Araştırma Çıktıları
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Item Translating Biotechnology to Knowledge-Based Innovation, Peace, and Development? Deploy a Science Peace Corps-An Open Letter to World Leaders(MARY ANN LIEBERT, INC, 2014-01-01) Hekim, Nezih; Coskun, Yavuz; Sinav, Ahmet; Abou-Zeid, Alaa H.; Agirbasli, Mehmet; Akintola, Simisola O.; Aynacioglu, Sukru; Bayram, Mustafa; Bragazzi, Nicola Luigi; Dandara, Collet; Dereli, Turkay; Dove, Edward S.; Elbeyli, Levent; Endrenyi, Laszlo; Erciyas, Kamile; Faris, Jack; Ferguson, Lynnette R.; Gogus, Fahrettin; Gungor, Kivanc; Gursoy, Mervi; Gursoy, Ulvi K.; Karaomerlioglu, M. Asim; Kickbusch, Ilona; Kilic, Turker; Kilinc, Metin; Kocagoz, Tanil; Lin, Biaoyang; LLerena, Adrian; Manolopoulos, Vangelis G.; Nair, Bipin; Ozkan, Bulent; Pang, Tikki; Sardas, Semra; Srivastava, Sanjeeva; Toraman, Cengiz; Ustun, Kemal; Warnich, Louise; Wonkam, Ambroise; Yakicier, Mustafa Cengiz; Yasar, Umit; Ozdemir, VuralScholarship knows no geographical boundaries. This science diplomacy and biotechnology journalism article introduces an original concept and policy petition to innovate the global translational science, a Science Peace Corps. Service at the new Corps could entail volunteer work for a minimum of 6 weeks, and up to a maximum of 2 years, for translational research in any region of the world to build capacity manifestly for development and peace, instead of the narrow bench-to-bedside model of life science translation. Topics for translational research are envisioned to include all fields of life sciences and medicine, as long as they are linked to potential or concrete endpoints in development, foreign policy, conflict management, post-crisis capacity building, and/or peace scholarship domains. As a new instrument in the global science and technology governance toolbox, a Science Peace Corps could work effectively, for example, towards elucidating the emerging concept of ``one health{''}-encompassing human, environmental, plant, microbial, ecosystem, and planet health-thus serving as an innovative crosscutting pillar of 21st century integrative biology. An interdisciplinary program of this caliber for development would link 21st century life sciences to foreign policy and peace, in ways that can benefit many nations despite their ideological differences. We note that a Science Peace Corps is timely. The Intergovernmental Panel on Climate Change (IPCC) of the United Nations released the Fifth Assessment Report on March 31, 2014. Worrisomely, the report underscores that no person or nation will remain untouched by the climate change, highlighting the shared pressing life sciences challenges for global society. To this end, we recall that President John F. Kennedy advocated for volunteer work that has enduring, transgenerational, and global impacts. This culminated in establishment of the Peace Corps in 1961. Earlier, President Abraham Lincoln aptly observed, ``nearly all men can stand adversity, but if you want to test a man's character, give him power.{''} We therefore petition President Barack Obama, other world leaders, and international development agencies in positions of power around the globe, to consider deploying a Science Peace Corps to cultivate the essential (and presently missing) ties among life sciences, foreign policy, development, and peace agendas. A Science Peace Corps requires support by a credible and independent intergovernmental organization or development agency for funding, and arbitration in the course of volunteer work when the global versus local (glocal) value-based priorities and human rights intersect in synergy or conflict. In all, Science Peace Corps is an invitation to a new pathway for competence in 21st century science that is locally productive and globally competitive. It can open up scientific institutions to broader considerations and broader inputs, and thus cultivate vital translational science in a world sorely in need of solidarity and sustainable responses to the challenges of 21st century science and society.Item Comparison of a novel antigen detection test with reverse transcription polymerase chain reaction assay for laboratory diagnosis of SARS-CoV-2 infection(SPRINGER HEIDELBERG, 2022-01-01) Cirit, Osman Sezer; Mutlu, Esvet; Sancak, Banu; Kocagoz, Tanil; Can, Ozge; Cicek, Candan; Sayiner, Ayca Arzu; Appak, Ozgur; Uyar, Neval Yurttutan; Kulah, Canan; Cicek, Aysegul Copur; Ozgumus, Osman Birol; Altintop, Yasemin Ay; Saatci, Esma; Karsligil, Tekin; Zer, Yasemin; Ozen, Nevgun Sepin; Cekin, Yesim; Karahan, Zeynep Ceren; Evren, Ebru; Karakoc, Ayse Esra; Orhan, Sultan Gulbahce; Mutlu, Derya; Bozdemir, Tugba; Cayci, Yeliz Tanriverdi; Cinar, Canberk; Tasbakan, Meltem; Mert, Merve; Cinar, Ece; Kutsoylu, Oya Ozlem Eren; Kocagoz, Sesin; Erturk, Ayse; Celik, Ilhami; Mete, Ayse Ozlem; Eneyli, Muge Gunalp; Akdemir, Irem; Karakok, Taliha; Inan, Dilara; Atilla, Aynur; Taflan, Sevket Onur; Yoruk, Kagan EtkaMolecular diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by real-time reverse transcription polymerase chain reaction (RT-PCR) in respiratory specimens is considered the gold standard method. This method is highly sensitive and specific but it has some limitations such as being expensive and requiring special laboratory equipment and skilled personnel. RapidFor (TM) Antigen Rapid Test Kit is a commercially available Ag-RDT which is produced in Turkey and designed to detect the nucleocapsid antigen of SARS-CoV-2 in nasopharyngeal swab samples. The aim of this study was to evaluate the performance of this novel SARS-CoV-2 antigen detection considering the RT-PCR method as the gold standard. Four hundred forty-four nasopharyngeal swab samples which were collected from the patients who met clinical criteria of COVID-19 from ten centers in Turkey between September 2020 and February 2021 were included in the study. All the nasopharyngeal swab samples were tested for SARS-CoV-2 RNA using commercial RT-PCR kits (Bioeksen and A1 Lifesciences, Istanbul, Turkey) according to the manufacturer's instructions. Viral loads were assessed according to the cycle threshold (Ct) values. RapidFor (TM) SARS-CoV-2 antigen test (Vitrosens Biotechnology, Istanbul, Turkey) was used to investigate the presence of SARS-CoV-2 antigen in all samples following the manufacturer's instructions. Out of 444 nasopharyngeal swab samples tested, 346 (77.9\%) were positive and 98 (22.1\%) were negative for SARS-CoV-2 RNA by RTPCR. Overall sensitivity of the RapidFor (TM). Antigen Rapid Test Kit was 80.3\% whereas specificity was found to be 87.8\%. Positivity rate of rapid antigen test in samples with Ct values over 25 and below 30 was 82.7\%, while it increased to 95.7\% in samples 20 <= Ct < 25 and reached 100\% in samples with Ct values below 20. RapidFor (TM) SARS-CoV-2 Ag test might be a good choice in the screening of symptomatic and asymptomatic patients and their contacts for taking isolation measures early, with advantages over RT-PCR as being rapid, easy and being applicable in every laboratory and even at point of care.Item 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, HuseyinToday, 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.Item Biologically modified microelectrode sensors provide enhanceds ensitivity for detection of nucleic acid sequences from Mycobacterium tuberculosis(ELSEVIER, 2020-01-01) Blair, Ewen O.; Hannah, Stuart; Vezza, Vincent; Avci, Huseyin; Kocagoz, Tanil; Hoskisson, Paul A.; Guzel, Fatma D.; Corrigan, Damion K.This paper describes improved sensitivity when using biosensors based on microfabricated microelectrodes to detect DNA, with the goal of progressing towards a low cost and mass manufacturable assay for antibiotic resistance in tuberculosis (TB). The microelectrodes gave an improvement in sensitivity compared to polycrystalline macroelectrodes. In addition, experimental parameters such as redox mediator concentration and experimental technique were investigated and optimised. It was found that lower concentrations of redox mediator gave higher signal changes when measuring hybridisation events and, at these lower concentrations, square wave voltammetry was more sensitive and consistent than differential pulse voltammetry. Together, this paper presents a quantifiable comparison of macroelectrode and microelectrode DNA biosensors. The final assay demonstrates enhanced sensitivity through reduction of sensor size, reduction of redox mediator concentration and judicious choice of detection technique, therefore maintaining manufacturability for incorporation into point of care tests and lab-on-a-chip devices.Item Multiplex-PCR-Based Screening and Computational Modeling of Virulence Factors and T-Cell Mediated Immunity in Helicobacter pylori Infections for Accurate Clinical Diagnosis(PUBLIC LIBRARY SCIENCE, 2015-01-01) Oktem-Okullu, Sinem; Tiftikci, Arzu; Saruc, Murat; Cicek, Bahattin; Vardareli, Eser; Tozun, Nurdan; Kocagoz, Tanil; Sezerman, Ugur; Yavuz, Ahmet Sinan; Sayi-Yazgan, AycaThe outcome of H. pylori infection is closely related with bacteria's virulence factors and host immune response. The association between T cells and H. pylori infection has been identified, but the effects of the nine major H. pylori specific virulence factorsItem A rapid, ultrasensitive voltammetric biosensor for determining SARS-CoV-2 spike protein in real samples(ELSEVIER ADVANCED TECHNOLOGY, 2021-01-01) Liv, Lokman; Coban, Gizem; Nakiboglu, Nuri; Kocagoz, TanilThe ongoing coronavirus disease 2019 (COVID-19) pandemic continues to threaten public health systems all around the world. In controlling the viral outbreak, early diagnosis of COVID-19 is pivotal. This article describes a novel method of voltammetrically determining severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein with a newly designed sensor involving bovine serum albumin, SARS-CoV-2 spike antibody and a functionalised graphene oxide modified glassy carbon electrode (BSA/AB/f-GO/GCE) or screen-printed electrode (BSA/AB/f-GO/SPE). The oxidation reaction based on the antibody-antigen protein interaction was evaluated as a response to SARS-CoV-2 spike protein at -200 mV and 1430 mV with the BSA/AB/f-GO/SPE and BSA/AB/fGO/GCE, respectively. The developed sensors, BSA/AB/f-GO/SPE and BSA/AB/f-GO/GCE, could detect 1 ag/mL of virus spike protein in synthetic, saliva and oropharyngeal swab samples in 5 min and 35 min, and both sensors demonstrated a dynamic response to the SARS-CoV-2 spike protein between 1 ag/mL and 10 fg/mL. Real-time polymerase chain reaction (RT-PCR), rapid antigen test and the proposed method were applied to saliva samples. When compared to RT-PCR, it was observed that the developed method had a 92.5\% specificity and 93.3\% sensitivity. Moreover, BSA/AB/f-GO/SPE sensor achieved 91.7\% accuracy compared to 66.7\% accuracy of rapid antigen test kit in positive samples. In view of these findings, the developed sensor provides great potential for the diagnosing of COVID-19 in real samples.Item Antimicrobial activities of phosphonium containing polynorbornenes(ROYAL SOC CHEMISTRY, 2016-01-01) Suer, N. Ceren; Demir, Ceren; Unubol, Nihan A.; Yalcin, Ozlem; Kocagoz, Tanil; Eren, TarikIn this study, amphiphilic polyoxanorbornene with different alkyl and aromatic phosphonium side chains was synthesized. The biological activities of these polymers were determined by the minimal inhibitory concentration (MIC) against E. coli, S. aureus, M. tuberculosis and the yeast C. albicans, and cytotoxicity studies on red blood cells were performed. A series of polymers with different alkyl and aromatic substituents (methyl, ethyl, tripropyl, tert-butyl, phenyl, and tris 4-methoxyphenyl) and two types different molecular weight, 3000 g mol(-1) and 10 000 g mol(-1), were prepared. It was observed that the biological activity of the polymers with aromatic group substituents had an MIC of 16, 8, 64 and 128 mu g mL(-1) against E. coli, S. aureus, M. tuberculosis and C. albicans, respectively, while those with nonaromatic carbons had a higher MIC compared to those with aromatic carbons. The aromaticity of the repeat unit had impressive effects on hemolytic activities as well. Zeta potential measurements of E. coli incubated with active and inactive polymer concentration revealed a relationship between the MIC and membrane surface charge density. Polymers bearing aromatic groups killed the bacteria with widespread damage after the polymers, holding the threshold concentration, were added to the bacteria.Item Simple concentration method enables the use of gargle and mouthwash instead of nasopharyngeal swab sampling for the diagnosis of COVID-19 by PCR(SPRINGER, 2021-01-01) Kocagoz, Tanil; Can, Ozge; Yurttutan Uyar, Neval; Aksoy, Ece; Polat, Tuba; Cankaya, Dilara; Karakus, Betul; Mozioglu, Erkan; Kocagoz, SesinSince its emergence in December 2019, SARS-CoV-2 is causing one of the most devastating pandemics in human history. Currently, the most important method for definitive diagnosis of COVID-19 is identification of SARS-CoV-2 RNA in nasopharyngeal swab samples by RT-PCR. Nasopharyngeal swab sampling is a discomforting procedure sometimes with adverse effects, which also poses a risk for infection for the personnel performing the sampling. We have developed a new method for concentrating biological samples, which enabled us to use gargle and mouthwash samples to be used in RT-PCR, for the diagnosis of COVID-19, as an alternative to nasopharyngeal swab samples. We have analyzed nasopharyngeal and gargle and mouthwash samples, before and after concentration, of 363 patients by RT-PCR for the presence of SARS-CoV-2. Among 114 patients in which SARS-CoV-2 was identified in at least one of their samples, the virus was identified in 76 (66.7\%), 67 (58.8\%), and 101 (88.6\%) of nasopharyngeal swab, gargle, and mouthwash samples before and after concentration, respectively. When concentrated by our new method, gargle and mouthwash samples can be used instead of nasopharyngeal samples in identification of SARS-CoV-2 by RT-PCR, with the same or better sensitivity. Eliminating the need for nasopharyngeal sampling will save the patients from an invasive and painful procedure and will lower the risk of infection for the healthcare personnel taking the sample. This easy sampling procedure may decrease the workload of hospitals, shorten the turnaround time of obtaining test results, and thus enable rapid isolation of infected patients.