Browsing by Author "Akcakoca, Iremnur"

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    Investigation of the Effect of Channel Structure and Flow Rate on On-Chip Bacterial Lysis
    (IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC, 2021-01-01) Dizaji, Araz Norouz; Ozturk, Yasin; Ghorbanpoor, Hamed; Cetak, Ahmet; Akcakoca, Iremnur; Kocagoz, Tanil; Avci, Huseyin; Corrigan, Damion; Guzel, Fatma Dogan
    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 (0.6-8 mu l/min) either at room temperature or 50 degrees 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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    Label-free molecular detection of antibiotic susceptibility forMycobacterium smegmatisusing a low cost electrode format
    (WILEY, 2021-01-01) Guzel, Fatma Dogan; Ghorbanpoor, Hamed; Dizaji, Araz Norouz; Akcakoca, Iremnur; Ozturk, Yasin; Kocagoz, Tanil; Corrigan, Damion K.; Avci, Huseyin
    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 vitroantibiotic susceptibility testing is becoming increasingly important. This research details the development of an antibiotic susceptibility test forMycobacterium smegmatisusing streptomycin as antibiotics. This strain was selected because it is a member of the slow growingMycobacteriumgenus and serves as a useful surrogate organism forM. 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 monitorM. smegmatisnucleic acid sequences using the techniques of square-wave voltammetry and electrochemical impedance spectroscopy. The results show that it was possible to detectM. smegmatissequences and distinguish antibiotic-treated cells from untreated cells with a label-free molecular detection. As a result, thein vitroantibiotic susceptibility test revealed thatM. smegmatisshowed 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.