Publications by authors named "Araz Norouz Dizaji"

7 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

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

imaging/detection of MRSA bacterial infections in mice using fluorescence labelled polymeric nanoparticles carrying vancomycin as the targeting agent.

J Biomater Sci Polym Ed 2020 02 25;31(3):293-309. Epub 2019 Nov 25.

Bioengineering Division, Institute of Graduate Studies, Hacettepe University, Beytepe, Ankara, Turkey.

This study aims to develop fluorescence labelled polymeric nanoparticle (NP) carrying vancomycin as the targeting agent for imaging of Methicillin-resistant bacterial infections in animal models. Maleimide functionalized 1,2-distearoyl-sn-glycero-3-phosphoethanolamine--[maleimide (polyethylene glycol)-2000] as the main was carrier matrix to prepare the NPs. A fluorescence probe, namely, poly[9,9'-bis (6″-,,-trimethylammonium) hexyl) fluorene-co-alt-4,7-(2,1,3-benzothiadiazole) dibromide] was encapsulated within these NPs by ultrasonication successfully. UV-Vis spectro- photometry of the NPs showed the characteristic shifting on the peak of conjugated polymers indicating successful packaging of this compound with lipid bilayers in nanoscales. Zeta-sizer and TEM analysis showed that the prepared NPs have a diameter of 80-100 nm in a narrow size distribution. Thiolated vancomycin was synthesized and attached to the NPs as the targeting agent. FTIR and MALDI-TOF spectroscopy analysis confirmed the immobilization. The specific targeting properties of the vancomycin conjugated NPs to the target bacteria were first confirmed in bacterial cultures in which was the non-target bacteria - using confocal microscopy and TEM. Imaging of bacterial infections was investigated in mice model using a non-invasive live animal fluorescence imaging technique. The results confirmed that bacterial infections can be detected using these novel polymeric NPs carrying fluorescence probes for imaging and vancomycin as the targeting agent - successfully.
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http://dx.doi.org/10.1080/09205063.2019.1692631DOI Listing
February 2020

Silver or gold deposition onto magnetite nanoparticles by using plant extracts as reducing and stabilizing agents.

Artif Cells Nanomed Biotechnol 2016 Jun 24;44(4):1109-15. Epub 2015 Mar 24.

a Department of Chemical Engineering , Bioengineering Division, Hacettepe University and Biyomedtek/Nanobiyomedtek , Beytepe, Ankara 06800 , Turkey.

In this paper, we describe an environmentally friendly procedure to produce silver (Ag) or gold (Au)-deposited magnetite nanoparticles by using plant extracts (Ligustrum vulgare) as reducing and stabilizing agents. Firstly, magnetite nanoparticles (∼6 nm) with superparamagnetic properties - SPIONs - were synthesized by co-precipitation of Fe(+ 2) and Fe(+ 3) ions. Color changes indicated the differing amounts of Au and Ag ions reduced and deposited on to the SPIONs when the plant extracts were used. UV-vis and transmission electron microscope (TEM) with energy dispersive X-ray (EDX) apparatus confirmed the metallic deposition. Magnetic saturation decreased when the amount of the metallic deposition increased, which was measured by vibrating sample magnetometry (VSM). Due to the molecules coming into contact with - and even remaining on - the surface of the nanoparticles after aggressive washing procedures, the Ag/Au-deposited SPIONs were stable, and almost no agglomeration was observed for months. Fourier Transform Infrared (FTIR) spectra depicted that functional groups such as carboxylic and ketone groups, which are most probably responsible for the reduction and stabilization of Ag/Au- carrying magnetite nanoparticles, originated from the plant extract. The proposed route was facile, viable, and reproducible, and it should be stressed that nanoparticles do contain only safe biomolecules as stabilizing agents on their surfaces.
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http://dx.doi.org/10.3109/21691401.2015.1019672DOI Listing
June 2016