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A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan
(Chemistry and Biodiversity, 2024-02) Yeğin, Zeynep; Mamatova, Zhanylbubu; Yurt, Mediha Nur Zafer; Taşbaşi, Behiye Büşra; Acar, Elif Esma; Uçak, Samet; Süleymanoğlu, Ali Anil; Aydın, Ali; Özalp, Veli Cengiz; Sudağıdan, Mert
Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.
Aptamer decorated PDA@magnetic silica microparticles for bacteria purifcation
(Microchimica Acta, 2024-04-23) Kavruk, Murat; Babaie, Zahra; Kibar, Güneş; Çetin, Barbaros; Yeşilkaya, Hasan; Amrani, Yassine; Dursun, Ali Doğan; Özalp, Veli Cengiz
One significant constraint in the advancement of biosensors is the signal-to-noise ratio, which is adversely affected by the presence of interfering factors such as blood in the sample matrix. In the present investigation, a specific aptamer binding was chosen for its affinity, while exhibiting no binding affinity towards non-target bacterial cells. This selective binding property was leveraged to facilitate the production of magnetic microparticles decorated with aptamers. A novel assay was developed to effectively isolate S. pneumoniae from PBS or directly from blood samples using an aptamer with an affinity constant of 72.8 nM. The capture experiments demonstrated efficiencies up to 87% and 66% are achievable for isolating spiked S. pneumoniae in 1 mL PBS and blood samples, respectively.
Bacterial and fungal microbiota of mould-ripened cheese produced in Konya
(International Journal of Dairy Technology, 2023-09-01) Yurt, Mediha Nur Zafer; Ömeroğlu, Esra Ersoy; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Altunbaş, Osman; Özalp, Veli Cengiz; Sudağıdan, Mert
Bacterial and fungal diversities of 24 mould-ripened cheeses originating from Konya-Türkiye were examined by metagenomic analysis. Firmicutes phylum, Enterococcus, Clostridium sensu stricto and Lactobacillus (Levilactobacillus) genera were the dominant bacteria. Ascomycota phylum and Penicillium and Pichia genera and Penicillium roqueforti and Pichia membranifaciens species were dominant fungi. Enterococcus faecium (n = 30) and Enterococcus faecalis (n = 6) were identified, and all strains were susceptible to penicillin, ampicillin, vancomycin, teicoplanin, chloramphenicol and linezolid. The highest resistance (n = 14) was against rifampin. Tetracycline resistance was determined in two strains. Biofilm-forming ability was found in nine E. faecium and 1 E. faecalis. E. faecium strains revealed 40–88.9%, and E. faecalis showed 59.2–100% homology by pulsed field gel electrophoresis.
Bacterial Skin Microbiota of Seabass from Aegean Fish Farms and Antibiotic Susceptibility of Psychrotrophic Pseudomonas
(Foods, 2023-05-11) Aydın, Ali; Sudağıdan, Mert; Mamatova, Zhanylbubu; Yurt, Mediha Nur Zafer; Özalp, Veli Cengiz; Zornu, Jacob; Tavornpanich, Saraya; Brun, Edgar
Farming seabass (Dicentrarchus labrax) is an essential activity in the Mediterranean basin including the Aegean Sea. The main seabass producer is Turkey accounting for 155,151 tons of produc tion in 2021. In this study, skin swabs of seabass farmed in the Aegean Sea were analysed with regard to the isolation and identification of Pseudomonas. Bacterial microbiota of skin samples (n = 96) from 12 fish farms were investigated using next-generation sequencing (NGS) and metabarcoding analysis. The results demonstrated that Proteobacteria was the dominant bacterial phylum in all samples. At the species level, Pseudomonas lundensis was identified in all samples. Pseudomonas, Shewanella, and Flavobacterium were identified using conventional methods and a total of 46 viable (48% of all NGS+) Pseudomonas were isolated in seabass swab samples. Additionally, antibiotic susceptibility was determined according to standards of the European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) in psychrotrophic Pseu domonas. Pseudomonas strains were tested for susceptibility to 11 antibiotics (piperacillin-tazobactam, gentamicin, tobramycin, amikacin, doripenem, meropenem, imipenem, levofloxacin, ciprofloxacin, norfloxacin, and tetracycline) from five different groups of antibiotics (penicillins, aminoglycosides, carbapenems, fluoroquinolones, and tetracyclines). The antibiotics chosen were not specifically linked to usage by the aquaculture industry. According to the EUCAST and CLSI, three and two Pseudomonas strains were found to be resistant to doripenem and imipenem (E-test), respectively. All strains were susceptible to piperacillin-tazobactam, amikacin, levofloxacin, and tetracycline. Our data provide insight into different bacteria that are prevalent in the skin microbiota of seabass sampled from the Aegean Sea in Turkey, and into the antibiotic resistance of psychrotrophic Pseudomonas spp
Biosensor for ATP detection via aptamer-modified PDA@POSS nanoparticles synthesized in a microfluidic reactor
(Microchimica Acta, 2024-02-23) Kibar, Güneş; Şahinoğlu, O. Berkay; Kılınçlı, Betül; Erdem, E. Yegan; Çetin, Barbaros; Özalp, Veli Cengiz
This study introduces aptamer-functionalized polyhedral oligomeric silsesquioxane (POSS) nanoparticles for adenosine triphosphate (ATP) detection where the POSS nanoparticles were synthesized in a one-step, continuous flow microfluidic reactor utilizing thermal polymerization. A microemulsion containing POSS monomers was generated in the microfluidic reactor which was designed to prevent clogging by using a continuous oil flow around the emulsion during thermal polymerization. Surfaces of POSS nanoparticles were biomimetically modified by polydopamine. The aptamer sequence for ATP was successfully attached to POSS nanoparticles. The aptamer-modified POSS nanoparticles were tested for affinity-based biosensor applications using ATP as a model molecule. The nanoparticles were able to capture ATP molecules successfully with an affinity constant of 46.5 μM. Based on this result, it was shown, for the first time, that microfluidic synthesis of POSS nanoparticles can be utilized in designing aptamer-functionalized nanosystems for biosensor applications. The integration of POSS in biosensing technologies not only exemplifies the versatility and efficacy of these nanoparticles but also marks a significant contribution to the field of biorecognition and sample preparation.
Clinical and Laboratory Evaluation of Acute Pericarditis Associated with Antinuclear Antibodies Positivity
(Current Vascular Pharmacology, 2023-02-16) Dursun, Ali Doğan; Sarıçam, Ersin; Erdem, Hakan; Türkmen-Sarıyıldız, Gülçin; Özyer, Eşref Umut; Bozkurt, Engin; İlkay, Erdoğan; Cantekin, Ömer Faruk
Background: Up to 30% of patients with acute pericarditis develop recurrent pericarditis. Acute pericarditis may be a manifestation of an underlying systemic autoimmune disease. Therefore, we evaluated the characteristics of patients with acute pericarditis according to antinuclear antibodies (ANA) positivity/negativity. Methods: Participants with acute pericarditis and negative ANA (n=29), recurrent pericarditis with positive ANA (n=30) and healthy controls (n=11) were examined. The groups were compared using serum parameters (ANA, C-reactive protein, leucocyte count, erythrocyte sedimentation rate, total antioxidant status, nitric oxide (NO), and oxidative stress index (OSI)) and imaging techniques (electrocardiogram, echocardiography, cardiovascular magnetic resonance, and venous Doppler ultrasound). Results: In females, acute pericarditis associated with ANA occurred more frequently (p<0.001). ANApositive acute pericarditis had significantly lower NO and OSI (p<0.05 and p<0.001, respectively) and pericardial inflammation on magnetic resonance. We found a pulmonary embolism in one patient with positive ANA. Slow venous flow (SVF) occurred more often in acute pericarditis associated with ANA than in the ANA-negative group on venous ultrasound (p<0.05). The prevalence of positive ANAs was 1.6 times higher among SVF patients than in controls. Conclusion: This study suggests that acute pericarditis associated with ANA is more common in middle- aged females. SVF and lower oxidative stress tests were more common in patients with ANAassociated acute pericarditis. Acute pericarditis associated with ANA could be considered as a hypercoagulable state. Therefore, all newly diagnosed pericarditis patients (especially females) should be checked for ANA positivity. Awareness of this coexistence should be promptly addressed to establish management strategies.
Determination of Bacterial Diversity of Propolis Microbiota
(Chemistry and Biodiversity, 2023-03) Ersoy-Ömeroğlu, Esra; Arserim-Uçar, Dilhun Keriman; Yeğin, Zeynep; Çağlayan, Nevzat; Zafer-Yurt, Mediha Nur; Taşbaşı, Behiye Büşra; Acar, Elif Esma; Uçak, Samet; Özalp, Veli Cengiz; Sudağıdan, Mert
Propolis is a natural resinous mixture produced by the excretions of honeybees. PCR amplification of the 16S rRNA gene region was achieved using DNA of pre-enriched propolis samples collected from Apis mellifera production hives (n=37) in Eastern Türkiye (Bingöl and its regions). Next-generation sequencing and metabarcoding techniques were used to identify bacterial communities in propolis samples. Firmicutes dominated the phylum structure, with Proteobacteria, Actinobacteria, Tenericutes, and Spirochaetes following. The top three bacterial families were Bacillaceae, Enterobacteriaceae, and Enterococcaceae. Bacillus (dominantly B. badius and B. thermolactis at the species level) was recognized at the genus level, followed by Enterococcus and Clostridium sensu stricto. Our study comprehensively identified the bacterial diversity of propolis samples. Further investigations targeting to enlighten the microbiota of propolis and its potential application fields are required to gain better insight into ecological, nutritional, and medicinal perspectives.
Development and validation of a sensitive assay for the quantification of arachidonoylcyclopropylamide (ACPA) in cell culture by LC–MS/MS
(Journal of Analytical Science and Technology, 2023-03-07) Boyacıoğlu, Özge; Reçber, Tuğba; Kır, Sedef; Korkusuz, Petek; Nemutlu, Emirhan
Synthetic and natural cannabinoid derivatives are highly investigated as drug candidates due to their antinociceptive, antiepileptic and anticancer potential. Arachidonoylcyclopropylamide (ACPA) is a synthetic cannabinoid with antiproliferative and apoptotic effects on non-small cell lung cancer and pancreatic and endometrial carcinoma. Thus, ACPA has a great potential for being used as an anticancer drug for epithelial cancers. Therefore, determining the levels of ACPA in biological fluids, cells, tissues and pharmaceutical dosage forms is crucial in monitoring the effects of various pharmacological, physiological and pathological stimuli on biological systems. However, the challenge in the quantification of ACPA is its short half-life and lack of UV signal. Therefore, we developed a liquid chromatography-tandem mass spectrometric (LC–MS/MS) method for sensitive and selective quantification of ACPA in cell culture medium and intracellular matrix. Multiple reaction monitoring in the positive ionization mode was used for detection with 344 → 203 m/z transitions. The separation of ACPA was performed on C18 column (50 × 3.0 mm, 2.1 μm) with the mobile phase run in the gradient mode with 0.1% formic acid (FA) in water and 0.1% FA in acetonitrile at a flow rate of 0.3 ml/min. The assay was linear in the concentration range of 1.8–1000 ng/mL (r = 0.999). The validation studies revealed that the method was linear, sensitive, accurate, precise, selective, repeatable, robust and rugged. Finally, the developed method was applied to quantify ACPA in cell culture medium and intracellular matrix.
Direct Detection of Viral Infections from Swab Samples by Probe-Gated Silica Nanoparticle-Based Lateral Flow Assay
(2024-02-08) Durdabak, Dilara Buse; Doğan, Soner; Tekol, Serap Demir; Çelik, Caner; Özalp, Veli Cengiz; Tuna, Bilge Güvenç
Point-of-care diagnosis is crucial to control the spreading of viral infections. Here, universal-modifiable probe-gated silica nanoparticles (SNPs) based lateral flow assay (LFA) is developed in the interest of the rapid and early detection of viral infections. The most superior advantage of the rapid assay is its utility in detecting various sides of the virus directly from the human swab samples and its adaptability to detect various types of viruses. For this purpose, a high concentration of fluorescein and rhodamine B as a reporting material was loaded into SNPs with excellent loading capacity and measured using standard curve, 4.19 μmol ⋅ g−1 and 1.23 μmol ⋅ g−1, respectively. As a model organism, severe acute respiratory syndrome coronavirus-2 (CoV-2) infections were selected by targeting its nonstructural (NSP9, NSP12) and envelope (E) genes as target sites of the virus. We showed that NSP12-gated SNPs-based LFA significantly outperformed detection of viral infection in 15 minutes from 0.73 pg ⋅ mL−1 synthetic viral solution and with a dilution of 1 : 103 of unprocessed human samples with an increasing test line intensity compared to steady state (n=12). Compared to the RT-qPCR method, the sensitivity, specificity, and accuracy of NSP12-gated SNPs were calculated as 100 %, 83 %, and 92 %, respectively. Finally, this modifiable nanoparticle system is a high-performance sensing technique that could take advantage of upcoming point-of-care testing markets for viral infection detections.
Fluorescent and electrochemical detection of nuclease activity associated with Streptococcus pneumoniae using specific oligonucleotide probes
(Analyst, 2024-01-19) Goikoetxea, Garazi; Akhtar, Khadija-Tul Kubra; Prysiazhniuk, Alona; Borsa, Barış A.; Aldağ, Mehmet Ersoy; Kavruk, Murat; Özalp, Veli Cengiz; Hernandez, Frank J.
Streptococcus pneumoniae (S. pneumoniae) represents a significant pathogenic threat, often responsible for community-acquired pneumonia with potentially life-threatening consequences if left untreated. This underscores the pressing clinical need for rapid and accurate detection of this harmful bacteria. In this study, we report the screening and discovery of a novel biomarker for S. pneumoniae detection. We used S. pneumoniae nucleases as biomarker and we have identified a specific oligonucleotide that works as substrate. This biomarker relies on a specific nuclease activity found on the bacterial membrane, forming the basis for the development of both fluorescence and electrochemical biosensors. We observed an exceptionally high sensitivity in the performance of the electrochemical biosensor, detecting as low as 102 CFU mL−1, whereas the fluorescence sensor demonstrated comparatively lower efficiency, with a detection limit of 106 CFU mL−1. Moreover, the specificity studies have demonstrated the biosensors’ remarkable capacity to identify S. pneumoniae from other pathogenic bacteria. Significantly, both biosensors have demonstrated the ability to identify S. pneumoniae cultured from clinical samples, providing compelling evidence of the potential clinical utility of this innovative detection system.
Higher rates of cefiderocol resistance among NDM producing Klebsiella bloodstream isolates applying EUCAST over CLSI breakpoints
(Infectious Diseases, 2023-06-30) İşler, Burcu; Vatansever, Cansel; Özer, Berna; Çınar, Güle; Aslan, Abdullah Tarık; Bauer, Michelle J.; Falconer, Caitlin; Forde, Brain; Şimşek, Funda; Tülek, Necla; Demirkaya, Hamiyet; Menekşe, Şirin; Akalin, Halis; Balkan, İlker İnanç; Aydın, Mehtap; Tigen, Elif Tükenmez; Demir, Safiye Koçulu; Kapmaz, Mahir; Keske , Şiran; Doğan, Özlem; Arabacı, Çiğdem; Yağcı, Serap; Hazırolan, Gülşen; Bakır, Veli Oğuzalp; Gönen, Mehmet; Saltoğlu, Neşe; Azap, Alpay; Azap, Özlem; Akova, Murat; Ergönül, Önder; Can, Füsun; Paterson, David L.; Harris, Patrick N. A.
Background: Cefiderocol is generally active against carbapenem-resistant Klebsiella spp. (CRK) with higher MICs against metallo-beta-lactamase producers. There is a variation in cefiderocol interpretive criteria determined by EUCAST and CLSI. Our objective was to test CRK isolates against cefiderocol and compare cefiderocol susceptibilities using EUCAST and CLSI interpretive criteria. Methods: A unique collection (n ¼ 254) of mainly OXA-48-like- or NDM-producing CRK bloodstream isolates were tested against cefiderocol with disc diffusion (Mast Diagnostics, UK). Beta-lactam resistance genes and multilocus sequence types were identified using bioinformatics analyses on complete bacterial genomes. Results: Median cefiderocol inhibition zone diameter was 24 mm (interquartile range [IQR] 24–26 mm) for all isolates and 18 mm (IQR 15–21 mm) for NDM producers. We observed significant variability between cefiderocol susceptibilities using EUCAST and CLSI breakpoints, such that 26% and 2% of all isolates, and 81% and 12% of the NDM producers were resistant to cefiderocol using EUCAST and CLSI interpretive criteria, respectively. Conclusions: Cefiderocol resistance rates among NDM producers are high using EUCAST criteria. Breakpoint variability may have significant implications on patient outcomes. Until more clinical outcome data are available, we suggest using EUCAST interpretive criteria for cefiderocol susceptibility testing.
Impact of vaccination on the presence and severity of symptoms in hospitalized patients with an infection of the Omicron variant (B.1.1.529) of the SARS-CoV-2 (subvariant BA.1)
(Clinical Microbiology and Infection, 2023-04-24) Beraud, Guillaume; Bouetard, Laura; Civljak, Rok; Michon, Jocelyn; Tülek, Necla; Lejeune, Sophie; Millot, Romain; Garchet-Beaudron, Aurelie; Lefebvre, Maeva; Velikov, Petar; Festou, Benjamin; Abgrall, Sophie; Lizatovic, Ivan K.; Baldolli, Aurelie; Esmer, Hüseyin; Blanchi, Sophie; Froidevaux, Gabrielle; Kapincheva, Nikol; Faucher, Jean-François; Duvnjak, Mario; Afşar, Elçin; Svitek, Luka; Yarımoğlu, Saliha; Yarımoğlu, Rafet; Janssen, Cecile; Epaulard, Olivier; EVASG (ESCMID vaccination study group)
Objectives The emergence of SARS-CoV-2 variants raised questions about the extent to which vaccines designed in 2020 have remained effective. We aimed to assess whether vaccine status was associated with the severity of Omicron SARS-CoV-2 infection in hospitalized patients. Methods We conducted an international, multi-centric, retrospective study in 14 centres (Bulgaria, Croatia, France, and Turkey). We collected data on patients hospitalized for ≥24 hours between 1 December 2021 and 3 March 2022 with PCR-confirmed infection at a time of exclusive Omicron circulation and hospitalization related or not related to the infection. Patients who had received prophylaxis by monoclonal antibodies were excluded. Patients were considered fully vaccinated if they had received at least two injections of either mRNA and/or ChAdOx1-S or one injection of Ad26.CoV2-S vaccines. Results Among 1215 patients (median age, 73.0 years; interquartile range, 57.0–84.0; 51.3% men), 746 (61.4%) were fully vaccinated. In multivariate analysis, being vaccinated was associated with lower 28-day mortality (Odds Ratio [95% Confidence Interval] (OR [95CI]) = 0.50 [0.32–0.77]), intensive care unit admission (OR [95CI] = 0.40 [0.26–0.62]), and oxygen requirement (OR [95CI] = 0.34 [0.25–0.46]), independent of age and comorbidities. When co-analysing these patients with Omicron infection with 948 patients with Delta infection from a study we recently conducted, Omicron infection was associated with lower 28-day mortality (OR [95CI] = 0.53 [0.37–0.76]), intensive care unit admission (OR [95CI] = 0.19 [0.12–0.28]), and oxygen requirements (OR [95CI] = 0.50 [0.38–0.67]), independent of age, comorbidities, and vaccination status. Discussion Originally designed vaccines have remained effective on the severity of Omicron SARS-CoV-2 infection. Omicron is associated with a lower risk of severe forms, independent of vaccination and patient characteristics.
Irisin pathways in hearts of Type 1 diabetic adult male rats following 6 weeks of moderate and high-volume aerobic exercise on a treadmill
(Sport Sciences for Health, 2023-06) Çelik, Hümeyra; Dursun, Ali Doğan; Tatar, Yakup; Ömercioğlu, Göktuğ; Baştuğ, Metin
Purpose Exercise-mediated protection from cardiomyopathy in diabetes through myokines raises the question of what volume of exercise should be performed. Irisin pathway molecules (consisting of peroxisome proliferator-activated receptor gamma coactivator 1-α (PGC-1α), irisin, peroxisome proliferator-activated receptors-α (PPAR-α) and uncoupling protein 1 (UCP1)), which have been shown to be mostly expressed in the heart, are thought to have beneficial effects on diabetic heart. The aim of the study is to evaluate the effects of different exercise protocols on irisin pathway in Type 1 diabetic heart. Methods Diabetic (60 mg/kg streptozotocin i.p.) and healthy Wistar Albino rats (n = 60) were trained under moderate and high-volume exercise protocols on rat treadmill for 6 weeks. After killing, mRNA transcript and protein abundance of PGC-1α, irisin, PPAR-α, and UCP1 were determined in the left ventricles of healthy and diabetic rats. Results PPAR-α, FNDC5, and UCP1 mRNA levels increased significantly in healthy moderate-volume exercise group (HMVE) compared to healthy high-volume exercise (HHVE) and diabetic moderate-volume exercise groups (DMVE). Moreover, protein levels of irisin and UCP1 also elevated significantly in the diabetic high-volume exercise group (DHVE) compared to the healthy control group (HC), although there was no significant difference between the groups in PPAR-α. Conclusion Irisin and UCP1 protein values increased due to HHEV in the heart of Type 1 diabetic rats, but PPAR-α values did not change; it shows that HHEV is suitable for the heart of Type 1 diabetic rats in terms of the benefits of the pathway of irisin.
Protective effects of hydrogen rich saline solution in rats with experimental myocardial ischemia reperfusion injury
(Heliyon, 2023-11) Köksal, Zeynep; Kurtipek, Ömer; Arslan, Mustafa; Doğan, Dursun Ali; Yığman, Zeynep; Özer, Abdullah
Aim The aim of our study is to show whether the administration of hydrogen-rich saline solution (HRSS) intraperitoneally before left main coronary artery (LAD) ischemia protects the myocardium against ischemia-reperfusion (IR) injury. Materials and methods After ethics committee approval, 24 Wistar Albino rats were divided into 4 groups, 6 rats in each group. For experimental IR, myocardial ischemia was performed by LAD ligation. Left thoracotomy was performed without ischemia in the Control group (Group C). Left thoracotomy was performed without myocardial ischemia to the rats in the HRSS group, and HRSS was given intraperitoneally (ip) at a rate of 10 ml/kg throughout the procedure. In the MIR-HRSS group, a single dose of 10 ml/kg HRSS was administered 5 min before reperfusion. Histopathological and biochemical parameters were compared in myocardial tissue samples taken at the end of the reperfusion period. Results When the groups were compared among themselves in terms of TOS and TAS levels, there was a significant difference between the groups (p = 0.006, p = 0.002). The severity of cardiomyocyte degeneration was significantly greater in MIR group than that in the control and HRSS groups (p = 0.002 and p = 0.001, respectively), as well as severity score of cardiomyocyte degeneration was higher in MIR-HRSS group compared with HRSS group (p = 0.035). Conclusion Our study shows that HRSS is protective in IR injury, with the application of HRSS 5 min before reperfusion, interstitial edema severity, subendocardial haemorrhage are reduced, and oxidant status parameters are increased, while antioxidant status parameters are decreased. We believe that when it is supported by other studies, the protective effects of HRSS on IR damage will be shown in detail and its indications will be expanded.
Quartz crystal microbalance–based aptasensor integrated with magnetic pre‑concentration system for detection of Listeria monocytogenes in food samples
(Microchimica Acta, 2024-04-03) Beyazıt, Fatma; Arıca, Mehmet Yakup; Açıkgoz‑Erkaya, İlkay; Özalp, Veli Cengiz; Bayramoğlu, Gülay
A fast and accurate identifcation of Listeria monocytogenes. A new quartz crystal microbalance (QCM) aptasensor was designed for the specific and rapid detection of L. monocytogenes. Before detection of the target bacterium from samples inthe QCM aptasensor, a magnetic pre-enrichment system was used to eliminate any contaminant in the samples. The preparedmagnetic system was characterized using ATR-FTIR, SEM, VSM, BET, and analytical methods. The saturation magnetizationvalues of the Fe3O4, Fe3O4@PDA, and Fe3O4@PDA@DAPEG particles were 57.2, 40.8, and 36.4 emu/g, respectively.The same aptamer was also immobilized on the QCM crystal integrated into QCM flow cell and utilized to quantitativelydetect L. monocytogenes cells from the samples. It was found that a specific aptamer-magnetic pre-concentration systemefficiently captured L. monocytogenes cells in a short time approximately 10 min). The Fe3O4@PDA@DA-PEG-Apt particlesprovided selective isolation of L. monocytogenes from the bacteria-spiked media up to 91.8%. The immobilized aptamercontent of the magnetic particles was 5834 μg/g using 500 ng Apt/mL. The QCM aptasensor showed a very high range ofanalytical performance to the target bacterium from 1.0 × 102and 1.0 × 107CFU/mL. The limit of detection (LOD) and limit of quantitation (LOQ) were 148 and 448 CFU/mL, respectively, from the feeding of the QCM aptasensor flow cell with the eluent of the magnetic pre-concentration system. The reproducibility of the aptasensor was more than 95%. The aptasensor was very specific to L. monocytogenes compared to the other Listeria species (i.e., L. ivanovii, L. innocua, and L. seeligeri) or other tested bacteria such as Staphylococcus aureus, Escherichia coli, and Bacillus subtilis. The QCM aptasensor was regenerated with NaOH solution, and the system was reused many times.
Serum irisin levels and osteoporosis in patients with advanced chronic kidney disease and renal transplant recipients
(International Urology and Nephrology, 2023-02-11) Demir, Canan; Dursun, Ali Doğan; Sarıyıldız, Gülçin Türkmen; Arslan, Aykut İlker
Aim To elucidate the association of serum irisin levels with bone mineral density (BMD) and calcium–phosphorus metabolism parameters in chronic kidney disease (CKD) patients and renal transplant recipients (RTRs). Methods This is a cross-sectional study involving CKD patients and RTRs. Healthy volunteers served as controls. Age, gender, and dialysis vintage were recorded. Serum irisin, creatinine, glucose, calcium, albumin, 25(OH) vitamin D, ferritin, C-reactive protein, A1C, and lipid profile were studied in all participants. Estimated glomerular filtration rate (eGFR), corrected calcium, and body mass index (BMI) were calculated. Results Overall, 49 patients (23 hemodialysis, 26 RTRs) and 25 control subjects were included. In hemodialysis (HD) group, 8 patients (34.8%) had osteoporosis, and 12 patients (52.2%) had osteopenia. In RTR group, 3 patients (11.5%) had osteoporosis, while 15 patients (57.7%) had osteopenia. Among controls, one had osteoporosis, and 7 had osteopenia. There was no significant difference between HD and RTRs; however, osteoporosis rate was significantly lower in control subjects. BMD measurements (femur and lumbar T- and Z-scores) were comparable between HD and RTR groups. Control group DEXA values were similar to RTRs; however, they were significantly higher compared to HD group. 25(OH) vitamin D levels were comparable between the HD and RTR groups, and these were significantly lower compared to values of the control group. Mean serum irisin level was 426.6 ± 191.2 pg/mL in hemodialysis group, 342.6 ± 174.8 in the RTR group, and 208.0 ± 186.1 in controls. Serum irisin levels were similar in RTR and HD groups, but their values were significantly higher compared to controls. When we compared serum irisin levels between patients with and without osteoporosis in the whole cohort and hemodialysis and RTR groups, there was no difference. Serum irisin was positively correlated with lumbar T-score both in hemodialysis and RTR groups. Conclusion Our study is the first in the literature revealing the positive correlation of serum irisin level with femur T-score in RTRs. Serum irisin level was also positively correlated with femur T-scores in hemodialysis patients.
Targeted multidrug delivery systems to kill antibiotic-resistant Staphylococcus aureus
(Journal of Drug Delivery Science and Technology, 2023-10-01) Özalp, Veli Cengiz; Uçak, Samet; Dursun, Ali D.; Sudağıdan, Mert; İçin, Öykü; Vakifahmetoglu, Çekdar; Henning, Laura M.; Simon, Ulla; Gurlo, Aleksander
Different ordered mesoporous silica (OMS) nanoparticles, ranging from regular COK-12 to COK-12 modified in terms of pore shape and size, have been employed as standard drug carriers for the controlled adsorption and release of drug molecules in comparison to well known OMS SBA-15 and MCM-41. The cytotoxicity analysis demonstrated that regular COK-12 particles were less harmful to mammalian cultured cells, causing lower apoptosis induction than modified COK-12, MCM-41, and SBA-15 particles. Thus, regular COK-12 was further used to prepare a dual antibiotic-loaded drug delivery material, followed by surface functionalization with Staphylococcus aureus-specific aptamers for targeting. The results demonstrated that the joint loading of lysozyme and vancomycin in regular COK-12 improved the ability of the antibiotic treatments to kill methicillin-resistant Staphylococcus strains via aptamer targeting. The minimum inhibitory concentration (MIC) values decreased 4.1-fold and 12-fold compared to the non-targeted use of the antimicrobial agents in homogeneous solutions for vancomycin and lysozyme, respectively, clearly demonstrating the high potential of COK-12 to be used as a carrier in multidrug therapy.
The Effect of Sevoflurane and Fullerenol C 60 on the Liver and Kidney in Lower Extremity Ischemia-Reperfusion Injury in Mice with Streptozocin-Induced Diabetes
(International Journal of Nanomedicine, 2023-11-12) Şengel, Necmiye; Küçük, Ayşegül; Özdemir, Çağrı; Sezen, Şaban Cem; Kip, Gülay; Er, Fatma; Dursun, Ali Doğan; Polat, Yücel; Kavutçu, Mustafa; Arslan, Mustafa
Objective: This study aimed to demonstrate whether fullerenol C60, sevoflurane anesthesia, or a combination of both had protective effects on the liver and kidneys in lower extremity ischemia-reperfusion injury (IRI) in mice with streptozocin-induced diabetes. Methods: A total of 46 Swiss albino mice were divided into six groups as follows: control group (group C, n=7), diabetes group (group D, n=7), diabetes-ischemia/reperfusion (group DIR, n=8), diabetes-ischemia/reperfusion-fullerenol C60 (group DIR-FC60, n=8), diabetes-ischemia/reperfusion-sevoflurane (group DIR-S, n=8), and the diabetes-ischemia/reperfusion-fullerenol C60-sevoflurane (group DIR-S-FC60, n=8). Fullerenol C60 (100mg/kg) was administered intraperitoneally 30 min before the ischemia-reperfusion procedure to the fullerenol groups (DIR-FC60 and DIR-S-FC60). In the DIR groups, 2 hours (h) ischemia-2h reperfusion periods were performed. In the sevoflurane groups, sevoflurane was applied during the ischemia-reperfusion period with 100% O2. Liver and kidney tissues were removed at the end of the reperfusion procedure for biochemical and histopathological examinations. Results: In liver tissue, hydropic degeneration, sinusoidal dilatation, pycnotic nuclei, prenecrotic cells, and mononuclear cell infiltration in parenchyma were significantly more frequent in group DIR than in groups D and group C. In terms of the histopathologic criteria examined, more positive results were seen in group DIR-FC60, and when group DIR-FC60 was compared with group DIR, the difference was significant. The best results in AST, ALT, glucose, TBARS levels, and SOD enzyme activities in liver tissue were in group DIR-FC60 compared with group DIR, followed by groups DIR-S-FC60 and DIR-S, respectively. Regarding TBARS levels and SOD enzyme activities in kidney tissue, the best results were in groups DIR-FC60, DIR-S-FC60, and DIR-S, respectively. Conclusion: According to our findings, it is clear that fullerenol C60 administered intraperitoneally 30 min before ischemia, alone or together with sevoflurane, reduces oxidative stress in distant organ damage caused by lower extremity IRI, and reduces liver and kidney tissue damage in histopathologic examinations.
The Effects of Antimicrobial Resistance and the Compatibility of Initial Antibiotic Treatment on Clinical Outcomes in Patients With Diabetic Foot Infection
(The International Journal of Lower Extremity Wounds, 2023) Saltoğlu, Neşe; Sürme, Serkan; Ezirmik, Elif; Kadanalı, Ayten; Kurt, Ahmet Furkan; Özdemir, Meryem Şahin; Ak, Öznur; Altay, Fatma Aybala; Acar, Ali; Çakar, Zeynep Şule; Tülek, Necla; Kınıklı, Sami; KLIMIK Society; Diabetic Foot Study Group
We aimed to determine pathogen microorganisms, their antimicrobial resistance patterns, and the effect of initial treatment on clinical outcomes in patients with diabetic foot infection (DFI). Patients with DFI from 5 centers were included in this multicenter observational prospective study between June 2018 and June 2019. Multivariate analysis was performed for the predictors of reinfection/death and major amputation. A total of 284 patients were recorded. Of whom, 193 (68%) were male and the median age was 59.9 ± 11.3 years. One hundred nineteen (41.9%) patients had amputations, as the minor (n = 83, 29.2%) or major (n = 36, 12.7%). The mortality rate was 1.7% with 4 deaths. A total of 247 microorganisms were isolated from 200 patients. The most common microorganisms were Staphylococcus aureus (n = 36, 14.6%) and Escherichia coli (n = 32, 13.0%). Methicillin resistance rates were 19.4% and 69.6% in S aureus and coagulase-negative Staphylococcus spp., respectively. Multidrug-resistant Pseudomonas aeruginosa was detected in 4 of 22 (18.2%) isolates. Extended-spectrum beta-lactamase-producing Gram-negative bacteria were detected in 20 (38.5%) isolates of E coli (14 of 32) and Klebsiella spp. (6 of 20). When the initial treatment was inappropriate, Klebsiella spp. related reinfection within 1 to 3 months was observed more frequently. Polymicrobial infection (p = .043) and vancomycin treatment (p = .007) were independent predictors of reinfection/death. Multivariate analysis revealed vascular insufficiency (p = .004), hospital readmission (p = .009), C-reactive protein > 130 mg/dL (p = .007), and receiving carbapenems (p = .005) as independent predictors of major amputation. Our results justify the importance of using appropriate narrow-spectrum empirical antimicrobials because higher rates of reinfection and major amputation were found even in the use of broad-spectrum antimicrobials.
The Effects of Paddy Cultivation and Microbiota Members on Arsenic Accumulation in Rice Grain
(Foods, 2023-05-26) Ömeroğlu, Esra Ersoy; Bayer, Aslı; Sudağıdan, Mert; Özalp, Veli Cengiz; Yaşa, İhsan
Access to safe food is one of the most important issues. In this context, rice plays a prominent role. Because high levels of arsenic in rice grain are a potential concern for human health, in this study, we determined the amounts of arsenic in water and soil used in the rice development stage, changes in the arsC and mcrA genes using qRT-PCR, and the abundance and diversity (with metabarcoding) of the dominant microbiota. When the rice grain and husk samples were evaluated in terms of arsenic accumulation, the highest values (1.62 ppm) were obtained from areas where groundwater was used as irrigation water, whereas the lowest values (0.21 ppm) occurred in samples from the stream. It was observed that the abundance of the Comamonadaceae family and Limnohabitans genus members was at the highest level in groundwater during grain formation. As rice development progressed, arsenic accumulated in the roots, shoots, and rice grain. Although the highest arsC values were reached in the field where groundwater was used, methane production increased in areas where surface water sources were used. In order to provide arsenic-free rice consumption, the preferred soil, water source, microbiota members, rice type, and anthropogenic inputs for use on agricultural land should be evaluated rigorously.

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