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Öğe Ameliorative effect of vitamin C on diabetes-induced damages in nucleic acids of testicular tissues(2023) Doğan, Ayça; Ergun, Sercan; Bilgin, Mehmet Dinçer; Severcan, Mete; Severcan, FerideBackground: Diabetes mellitus (DM) can be characterized by over-production and under-utilization of carbohydrates and varying degrees of abnormal lipid and protein metabolism. The complications of diabetes mellitus affect various organs and systems in the body including the reproductive system. Vitamin C (ascorbic acid) is an essential micronutrient for maintaining normal metabolic processes and homeostasis within the human body. In the current study, the diabetes-induced alterations on the nucleic acids of rat testicular tissues and the effects of low and high doses of ascorbic acid administration were investigated using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy coupled with an unsupervised technique, namely principal component analysis (PCA). Methods: Male Wistar rats were treated with streptozotocin (STZ) to induce DM. One week after STZ administration, the diabetic rats were treated with a low dose of ascorbic acid (15 mg/kg) and a high dose of ascorbic acid (100 mg/kg) for 6 weeks. The dissected testicular tissues were studied by FTIR spectroscopy. PCA was applied to their spectra. Results: This study revealed diabetes-induced global contextual alterations on nucleic acids, particularly RNAs and DNAs in diabetic samples. Low dose ascorbic acid administration was found to be more effective than higher doses in restoring the effect of diabetes on nucleic acids. The PCA results presented a successful discrimination of the diabetic group from the control and Vitamin C treated groups, and showed especially the ameliorative effect of low dose Vitamin C. Conclusion: Low dose Vitamin C was found to be more effective in combating diabetes-induced alterations in nucleic acids. ATRFTIR spectroscopy combined with multivariate data analyses demonstrated the beneficial effect of Vitamin C administration on nucleic acid content of diabetic testicular tissue based on the spectral differences.Öğe CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics(TÜBİTAK, 2021) Doğan, Ayça; Gurbaov, Rafig; Severcan, Mete; Severcan, FerideFrom the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes in some functional groups belonging to lipids, proteins and nucleic acids. In addition, the non-vaccinated and vaccinated groups were successfully separated from each other by principal component analysis (PCA) and linear discriminant analysis (LDA). This proof-of-concept study will encourage future studies on CoronaVac as well as other vaccines and will lead to make a comparison between different vaccines to establish a better understanding of the vaccination outcomes on serum biomolecules.Öğe Decoding myasthenia gravis: advanced diagnosis with infrared spectroscopy and machine learning(2024) Severcan, Feride; Özyurt, İpek; Doğan, Ayça; Severcan, Mete; Gurbanov, Rafig; Küçükcankurt, Fulya; Elibol, Birsen; Tiftikçioğlu, İrem; Gürsoy, Esra; Yangın, Melike Nur; Zorlu, YaşarMyasthenia Gravis (MG) is a rare neurological disease. Although there are intensive efforts, the underlying mechanism of MG still has not been fully elucidated, and early diagnosis is still a question mark. Diagnostic paraclinical tests are also time-consuming, burden patients financially, and sometimes all test results can be negative. Therefore, rapid, cost-effective novel methods are essential for the early accurate diagnosis of MG. Here, we aimed to determine MG-induced spectral biomarkers from blood serum using infrared spectroscopy. Furthermore, infrared spectroscopy coupled with multivariate analysis methods e.g., principal component analysis (PCA), support vector machine (SVM), discriminant analysis and Neural Network Classifier were used for rapid MG diagnosis. The detailed spectral characterization studies revealed significant increases in lipid peroxidation; saturated lipid, protein, and DNA concentrations; protein phosphorylation; PO2-asym + sym /protein and PO2-sym/lipid ratios; as well as structural changes in protein with a significant decrease in lipid dynamics. All these spectral parameters can be used as biomarkers for MG diagnosis and also in MG therapy. Furthermore, MG was diagnosed with 100% accuracy, sensitivity and specificity values by infrared spectroscopy coupled with multivariate analysis methods. In conclusion, FTIR spectroscopy coupled with machine learning technology is advancing towards clinical translation as a rapid, low-cost, sensitive novel approach for MG diagnosis.Öğe Diagnosis of malignant pleural mesothelioma from pleural fluid by Fourier transform-infrared spectroscopy coupled with chemometrics(Spie-Soc Photo-Optical Instrumentation Engineers, 2018) Abbas, Sherif; Özek, Nihal Şimşek; Emri, Salih; Köksal, Deniz; Severcan, Mete; Severcan, FerideThis study was conducted to differentiate malignant pleural mesothelioma (MPM) from lung cancer (LC) and benign pleural effusion (BPE) from pleural fluids using the diagnostic power of Fourier transform-infrared spectroscopy with attenuated total reflectance mode coupled with chemometrics. Infrared spectra of MPM (n = 24), LC (n = 20), and BPE (n = 25) were collected, and hierarchical cluster analysis (HCA) and principal component analysis (PCA) were applied to their spectra. HCA results indicated that MPM was differentiated from LC with 100% sensitivity and 100% specificity and from BPE, with 100% sensitivity and 88% specificity, which were also confirmed by PCA score plots. PCA loading plots indicated that these separations originated mainly from lipids, proteins, and nucleic acids-related spectral bands. There was significantly higher lipid, protein, nucleic acid, and glucose contents in the MPM and LC. However, the significant changes in triglyceride and cholesterol ester content, protein and nucleic acid structure, a lower membrane fluidity, and higher membrane order were only observed in the MPM. To check the classification success of some test samples/each group, soft independent modeling of class analogies was performed and 96.2% overall classification success was obtained. This approach can provide a rapid and inexpensive methodology for the efficient differentiation of MPM from other pleural effusions. (C) 2018 Society of Photo-Optical Instrumentation Engineers (SPIE)Öğe Diagnosis of malignant pleural mesothelioma from pleural fluid by Fourier transform-infrared spectroscopy coupled with chemometrics (vol 23, 105003, 2018)(Spie-Soc Photo-Optical Instrumentation Engineers, 2018) Abbas, Sherif; Ozek, Nihal Simsek; Emri, Salih; Koksal, Deniz; Severcan, Mete; Severcana, FerideChlorobenzene is a commonly used toxic solvent and listed as a priority environmental pollutant by the US Environmental Protection Agency. Here, we report that Escherichia coli TG1 cells expressing toluene o-xylene monooxygenase (ToMO) can successfully oxidize chlorobenzene to form dihydroxy chloroaromatics, which are valuable industrial compounds. Toluene o-xylene monooxygenase (ToMO) was found to oxidize chlorobenzene to form 2-chlorophenol (2-CP, 4%), 3-CP (12%), and 4-CP (84%) with a total product formation rate of 1.2 +/- 0.17 nmol/min/mg protein. It was also discovered that ToMO forms 4-chlorocatechol (4-CC) from 3-CP and 4-CP with initial rates of 0.54 +/- 0.10 and 0.40 +/- 0.04 nmol/min/mg protein, respectively, and chlorohydroquinone (CHQ, 13%), 4-chlororesorcinol (4-CR, 3%), and 3-CC (84%) from 2-CP with an initial product formation rate of 1.1 +/- 0.32 nmol/min/mg protein. To increase the oxidation rate and alter the oxidation regiospecificity of chloroaromatics, as well as to study the roles of active site residues L192 and A107 of the alpha hydroxylase fragment of ToMO (TouA), we used the saturation mutagenesis approach of protein engineering. Thirteen TouA variants were isolated, among which some of the best substitutions uncovered here have never been studied before. Specifically, TouA variant L192V was identified which had 1.8-, 1.4-, 2.4-, and 4.8-fold faster hydroxylation activity toward chlorobenzene, 2-CP, 3-CP, and 4-CP, respectively, compared to the native ToMO. The L192V variant also had the regiospecificity of chlorobenzene changed from 4% to 13% 2-CP and produced the novel product 3-CC (4%) from 3-CP. Most of the isolated variants were identified to change the regiospecificity of oxidation. For example, compared to the native ToMO, variants A107T, A107N, and A107M produced 6.3-, 7.0-, and 7.3-fold more 4-CR from 2-CP, respectively, and variants A107G and A107G/L192V produced 3-CC (33 and 39%, respectively) from 3-CP whereas native ToMO did not. IMPORTANCE Chlorobenzene is a commonly used toxic solvent and listed as a priority environmental pollutant by the US Environmental Protection Agency. Here, we report that Escherichia coli TG1 cells expressing toluene o-xylene monooxygenase (ToMO) can successfully oxidize chlorobenzene to form dihydroxy chloroaromatics, which are valuable industrial compounds. ToMO performs this at room temperature in water using only molecular oxygen and a cofactor supplied by the cells. Using protein engineering techniques, we also isolated ToMO variants with enhanced oxidation activity as well as fine-tuned regiospecificities which make direct microbial oxygenations even more attractive. The significance of this work lies in the ability to degrade environmental pollutants while at the same time producing valuable chemicals using environmentally benign biological methods rather than expensive, complex chemical processes.Öğe Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra(Academic Press Inc Elsevier Science, 2020) Kepenek, Eda Şeyma; Severcan, Mete; Gözen, Ayşe Gül; Severcan, FerideHeavy metal acclimated bacteria are profoundly the preferred choice for bioremediation studies. Bacteria get acclimated to toxic concentrations of heavy metals by induction of specific enzymes and genetic selection favoring new metabolic abilities leading to activation of one or several of resistance mechanisms creating bacterial populations with differences in resistance profile and/or level. Therefore, to use in bioremediation processes, it is important to discriminate acclimated bacterial populations and choose a more resistant strain. In this study, we discriminated heavy metal acclimated bacteria by using Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) spectroscopy and multivariate analysis methods namely Hierarchical Cluster Analysis (HCA), Principal Component Analysis (PCA) and Soft Independent Modeling of Class Analogy (SIMCA). Two acclimation methods, acute and gradual, were used which cause differences in molecular changes resulting in bacterial populations with different molecular and resistance profiles. Brevundimonas sp., Gordonia sp., and Microbacterium oxydans were exposed to the toxic concentrations of Cd (30 mu g/ml) or Pb (90 mu g/ml) by using broth medium as a growth media. Our results revealed that PCA and HCA clearly discriminated the acute-acclimated, gradual acclimated, and control bacteria from each other in protein, carbohydrate, and whole spectral regions. Furthermore, we classified acclimated (acute and gradual) and control bacteria more accurately by using SIMCA with 99.9% confidence. This study demonstrated that heavy metal acclimated and control group bacteria can be discriminated by using chemometric analysis of FTIR spectra in a powerful, cost-effective, and handy way. In addition to the determination of the most appropriate acclimation procedure, this approach can be used in the detection of the most resistant bacterial strains to be used in bioremediation studies.Öğe Dose-dependent differentiation of gamma-irradiated hazelnut samples by mid-infrared spectroscopy coupled with chemometrics(Hindawi Ltd, 2020) Doğan, Ayça; Severcan, Mete; Severcan, FerideGamma irradiation is used as a food preservation method. It is known that high-dose irradiation causes several structural and functional damages. Therefore, the detection of high-dose irradiated food samples is a critical issue in international trade. The objective of this work is to evaluate the potential of Fourier transform infrared (FTIR) spectroscopy for the differentiation of gamma-irradiated hazelnuts at higher doses (3 kGy and 10 kGy) from the lower (1.5 kGy) and nonirradiated ones using multivariate statistical analysis, namely, principal component analysis (PCA) and hierarchical cluster analysis (HCA). This study showed that high-dose irradiated hazelnut samples can be clearly differentiated from the low-dose irradiated samples using unsupervised methods based on the spectral differences. Furthermore, dose-dependent discrimination was also achieved. In conclusion, FTIR spectroscopy combined with multivariate statistical analysis has potential for the development of a reliable and fast methodology for separation of high-dose irradiated food samples.Öğe Rapid diagnosis of malignant pleural mesothelioma and its discrimination from lung cancer and benign exudative effusions using blood serum(2022) Yonar, Dilek; Severcan, Mete; Gurbanov, Rafig; Sandal, Abdulsamet; Yılmaz, Ülkü; Emri, Salih; Severcan, FerideMalignant pleural mesothelioma (MPM), an aggressive cancer associated with exposure to fibrous minerals, can only be diagnosed in the advanced stage because its early symptoms are also connected with other respiratory diseases. Hence, understanding the molecular mechanism and the discrimination of MPM from other lung diseases at an early stage is important to apply effective treatment strategies and for the increase in survival rate. This study aims to develop a new approach for characterization and diagnosis of MPM among lung diseases from serum by Fourier transform infrared spectroscopy (FTIR) coupled with multivariate analysis. The detailed spectral characterization studies indicated the changes in lipid biosynthesis and nucleic acids levels in the malignant serum samples. Furthermore, the results showed that healthy, benign exudative effusion, lung cancer, and MPM groups were successfully separated from each other by applying principal component analysis (PCA), support vector machine (SVM), and especially linear discriminant analysis (LDA) to infrared spectra.Öğe Strain and depot-specific differences in adipose tissues of obese BFMI mice(2023) Doğan, Ayça; Şen, İlke; Severcan, Mete; Brockmann, Gudrun; Severcan, FerideBackground/aim: Obesity is associated with the structural and functional disorders related to the molecules of the tissues, cells, and membranes. This study aimed to examine the alterations in the secretion of inflammatory cytokines and metabolic factors and structural changes in inguinal (IF) and gonadal (GF) adipose tissues at the molecular level. Materials and methods: The IF and GF tissues of Berlin Fat Mouse Inbred (BFMI) lines namely BFMI852, BFMI856, BFMI860, BFMI861 obese and DBAJ control mouse lines were used for mRNA expression and Attenuated Total Reflection - Fourier Transform Infrared Spectroscopy (ATR-FTIR) studies. The mRNA levels of inflammatory cytokines including leptin, interleukin 6 (IL-6), tumor necrosis factor-alpha (Tnf-α), and insulin-like growth factor-1 (Igf-1), and peroxisome proliferator-activated receptor gamma 2 (Pparγ-2), were investigated using quantitative reverse transcriptase real-time PCR (qRT-PCR). Infrared spectroscopy does not provide information about specific proteins, instead, it gives information about overall (total) proteins, which is called global information. Therefore, in the current study, adequate information about secondary structures of adipose tissues proteins was obtained using artificial neural network (ANN) and secondary derivative-vector normalization methods based on the spectral profiles. Results: According to the mRNA expression studies, high leptin resistance was found in all BFMI lines. Differences were observed in the levels of measured factors except for Igf-1 among BFMI lines. Protein secondary structure studies showed an increase in random coil contents, especially for BFMI860, which indicates denaturation of the proteins. Conclusion: Among the spontaneous obese BFMI mouse lines, the BFMI860 line is the most suitable for obesity studies. Obesity-induced effect on the adipose tissues varies considerably with location, type of adipose tissue, and animal line.Öğe Structural effects of simvastatin on liver rate tissue: Fourier transform infrared and Raman microspectroscopic studies(Spie-Soc Photo-Optical Instrumentation Engineers, 2016) Garip, Şebnem; Bayari, Sevgi Haman; Severcan, Mete; Abbas, Sherif; Lednev, Igor K.; Severcan, FerideSimvastatin is one of the most frequently prescribed statins because of its efficacy in the treatment of hypercholesterolemia, reducing cardiovascular risk and related mortality. Determination of its side effects on different tissues is mandatory to improve safe use of this drug. In the present study, the effects of simvastatin on molecular composition and structure of healthy rat livers were investigated by Fourier transform infrared and Raman imaging. Simvastatin-treated groups received 50 mg/kg/day simvastatin for 30 days. The ratio of the area and/or intensity of the bands assigned to lipids, proteins, and nucleic acids were calculated to get information about the drug-induced changes in tissues. Loss of unsaturation, accumulation of end products of lipid peroxidation, and alterations in lipid-to-protein ratio were observed in the treated group. Protein secondary structure studies revealed significant decrease in alpha-helix and increase in random coil, while native beta-sheet decreases and aggregated beta-sheet increases in treated group implying simvastatin-induced protein denaturation. Moreover, groups were successfully discriminated using principal component analysis. Consequently, high-dose simvastatin treatment induces hepatic lipid peroxidation and changes in molecular content and protein secondary structure, implying the risk of liver disorders in drug therapy. (C) 2016 Society of Photo-Optical Instrumentation Engineers (SPIE)Öğe Structural effects of simvastatin on rat liver tissue: Fourier transform infrared and Raman microspectroscopic studies (vol 21, 025008, 2016)(Spie-Soc Photo-Optical Instrumentation Engineers, 2016) Garip, Şebnem; Bayari, Sevgi Haman; Severcan, Mete; Abbas, Sherif; Lednev, Igor K.; Severcane, FerideSimvastatin is one of the most frequently prescribed statins because of its efficacy in the treatment of hypercholesterolemia, reducing cardiovascular risk and related mortality. Determination of its side effects on different tissues is mandatory to improve safe use of this drug. In the present study, the effects of simvastatin on molecular composition and structure of healthy rat livers were investigated by Fourier transform infrared and Raman imaging. Simvastatin-treated groups received 50 mg/kg/day simvastatin for 30 days. The ratio of the area and/or intensity of the bands assigned to lipids, proteins, and nucleic acids were calculated to get information about the drug-induced changes in tissues. Loss of unsaturation, accumulation of end products of lipid peroxidation, and alterations in lipid-to-protein ratio were observed in the treated group. Protein secondary structure studies revealed significant decrease in alpha-helix and increase in random coil, while native beta-sheet decreases and aggregated beta-sheet increases in treated group implying simvastatin-induced protein denaturation. Moreover, groups were successfully discriminated using principal component analysis. Consequently, high-dose simvastatin treatment induces hepatic lipid peroxidation and changes in molecular content and protein secondary structure, implying the risk of liver disorders in drug therapy. (C) 2016 Society of Photo-Optical Instrumentation Engineers (SPIE)Öğe The structural effects of Vitamin A deficiency on biological macromolecules due to ethanol consumption and withdrawal: An FTIR study with chemometrics(2022) Elibol, Birsen; Severcan, Mete; Jakubowska-Dogru, Ewa; Dursun, Ilknur; Severcan, FerideThe structural effects of vitamin A-deficiency were examined on the molecular profiles of biomolecules of male rat hippocampus during prolonged ethanol intake/withdrawal using FT-IR spectroscopy coupled with chemometrics. Liquid ethanol diet with/without vitamin A was maintained to adult rats for 3-months. The rats were decapitated at different ethanol withdrawal times and FT-IR spectra were obtained. Ethanol consumption/withdrawal produced significant changes in proteins' conformations, while having insignificant structural effects on lipids. In vitamin A deficiency, ethanol produced structural changes in lipids by lipid ordering especially in the early-ethanol withdrawal. Furthermore, an increase in lipid and protein content, saturated/unsaturated lipid ratio, a decrease in nucleic acids content and decrease in membrane fluidity were observed. These changes were less severe in the presence of Vitamin A. This study is clinically important for individuals with vitamin A deficiency because they have to be more cautious when consuming alcohol to protect themselves from cognitive dysfunctions.Öğe Yapay sinir ağları kullanılarak FTIR spektroskopik sinyallerinden proteinlerin ikincil yapılarının saptanması(2003) Severcan, Mete; Severcan, FerideProtein ikincil yapılarının, Fourier Transform Infrared (FTIR) spektrumlarmdan, yapay sinir ağları kullanılarak hassas bir şekilde kestirimi amacıyla yöntemler geliştirildi. Yapay sinir ağları ile protein ikincil yapıları kestiriminde en önemli sorun sinir ağının öğrenmesi için gerekli eğitim örneklerinin sınırlı sayıda olması, bu nedenle sinir ağının genelleştirme özelliğinin iyi olmamasıdır. Bu çalışmada, genelleştirme başarımmı iyileştirecek algoritmalar geliştirildi ve eğitim örneklerinin sayısını artırmak için de x-ışını karakterizasyonu bilinen yeni protein FTIR spektrumları elde edildi. Sinir ağlarındaki genelleştirmeyi iyileştirmek için eğitim verilerinin önişlemesi, düzenlileştirilmiş sinir ağı yapıları, ve çok sayıda sinir ağı çıktılarının tümleştirilmesi üzerine çalışmalar yapıldı. Yapay olarak çoğaltılmış spektrumların ayrık cosinüs dönüşümlerinin girdi olarak uygulandığı, Bayes düzenlileştirilmiş ve eniyileştirilmiş bir sinir ağı mimarisi en başarılı sonucu verdi. Sinir ağları çıktıları maksimum olabilirlik kuralı ile tümleştirilerek kestirimler elde edildi. Çalışmanın başında, ikincil yapı parametreleri, $\\alpha$ -heliks, $\\beta$ -tabaka ve dönme için, o zaman için literatürde en düşük değerler olarak elde ettiğimiz standart kestirim hataları sırasıyla, %7.7, %6.4, ve %4.8 idi. Bu değerler bu çalışma sonucunda sırasıyla %4.2, %3.5, ve %3.2 düzeylerine düşürüldü. Belirtilen sonuçlar, geliştirilen algoritmanın şu anda literatürde aynı veri kümesini kullanan diğer algoritmalara göre başarımının daha üstün olduğunu göstermektedir. Raporun sonunda, geliştirdiğimiz bu yöntemin tıpta değişik hastalıkların protein ikincil yapılarında oluşturduğu değişiklikleri saptayabileceğini göstermek amacıyla bir uygulama sunuldu. Bu uygulamada, geliştirilen kestirim yöntemi kullanılarak diğer yöntemlere göre oldukça kısa bir sürede ve daha doğru olarak, diyabetin mikrosomal membran proteinlerinin ikincil yapılarda oluşturduğu değişimler saptandı ve değişik antioksidant karışımlarının diyabetin neden olduğu hasarı onardığı gözlendi.
