Publications by authors named "Fatma Dogan Guzel"

6 Publications

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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

Towards understanding single-channel characteristics of OccK8 purified from Pseudomonas aeruginosa.

Eur Biophys J 2021 Jan 22;50(1):87-98. Epub 2021 Jan 22.

School of Engineering and Science, Jacobs University Bremen, Campus Ring 1, 28759, Bremen, Germany.

Antibiotic resistance in Gram-negative bacteria causes serious health issues worldwide. Bacteria employ several resistance mechanisms to cope with antimicrobials. One of their strategies is to reduce the permeability of antibiotics either through general diffusion porins or substrate-specific channels. In this study, one of the substrate-specific channels from Pseudomonas aeruginosa, OccK8 (also known as OprE), was investigated using single-channel electrophysiology. The study also includes the investigation of permeability properties of several amino acids with different charged groups (i.e. arginine, glycine and glutamic acid) through OccK8. We observed four different conformations of the same OccK8 channel when inserted in lipid bilayers. This is in contrast to previous studies where heterologous expressed OccK8 in E. coli showed only one conformation. We hypothesized that the difference in our study was due to the expression and purification of the native channel from P. aeruginosa. The single-channel uptake characteristics of the porin showed that negatively charged glutamic acid preferentially interacted with the channel while the positively charged arginine molecule showed infrequent interaction with OccK8. The neutral amino acid glycine did not show any interaction at the physiological conditions.
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http://dx.doi.org/10.1007/s00249-021-01498-5DOI Listing
January 2021

Investigation of the Effect of Channel Structure and Flow Rate on On-Chip Bacterial Lysis.

IEEE Trans Nanobioscience 2021 Jan 30;20(1):86-91. Epub 2020 Dec 30.

Successful lysis of cells/microorganisms is a key step in the sample preparation in fields like molecular biology, bioengineering, and biomedical engineering. This study therefore aims to investigate the lysis of bacteria on-chip and its dependence on both microfluidic channel structure and flow rate. Effects of temperature on lysis on-chip were also investigated. To perform these investigations, three different microfluidic chips were designed and produced (straight, zigzag and circular configurations), while the length of the channels were kept constant. As an exemplary case, Mycobacterium smegmatis was chosen to represent the acid-fast bacteria. Bacterial suspensions of 1.5 McFarland were injected into the chips at various flow rates (0.6- [Formula: see text]/min) either at room temperature or 50° C. In order to understand the on-chip lysis performance fully, off-chip experiments were carried out at durations which are equal to those bacteria spent in the channel from inlet to the outlet at different flow rates. We also performed COMSOL multiphysics program simulations to evaluate further the effect of the applied parameters. As a result, we found that the structure and the flow rate do not affect lysis over all in all investigated channel types, however on-chip experiments at room temperature produced more effective lysis compared to the on-chip and the off-chip samples performed at higher temperatures. Interestingly on-chip experiments at higher tempratures do not result in effective lysis.
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http://dx.doi.org/10.1109/TNB.2020.3031346DOI Listing
January 2021

Label-free molecular detection of antibiotic susceptibility for Mycobacterium smegmatis using a low cost electrode format.

Biotechnol Appl Biochem 2020 Sep 25. Epub 2020 Sep 25.

Department of Metallurgical and Materials Engineering & Cellular Therapy and Stem Cell Research Center, Eskisehir Osmangazi University, Eskisehir, Turkey.

Today, the emergence of antibiotic resistance in pathogenic bacteria is considered an important problem for society. Excessive consumption of antibiotics, long-term treatments, and inappropriate prescriptions continually increase the severity of the problem. Improving antibiotic stewardship requires improved diagnostic testing, and, therefore, in vitro antibiotic susceptibility testing is becoming increasingly important. This research details the development of an antibiotic susceptibility test for Mycobacterium smegmatis using streptomycin as antibiotics. This strain was selected because it is a member of the slow growing Mycobacterium genus and serves as a useful surrogate organism for M. tuberculosis. A commercially available and low-cost screen-printed gold electrode in combination with a specifically developed nucleic acid probe sequence for the 16SrRNA region of the mycobacterial genome was employed to monitor M. smegmatis nucleic acid sequences using the techniques of square-wave voltammetry and electrochemical impedance spectroscopy. The results show that it was possible to detect M. smegmatis sequences and distinguish antibiotic-treated cells from untreated cells with a label-free molecular detection. As a result, the in vitro antibiotic susceptibility test revealed that M. smegmatis showed sensitivity to streptomycin after a 24-H incubation, with the developed protocol representing a potential approach to determining antibiotic susceptibility more quickly and economically than current methods.
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http://dx.doi.org/10.1002/bab.2037DOI Listing
September 2020

Decellularized inner body membranes for tissue engineering: A review.

J Biomater Sci Polym Ed 2020 07 26;31(10):1287-1368. Epub 2020 Apr 26.

Faculty of Engineering and Architecture, Department of Metallurgical and Materials Engineering, Eskisehir Osmangazi University, Eskisehir, Turkey.

Body membranes are thin sheets/layers of cells or tissues which cover the surface of internal organs, the outside of the body and lines various body cavities. These membranes are separated into two main groups which are epithelial membranes and connective tissue membranes. Decellularized forms of inner body membranes in the groups of epithelial membranes (amniotic membrane, mesentery, omentum, pericardium, peritoneum, pleura) and connective tissue membranes (fascia, periosteum, synovial membrane) have been used in tissue engineering studies for preparation and regeneration of various tissues such as bone, tendon, cartilage, skin, cornea, ocular surface, uterine, periodontium, vascular and cardiovascular structures. Decellularized inner body membranes have high biocompatibility and support cell attachment, cell growth and angiogenesis which are desired properties for using as versatile tools in tissue engineering applications. Even though, decellularized forms of these membranes have been used in many studies, it is necessary to develop new decellularization methods for more effective cell removal and less destructive properties on tissue structures. Moreover, development of decellularization agents which target removal of antigens of donor tissues is also essential because these antigens are one of the main reasons for tissue-organ rejections in allogeneic and xenogeneic tissue-organ implantations. This review provides comprehensive information and analysis about the current state of the art in the literature on decellularized inner body membranes and applications of these membranes in tissue engineering.
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http://dx.doi.org/10.1080/09205063.2020.1751523DOI Listing
July 2020

Development of an On-Chip Antibiotic Permeability Assay With Single Molecule Detection Capability.

IEEE Trans Nanobioscience 2018 04;17(2):155-160

Electrophysiology is the method of choice to characterize membrane channels. In this paper, we demonstrate a patch pipette based simple miniaturization that allows performing conductance measurements on a planar lipid bilayer in a microfluidic channel. Membrane proteins were reconstituted into Giant Unilamellar Vesicles (GUVs) by electroswelling, and GUVs with a single channel insertion were patched at the tip of pipette. We applied this approach to investigate the interactions of porins from E.coli with single antibiotics, and this will potentially provide information on the permeability rates. The results of this paper suggest that this approach can be extended to the integration of several pipettes into the microfluidic channel from different positions, allowing the multiplexed recordings and also reducing the substrate consumption below volumes.
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http://dx.doi.org/10.1109/TNB.2018.2809592DOI Listing
April 2018