Publications by authors named "Cihan Darcan"

6 Publications

  • Page 1 of 1

Rapid fabrication of teflon apertures by controlled high voltage pulses for formation of free standing planar lipid bilayer membrane.

Biomed Microdevices 2021 Feb 27;23(1):12. Epub 2021 Feb 27.

Department of Biomedical Engineering, Ankara Yıldırım Beyazıt University, Ankara, Turkey.

Free standing artificial lipid bilayers are widely used in the study of biological pores. In these types of studies, the free standing planar lipid bilayer is formed over a micron-sized aperture consisting of either polymer such as Polytetrafluoroethylene (PTFE, Teflon) or glass. Teflon is chemically inert, has a low dielectric constant, and has a high electrical resistance which combined allow for obtaining low noise recordings. This study investigates the reproducible generation of micropores in the range of 50-100 microns in diameter in a Teflon film using a high energy discharge set-up. The discharger set-up consists of a microprocessor, a transformer, a voltage regulator, and is controlled by a computer. We compared two approaches for pore creation: single and multi-pulse methods. The results showed that the multi-pulse method produced narrower aperture size distributions and is more convenient for lipid bilayer formation, and thus would have a higher success rate than the single-pulse method. The bilayer stability experiments showed that the lipid bilayer lasts for more than 33 h. Finally, as a proof-of-concept, we show that the single and multi-channel electrophysiology experiments were successfully performed with the apertures created by using the mentioned discharger. In conclusion, the described discharger provides reproducible Teflon-pores in a cheap and easy-to-operate manner.
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http://dx.doi.org/10.1007/s10544-021-00553-4DOI Listing
February 2021

The role of oxidative stress genes and effect of pH on methylene blue sensitized photooxidation of Escherichia coli.

Acta Biol Hung 2016 Mar;67(1):85-98

Department of Molecular Biology and Genetics, Faculty of Arts and Science, Bilecik Şeyh Edebali University , Bilecik , Turkey.

In this study, the survival time of wild type E. coli W3110 and 11 mutants was analysed with a plate count method in methylene blue added or control groups under daylight fluoroscence illumination (4950 lux) at different pH values (5.0, 6.0, 7.0, and 8.0) in phosphate buffer. As a result, while the number of bacteria did not decrease under photooxidative stress at pH 5.0 and 6.0 during a 6-hour incubation, the wild type and all mutants decreased more than 2 log. at pH 8.0, and approximately one log. at pH 7.0. It was determined that a 2 log decrease in wild type E. coli takes 3.7 h according to t99 value at pH 8, these values were 2.39 h in the katE mutant, 2.64 h in the soxR mutant, 2.67 h in the oxyR mutant, 2.71 h in the sodB mutant, 3 h in the btuE mutant, 3.38 h in the zwf mutant and 3.40 h in the soxS mutant, respectively (p < 0.05). The roles of these genes were proved with complement tests. Finally, it is found that the effectiveness of photooxidative stress is in direct relation with pH, and the katE, soxR, oxyR, sodB, btuE, zwf, and soxS genes are important for the protection against this stress.
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http://dx.doi.org/10.1556/018.67.2016.1.7DOI Listing
March 2016

The effect of some boron derivatives on kanamycin resistance and survival of E. coli and P. aeruginosa in lake water.

Biomed Environ Sci 2012 Aug;25(4):476-82

Department of Biology, Faculty of Art and Sciences, Dumlupinar University, 43100, Kütahya-Turkey.

Objective: To study MIC value of 7 boron derivatives namely [Boric acid (H(3)BO(3)), Anhydrous Borax (Na(2)B(4)O(7)), Sodium Borate (NaBO(2)), Diammonium Tetraborate (NH(4))(2)B(4)O(7), Sodium Perborate (NaBO(3)), Boron Trioxide (B(2)O(3)), Potassium Tetraborate (K(2)B(4)O(7))] on E. coli and P. aeruginosa and their effects on survival of bacteria in lake water and resistance against kanamycin antibiotic.

Methods: MIC values of Boron derivatives and antibiotic were studied by broth microdilution method. The effect of boron derivatives on survival of bacteria in lake water were also determined with plate count.

Results: Sodium perborate was determined as the most effective substance among the studied substances. Effectiveness increased as temperature increased. E. coli was more affected from P. aeruginosa in 8 mg/mL sodium perborate concentration in lake water. Moreover, it was determined that MIC value of kanamycin antibiotic decreased 200 times by especially treating P. aeruginosa with sodium perborate in lake water. However, it can be stated that this change in resistance did not arise from microorganisms.

Conclusion: Sodium perborate solution can be used supportedly in kanamycin antibiotic applications for P. aeruginosa. Future studies are necessary to explore the relation between sodium perborate and kanamycin which is effective on P. aeruginosa in lake water.
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http://dx.doi.org/10.3967/0895-3988.2012.04.014DOI Listing
August 2012

Screening of antioxidant, antimicrobial activities and chemical contents of edible mushrooms wildly grown in the black sea region of Turkey.

Comb Chem High Throughput Screen 2011 Feb;14(2):72-84

Department of Chemistry, Faculty of Art and Sciences, Ondokuz Mayis University, 55139-Samsun, Turky. Turkey.

The antioxidative activity of the methanol extracts obtained from twelve commonly consumed wild edible mushrooms was investigated according to the phosphomolybdenum method, inhibition of linoleic acid peroxidation, reducing power, metal chelating, O(2)(˙-), DPPH(˙), peroxide and H(2)O(2) scavenging activity in the Black Sea Region of Turky, and compared to standard antioxidant compounds such as a-tocopherol, butylated hydroxyanisole (BHA), butylated hydroxytoluene (BHT), and trolox. Total phenolic compounds, flavonoids, anthocyanins, ascorbic acid, β-carotene and lycopene in the extracts were measured. The antimicrobial activities of extracts were also evalated against gram (-) and (+) bacteria and yeast with disc diffusion method. Hydnum repandum, Lactarius delicious, Lactarius camphoratus, Lactarius piperatus, Ramaria flava, and Agaricus bisporus were greater than α-tocopherol and BHT on antioxidant activity. The lipid peroxidation of L. camphoratus and Lactarius volemus was excellent, and was 58.05% and 61.44% respectively. The DPPH(˙) scavenging effects decreased in the order of R. flava>BHT> Macrolepiota procera>L. camphoratus>L. piperatus>Lactarius volemus>a-tocopherol and were, at 500 µg/ml and were 80.38, 76.61, 69.74, 61.55, 61.47, 61.09, 60.65%, respectively. All the extracts of mushroom also had the stronger chelating effect according to standards. The O(2)(˙-) scavenging effect of extracts of the mushroom species was in order of R. flava>Boletus edulis>Leatiporus sulphureus>M. procera>standards. L. piperatus, L. camphorates, L. volemus, A. bisporus, Chanterellus cibarius, L. sulphureus, H. repandum showed strong antimicrobial activity, especially on E. coli. H. repandum exhibited to be more effective on P. aeruginosa than other bacterial strains.
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http://dx.doi.org/10.2174/138620711794474079DOI Listing
February 2011

Escherichia coli: dominance of red light over other visible light sources in establishing viable but nonculturable state.

Photochem Photobiol 2010 Jan-Feb;86(1):104-9. Epub 2009 Nov 12.

Science Education Department, Faculty of Education, Amasya University, Amasya, Turkey.

In this study, the effect of UV-A and different wavelengths of visible light irradiations combined with or without a photosensitizer (methylene blue, MB) on the establishment of viable but nonculturable (VBNC) state in Escherichia coli was investigated. Survival of the E. coli was investigated by measuring plate counts, respiring cell count (RCC), direct viable count (DVC) and total counts over a period of up to 72 h. The inhibition rates of various light sources in the presence or absence of MB on E. coli in seawater were ranked in the order UV-A>red light>white light>blue light>green light (from greatest to least activation). E. coli survived for 10.2, 19.0, 21.3 and 24.04 h under exposure to red, white, blue and green light and for 6.8 h under exposure to UV-A in the presence of MB according to t(99). Although the VC declined to undetectable levels in a relatively short time, the RCC showed that some cells were still capable of respiration and, therefore, are assumed to have entered the VBNC phase. This is the first time that red light has been shown to have a stronger effect on E. coli survival and VBNC than white, green and blue light in seawater environment.
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http://dx.doi.org/10.1111/j.1751-1097.2009.00636.xDOI Listing
August 2010

Viable but non-culturable state (VBNC) of Escherichia coli related to EnvZ under the effect of pH, starvation and osmotic stress in sea water.

Pol J Microbiol 2009 ;58(4):307-17

Department of Biology, Faculty of Art and Sciences, Dumlupinar University, Kütahya, Turkey.

When exposed extreme environmental conditions such as sea water, bacteria have been shown different survival strategy for continue their life. One of this strategy known as viable but nonculturable (VBNC) state which is very important for nondifferiation bacteria. VBNC cells cause serious human health problems. Little is known, however, about the genetic mechanisms underlying the VBNC state. Under different environmental conditions, porins are important in the survival strategy of bacteria. EnvZ/OmpR work together as regulators of ompF and ompC gene expression. It is known that the EnvZ system has a role in VBNC state. In this study we tried to find out the viability of EnvZ, OmpC and OmpF mutant E. coli under stress effect of osmolarity, pH and starvation. Bacteria were suspended in filtered-autoclaved sea water microcosms and numbers determined over 25 day incubation periods by plate count (PC), direct viable count (DVC) and count of cells capable of respiration (RCC). As regard to results, alkaline pH affected E. coli more than acidic pH, which led to decline in number. On the contrary glycine betaine addition to sea water protected E. coli porin mutants and also reduced the death rate of bacteria. Under the effect of pH, osmotic stress and starvation stress, wild type E. coli and porin mutants entered a dormant state or became VBNC with the exception of MSZ31 (envZ mutant) E. coli cells which did not enter the VBNC state under the three tested stress conditions. This study is the first report to demonstrate that E. coli could not enter the VBNC state in the lack of EnvZ product under the stress of osmolarity, pH and starvation and the relationship between EnvZ and VBNC state are not affected by pH, osmolarity and starvation.
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April 2010