus sp. AH1 NB besiyerinde üretildi ve değişik inkübasyon sürelerinde ?-amilaz aktivitesi ölçüldü. Maksimum enzim üretimi 12?24 saatleri arasında tespit edildi. pH ve sıcaklık etkisi sırasıyla pH 4.0?11.0 ve 30?90 oC'de hem ham enzimde hemde kısmi olarak saflaştırılan enzimde araştırıldı. Enzimin optimum pH ve sıcaklık değerleri sırasıyla 7.0 ve 60 oC olarak bulundu. Enzim üretimi üzerine değişik besiyerlerinin, % 1'lik farklı azot ve % 0.5-% 1 oranlarında farklı karbon kaynaklarının ve nişastaların etkisi incelendi. Maksimum enzim üretimi NB1 besiyerinde elde edildi. En iyi azot kaynağı pepton ve beef ekstrakt, en iyi karbon kaynağı ise % 0.5 oranlarındaki maltoz, glukoz ve laktoz olarak belirlendi. Ayrıca % 0.5 ve % 1 oranlarındaki patates nişastasının ve % 1 oranında çözünebilir nişastanın enzim üretimini arttırdığı tespit edildi. Enzim üretimi üzerine çeşitli konsantrasyonlarda CaCl2'nin etkisi araştırıldı. CaCl2 varlığında enzim üretiminin arttığı tespit edildi. Maksimum enzim üretimi 20 mM'da elde edildi. Anoxybcillus sp. AH1'de ?-amilaz kısmi olarak saflaştırıldı ve enzim aktivitesi üzerine bazı kimyasalların, metallerin, metal şelatörlerin ve deterjanların etkisi incelendi. MgCl2 (8 mM'da % 41) ve CaCl2'nin (8 mM'da % 70) ?-amilaz aktivitesini belirli oranlarda arttırdığı, ZnCl2 (0.5 mM'da % 85 ve 1 mM'da % 93), CuCl2'nin (0.5 mM'da % 76 ve 1 mM'da % 100) ve metal şelatörleri olan EDTA (10 mM'da % 63) ve 1,10-phenanthroline'nin (10 mM'da % 22) ise yüksek oranda inhibe ettiği tespit edildi. ß-mercaptoethanol (10 mM'da % 64) ve DTT'nin (10mM'da % 100) ?-amilaz aktivitesini geniş ölçüde arttırdığı, PCMB (4mM'da % 52) ve PMSF'nin (4mM'da % 60) ise enzim aktivitesini belirli oranlarda inhibe ettiği tespit edildi. Iodaacetamide ve N-ethylmaleimide'nin enzim aktivitesini çok az etkilediği görüldü. Enzim aktivitesinin çeşitli deterjanlar varlığında arttığı; fakat üre tarafından güçlü bir şekilde inhibe edildiği tespit edildi. Km ve Vmax gibi kinetik parametreleri ?-amilazın % 0.5-% 3 (w/v) oranlarında tamponda hazırlanan çözünebilir nişasta ile inkübasyona bırakılarak hesaplandı. Km ve Vmax değerleri Lineweaver?Burk plot'a göre sırasıyla 0.102 mM ve 0.929 µmol/dk. olarak hesaplandı. Enzimin 45 oC'nin üzerindeki sıcaklıklara duyarlı olduğu ve termal stabilitesinin gliserol ve sorbitol tarafından arttırıldığı belirlendi. % 30 gliserol varlığında enzimin 55 oC ve 60 oC' de 120 dakika sonunda orijinal aktivitesini sırasıyla % 99 ve % 85 oranında koruduğu tespit edildi. Enzimin elektroforetik analizi nondenatüre poliakrilamid jel elektroforezi ile yapıldı. Anahtar Kelimeler:, Anoxybacillus sp. AH1, Biyoteknoloji, ? -amilaz enzim üretimi, enzim karakterizasyonu