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Öğe Characterization of Bacillus species by numerical analysis of their SDS-PAGE protein profiles(Journal of Cell and Molecular Biology, 2004) Berber, İsmetIn the present study nine reference Bacillus strains were characterized by whole-cell protein profiles using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). A numerical classification of the protein profiles revealed two distinct clusters at 47% similarity level. Cluster 1 comprised four strains belongs to B. subtilis and B. megaterium species at similarity levels changed between 67 and 85%, while cluster 2 consisted five strains belongs to various Bacillus species at similarity levels changed between 50 and 70%. The strains of the cluster 2 were clearly separated from that of cluster 1 by numerical analysis. Our results indicates that SDS-PAGE method combined with computerized analysis of cellular protein profiles provide an effective approach to investigate of taxonomic relationships within Bacillus species.Öğe Characterization of bean (Phaseolus vulgaris L.) cultivars grown in turkey by SDS-page of seed proteins(Pakistan Journal of Botany, 2011) Berber, İsmet; Yaşar, FikretIn the present research, a total 28 bean cultivars grown in Turkey were characterized by the numerical analysis of seed protein profiles obtained by using sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) technique. The numerical analysis of seed protein profiles generated two major clusters at similarity levels of 82.52% or above. The first cluster included 5 reference bean cultivars at the intra-cluster similarity values of 91.25% or above. The second cluster comprised the all remaining genotypes at similarity values between 84.46% and 100%. Our results also indicated that Gina standard cultivar together with all eastern genotypes belonged to subcluster IIc, having the highest intra-cluster similarities between 95.54% and 100%. In this sense, it is suggested that probably there may be a very close genetic relationship between eastern genotypes and Gina cultivar. In conclusion, this study indicated that the numerical analysis of seed protein profiles offer no final answer to the identity of bean genotypes, however, the method can provide of extra banding pattern for the discrimination of bean genotypes cultivated in Turkey.Öğe Determination of Total Cell Protein Profiles of Streptomyces Species(Journal of Experimental Biology and Agricultural Sciences, 2013) Özdemir, K.; Berber, İsmet; Öğün, E.; Atalan, E.Present study has been conducted for finding out the total protein profile of bacterial strain Streptomyces sps by sodium dodecyl sulphate polyacrylamide gel electrophoresis. Total 139 isolates of Streptomyces have been isolated from the soil. Amongst all isolated strain, total 20 isolates were used for getting protein profile by SDS PAGE. Amongst all isolates, 20 isolates were selected for protein profiling and these were divided in two groups. Two strains of Streptomyces i.e. S. violaceus and S. albidoflavus were selected as a reference strain for both groups. Band profile were analyzed and assessed by computer added program BioRad Quantity with the use of Unweighted Pair Group Method of Analysis (UPGMA). As a result of this computer assisted numeric analysis study, approximately 40 different types of protein bands were reported between 10 or 100 kD molecular weight. Analysis of acquired dendogram on the basis of similarities ratios, all 40 proteins can be divided in to 7 groups. In addition, the isolates A4B3G, D145B, S5036.6 and reference isolate S. violaceus were available in the same group, while 805A, C804B, F1705 isolates and reference sample S. albidoflavus were detected in the same group. The test organisms which were similar to each other in terms of morphological and biochemical characters delivered the same protein bands. SDS-PAGE method is an effective method in terms of determining taxonomical relations between the various species of genus Streptomyces.Öğe Discrimination and numerical analysis of human pathogenic Candida albicans strains based on SDS-PAGE protein profiles(African Journal of Biotechnology, 2008) Berber, İsmet; Ekin, SuatIn the present study, 21 Candida albicans strains were investigated using the commercial kit API 20C AUX system and the numerical analysis of whole-cell protein profiles. The results of the commercial kit confirmed that the all the strains belonged to C. albicans species. However, the research indicated that SDS-PAGE of polypeptides of whole-cell extracts can provide more valuable taxonomic information than conventional yeast test kits at the subspecies level. Despite the fact that C. albicans subtypes isolated from different anatomical sites had similar protein profiles, there were some distinctive protein bands. Numerical analysis of whole-cell protein profiles of all strains revealed 2 major clusters at similarity degrees of between 46.26 and 100%. Moreover, the results of numerical analysis confirmed that each cluster had characteristic and distinctive protein profiles. The research showed that, the morphological examination of yeast isolates remains essential to obtaining a correct identification, both the commercial yeast kit system and the numerical analysis of whole-cell protein patterns can be useful for the more reliable identification of C. albicans strains.Öğe Effect of Gramoxone Herbicide on Spore Viability and Larvicidal activity of Bacillus sphaericus 2362 and 1593 strains(Fresenius Environmental Bulletin, 2003) Berber, İsmet; Atalan, Ekrem; Çökmüş, CumhurSpore viability and larvacidal activity of B. sphaeri-cus 2362 and 1593 strains were monitored in media con-taining Gramaxone® herbicide. Minimal Inhibitory Con-centrations (MICs) of the herbicide were determined for each of the mosquito pathogenic strains. Addition of paraquat into the media suppressed the spore germination after 24 and 48 h, but no influence was observed on parasporal inclusions containing insecticidal toxin pro-teins. SDS-PAGE analysis confirmed the presence of the so-called binary toxin comprising two proteins that are deposited in parasporal crystals treated with the herbicide. Moreover, the number of heat-resistant spores and total cell numbers of test strains were reduced drastically when test strains were grown in media containing 50, 100 and 200 mg ml-1 of paraquat. In contrast, there were no differ-ences between heat-resistant spore counts of both strains when grown under diet concentrations of less than 50 mg ml-1. This study revealed that B. sphaericus 2362 strain has a higher mosquito larvacidal activity than 1593 strain in the presence of paraquat in the media. Thus, the use of Gramaxone® herbicide can have harmful effects on mos-quitocidal biological control agents.Öğe Effects of Some Pesticides on Spore Germination and Larvicidal Activity of Bacillus thuringiensis var. israelensis and Bacillus sphaericus 2362 Strain(Turkish Journal of Biology, 2004) Berber, İsmet; Çökmüş, Cumhur; Atalan, EkremThe effects of 9 commercial pesticides used commonly in agriculture on spore germination and larvicidal activity of the mosquito pathogenic B. thuringiensis var. israelensis and B. sphaericus 2362 strain were examined. Six of the pesticides was had an inverse impact on spore germination and growth of the test strains. It was determined that the pesticides with the most adverse effect were copper sulfate, methiocarb, and dalapon on spore germination of the microorganisms. Higher concentrations or MIC values of the pesticides reduced the heat-resistant spore numbers of both bioinsecticides, suppressing spore germination. These results indicated that the spores of the bacteria are sensitive to chemical pesticides at the same level. Moreover, the study revealed that the spore germination and larvicidal activity of both biological control agents are affected by pesticides equally. The findings should be considered for assessing the effects of pesticides when both microbial agents are used in field applications.Öğe Identification and Protein Fingerprinting of Staphylococcus aureus Species Isolated from Tooth Decay(Springer India, 2017) Bilgin Çine, Nevra; Berber, İsmet; Avşar, CumhurStaphylococcusaureus is the most prevalent human pathogenic microorganism worldwide. In the present study, a total of 57 S. aureus strains, including 54 clinical isolates obtained from dental hospitals and three reference strains were characterized by phenotypic characteristics and SDS-PAGE protein profiling. Out of the 132 clinical specimens, 54 S. aureus strains were isolated and identified according to their morphological and physiological characteristics. The strains were tested against 13 standard antibiotics by using disc diffusion procedure. Antibiogram results showed that the highest resistance among the isolates was determined against ampicillin (83.6 %), whereas they were susceptible to sulfamethoxazole/trimethoprim, cefoperazone/sulbactam, vancomycin and imipenem. In addition, multidrug resistance index values of 12 (22.2 %) of the isolates were higher than the reference value of 0.2. The numerical analysis of whole-cell protein profiles of S. aureus strains revealed 2 major clusters at similarity levels of 57 % or above. Furthermore, the numerical analysis of extra-cellular protein profiles of S. aureus strains yielded 2 major clusters at similarity levels of 48 % or above. In conclusion, the present findings revealed that use of conventional methods with the numerical analysis of whole-cell and extra-cellular protein profiles might be useful for the more reliable identification of S. aureus strains isolated from tooth decay. © 2015, The National Academy of Sciences, India.Öğe Identification of Alkaliphilic Bacillus Species Isolated from Lake Van and Its Surroundings by Computerized Analysis of Extracellular Protein Profiles(Turkish Journal of Biology, 2005) Berber, İsmet; Yenidünya, ElçinFive reference Bacillus species and 17 native alkaliphilic Bacillus strains, isolated from the water of Lake Van and the soil surrounding it, were identified using phenotypic characteristics and extracellular protein profiles by the method of sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). According to the phenotypic characteristics, all the native isolates were Gram-positive, aerobic, endospore-forming, motile, facultatively alkaliphilic Bacillus spp. It was also found that the native alkaliphilic Bacillus isolates were distinguished phenotypically from other Bacillus species. A numerical analysis based on the resulting extracellular protein profiles revealed 5 distinct clusters: native isolates and B. megaterium formed 4 clusters that varied between 69% and 100% similarity, and the other reference Bacillus species formed a cluster with a similarity of above 70%. The research showed that extracellular protein profiles obtained by SDS-PAGE provide an effective approach to the investigation of taxonomic relationships within native alkaliphilic Bacillus isolates and other Bacillus species.Öğe Numerical Analysis of SDS-PAGE Protein Patterns of Facultative Alkaliphilic Bacillus Species Isolated From Lake Van, Turkey(Fresenius Environmental Bulletin, 2006) Berber, İsmet; Berber, ŞerifeIn the present study, seven reference Bacillus species and a total of eighteen new facultative alkaliphilic Bacil-lus strains, isolated from the water of Lake Van and its soil surroundings, were identified using phenotypic charac-teristics and the numerical analysis of whole-cell protein profiles. According to morphological, biochemical and physiological characteristics, it was found that the new isolated strains belonged to Bacillus genus. In addition, the research indicated that SDS-PAGE of polypeptides of whole-cell extracts can provide more valuable taxonomic information than conventional tests based on the pheno-typic characteristics at the species and subspecies levels. Numerical analysis of whole-cell protein profiles of test strains revealed 4 basic clusters (I-IV) at dissimilarity val-ues of 18.9 % or above. The results of numerical analysis confirmed that each cluster had characteristic and distinc-tive protein profiles. Indeed, this study showed that the application of numerical analysis, coupled with the utiliza-tion of a standardized identification system instead of sim-ple quantitative comparison of protein patterns, greatly enhanced the utilization of whole-cell protein profiles for identification of the facultative alkaliphilic Bacillus species.Öğe Sinop İlindeki hamsi ve zargana balıklarından Vibrio spp. izolasyonu ve karakterizasyonu(2016) Avşar, Cumhur; Berber, İsmet; Yildirim, Ahmet KenanAmaç: Bu çalışmada, Sinop İlindeki balıkçılardan temin edilen hamsi ve zargana balık örneklerinden izole edilen Vibrio türlerinin karekterizasyonu ile bu izolatların antibiyotik dirençlilikleri, plazmid DNA ve SDS-PAGE (sodyum dodesil sülfat poliakrilamid jel elektroforezis) toplam hücre protein profillerinin belirlenmesi amaçlanmıştır. Yöntem: Balık örnekleri taze olarak alınmış, buz üzerinde korunarak laboratuvara getirilmiş ve hemen analize alınmıştır. Balık örnekleri 25 g tartılarak zenginleştirme amacıyla %3 NaCl içeren steril alkali peptonlu su (225 mL) besiyerine ilave edilmiş ve 37 OC'de 18-24 saat inkübasyona bırakılmıştır. İnkübasyon sonrası Tiyosülfat Sitrat Safra Sükroz (TCBS) agar besiyerinde gelişen sarı, yeşil veya mavi-yeşil koloniler Tripton Soya Agar (TSA) besiyerine ekilmiş ve izolatların daha sonraki tanımlaması için bir gece süreyle inkübe edilmiştir. İzolatlar morfolojik, fizyolojik ve biyokimyasal testlere göre tanımlanmıştır. Bunlara ek olarak izolatların yedi farklı antibiyotiğe karşı dirençliliği disk-difüzyon yöntemiyle belirlenmiştir. Ayrıca, izolatların SDSPAGE hücresel protein ve plazmid DNA profilleri de çıkartılmıştır. Bulgular: Toplam 44 adet balık örneği Vibrio türlerinin belirlenmesine yönelik çalışılmış ve morfolojik, biyokimyasal özellikleri yönünden incelenmiştir. İnceleme sonucunda; 12 adet Vibrio spp. belirlenmiştir. zolatların, seftazidime %66,6, gentamisine %25, tetrasikline %16,6, seftriazona %91,6, amikasine %16,6, ofloksine %25 ve penisilin G'ye %58,3 oranında antibiyotik dirençlikleri saptanmıştır. Ayrıca, test edilen izolatların MARI (Çoklu Antibiyotik Dirençlilik İndeks) değeri 0,41 oranında bulunmuştur. Vibrio spp. izolatlarının SDSPAGE toplam hücre protein profillerine göre oluşturulan nümerik analiz %80 ve üzerinde benzerlik seviyesinde iki temel küme oluşturmuştur. Vibrio spp. izolatların tümünde 1-4 plazmid DNA (1590 - 27000 bp aralığında) tespit edilmiştir. Sonuç: Sonuç olarak, balıklar yakalandıktan sonra yeterince dondurularak, pişirilerek ve uygun şartlarda depolanarak; ayrıca paketleme esnasında çapraz bulaşlara engel olunarak mikrobiyal enfeksiyonların önlenebileceğini söylemek mümkündür. Ayrıca, bakterilerden dolayı kıyı sularında meydana gelen bulaşlar, deniz suyu kaynaklarının kalitesinde düşüşlere ve bu yolla da insan sağlığında riske ve ekonomik kayıplara yol açmaktadır. Çalışmamız, sağlık için potansiyel risk olabilen ve balıklardan izole edilebilen, antibiyotiklere dirençli Vibrio spp. suşlarının varlığını göstermektirÖğe Sinop’da Yetişen Bazı Bitkilerin Metanolik Ekstraktlarının Antibakteriyal ve Antifungal Aktivitelerinin Belirlenmesi(Karaelmas Science and Engineering Journal, 2013) Berber, İsmet; Avşar, Cumhur; Çine, Nevra; Bozkurt, Nevin; Elmas, EmireBu çalışmada, Sinop’da yetişen 15 farklı bitki türünden elde edilen metanol ekstraktların antimikrobiyal aktiviteleri 3 Gram-pozitif (Staphylococcus aureus ATCC 6538, Micrococcus luteus ATCC 9345, Bacillus cereus ATCC 7064), 2 Gram-negatif (Escherichia coli ATCC 11293 ve Enterococcus faecalis ATCC 51299) ve 3 maya (Candida krusei ATCC 6258, C. parapilosis ATCC 22019 ve C. albicans ATCC 14053) suşlarına karşı disk difüzyon yöntemi kullanılarak test edildi. Antimikrobiyal etkisi incelenen bitki türlerinin tümünün bir veya daha fazla mikroorganizmaya karşı etkili olduğu bulundu. Ayrıca, Sinop’a endemik olan Crocus speciosus subsp. xantholaimos’ın test edilen Gram-pozitif ve Gram-negatif bakterilere karşı yüksek antibakteriyal aktiviteye sahip olduğu belirlendi. Buna karşın, Laurus nobilis yaprak ve meyve özütleri 3 Candida türüne karşı daha yüksek antifungal aktivite gösterdi. Genel olarak bu çalışmadan elde edilen sonuçlar, incelen bitki ekstraktlarının antibakteriyal ve antifungal aktiviteleri arasında önemli bir farkın olmadığını gösterdi.Öğe Synthesis, characterization, and antimicrobial activity of a new pyrimidine Schiff base and its Cu(II), Ni(II), Co(II), Pt(II), and Pd(II) complexes(Turkish Journal of Chemistry, 2012) Gülcan, Mehmet; Sönmez, Mehmet; Berber, İsmetA new Schiff base, {1-[(5-bromo-2-hydroxy-benzylidene)- amino]-4-phenyl-2-thioxo-1,2-dihyro-pyrimidin-5-yl}-phenyl-methanone, was synthesized from N-amino pyrimidine-2-thione and 5-bromsalicylaldehyde. Metal complexes of the Schiff base were prepared from acetate salts of Cu(II), Ni(II), Co(II), Pd(II), and PtCl2 in methanol. The chemical structures of the Schiff base ligand and its metal complexes were confirmed by spectroscopic analysis. All of the compounds were evaluated for their antimicrobial against 4 gram-positive bacteria, 1 gram-negative bacterium, and 3 yeast strains. The Schiff base and the Cu(II) and Co(II) complexes showed good biological activity against all tested bacteria and yeast strains.Öğe Synthesis, characterization, antioxidant and antimicrobial studies of Cu(II), Co(II), Ni(II) and Mn(II) complexes with a new schiff base ligand containing a pyrimidine moiety(Sphinx Knowledge House, 2016) Soğukömeroğullari, Hatice Gamze; Sönmez, Mehmet; Berber, İsmetThe new Schiff base ligand derived from 2-hydroxy-5-methoxybenzaldehyde and 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-one and its metal complexes (Cu(II), Co(II), Ni(II) and Mn(II)) have been synthesized. Schiff base ligand and its complexes were characterized by elemental analysis, magnetic measurement, molar conductivity, IR, NMR (for ligand) and Mass spectral studies. All the compounds have encouraged us to study on their antioxidant properties and antimicrobial activities against Gram-positive, Gram-negative bacteria and fungi using microdilution procedure. Cu(II) (1a) and Co(II) (1b) metallic complexes might be possible as substances to eliminate the free radicals and against the antimicrobial agent. © 2016, Sphinx Knowledge House. All rights reserved.Öğe Synthesis, characterization, biological studies, and molecular modeling of mixed ligand bivalent metal complexes of Schiff bases based on N-aminopyrimidine-2-one/2-thione(2015) Soğukömeroğullari, Hatice Gamze; Taşkin, Tuğba Tok; Yilmaz, Feyza; Sönmez, Mehmet; Berber, İsmetAbstract: New mixed Schiff bases, Cu(II), Co(II), Ni(II), and Mn(II) complexes, were synthesized derived from 5-chloro-2-hydroxyacethophenone and 1-amino-5-benzoyl-4-phenyl-1H-pyrimidine-2-one/thione. These complexes were characterized by elemental analysis, magnetic measurements, molar conductivity, IR, electronic, NMR, and mass spectral studies. All the complexes showed nonelectrolytic behavior. Moreover, the newly synthesized mixed ligand complexes were evaluated for their in vitro antimicrobial efficiency against bacteria and yeast. The compound named Co(L1L) had good antifungal activity against Candida species, but no profound antibacterial effect against bacterial strains. In addition, the ground state geometries of the complexes were optimized using a semi-empirical method at PM6 level, which is a suitable and effective basis set for organometallic and large structures to obtain information about their 3D geometries and electronic structures.Öğe The Influence of Pesticides on the Spore Viability, Toxin Stability and Larvicidal Activity of Bacillus sphaericus 2362 Strain(Fresenius Environmental Bulletin, 2004) Berber, İsmet; Atalan, Ekrem; Çökmüş, CumhurIn this study, 12 different commercial pesticides, in-cluding 5 fungicides, 5 herbicides, 1 aphicide and 1 acari-cide, were investigated for their effects on spore viability, toxin stability and larvicidal activity of a mosquito patho-genic B. sphaericus 2362 strain. Minimal inhibitory con-centrations (MICs) of each pesticide were determined after 48 h incubation of B. sphaericus 2362 strain. Ac-cording to MIC results, all pesticides showed various inhibitory effects on the growth of the test bacterium. Particularly, the pesticides which contain TCA, hymexa-zol, copper sulphate, hexythiazox, 2,4-D Amine, copper inhibited spore germination significantly and bacterial growth even at the lowest tested concentrations. Our re-sults indicated that various commercial pesticides in dif-ferent concentrations reduced the spore viability signifi-cantly and heat-resistant spore numbers of B. sphaericus 2362 strain. In general, the pesticides decreased the spore numbers 104-105-fold compared to initial ones. Further-more, it was observed that the larvicidal activity was completely lost when it was grown at the concentration of MIC values or higher. Indeed, SDS-PAGE analysis con-firmed that the binary toxin proteins, 41.9 kDa and 51.4 kDa, were lost at the MIC values and higher concentra-tions although parasporal crystals did not disappear in the much lower pesticide concentration.Öğe The levels of nitrite and nitrate, proline and protein profiles in tomato plants infected with Pseudomonas syringae(Pakistan Journal of Botany, 2012) Berber, İsmet; Önlü, HarunIn this study, the contents of nitrite-nitrate and free L-proline, and pathogenesis-related (PR) proteins in tomato plants following inoculation with Pseudomonas syringae pv. tomato strain were examined. The results of the nitrite and nitrate indicated that there was a reduction in the levels of nitrate in the infected tomato plants through 1-8 study days, compared with the healthy plants. On the other hands, when the nitrite amounts increased in the first and second days, the nitrite concentrations reduced in infected plants at subsequent time periods, compared with uninfected plants. The accumulation of free proline increased in the infected plants, according to control plants. The whole-cell protein profiles displayed that the levels of the protein bands of molecular masses 204.6 kDa and 69.9 kDa significantly increased in infected and uninfected plants during 2-10 study days. In additionally, in the quantities of the protein bands of molecular weights 90.3 and 79.4 kDa were observed an increase in the infected and healthy plants after the fourth day. However, the protein band of molecular weight 54.3 kDa was visible only in uninfected plants for the fourth and eighth days. Finally, the study suggest that there were the sophisticate relationships among the proline accumulation, the conversion of nitrate to nitrite and the induction of PR protein genes in the regulation of defense mechanisms toward microbial invaders. Our results also indicated that the increases in nitrite and proline contents might be useful indicator for the response toward pathogen attacks.
