PubMed İndeksli Yayınlar Koleksiyonu / PubMed Indexed Publications Collection
Permanent URI for this collectionhttps://hdl.handle.net/11147/7645
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Article Citation - WoS: 15Citation - Scopus: 17Improved Activity of Alpha-L From Geobacillus Vulcani Gs90 by Directed Evolution: Investigation on Thermal and Alkaline Stability(John Wiley and Sons Inc., 2019) Sürmeli, Yusuf; İlgü, Hüseyin; Şanlı Mohamed, Gülşahalpha-L-Arabinofuranosidase (Abf) is a potential enzyme because of its synergistic effect with other hemicellulases in agro-industrial field. In this study, directed evolution was applied to Abf from Geobacillus vulcani GS90 (GvAbf) using one round error-prone PCR and constructed a library of 73 enzyme variants of GvAbf. The activity screening of the enzyme variants was performed on soluble protein extracts using p-nitrophenyl alpha-L-arabinofuranoside as substrate. Two high activity displaying variants (GvAbf L307S and GvAbf Q90H/L307S) were selected, purified, partially characterized, and structurally analyzed. The specific activities of both variants were almost 2.5-fold more than that of GvAbf. Both GvAbf variants also exhibited higher thermal stability but lower alkaline stability in reference to GvAbf. The structural analysis of GvAbf model indicated that two mutation sites Q90H and L307S in both GvAbf variants are located in TIM barrel domain, responsible for catalytic action in many Glycoside Hydrolase Families including GH51. The structure of GvAbf model displayed that the position of L307S mutation is closer to the catalytic residues of GvAbf compared with Q90H mutation and also L307S mutation is conserved in both variants of GvAbf. Therefore, it was hypothesized that L307S amino acid substitution may play a critical role in catalytic activity of GvAbf. (C) 2018 International Union of Biochemistry and Molecular Biology, Inc.Article Citation - WoS: 16Citation - Scopus: 16Secular Trends in Opportunistic Infections, Cancers and Mortality in Patients With Aids During the Era of Modern Combination Antiretroviral Therapy(John Wiley and Sons Inc., 2018) Sezgin, Efe; Van Natta, Mark L.; Thorne, Jennifer E.; Puhan, M. A.; Jabs, D. A.Objectives: The aim of the study was to estimate the incidence of, determine risk factors for, and investigate the consequences of opportunistic infections (OIs) and malignancies among patients with the acquired immune deficiency syndrome (AIDS) in the era of modern combination antiretroviral therapy (cART). Methods: Three enrolment periods (1998–2002, 2003–2005 and 2006–2012), corresponding to changes in predominant cART regimens, were compared among 1889 participants enrolled in a prospective cohort study, the Longitudinal Study of Ocular Complications of AIDS (LSOCA). Incidences of AIDS-related OIs and cancers were estimated. Multivariate logistic and Cox regression models were used to determine the effect of demographic and clinical characteristics on OIs and mortality. Results: Between participants enrolled in the 1998–2002 and 2006–2012 enrolment periods, the incidence of OIs decreased from 27 per 1000 person-years (PY) to 11 per 1000 PY (P < 0.001), and mortality decreased from 41 per 1000 PY to 18 per 1000 PY (P < 0.0001), corresponding to improvements in cART regimens. Conclusions: Improvements in cART regimens led to a progressive decline in the incidence of OIs and mortality between 1999 and 2013 among patients with AIDS in the era of modern cART.Article Citation - WoS: 59Citation - Scopus: 57Cmos Enabled Microfluidic Systems for Healthcare Based Applications(John Wiley and Sons Inc., 2018) Hussian, Muhammad M.; Khan, Sherjeel M.; Gümüş, Abdurrahman; Nassar, Joanna M.With the increased global population, it is more important than ever to expand accessibility to affordable personalized healthcare. In this context, a seamless integration of microfluidic technology for bioanalysis and drug delivery and complementary metal oxide semiconductor (CMOS) technology enabled data-management circuitry is critical. Therefore, here, the fundamentals, integration aspects, and applications of CMOS-enabled microfluidic systems for affordable personalized healthcare systems are presented. Critical components, like sensors, actuators, and their fabrication and packaging, are discussed and reviewed in detail. With the emergence of the Internet-of-Things and the upcoming Internet-of-Everything for a people–process–data–device connected world, now is the time to take CMOS-enabled microfluidics technology to as many people as possible. There is enormous potential for microfluidic technologies in affordable healthcare for everyone, and CMOS technology will play a major role in making that happen.Article Citation - WoS: 56Citation - Scopus: 55A Bodipy-Based Fluorescent Probe To Visually Detect Phosgene: Toward the Development of a Handheld Phosgene Detector(John Wiley and Sons Inc., 2018) Sayar, Melike; Karakuş, Erman; Güner, Tuğrul; Yıldız, Büşra; Yıldız, Ümit Hakan; Emrullahoğlu, MustafaA boron-dipyrromethene (BODIPY)-based fluorescent probe with a phosgene-specific reactive motif shows remarkable selectivity toward phosgene, in the presence of which the nonfluorescent dye rapidly transforms into a new structure and induces a fluorescent response clearly observable to the naked eye under ultraviolet light. Given that dynamic, a prototypical handheld phosgene detector with a promising sensing capability that expedites the detection of gaseous phosgene without sophisticated instrumentation was developed. The proposed method using the handheld detector involves a rapid response period suitable for issuing early warnings during emergency situations.Article Citation - WoS: 87Citation - Scopus: 94Factors Related To Recurrence of Idiopathic Granulomatous Mastitis: What Do We Learn From a Multicentre Study?(John Wiley and Sons Inc., 2018) Uysal, Erdal; Soran, Atilla; Sezgin, Efe; Granulomatous Mastitis Study GroupBackground: Idiopathic granulomatous mastitis (IGM) is a rare chronic inflammatory disease of the breast with unknown aetiology. Its treatment is controversial and the recurrence rate is high. The objectives of this study were to examine the demographic, sociocultural and clinical characteristics observed among a large cohort of IGM patients from Turkey and to identify factors related to the recurrence of IGM. Methods: The study was designed as a multicentre retrospective study including 22 breast centres in Turkey. A total of 720 IGM patients are included in the study. Patient data were obtained from the patient's files and electronic records based on the study protocol. Patients’ demographic, clinical, radiological, treatment and recurrence of IGM related characteristics were recorded. Results: Our results revealed a statistically significant association between IGM recurrence and history of pregnancy, breastfeeding, breast infection and smoking (P < 0.05). Having a chronic systematic disease, oral contraceptive, analgesic and herbal medicine consumptions, treatment choice, education, place of birth and current residence were not found to be associated with IGM recurrence (P > 0.05). Conclusion: Our findings show that history of pregnancy, breastfeeding, breast infection and smoking were the risk factors for IGM recurrence. As current treatment methods did not affect IGM recurrence, recurrence-related factors, such as breast infection and smoking, should be considered to eliminate while focusing on less invasive local treatment research.Article Citation - WoS: 21Citation - Scopus: 22First-Principle Phonon Transport Properties of Nanoscale Graphene Grain Boundaries(John Wiley and Sons Inc., 2018) Sandonas, Leonardo Medrano; Sevinçli, Haldun; Gutierrez, Rafael; Cuniberti, GianaurelioThe integrity of phonon transport properties of large graphene (linear and curved) grain boundaries (GBs) is investigated under the influence of structural and dynamical disorder. To do this, density functional tight-binding (DFTB) method is combined with atomistic Green's function technique. The results show that curved GBs have lower thermal conductance than linear GBs. Its magnitude depends on the length of the curvature and out-of-plane structural distortions at the boundary, having stronger influence the latter one. Moreover, it is found that by increasing the defects at the boundary, the transport properties can strongly be reduced in comparison to the effect produced by heating up the boundary region. This is due to the large reduction of the phonon transmission for in-plane and out-of-plane vibrational modes after increasing the structural disorder in the GBs.Article Citation - WoS: 27Citation - Scopus: 37Nanofibrous Gelatine Scaffolds Integrated With Nerve Growth Factor-Loaded Alginate Microspheres for Brain Tissue Engineering(John Wiley and Sons Inc., 2018) Büyüköz, Melda; Erdal, Esra; Alsoy Altınkaya, SacideNeural regeneration research is designed in part to develop strategies for therapy after nerve damage due to injury or disease. In this study, a new gelatine-based biomimetic scaffold was fabricated for brain tissue engineering applications. A technique combining thermally induced phase separation and porogen leaching was used to create interconnected macropores and nanofibrous structure. To promote tissue regeneration processes, the scaffolds were integrated with nerve growth factor (NGF)-loaded alginate microspheres. The results showed that nanofibrous matrix could only be obtained when gelatine concentration was at least 7.5% (w/v). The scaffold with a modulus value (1.2 kPa) similar to that of brain tissue (0.5–1 kPa) was obtained by optimizing the heat treatment time, macropore size and gelatine concentration. The encapsulation efficiencies of NGF into 0.1% and 1% alginate microspheres were 85% and 100%, respectively. The release rate of NGF from the microspheres was controlled by the alginate concentration and the poly(L-lysine) coating. The immobilization of the microspheres in the scaffold reduced burst release and significantly extended the release period. The nanofibrous architecture and controlled release of NGF from the microspheres induced neurite extension of PC12 cells, demonstrating that the released NGF was in an active form. The results suggest that the scaffolds prepared in this study may have potential applications in brain tissue engineering due to topologic and mechanical properties similar to brain tissue and pore structure suitable for cell growth and differentiation.Article Citation - WoS: 15Citation - Scopus: 13Environmentally Responsive Dual-Targeting Nanoparticles: Improving Drug Accumulation in Cancer Cells as a Way of Preventing Anticancer Drug Efflux(John Wiley and Sons Inc., 2018) Dağlıoğlu, CenkDrug targeting and stimuli-responsive drug release are 2 active areas of cancer research and hold tremendous potential in the management of cancer drug resistance. In this study, I addressed this issue and focused on the synthesis and characterization of pH-responsive Fe3O4@SiO2(FITC)-BTN/folic acid/DOX multifunctional nanoparticles aiming to increase drug accumulation in malignancies with both dual active targeting and endosomal drug release properties. Dye-doped silica magnetic-fluorescent composite was constructed by a simple coprecipitation of Fe+2/Fe+3 salts followed by sol-gel formation and dual-targeting function was obtained by conjugating folate and biotin moieties on the silica surface of nanoparticles via an esterification reaction. Doxorubicin was then successfully attached on the amine-functionalized nanoparticles using a pH-sensitive Schiff-base formation. The physicochemical characterization of the structure was performed by dynamic light scattering, zeta potential measurement, X-ray diffraction, Fourier transform infrared spectroscopy, electron microscopy techniques, and an in vitro pH-dependent release study. Cellular uptake and cytotoxicity experiments demonstrated an enhanced intracellular delivery and reduction of cancer cell viability in the cervical carcinoma HeLa cell line. Furthermore, proapoptotic studies showed that the nanoparticles increased the apoptotic rates within the same cancer cells. The preliminary cell tests confirm the potential of these multifunctional nanoparticles against the development of drug resistance in cancer cells.Article Citation - WoS: 3Citation - Scopus: 8Way-Finding Strategies of Blind Persons in Urban Scale(John Wiley and Sons Inc., 2017) Kan Kılıç, Didem; Doğan, FehmiThe aim of this study was to determine whether urban environments with different prominent sensory inputs have an impact on the way-finding strategies of blind people and to identify these impacts, where applicable. We specifically investigated how blind people use their senses to compensate for the lack of visual information and how the priority of senses changes according to the urban context. The participants of the study consisted of nine congenitally blind individuals and the study took place in two urban settings: a dense urban district, Kemeralti district in İzmir; and an urban park, the İzmir Fair Park. During the learning phase, a first trial along the selected routes was conducted for each participant individually along with one of the researchers. In the test phase, the participants were requested to re-walk the route and verbally report the environmental cues they attended to. The participants’ verbal reports were recorded and transcripts of the recordings were coded according to the environmental sensory inputs. In addition, the short-term memory of each participant was also evaluated. The results show that the characteristics of the urban environment seem to have an impact on way-finding strategies of blind individuals. It was found that the sound of the city and the echo from the environment are the most important factors for blind participants in the dense urban environment. Environmental boundaries provided echoes and gave a sense of enclosure that helped them orient themselves, whereas, in the park environment, the sense of enclosure was not enhanced due to a lack of boundaries in the environment.Article Citation - WoS: 13Citation - Scopus: 18Effect of Physicochemical Parameters on the Polygalacturonase of an Aspergillus Sojae Mutant Using Wheat Bran, an Agro-Industrial Waste, Via Solid-State Fermentation(John Wiley and Sons Inc., 2016) Demir, Hande; Tarı, CananBACKGROUND: Polygalacturonases (PGs) are valuable enzymes of the food industry; therefore it is of great importance to discover new and GRAS PG-producing microbial strains. In this study, PG enzyme produced from a high PG activity producer mutant Aspergillus sojae using wheat bran at the flask scale under pre-optimized conditions of solid-state fermentation (SSF) was biochemically characterized. RESULTS: The crude PG enzyme showed optimum activity in the pH range 4.0–5.0 and was stable in the pH range 3.0–7.0. The optimum temperature for the PG was 40 °C and it retained 99% of its activity at 50 °C. The mutant A. sojae PG could preserve more than 50% of its stability between 25 and 50 °C, both for 30 and 60 min, and was found to be stable in the presence of most of the tested compounds and metal ions. The inactivation energy (Ed) was determined as 125.3 kJ mol−1. The enthalpy (ΔH*), free energy (ΔG*) and entropy (ΔS*) of inactivation were found to be stable with increasing temperature. CONCLUSION: The mutant A. sojae PG could be suitable for the clarification (depectinization) of orange and grape juices and wine. © 2015 Society of Chemical Industry.