Browsing by Author "Sevgi, Tuba"

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Analysis by scanning electron microscopy of polyethylene terephthalate and nylon biodegradation abilities of Bacillus sp. strains isolated from soil
(Bursa Uludağ Üniversitesi, 2020-12-07) Demirkan, Elif; Güler, Baran Enes; Sevgi, Tuba; Bursa Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü.
Plastic pollution, the aggregation of synthetic plastic products in the environment generates serious problems for wildlife, habitats and the human population. Plastic accumulates at ocean, creating areas called the seventh continent, a mass of plastic garbage. Plastic wastes are disposed of by recycling, burying and incineration. However, these also have disadvantages. They are developing bioplastics as new solutions to plastic problems. Other alternative solutions may be microorganisms. Compared to other conventional technologies, it is extremely inexpensive and efficient in terms of cost and simplicity because it is based on the capabilities of microorganisms. In this study, we have reported the degradation abilities of B. subtilis and B. cereus strains on polyethylene terephthalate (PET, water bottle) and nylon (plastic bag). In the nylon medium with Bacillus subtilis ET18 and Bacillus cereus ET30 was observed red pigment formation. All bacteria showed biofilm formation in the presence of nylon. The surface morphology changes of the PET and nylon were determined by light microscope and SEM. The bacteria used in this study were found to biodegrade nylon more easily than PET. The activities of lipase, protease and α-amylase were determined. Among the enzymes, lipase was detected in the presence of both PET and nylon.
Cellulose monoacetate/polycaprolactone and cellulose monoacetate/polycaprolactam blended nanofibers for protease immobilization
(Wiley, 2017-06-25) Aykut, Yakup; Sevgi, Tuba; Demirkan, Elif; Uludağ Üniversitesi/Mühendislik Fakültesi/Tekstil Mühendisliği Bölümü.; Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü.; 0000-0002-7528-9529; ABI-4472-2020; AAG-7112-2021; 55320835000; 57191880859; 23469245200
Enzymes can be used multiple times when they are immobilized on a support. More enzymes can be immobilized on a surface when nanofibers are used as a supporting surface because the specific surface area increases tremendously. In this regard, polycaprolactam/cellulose monoacetate (PA6/CMA) and polycaprolactone/cellulose monoacetate (PCL/CMA) blended nanofibers (NFs) were prepared via an electrospinning process. Protease enzymes were immobilized on neat PA6, PCL, PA6/CMA, and PCL/CMA nanofibers and glutaraldehyde (GA) activated analogs through the physical adsorption method. The immobilized enzyme activity was measured by using a casein substrate, and the results were compared with free enzyme activity. Among all of the samples, the highest immobilization yield of about 82% was obtained with GA-activated neat PCL NF samples. The best remaining activity of the immobilized enzymes on pure CMA NFs was found to be 59% after seven reuses. Even after nine reuses, enzyme activities are still observed on the CMA NF samples. It was expected that the addition of CMA in PCL and PA6 NFs would increase the reusability number to reach the reusability of CMA NFs, but it was not significantly enhanced. If CMA chains could be mostly collected on the sheath or close to the sheath of the NFs during the electrospinnig process, this target could be achieved.
Evaluation of the effects of temperature, light, and UV-C radiation on HSP70A expression in chlamydomonas reinhardtii
(Tübitak Bilimsel ve Teknolojik Araştırma Kurumu, 2021-01-01) Sevgi, Tuba; Demirkan, Elif; SEVGİ, TUBA; DEMİRKAN, ELİF; Bursa Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü; 0000-0002-5292-9482; 0000-0002-7528-9529; AAG-7112-2021; ABI-4472-2020
In this study, various physical parameters (temperature, light intensity and UV-C radiation) which could be effective in heat shock response on C.reinhardtii by using molecular tools were investigated. In total, 256 transformants were obtained, among them, 160 transformants had continuous expression while 96 of them had heat-inducible expression. In these transformants, arylsulfatase activities were detected qualitatively and quantitatively. The best two transformants were selected and used in studies. To determine the effect of temperature, the cells were shifted from 23 degrees C to 35 degrees C, 37 degrees C, 40 degrees C and 42 degrees C. The heat shock response was induced at all temperatures. In investigating the effect of light intensity, 0, 14, 28, 70, 140 mu mol E.m(-2)s(-1) were used. It was found that the light intensity of 28 mu mol E.m(-2)s(-1) and above increased ARS activity. On the other hand, ultraviolet C radiation application was carried out for periods of 2, 6 and 12 h, and no significant change in ARS activity was observed. In order to compare the selected arylsulfatase activity results in the study, real-time polymerase chain reaction trials were conducted at the transcript level, and parallel results were obtained. As a result of the study, it was determined that the heat shock response was triggered by temperature and light intensity. These might be also important for plant stress and ecological studies.
Immobilization of bacillus subtilis e6-5 protease and commercial protease in nanofibrils containing different amino acids
(Trakya Univ Balkan Yerlesesi Enstituler Binasi, 2020-04-01) Güler, Baran Enes; Demirkan, Elif; DEMİRKAN, ELİF; Sevgi, Tuba; SEVGİ, TUBA; Bursa Uludağ Üniversitesi/Fen Edebiyat Fakültesi/ Biyoloji Anabilim Dalı.; 0000-0001-7967-9041; 0000-0002-5292-9482; GWU-7780-2022; AAG-7112-2021; ABI-4472-2020
In this study, polyamide 6 polymer surfaces that have a high surface area were produced by electrospinning method with the participation of Glycine, Tyrosine and Glutamic acid amino acids, and lyophilized Bacillus subtilis E6-5 protease and commercial protease enzymes were immobilized on nanofibrils. Enzyme reusability were investigated. The immobilization efficiencies of the enzymes were approximately between 50-55 %. In studies with lyophilized Bacillus protease, glutaraldehyde activated PA6 nanofibrils and glutaraldehyde unactivated PA6 nanofibrils were found to be more immobilized in the presence of Glutamic acid. Although the lyophilized protease enzyme immobilized on non-glutaraldehyde activated and activated surfaces has been used 4 times, the best functional stability has been achieved with 2 times use. In pure PA6/Glutamic acid nanofibrils, the immobilization yield of the two times used enzymes was found to be 38 %. In glutaraldehyde-activated PA6 nanofibrils, the PA6/Glutamic acid nanofibril surfaces were found to have 65 % immobilization yield of the two repetitive used enzymes. The enzyme immobilization efficiency has been doubled by glutaraldehyde activation of the nanofibrils. In studies with commercial protease, the most functional stability was obtained for 3 repeated uses, although the enzyme was used 6 times on the non-glutaraldehyde activated nanofibril surfaces. The most successful immobilization was found in 58 % of PA6 nanofibrils. In glutaraldehyde-activated PA6 nanofibrils, the enzyme was found to be used 6 times, but the functional stability was maintained as much as 4 times of repeated use.
Investigation of effects of protease enzyme produced by Bacillus subtilis 168 E6-5 and commercial enzyme on physical properties of woolen fabric
(Taylor, 2019-06-04) Demirkan, Elif; Kut, Dilek; Sevgi, Tuba; Doğan, Meral; Baygın, Eren; DEMİRKAN, ELİF; KUT, YAŞAR DİLEK; SEVGİ, TUBA; Doğan, Meral; Baygın, Eren; Bursa Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü; Bursa Uludağ Üniversitesi/Mühendislik Fakültesi/Tekstil Mühendisliği Bölümü; 0000-0002-5292-9482; 0000-0002-9059-0838; 0000-0002-7528-9529; AAG-7112-2021; AAH-4335-2021; ABI-4472-2020; CMN-9718-2022; CFF-0023-2022
Wool is one of the most important fibers in textile industry, and has been commonly used for producing value added products due to its properties of lightness, warmth, softness, and smoothness. However, the special scale structure in wool cuticle can cause felting shrinkage of wool fabrics. Proteases have been widely used to modify the surface of wool to prevent wool felting, due to their ability to catalyze the hydrolysis of peptide bonds in wool scales. Although the treatment of wool with proteases was considered as an environmentally friendly technique to provide wool fabrics with shrink resistance properties, proteases exhibited low efficacy in removing the cuticle scales because of the highly cross-linked barriers. In this study, wool fabric was treated with protease enzyme obtained from novel isolated bacteria and commercial protease enzyme, and the results were compared. The tear strength, pilling changes in Delta E values, whiteness and yellowness values of wool were controlled. Results showed that treatment with Bacillus subtilis 168 E6-5 protease enzyme yielded improvements in the physical properties of wool fabric compared with commercial enzyme.
Optimization of culture medium for the production and partial purification and characterization of an antibacterial activity from brevibacillus laterosporus strain EA62
(Ars Docendi, 2019-07-01) Usta, Alev A. K.; Demirkan, Elif; Cengiz, Murat; Sevgi, Tuba; Zeren, Behice; Abdou, Maoulida; Usta, Alev A. K.; DEMİRKAN, ELİF; CENGİZ, MURAT; SEVGİ, TUBA; Zeren, Behice; Abdou, Maoulida; Bursa Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü.; Bursa Uludağ Üniversitesi/Veteriner Fakültesi/Farmakoloji ve Toksikoloji Anabilim Dalı.; 0000-0002-5292-9482; ABI-4472-2020; ABE-5935-2020; IPA-7484-2023; ISY-3462-2023; EID-6407-2022; CAU-1487-2022
The present study was performed to report the bacterial identification, optimization of culture conditions and characterization of a novel antibiotic substance from a Bacillus sp. EA62 strain isolated from soil. The EA62 strain was identified based on 16S rRNA analysis. The new isolate EBD 9-1 showed 100% sequence identity with Brevibacillus laterosporus. The antibacterial activity of the new substance was examined against five pathogenic bacteria and was observed to be the most effective against Escherichia coli. An agar diffusion assay was performed to evaluate the antibacterial activity of the substance. The effects of some nutritional (amino acid, carbon, nitrogen and metal sources) and physical factors (pH and temperature) and incubation time on the antibiotic activity were studied. Antibiotic activity in basal medium reached the maximum levels after 72 h of incubation. The best antibiotic activity was obtained in the presence of glucose as a carbon source, yeast extract as a nitrogen source, glutamic acid as an amino acid source and MgSO4+CaCO3 as metal ion sources. For physical parameters, the best results were obtained at 37 degrees C, pH 7.0. The antibiotic substance was partially purified, and the estimated molecular weight was 6.3 kDa. The minimum inhibitory concentration (MIC) values determined against five pathogen bacteria were >256 mu g/ml. The substance was identified by thin-layer chromatography, and its Rf value was measured as 0.04 cm.
Optimization of phytase production by new isolate bacillus sp. EBD 9-1 strain using statistical experimental design
(Uludağ Üniversitesi, 2015-10-08) Murat, Dilek; Demirkan, Elif; Sevgi, Tuba; Baygın, Eren; Uludağ Üniversitesi/İktisadi ve İdari Bilimler Fakültesi.; Uludağ Üniversitesi/Fen Edebiyat Fakültesi/Biyoloji Bölümü.
In this study, face centered central composite design (FCCCD) of response surface methodology (RSM) was applied to describe the relationship between the tested variables, pH, temperature, rpm, incubation period and phytase production by novel isolate Bacillus sp. EBD 9-1. The design was employed by selecting pH, temperature, rpm and incubation period as the model factors and to achieve maximum yield, interaction of these factors was studied by RSM. A second order quadratic model and response surface method showed that the optimum conditions for phytase production were pH, 8.0; temperature, 38.13°C; rpm, 113.64 and incubation period, 45 h. Under these conditions, phytase activity was found to be about 228 Uml-1.
Partial purification, characterization and wheat bran degradation studies of a new phytase from the Bacillus megaterium EBD 9-1 strain
(Walter de Gruyter, 2016-07-27) Demirkan, Elif; Sevgi, Tuba; Akçakoca, Dilara; Ersoy, Figen; Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü.; Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Moleküler Biyoloji ve Genetik Bölümü.; 0000-0002-7528-9529; ABI-4472-2020; AAI-6817-2021; AAG-7112-2021; 23469245200; 57191880859; 57194708199; 55088196700
Objective: The present study was designed to report the bacterial identification and characterization of a new phytase enzyme from a Bacillus sp. strain isolated from soil. Methods: Bacillus sp. strain was identified based on 16S rRNA analysis. The phytase was partially purified through ammonium sulfate precipitation and Sephadex G100 gel filtration steps, and characterized for its activity and stability. Results: The new isolate EBD 9-1 showed 100% sequence identity with Bacillus megaterium. The partially purified enzyme had the maximum activity at pH 7.0 and 60 degrees C. The activity of the enzyme was stimulated in the presence of Ca+2, V-max and K-m for enzyme were found to be 333 U/mL and 2 mM, respectively. The estimated molecular weight of enzyme was 45 kDa. The storage stability of phytase was 93% of the initial activity after 6 months at 4 degrees C and -20 degrees C. This study represents the partial purification, characterization and wheat bran degradation studies for B. megaterium phytase. Conclusion: Consequently, due to the characteristics such as significant stability at higher temperatures, alkaline pH and storage of the novel phytase enzyme produced by B. megaterium EBD 9-1, the enzyme may be suitable for supplementing animal feeds to improve the availability of phosphorus from phytates.
Rekombinant Chlamydomonas reinhardtii suşları kullanılarak ısı şoku yanıtına bazı fiziksel ve kimyasal parametrelerin etkisinin araştırılması
(Bursa Uludağ Üniversitesi, 2019-07-12) Sevgi, Tuba; Demirkan, Elif; Bursa Uludağ Üniversitesi/Fen Bilimleri Enstitüsü/Biyoloji Anabilim Dalı.
Bu çalışmada ısı şok yanıtında etkili olduğu düşünülen çeşitli kimyasal ve fiziksel parametreler moleküler araçlardan faydalanılarak C.reinhardtii üzerinde araştırılmıştır. Sürekli ekspresyona sahip 160 adet, ısıyla indüklenebilir ekspresyona sahip 96 tadet olmak üzere toplamda 256 adet transformant elde edilmiş ve bu transformantlar ARS aktivitesi bakımında kalitatif ve kantitatif olarak taranmıştır. Çalışmalara seçilen βTub II-32 ve HSP70A III-1 transformantları ile devam edilmiştir. Fiziksel parametre olarak sıcaklık, ışık şiddeti ve UV-B radyasyonun, kimyasal parametre olarak ise tuzluluğun, kalsiyumun ve kalsiyum şelatlayıcıları ve bloklayıcıların etkisi araştırılmıştır. Sıcaklığın etkisini incelemede hücreler 23 °C'den 35 °C, 37 °C, 40 °C ve 42 °C'ye kaydırılmış ve hücrelerin 35°C' ye dahi çıkarıldığında ısı şok yanıtının indüklendiği görülmüştür. Kalsiyumun 100 mM'ın üstünde ARS aktivitesini arttırdığı belirlenmiştir. Kalsiyum şelatlayıcıları olan EGTA ve BAPTA varlığında ısı stres yanıtının tetiklendiği gözlenmiştir. 100 µM lantan ve 250 µM gadolinyumun yükselen ARS aktivitesini düşürmede etkili olduğu saptanmıştır. Ancak verapamilin etki göstermediği belirlenmiştir. 2 000 lux ve üzeri ışık şiddetinin ise ARS aktivitesini arttığı saptanmıştır. UV-B uygulamasının ve tuzluluğun ARS aktivitesine herhangi bir etkisi bulunmamıştır. Tüm ARS enzim aktivite sonuçları RT-qPCR sonuçları ile karşılaştırmalı olarak değerlendirilmiş, paralel sonuçlar elde edildiği görülmüştür. Rekombinant C. reinhardtii ile elde edilen bu veriler bitki stresi ve ekolojik çalışmalar için önem taşıyabilir.
Strain improvement by UV mutagenesis for protease overproduction from bacillus subtilis E6-5 and nutritional optimization
(Bursa Uludağ Üniversitesi, 2018-08-01) Demirkan, Elif; Sevgi, Tuba; Gokoz, Meltem; Guler, Baran Enes; Zeren, Behice; Ozalpar, Busra; Abdou, Maoulida; Bursa Uludağ Üniversitesi/Fen Edebiyat Fakültesi/Biyoloji Bölümü.
The purpose of the present study was to enhance the protease production of the parental type Bacillus subtilis E6-5 by UV irradiation. The parental type was subjected to UV irradiation at different distances (5-15 cm) for different time intervals ( 1-120 min). After each treatment, total 400 mutants were obtained. The mutants were screened on skim milk agar plates for the selection of best proteolytic mutant. Among mutants, the mutant MET39, which obtained at 15 cm distance and irradiation time 5 min of exposure, was selected as best mutant produced 1.5 fold more enzyme over the parent strain. The effects of nutritional factors (various carbon, nitrogen sources and metal ions) on the protease production from MET39 mutant strain were studied. The best carbon source was found as glycerol. Among the inorganic nitrogen sources, the highest enzyme production was obtained in the presence of tryptone. The metal ions did not indicate significant effect on enzyme production. In order to enhance the yield, new modified medium was obtained by combining the best carbon and nitrogen sources. In this medium, enzyme yield was enhanced 88% compared to basal medium. MET39 mutant strain might have a great potential for protease production at industrial scale.
Synthesis and crystal structures of novel copper(II) complexes with glycine and substituted phenanthrolines: reactivity towards DNA/BSA and in vitro cytotoxic and antimicrobial evaluation
(Springer, 2017-01) Zorlu, Yunus; Yerli, Yusuf; Coşut, Bünyemin; İnci, Duygu; Aydın, Rahmiye; Vatan, Özgür; Sevgi, Tuba; Yılmaz, Dilek; Demirkan, Elif; Cinkılıç, Nilüfer; Uludağ Üniversitesi/Fen-Edebiyet Fakültesi/Kimya Bölümü.; Uludağ Üniversitesi/Fen-Edebiyat Fakültesi/Biyoloji Bölümü.; 0000-0002-0483-9642; 0000-0002-7687-3284; 0000-0002-7528-9529; 0000-0002-3595-6286; G-2201-2019; AAH-8936-2021; O-7508-2015; AAG-7112-2021; ABI-4472-2020; AAH-5296-2021; 55082306300; 56261495600; 16235098100; 57191880859; 6701369462; 23469245200; 26533892300
New copper(II) complexes-dimeric-[Cu(nphen)(gly)(H2O)](+) (1) and [Cu(dmphen)(gly)(NO3)(H2O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline, and gly = glycine)-have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR, EPR spectroscopy, and cyclic voltammetry. The CT-DNA-binding properties of these complexes have been investigated by thermal denaturation measurements and both absorption and emission spectroscopy. The DNA cleavage activity of these complexes has been studied on supercoiled pUC19 plasmid DNA by gel electrophoresis experiments in the absence and presence of H2O2. Furthermore, the interaction of these complexes with bovine serum albumin (BSA) has been investigated using absorption and emission spectroscopy. The thermodynamic parameters, free-energy change (Delta G), enthalpy change (Delta H), and entropy change (Delta S) for BSA + complexes 1 and 2 systems have been calculated by the van't Hoff equation at three different temperatures (293.2, 303.2, and 310.2 K). The distance between the BSA and these complexes has been determined using fluorescence resonance energy transfer (FRET). Conformational changes of BSA have been observed using the synchronous fluorescence technique. In addition, in vitro cytotoxicities of these complexes on tumor cell lines (Caco-2, A549, and MCF-7) and healthy cells (BEAS-2B) have been examined. The antimicrobial activity of the complexes has also been tested on certain bacteria cells. The effect of mono and dimeric in the above complexes is presented and discussed. New copper(II) complexes-dimeric-[Cu(nphen)(gly)(H2O)](+) (1) and [Cu(dmphen)(gly) (NO3)(H2O)] (2) (nphen = 5-nitro-1,10-phenanthroline, dmphen = 4,7-dimethyl-1,10-phenanthroline and gly = glycine)-have been synthesized and characterized by CHN analysis, single-crystal X-ray diffraction techniques, FTIR and EPR spectroscopy. They have been tested for their in vitro DNA/BSA interactions by the spectroscopic methods. These complexes exhibited higher cytotoxic and antimicrobial activities. Complex 1 shows better DNA / BSA interactions in comparison to complex 2.
Synthesis, crystal structure, stability studies, DNA/albumin interactions, and antimicrobial activities of two Cu(II) complexes with amino acids and 5-nitro-1,10-phenanthroline
(Taylor & Francis, 2016-11) Zorlu, Yunus; İnci, Duygu; Aydın, Rahmiye; Sevgi, Tuba; Demirkan, Elif; Uludağ Üniversitesi/Fen-Edebiyet Fakültesi/Kimya Bölümü.; Uludağ Üniversitesi/Fen-Edebiyet Fakültesi/Biyoloji Bölümü.; 0000-0002-0483-9642; 0000-0002-7528-9529; G-2201-2019; AAH-8936-2021; AAG-7112-2021; ABI-4472-2020; 55082306300; 56261495600; 57191880859; 23469245200
One-dimensional (1-D) coordination polymer and mononuclear copper(II) complexes, ([Cu(nphen)(asn)]ClO4)(n) (1) and [Cu(nphen) (gln)(H2O)]ClO4 center dot H2O (2) (nphen = 5-nitro-110-phenanthroline, asn = asparagine, gln = glutamine), have been synthesized and characterized by IR spectroscopy, ESI-MS, CHN analysis, and singlecrystal X-ray diffraction. These binary and ternary complexes of copper(II) with nphen, asn, and gln have been investigated using potentiometric methods in 0.1 MKCl aqueous ionic media at 298.2 K. The protonation constants of the ligands and the stability constants of 1 and 2 have been calculated from the potentiometric data using the "BEST" software package. The potentiometric results have been analyzed using the "SPE" software package, and the distribution curves for the copper-containing species have been determined for the ternary systems. The CT-DNA-binding properties of these complexes have been investigated by thermal denaturation measurements and both absorption and emission spectroscopy. Further, the interaction of these complexes with bovine serum albumin (BSA) and human serum albumin (HSA) has been investigated using absorption and emission spectroscopy. The thermodynamic parameters, free energy change (Delta G), enthalpy change (Delta H), and entropy change (Delta S) were calculated by the van't Hoff equation and discussed. The distances between the serum albumins and 1 and 2 have been obtained according to fluorescence resonance energy transfer (FRET). Conformational changes of serum albumins have been observed from synchronous fluorescence technique. The antimicrobial activity of the complexes has also been tested on some bacteria. The effect of different amino acids on the copper(II) complexes are discussed.