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Erdem Ö, Eş I, Akceoglu GA, Saylan Y, Inci F. Recent Advances in Microneedle-Based Sensors for Sampling, Diagnosis and Monitoring of Chronic Diseases. BIOSENSORS 2021; 11:296. [PMID: 34562886 PMCID: PMC8470661 DOI: 10.3390/bios11090296] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 08/20/2021] [Indexed: 12/14/2022]
Abstract
Chronic diseases (CDs) are noncommunicable illnesses with long-term symptoms accounting for ~70% of all deaths worldwide. For the diagnosis and prognosis of CDs, accurate biomarker detection is essential. Currently, the detection of CD-associated biomarkers is employed through complex platforms with certain limitations in their applicability and performance. There is hence unmet need to present innovative strategies that are applicable to the point-of-care (PoC) settings, and also, provide the precise detection of biomarkers. On the other hand, especially at PoC settings, microneedle (MN) technology, which comprises micron-size needles arranged on a miniature patch, has risen as a revolutionary approach in biosensing strategies, opening novel horizons to improve the existing PoC devices. Various MN-based platforms have been manufactured for distinctive purposes employing several techniques and materials. The development of MN-based biosensors for real-time monitoring of CD-associated biomarkers has garnered huge attention in recent years. Herein, we summarize basic concepts of MNs, including microfabrication techniques, design parameters, and their mechanism of action as a biosensing platform for CD diagnosis. Moreover, recent advances in the use of MNs for CD diagnosis are introduced and finally relevant clinical trials carried out using MNs as biosensing devices are highlighted. This review aims to address the potential use of MNs in CD diagnosis.
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Can ND, Basturk E, Kizilboga T, Akcay IM, Dingiloglu B, Tatli O, Acar S, Ozfiliz Kilbas P, Elbeyli E, Muratcioglu S, Jannuzzi AT, Gursoy A, Keskin O, Doganay HL, Karademir Yilmaz B, Dinler Doganay G. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation. PLoS One 2021; 16:e0256640. [PMID: 34428256 PMCID: PMC8384158 DOI: 10.1371/journal.pone.0256640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/11/2021] [Indexed: 11/24/2022] Open
Abstract
Bag-1 is a multifunctional protein that regulates Hsp70 chaperone activity, apoptosis, and proliferation. The three major Bag-1 isoforms have different subcellular localizations and partly non-overlapping functions. To identify the detailed interaction network of each isoform, we utilized mass spectrometry-based proteomics and found that interactomes of Bag-1 isoforms contained many common proteins, with variations in their abundances. Bag-1 interactomes were enriched with proteins involved in protein processing and degradation pathways. Novel interaction partners included VCP/p97; a transitional ER ATPase, Rad23B; a shuttling factor for ubiquitinated proteins, proteasome components, and ER-resident proteins, suggesting a role for Bag-1 also in ER-associated protein degradation (ERAD). Bag-1 pull-down from cells and tissues from breast cancer patients validated these interactions and showed cancer-related prominence. Using in silico predictions we detected hotspot residues of Bag-1. Mutations of these residues caused loss of binding to protein quality control elements and impaired proteasomal activity in MCF-7 cells. Following CD147 glycosylation pattern, we showed that Bag-1 downregulated VCP/p97-dependent ERAD. Overall, our data extends the interaction map of Bag-1, and broadens its role in protein homeostasis. Targeting the interaction surfaces revealed in this study might be an effective strategy in the treatment of cancer.
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Hamawandi B, Batili H, Paul M, Ballikaya S, Kilic NI, Szukiewicz R, Kuchowicz M, Johnsson M, Toprak MS. Minute-Made, High-Efficiency Nanostructured Bi 2Te 3 via High-Throughput Green Solution Chemical Synthesis. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2053. [PMID: 34443884 PMCID: PMC8400796 DOI: 10.3390/nano11082053] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022]
Abstract
Scalable synthetic strategies for high-quality and reproducible thermoelectric (TE) materials is an essential step for advancing the TE technology. We present here very rapid and effective methods for the synthesis of nanostructured bismuth telluride materials with promising TE performance. The methodology is based on an effective volume heating using microwaves, leading to highly crystalline nanostructured powders, in a reaction duration of two minutes. As the solvents, we demonstrate that water with a high dielectric constant is as good a solvent as ethylene glycol (EG) for the synthetic process, providing a greener reaction media. Crystal structure, crystallinity, morphology, microstructure and surface chemistry of these materials were evaluated using XRD, SEM/TEM, XPS and zeta potential characterization techniques. Nanostructured particles with hexagonal platelet morphology were observed in both systems. Surfaces show various degrees of oxidation, and signatures of the precursors used. Thermoelectric transport properties were evaluated using electrical conductivity, Seebeck coefficient and thermal conductivity measurements to estimate the TE figure-of-merit, ZT. Low thermal conductivity values were obtained, mainly due to the increased density of boundaries via materials nanostructuring. The estimated ZT values of 0.8-0.9 was reached in the 300-375 K temperature range for the hydrothermally synthesized sample, while 0.9-1 was reached in the 425-525 K temperature range for the polyol (EG) sample. Considering the energy and time efficiency of the synthetic processes developed in this work, these are rather promising ZT values paving the way for a wider impact of these strategic materials with a minimum environmental impact.
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Turkoglu G, Koygun GK, Zafer Yurt MN, Pirencioglu SN, Erbas-Cakmak S. A therapeutic keypad lock decoded in drug resistant cancer cells. Chem Sci 2021; 12:9754-9758. [PMID: 34349948 PMCID: PMC8293978 DOI: 10.1039/d1sc02521j] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 06/17/2021] [Indexed: 12/23/2022] Open
Abstract
A molecular keypad lock that displays photodynamic activity when exposed to glutathione (GSH), esterase and light in the given order, is fabricated and its efficacy in drug resistant MCF7 cancer cells is investigated. The first two inputs are common drug resistant tumor markers. GSH reacts with the agent and shifts the absorption wavelength. Esterase separates the quencher from the structure, further activating the agent. After these sequential exposures, the molecular keypad lock is exposed to light and produces cytotoxic singlet oxygen. Among many possible combinations, only one 'key' can activate the agent, and initiate a photodynamic response. Paclitaxel resistant MCF7 cells are selectively killed. This work presents the first ever biological application of small molecular keypad locks.
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Torul H, Yarali E, Eksin E, Ganguly A, Benson J, Tamer U, Papakonstantinou P, Erdem A. Paper-Based Electrochemical Biosensors for Voltammetric Detection of miRNA Biomarkers Using Reduced Graphene Oxide or MoS 2 Nanosheets Decorated with Gold Nanoparticle Electrodes. BIOSENSORS 2021; 11:236. [PMID: 34356708 PMCID: PMC8301884 DOI: 10.3390/bios11070236] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 07/04/2021] [Accepted: 07/05/2021] [Indexed: 12/13/2022]
Abstract
Paper-based biosensors are considered simple and cost-efficient sensing platforms for analytical tests and diagnostics. Here, a paper-based electrochemical biosensor was developed for the rapid and sensitive detection of microRNAs (miRNA-155 and miRNA-21) related to early diagnosis of lung cancer. Hydrophobic barriers to creating electrode areas were manufactured by wax printing, whereas a three-electrode system was fabricated by a simple stencil approach. A carbon-based working electrode was modified using either reduced graphene oxide or molybdenum disulfide nanosheets modified with gold nanoparticle (AuNPs/RGO, AuNPs/MoS2) hybrid structures. The resulting paper-based biosensors offered sensitive detection of miRNA-155 and miRNA-21 by differential pulse voltammetry (DPV) in only 5.0 µL sample. The duration in our assay from the point of electrode modification to the final detection of miRNA was completed within only 35 min. The detection limits for miRNA-21 and miRNA-155 were found to be 12.0 and 25.7 nM for AuNPs/RGO and 51.6 and 59.6 nM for AuNPs/MoS2 sensors in the case of perfectly matched probe-target hybrids. These biosensors were found to be selective enough to distinguish the target miRNA in the presence of single-base mismatch miRNA or noncomplementary miRNA sequences.
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Giovanis E, Akdede SH, Ozdamar O. Impact of the EU Blue Card programme on cultural participation and subjective well-being of migrants in Germany. PLoS One 2021; 16:e0253952. [PMID: 34252092 PMCID: PMC8274866 DOI: 10.1371/journal.pone.0253952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/16/2021] [Indexed: 12/05/2022] Open
Abstract
The first aim of this study is to investigate the role of the EU Blue Card programme implemented in 2012 in Germany. In particular, we aim to explore the impact on the participation in cultural activities of first-generation non-European Union (EU) and non-European Economic Area (EEA) migrants, such as attendance to cinema, concerts and theatre. The second aim is to examine the impact of cultural activities on subjective well-being (SWB), measured by life satisfaction. We compare the cultural participation and life satisfaction between the treatment group that is the non-EU/EEA first-generation immigrants and the control group that consists, not only of natives and second-generation immigrants but also composes of EU/EEA first-generation immigrants who are not eligible to the programme. We will apply a sharp and a fuzzy regression discontinuity design (RDD) within a seemingly unrelated regression equations (SURE) system using the Ordered Probit method. The empirical analysis relies on data from the German Socio-Economic Panel (GSOEP) survey over the period 2015–2018. The results show that the treated subjects experience an increase in cultural participation activities and an improvement in their SWB, as a result of the EU Blue Card programme, compared to the control group. Participation in classical music performance, opera or theatre influences more the SWB compared to other cultural activities. Policies that promote labour market integration and participation in cultural activities will enable immigrants to integrate into the social norms of the host societies and improve their SWB.
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Uluisik S. Chemical and structural quality traits during postharvest ripening regulated by chromosome segments from a wild relative of tomato Solanum pennellii IL4-2 and IL5-1. J Food Biochem 2021; 45:e13858. [PMID: 34251032 DOI: 10.1111/jfbc.13858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/11/2021] [Accepted: 06/27/2021] [Indexed: 11/29/2022]
Abstract
Tomato is usually harvested at an early ripening stage with high firmness suitable for storage and transportation but lacks many quality parameters such as sugars, organic acids, and phenolics. In a recent study, we have selected introgression lines (ILs) IL4-2 and IL5-1, developed from a cross between the Solanum pennellii and the Solanum lycopersicum M82, that exhibit differentiated postharvest shelf-life characteristics in the fruit compared to M82 and the rest of the ILs. Here, we first structurally and biochemically characterized IL4-2, IL5-1, and their parent M82 to decipher the cell wall mechanistic difference between soft (IL4-2) and firm (IL5-1) lines at two postharvest ripening periods. Generally, IL4-2 had more active cell wall modifications in terms of ripening-related gene expression, water-soluble pectin, and cell wall structure under the microscope, which probably makes this line softer than IL5-1. We also evaluated these lines based on commercial quality parameters, sugars, phenolics, organic, and amino acids to gain insight into their commercial and functional quality and reveal noticeable differences. In summary, the contribution of the S. pennellii IL5-1 and IL4-2 to the shelf life of the tomato was structurally characterized, and the component differences meeting the quality criteria were revealed.
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Kayabolen A, Yilmaz E, Bagci-Onder T. IDH Mutations in Glioma: Double-Edged Sword in Clinical Applications? Biomedicines 2021; 9:799. [PMID: 34356864 PMCID: PMC8301439 DOI: 10.3390/biomedicines9070799] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 01/03/2023] Open
Abstract
Discovery of point mutations in the genes encoding isocitrate dehydrogenases (IDH) in gliomas about a decade ago has challenged our view of the role of metabolism in tumor progression and provided a new stratification strategy for malignant gliomas. IDH enzymes catalyze the conversion of isocitrate to alpha-ketoglutarate (α-KG), an intermediate in the citric acid cycle. Specific mutations in the genes encoding IDHs cause neomorphic enzymatic activity that produces D-2-hydroxyglutarate (2-HG) and result in the inhibition of α-KG-dependent enzymes such as histone and DNA demethylases. Thus, chromatin structure and gene expression profiles in IDH-mutant gliomas appear to be different from those in IDH-wildtype gliomas. IDH mutations are highly common in lower grade gliomas (LGG) and secondary glioblastomas, and they are among the earliest genetic events driving tumorigenesis. Therefore, inhibition of mutant IDH enzymes in LGGs is widely accepted as an attractive therapeutic strategy. On the other hand, the metabolic consequences derived from IDH mutations lead to selective vulnerabilities within tumor cells, making them more sensitive to several therapeutic interventions. Therefore, instead of shutting down mutant IDH enzymes, exploiting the selective vulnerabilities caused by them might be another attractive and promising strategy. Here, we review therapeutic options and summarize current preclinical and clinical studies on IDH-mutant gliomas.
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Kursunel MA, Taskiran EZ, Tavukcuoglu E, Yanik H, Demirag F, Karaosmanoglu B, Ozbay FG, Uner A, Esendagli D, Kizilgoz D, Yilmaz U, Esendagli G. Small cell lung cancer stem cells display mesenchymal properties and exploit immune checkpoint pathways in activated cytotoxic T lymphocytes. Cancer Immunol Immunother 2021; 71:445-459. [PMID: 34228218 PMCID: PMC8783896 DOI: 10.1007/s00262-021-02998-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 06/19/2021] [Indexed: 02/07/2023]
Abstract
Small cell lung cancer (SCLC) is an aggressive tumor type with early dissemination and distant metastasis capacity. Even though optimal chemotherapy responses are observed initially in many patients, therapy resistance is almost inevitable. Accordingly, SCLC has been regarded as an archetype for cancer stem cell (CSC) dynamics. To determine the immune-modulatory influence of CSC in SCLC, this study focused on the characterization of CD44+CD90+ CSC-like subpopulations in SCLC. These cells displayed mesenchymal properties, differentiated into different lineages and further contributed to CD8+ cytotoxic T lymphocytes (CTL) responses. The interaction between CD44+CD90+ CSC-like cells and T cells led to the upregulation of checkpoint molecules PD-1, CTLA-4, TIM-3, and LAG3. In the patient-derived lymph nodes, CD44+ SCLC metastases were also observed with T cells expressing PD-1, TIM-3, or LAG3. Proliferation and IFN-γ expression capacity of TIM-3 and LAG3 co-expressing CTLs are adversely affected over long-time co-culture with CD44+CD90+ CSC-like cells. Moreover, especially through IFN-γ secreted by the T cells, the CSC-like SCLC cells highly expressed PD-L1 and PD-L2. Upon a second encounter with immune-experienced, IFN-γ-stimulated CSC-like SCLC cells, both cytotoxic and proliferation capacities of T cells were hampered. In conclusion, our data provide evidence for the superior potential of the SCLC cells with stem-like and mesenchymal properties to gain immune regulatory capacities and cope with cytotoxic T cell responses. With their high metastatic and immune-modulatory assets, the CSC subpopulation in SCLC may serve as a preferential target for checkpoint blockade immunotherapy
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Erdoğan S, Haktanır G, Kuru N, Parpucu N, Tüylü DK. The effect of the e-mentoring-based education program on professional development of preschool teachers. EDUCATION AND INFORMATION TECHNOLOGIES 2021; 27:1023-1053. [PMID: 34248385 PMCID: PMC8254052 DOI: 10.1007/s10639-021-10623-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
The qualification of a preschool teacher is one of the important factors that determine the quality of preschool education. To increase the quality in education, teachers should be equipped with the necessary knowledge starting from pre-service training, and in-service training should support the upgrading of their knowledge. Thus, the aim of this study was to develop an e-Mentoring-Based Education Program (e-MENTE:PT) for preschool teachers and to test its effectiveness on their professional development during the in-service support period. The study used a design-based research approach. First, focus group interviews were conducted with one-hundred-and-five preschool teachers to find out their needs. Then, an e-MENTE:PT Program was developed based on these needs and devised to be used on the Canvas learning management system (LMS), which involves all opportunities of e-learning and allows one-to-one e-mentoring. The e-MENTE:PT Program involved twelve modules related to the pedagogical content knowledge of the preschool education program. Each module included contents, goals, module materials, e-books, videos, pre- and post-module evaluation questions, discussion questions, live lessons and e-portfolios, all of which were integrated in the LMS. Next, eighteen full-time and nine substitute voluntary teachers from five different provinces were selected as mentees by means of criterion sampling. Nine academicians working in these provinces acted as mentors and implemented the application, each working with two mentees for two months. Qualitative data were analysed by means of descriptive analysis and quantitative data were analysed by means of the Wilcoxon signed rank test. The research concluded that the e-MENTE:PT program supported preschool teachers' professional knowledge, learning environments and classroom applications, and an e-mentoring based teaching management system was effective on professional development.
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86
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Nadeem MA, Habyarimana E, Karaköy T, Baloch FS. Genetic dissection of days to flowering via genome-wide association studies in Turkish common bean germplasm. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1609-1622. [PMID: 34366600 PMCID: PMC8295450 DOI: 10.1007/s12298-021-01029-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Common bean is a nutrient-dense legume crop serving as a source of food for millions of people. Characterization of unexplored common bean germplasm to unlock the phenotypic and genetic variations is still needed to explore the breeding potential of this crop. The current study aimed to dissect the genetic basis having association for days to flowering (DF). A total of 188 common bean accessions collected from 19 provinces of Turkey were used as plant material under five environments and two locations. Analysis of variance (ANOVA) revealed that genotypes and genotype by environment interaction have significant effects on DF. A total of 10 most stable accessions were evaluated from stability analysis. Overall maximum (75) and minimum (54) DF were observed for Hakkari-51 and Mus-46 accessions, respectively. The implemented constellation plot divided studied germplasm according to their DF and growth habit. A total of 7900 DArTseq markers were used for association analysis. Mixed linear model using the Q + K Model resulted a total of 18 DArTseq markers from five environments. DArT-8668385 marker identified in Bolu during 2016 was also associated with DF in Sivas during 2017. Combined data of five years resulted a total of four markers (DArT-22346534, DArT-3369768, DArT-3374613, and DArT-3370801) having significant association ( p < 0.01 ) for DF. DArT-22346534 present on Pv 08 accounted a maximum of 9.89% variation to the studied trait. A total of four putative candidate genes were predicted from sequences reflecting homology to identified four DArTseq markers. We envisage that exploitation of identified DArTseq markers will hopefully beneficial for the development of new common bean varieties having better adaptation ability to changing climatic conditions. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01029-8.
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87
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Tunçer E, Sandalci T, Pusat S, Balcı Ö, Karagöz Y. Cycle-skipping strategy with intake air cut off for natural gas fueled Si engine. Sci Prog 2021; 104:368504211031074. [PMID: 34281435 PMCID: PMC10358453 DOI: 10.1177/00368504211031074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this study, cycle-skipping was investigated for a natural gas engine which has single cylinder, unsupercharged with 1.16 L volume and spark ignition. Additionally, inlet manifold air was switched off during cycle-skipping to minimize pumping losses. Thus, cycle-skipping strategy was carried out, and its effects on emission and engine performance were investigated. Indicated mean effective pressure, indicated efficiency, specific emissions (CO, HC, and NOX) and combustion characteristics (in-cylinder pressure and rate of heat release) were investigated in the study. As a result of performed study, it is predicted that a significant improvement can be achieved in indicated thermal efficiency as 22.8% and 13.4% by different cycle-skipping strategies. However, there is not a continuous change in emissions for different cycle-skipping strategies. While CO and NOX emissions increased in 3N1S (three normal, one cycle-skip) condition, HC emissions decreased in accordance with normal condition. For both cycle-skipping strategies, all the emissions have an increase in accordance with normal condition. In 3N1S and 2N1S (two normal, one cycle-skip) cycle skip engine operating conditions, compared to engine operating under normal condition, CO emissions increased by 14.7 and 51.7 times, respectively. In terms of HC emissions, while emission values decreased by 27.8% under 3N1S operating conditions, they increased by 67.2% under 2N1S operating conditions. Finally, in 3N1S and 2N1S cycle skip engine operating conditions, NOx emissions increased by 3.7 and 6.9 times, respectively, compared to normal operating condition. Another significant result of this study is that peak in-cylinder pressure increased as the cycle-skipping rate increased.
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Sheraz A, Mehmood N, Çiçek MM, Ergün İ, Rasouli HR, Durgun E, Kasırga TS. High elasticity and strength of ultra-thin metallic transition metal dichalcogenides. NANOSCALE ADVANCES 2021; 3:3894-3899. [PMID: 36133020 PMCID: PMC9419869 DOI: 10.1039/d1na00225b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/24/2021] [Indexed: 06/16/2023]
Abstract
Mechanical properties of transition metal dichalcogenides (TMDCs) are relevant to their prospective applications in flexible electronics. So far, the focus has been on the semiconducting TMDCs, mostly MoX2 and WX2 (X = S, Se) due to their potential in optoelectronics. A comprehensive understanding of the elastic properties of metallic TMDCs is needed to complement the semiconducting TMDCs in flexible optoelectronics. Thus, mechanical testing of metallic TMDCs is pertinent to the realization of the applications. Here, we report on the atomic force microscopy-based nano-indentation measurements on ultra-thin 2H-TaS2 crystals to elucidate the stretching and breaking of the metallic TMDCs. We explored the elastic properties of 2H-TaS2 at different thicknesses ranging from 3.5 nm to 12.6 nm and find that the Young's modulus is independent of the thickness at a value of 85.9 ± 10.6 GPa, which is lower than the semiconducting TMDCs reported so far. We determined the breaking strength as 5.07 ± 0.10 GPa which is 6% of the Young's modulus. This value is comparable to that of other TMDCs. We used ab initio calculations to provide an insight into the high elasticity measured in 2H-TaS2. We also performed measurements on a small number of 1T-TaTe2, 3R-NbS2 and 1T-NbTe2 samples and extended our ab initio calculations to these materials to gain a deeper understanding on the elastic and breaking properties of metallic TMDCs. This work illustrates that the studied metallic TMDCs are suitable candidates to be used as additives in composites as functional and structural elements and for flexible conductive electronic devices.
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Temiz E, Koyuncu I, Durgun M, Caglayan M, Gonel A, Güler EM, Kocyigit A, Supuran CT. Inhibition of Carbonic Anhydrase IX Promotes Apoptosis through Intracellular pH Level Alterations in Cervical Cancer Cells. Int J Mol Sci 2021; 22:6098. [PMID: 34198834 PMCID: PMC8201173 DOI: 10.3390/ijms22116098] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/29/2021] [Accepted: 06/03/2021] [Indexed: 02/07/2023] Open
Abstract
Carbonic anhydrase IX (CAIX) is a hypoxia-related protein that plays a role in proliferation in solid tumours. However, how CAIX increases proliferation and metastasis in solid tumours is unclear. The objective of this study was to investigate how a synthetic CAIX inhibitor triggers apoptosis in the HeLa cell line. The intracellular effects of CAIX inhibition were determined with AO/EB, AnnexinV-PI, and γ-H2AX staining; measurements of intracellular pH (pHi), reactive oxygen species (ROS), and mitochondrial membrane potential (MMP); and analyses of cell cycle, apoptotic, and autophagic modulator gene expression (Bax, Bcl-2, caspase-3, caspase-8, caspase-9, caspase-12, Beclin, and LC3), caspase protein level (pro-caspase 3 and cleaved caspase-3, -8, -9), cleaved PARP activation, and CAIX protein level. Sulphonamide CAIX inhibitor E showed the lowest IC50 and the highest selectivity index in CAIX-positive HeLa cells. CAIX inhibition changed the morphology of HeLa cells and increased the ratio of apoptotic cells, dramatically disturbing the homeostasis of intracellular pHi, MMP and ROS levels. All these phenomena consequent to CA IX inhibition triggered apoptosis and autophagy in HeLa cells. Taken together, these results further endorse the previous findings that CAIX inhibitors represent an important therapeutic strategy, which is worth pursuing in different cancer types, considering that presently only one sulphonamide inhibitor, SLC-0111, has arrived in Phase Ib/II clinical trials as an antitumour/antimetastatic drug.
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90
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Özkan M, Eskiocak YC, Wingender G. Macrophage and dendritic cell subset composition can distinguish endotypes in adjuvant-induced asthma mouse models. PLoS One 2021; 16:e0250533. [PMID: 34061861 PMCID: PMC8168852 DOI: 10.1371/journal.pone.0250533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022] Open
Abstract
Asthma is a heterogeneous disease with neutrophilic and eosinophilic asthma as the main endotypes that are distinguished according to the cells recruited to the airways and the related pathology. Eosinophilic asthma is the treatment-responsive endotype, which is mainly associated with allergic asthma. Neutrophilic asthma is a treatment-resistant endotype, affecting 5-10% of asthmatics. Although eosinophilic asthma is well-studied, a clear understanding of the endotypes is essential to devise effective diagnosis and treatment approaches for neutrophilic asthma. To this end, we directly compared adjuvant-induced mouse models of neutrophilic (CFA/OVA) and eosinophilic (Alum/OVA) asthma side-by-side. The immune response in the inflamed lung was analyzed by multi-parametric flow cytometry and immunofluorescence. We found that eosinophilic asthma was characterized by a preferential recruitment of interstitial macrophages and myeloid dendritic cells, whereas in neutrophilic asthma plasmacytoid dendritic cells, exudate macrophages, and GL7+ activated B cells predominated. This differential distribution of macrophage and dendritic cell subsets reveals important aspects of the pathophysiology of asthma and holds the promise to be used as biomarkers to diagnose asthma endotypes.
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Unal MA, Bayrakdar F, Nazir H, Besbinar O, Gurcan C, Lozano N, Arellano LM, Yalcin S, Panatli O, Celik D, Alkaya D, Agan A, Fusco L, Suzuk Yildiz S, Delogu LG, Akcali KC, Kostarelos K, Yilmazer A. Graphene Oxide Nanosheets Interact and Interfere with SARS-CoV-2 Surface Proteins and Cell Receptors to Inhibit Infectivity. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2101483. [PMID: 33988903 PMCID: PMC8236978 DOI: 10.1002/smll.202101483] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Indexed: 05/19/2023]
Abstract
Nanotechnology can offer a number of options against coronavirus disease 2019 (COVID-19) acting both extracellularly and intracellularly to the host cells. Here, the aim is to explore graphene oxide (GO), the most studied 2D nanomaterial in biomedical applications, as a nanoscale platform for interaction with SARS-CoV-2. Molecular docking analyses of GO sheets on interaction with three different structures: SARS-CoV-2 viral spike (open state - 6VYB or closed state - 6VXX), ACE2 (1R42), and the ACE2-bound spike complex (6M0J) are performed. GO shows high affinity for the surface of all three structures (6M0J, 6VYB and 6VXX). When binding affinities and involved bonding types are compared, GO interacts more strongly with the spike or ACE2, compared to 6M0J. Infection experiments using infectious viral particles from four different clades as classified by Global Initiative on Sharing all Influenza Data (GISAID), are performed for validation purposes. Thin, biological-grade GO nanoscale (few hundred nanometers in lateral dimension) sheets are able to significantly reduce copies for three different viral clades. This data has demonstrated that GO sheets have the capacity to interact with SARS-CoV-2 surface components and disrupt infectivity even in the presence of any mutations on the viral spike. GO nanosheets are proposed to be further explored as a nanoscale platform for development of antiviral strategies against COVID-19.
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92
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Zanin M, Ivanoska I, Güntekin B, Yener G, Loncar-Turukalo T, Jakovljevic N, Sveljo O, Papo D. A Fast Transform for Brain Connectivity Difference Evaluation. Neuroinformatics 2021; 20:285-299. [PMID: 33843024 PMCID: PMC9546979 DOI: 10.1007/s12021-021-09518-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 12/30/2022]
Abstract
Anatomical and dynamical connectivity are essential to healthy brain function. However, quantifying variations in connectivity across conditions or between patient populations and appraising their functional significance are highly non-trivial tasks. Here we show that link ranking differences induce specific geometries in a convenient auxiliary space that are often easily recognisable at mere eye inspection. Link ranking can also provide fast and reliable criteria for network reconstruction parameters for which no theoretical guideline has been proposed.
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93
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Balci FM, Sarisozen S, Polat N, Guvenc CM, Karadeniz U, Tertemiz A, Balci S. Laser assisted synthesis of anisotropic metal nanocrystals and strong light-matter coupling in decahedral bimetallic nanocrystals. NANOSCALE ADVANCES 2021; 3:1674-1681. [PMID: 36132566 PMCID: PMC9418786 DOI: 10.1039/d0na00829j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 01/19/2021] [Indexed: 06/15/2023]
Abstract
The advances in colloid chemistry and nanofabrication allowed us to synthesize noble monometallic and bimetallic nanocrystals with tunable optical properties in the visible and near infrared region of the electromagnetic spectrum. In the strong coupling regime, surface plasmon polaritons (SPPs) of metal nanoparticles interact with excitons of quantum dots or organic dyes and plasmon-exciton hybrid states called plexcitons are formed. Until now, various shaped metal nanoparticles such as nanorods, core-shell nanoparticles, hollow nanoparticles, nanoprisms, nanodisks, nanorings, and nanobipyramids have been synthesized to generate plasmon-exciton mixed states. However, in order to boost plasmon-exciton interaction at nanoscale dimensions and expand the application of plexcitonic nanocrystals in a variety of fields such as solar cells, light emitting diodes, and nanolasers, new plexcitonic nanocrystals with outstanding optical and chemical properties remain a key goal and challenge. Here we report laser-assisted synthesis of decahedral shaped noble metal nanocrystals, tuning optical properties of the decahedral shaped nanocrystals by galvanic replacement reactions, colloidal synthesis of bimetallic decahedral shaped plexcitonic nanocrystals, and strong plasmon-plasmon interaction in bimetallic decahedral shaped noble metal nanocrystals near a metal film. We photochemically synthesize decahedral Ag nanoparticles from spherical silver nanoparticles by using a 488 nm laser. The laser assisted synthesis of silver nanoparticles yields decahedral (bicolored) and prism (monocolored) shaped silver nanocrystals. The decahedral shaped nanoparticles were selectively separated from prism shaped nanoparticles by centrifugation. The optical properties of decahedral nanocrystals were tuned by the galvanic replacement reaction between gold ions and silver atoms. Excitons of J-aggregate dyes and SPPs of decahedral bimetallic nanoparticles strongly couple and hence decahedral shaped plexcitonic nanoparticles are prepared. In addition, localized SPPs of decahedral shaped bimetallic nanocrystals interact strongly with the propagating SPPs of a flat silver film and hence new hybrid plasmonic modes (plasmonic nanocavities) are generated. The experimental results are further fully corroborated by theoretical calculations including decahedral shaped plexcitonic nanoparticles and decahedral nanoparticles coupled to flat metal films.
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94
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Senol SP, Temiz-Resitoglu M, Guden DS, Sari AN, Sahan-Firat S, Tunctan B. Suppression of TLR4/MyD88/TAK1/NF-κB/COX-2 Signaling Pathway in the Central Nervous System by Bexarotene, a Selective RXR Agonist, Prevents Hyperalgesia in the Lipopolysaccharide-Induced Pain Mouse Model. Neurochem Res 2021; 46:624-637. [PMID: 33389386 DOI: 10.1007/s11064-020-03197-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/03/2020] [Accepted: 12/07/2020] [Indexed: 12/26/2022]
Abstract
A selective RXR agonist, bexarotene, has been shown to have anti-inflammatory, anti-nociceptive, and neuroprotective effects in several models of numerous neurological diseases characterized by systemic inflammation. The mechanisms underlying these effects remains unknown. To elucidate these mechanisms, we investigated whether the TLR4/MyD88/TAK1/NF-κB/COX-2 signaling pathway in the CNS mediates the effect of bexarotene to prevent hyperalgesia in the LPS-induced inflammatory pain mouse model. The reaction time to thermal stimuli within 30 s was evaluated by the hot plate test in male mice treated with saline, LPS (10 mg/kg), DMSO, and/or bexarotene (0.1, 1, 3, or 10 mg/kg) after 6 h. The latency to the thermal stimulus (18.11 ± 1.36 s) in the LPS-treated mice was significantly decreased by 30% compared with saline-treated mice (25.84 ± 1.99 s). Treatment with bexarotene only at a dose of 10 mg/kg showed a significant increase in the latency by 22.49 ± 1.00 s compared with LPS-treated mice. Bexarotene also prevented the reduction in RXRα protein expression associated with a rise in the expression of TLR4, MyD88, phosphorylated TAK1, NF-κB p65, phosphorylated NF-κB p65, COX-2, and IL-1β proteins, in addition to COX-2 activity and levels of PGE2 and IL-1β in the brains and spinal cords of the LPS-treated animals. Likely, decreased activity of TLR4/MyD88/TAK1/NF-κB/COX-2 signaling pathway in addition to increased pro-inflammatory cytokine formation in the CNS of mice participates in the protective effect of bexarotene against hyperalgesia induced by LPS.
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95
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Altay BN, Turkani VS, Pekarovicova A, Fleming PD, Atashbar MZ, Bolduc M, Cloutier SG. One-step photonic curing of screen-printed conductive Ni flake electrodes for use in flexible electronics. Sci Rep 2021; 11:3393. [PMID: 33564062 PMCID: PMC7873258 DOI: 10.1038/s41598-021-82961-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 01/27/2021] [Indexed: 11/08/2022] Open
Abstract
Photonic curing has shown great promise in maintaining the integrity of flexible thin polymer substrates without structural degradation due to shrinkage, charring or decomposition during the sintering of printed functional ink films in milliseconds at high temperatures. In this paper, single-step photonic curing of screen-printed nickel (Ni) electrodes is reported for sensor, interconnector and printed electronics applications. Solid bleached sulphate paperboard (SBS) and polyethylene terephthalate polymer (PET) substrates are employed to investigate the electrical performance, ink transfer and ink spreading that directly affect the fabrication of homogeneous ink films. Ni flake ink is selected, particularly since its effects on sintering and rheology have not yet been examined. The viscosity of Ni flake ink yields shear-thinning behavior that is distinct from that of screen printing. The porous SBS substrate is allowed approximately 20% less ink usage. With one-step photonic curing, the electrodes on SBS and PET exhibited electrical performances of a minimum of 4 Ω/sq and 16 Ω/sq, respectively, at a pulse length of 1.6 ms, which is comparable to conventional thermal heating at 130 °C for 5 min. The results emphasize the suitability of Ni flake ink to fabricate electronic devices on flexible substrates by photonic curing.
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96
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Çulha Erdal Ş, Eyidoğan F, Ekmekçi Y. Comparative physiological and proteomic analysis of cultivated and wild safflower response to drought stress and re-watering. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:281-295. [PMID: 33707869 PMCID: PMC7907392 DOI: 10.1007/s12298-021-00934-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 12/01/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Drought is one of the major environmental stress that adversely affect the growth and development of oil seed plant, safflower. There is a limited knowledge on proteomic responses to support physiological, biochemical changes in how safflowers can regulate growth and metabolism under drought conditions and followed by re-watering. The changes in morphological, physiological, biochemical and proteomics of safflower genotypes (Carthamus tinctorius L.; Remzibey-05 and Linas, tolerant and sensitive cultivars, respectively, and C. oxyacantha M. Bieb., wild type) after exposure to drought and followed by re-watering have been examined. Drought negatively affected the shoot weight, water content, chlorophyll fluorescence, and biochemical parameters, including photosynthetic pigment, proline, MDA, and H2O2 contents and antioxidant enzyme activities in all genotypes, while the re-watering period allowed Remzibey-05 to recover, and it even provided the wild type completely recovered (approximately 100%). A total of 72 protein spots were observed as differently accumulated under treatments. The identified proteins were mainly involved in photosynthesis and carbohydrate, protein, defense, and energy metabolisms. Protein accumulation related to these metabolisms in Remzibey-05 were decreased under drought, while increased following re-watering. However, sensitive cultivar, Linas, could not exhibit an effective performance under drought and recovery when compared with other safflower genotypes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s12298-021-00934-2).
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97
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Bostanabad SY, Noyan S, Dedeoglu BG, Gurdal H. Overexpression of β-Arrestins inhibits proliferation and motility in triple negative breast cancer cells. Sci Rep 2021; 11:1539. [PMID: 33452359 PMCID: PMC7810837 DOI: 10.1038/s41598-021-80974-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 12/31/2020] [Indexed: 01/29/2023] Open
Abstract
β-Arrestins (βArrs) are intracellular signal regulating proteins. Their expression level varies in some cancers and they have a significant impact on cancer cell function. In general, the significance of βArrs in cancer research comes from studies examining GPCR signalling. Given the diversity of different GPCR signals in cancer cell regulation, contradictory results are inevitable regarding the role of βArrs. Our approach examines the direct influence of βArrs on cellular function and gene expression profiles by changing their expression levels in breast cancer cells, MDA-MB-231 and MDA-MB-468. Reducing expression of βArr1 or βArr2 tended to increase cell proliferation and invasion whereas increasing their expression levels inhibited them. The overexpression of βArrs caused cell cycle S-phase arrest and differential expression of cell cycle genes, CDC45, BUB1, CCNB1, CCNB2, CDKN2C and reduced HER3, IGF-1R, and Snail. Regarding to the clinical relevance of our results, low expression levels of βArr1 were inversely correlated with CDC45, BUB1, CCNB1, and CCNB2 genes compared to normal tissue samples while positively correlated with poorer prognosis in breast tumours. These results indicate that βArr1 and βArr2 are significantly involved in cell cycle and anticancer signalling pathways through their influence on cell cycle genes and HER3, IGF-1R, and Snail in TNBC cells.
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98
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Ozcelik A, Aslan Z. A practical microfluidic pump enabled by acoustofluidics and 3D printing. MICROFLUIDICS AND NANOFLUIDICS 2021; 25:5. [PMID: 33424526 PMCID: PMC7780904 DOI: 10.1007/s10404-020-02411-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 12/04/2020] [Indexed: 05/09/2023]
Abstract
Simple and low-cost solutions are becoming extremely important for the evolving necessities of biomedical applications. Even though, on-chip sample processing and analysis has been rapidly developing for a wide range of screening and diagnostic protocols, efficient and reliable fluid manipulation in microfluidic platforms still require further developments to be considered portable and accessible for low-resource settings. In this work, we present an extremely simple microfluidic pumping device based on three-dimensional (3D) printing and acoustofluidics. The fabrication of the device only requires 3D-printed adaptors, rectangular glass capillaries, epoxy and a piezoelectric transducer. The pumping mechanism relies on the flexibility and complexity of the acoustic streaming patterns generated inside the capillary. Characterization of the device yields controllable and continuous flow rates suitable for on-chip sample processing and analysis. Overall, a maximum flow rate of ~ 12 μL/min and the control of pumping direction by frequency tuning is achieved. With its versatility and simplicity, this microfluidic pumping device offers a promising solution for portable, affordable and reliable fluid manipulation for on-chip applications. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10404-020-02411-w.
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Tarim EA, Karakuzu B, Oksuz C, Sarigil O, Kizilkaya M, Al-Ruweidi MKAA, Yalcin HC, Ozcivici E, Tekin HC. Microfluidic-based virus detection methods for respiratory diseases. EMERGENT MATERIALS 2021; 4:143-168. [PMID: 33786415 PMCID: PMC7992628 DOI: 10.1007/s42247-021-00169-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
With the recent SARS-CoV-2 outbreak, the importance of rapid and direct detection of respiratory disease viruses has been well recognized. The detection of these viruses with novel technologies is vital in timely prevention and treatment strategies for epidemics and pandemics. Respiratory viruses can be detected from saliva, swab samples, nasal fluid, and blood, and collected samples can be analyzed by various techniques. Conventional methods for virus detection are based on techniques relying on cell culture, antigen-antibody interactions, and nucleic acids. However, these methods require trained personnel as well as expensive equipment. Microfluidic technologies, on the other hand, are one of the most accurate and specific methods to directly detect respiratory tract viruses. During viral infections, the production of detectable amounts of relevant antibodies takes a few days to weeks, hampering the aim of prevention. Alternatively, nucleic acid-based methods can directly detect the virus-specific RNA or DNA region, even before the immune response. There are numerous methods to detect respiratory viruses, but direct detection techniques have higher specificity and sensitivity than other techniques. This review aims to summarize the methods and technologies developed for microfluidic-based direct detection of viruses that cause respiratory infection using different detection techniques. Microfluidics enables the use of minimal sample volumes and thereby leading to a time, cost, and labor effective operation. Microfluidic-based detection technologies provide affordable, portable, rapid, and sensitive analysis of intact virus or virus genetic material, which is very important in pandemic and epidemic events to control outbreaks with an effective diagnosis.
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100
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Emisoglu-Kulahli H, Gul S, Morgil H, Ozcan O, Aygenli F, Selvi S, Kavakli IH, Ozturk N. Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects. Funct Integr Genomics 2021; 21:1-16. [PMID: 33111200 DOI: 10.1007/s10142-020-00757-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 12/26/2022]
Abstract
We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its contribution to the pathways that are effective in the multistage carcinogenesis process. BMAL1 deletion sensitized nearly normal breast epithelial (MCF10A) and invasive breast cancer cells (MDA-MB-231) to cisplatin- and doxorubicin-induced apoptosis, while this deletion also aggravated the invasive potential of MDA-MB-231 cells. However, the mechanistic relationship of the seemingly opposite contribution of BMAL1 deletion to carcinogenesis process is not known at genome-wide level. In this study, an RNA-seq approach was taken to uncover the differentially expressed genes (DEGs) and pathways after treating BMAL1 knockout (KO) or wild-type (WT) MDA-MB-231 cells with cisplatin and doxorubicin to initiate apoptosis. Gene set enrichment analysis with the DEGs demonstrated that enrichment in multiple genes/pathways contributes to sensitization to cisplatin- or doxorubicin-induced apoptosis in BMAL1-dependent manner. Additionally, our DEG analysis suggested that non-coding transcript RNA (such as lncRNA and processed pseudogenes) may have role in cisplatin- or doxorubicin-induced apoptosis. Protein-protein interaction network obtained from common DEGs in cisplatin and doxorubicin treatments revealed that GSK3β, NACC1, and EGFR are the principal genes regulating the response of the KO cells. Moreover, the analysis of DEGs among untreated BMAL1 KO and WT cells revealed that epithelial-mesenchymal transition genes are up-regulated in KO cells. As a negative control, we have also analyzed the DEGs following treatment with an endoplasmic reticulum (ER) stress-inducing agent, tunicamycin, which was affected by BMAL1 deletion minimally. Collectively, the present study suggests that BMAL1 regulates many genes/pathways of which the alteration in BMAL1 KO cells may shed light on pleotropic phenotype observed.
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