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Öğe Assessment of oxidative stress effects in serum determined by FT-IR spectroscopy in cholangiocarcinoma patients(AMG Transcend Association, 2023) Bulut, Huri; Tarhan, Nevzat; Büyük, Melek; Serin, Kürşat Rahmi; Ulukaya, Engin; Depciuch, Joanna; Parlinska-Wojtan, Magdalena; Güleken, ZozanCholangiocarcinoma (CCA) is a heterogeneous malignant tumor containing intrahepatic and extrahepatic bile ducts and gallbladder carcinoma. Mostly diagnosed at an advanced stage with a <5% cure chance. Early-stage diagnosis may increase the number of patients who reach curative treatment. Fourier Transform InfraRed (FT-IR) spectroscopy was used to detect chemical changes in serum collected from CCA patients vs. healthy individuals. The study aims to correlate the FTIR spectra with biochemical indices such as TAS, TOS, OSI, and total protein levels. Decreased TAS and increased TOS, OSI, and total protein levels in CCA patients vs. healthy individuals were found. FTIR spectra showed higher absorbance of the peaks corresponding to C–O and bending vibration of C–O–H groups in CCA patients, while more CH2 functional groups than lipids could be seen in the FTIR spectra of controls serum. PLS analysis showed IR ranges of 1500 cm-1 to 1700 cm-1, and 2700 cm-1 to 3000 cm-1 were able to distinguish between CCA from controls, respectively. PCA confirmed this, while HCA did not differentiate between CCA and those without the disease. Lipids and some functional groups changes caused by oxidative stress can be applied to predict CCA by using FTIR spectroscopy. © 2022 by the authors.Öğe Assessment of structural protein expression by FTIR and biochemical assays as biomarkers of metabolites response in gastric and colon cancer(Elsevier B.V., 2021) Güleken, Zozan; Bulut, Huri; Gültekin, Güldal İnal; Arıkan, Soykan; Yaylım, İlhan; Hakan, Mehmet Tolgahan; Sönmez, Dilara; Tarhan, Nevzat K.; Depciuch, JoannaColon and gastric cancers are the widespread benign types of cancers which are synchronous and metachronous neoplasms. In terms of the progression and progress of the disease, metabolic processes and differentiation in protein structures have an important role in for treatment of the disease. In this study we proposed to investigate the metabolic process and the differentiation of protein secondary structure among colon and gastric cancer as well as healthy controls using biochemistry and Fourier Transform InfraRed spectroscopy (FTIR) methods. For this purpose, we measured blood serum of 133 patients, which were conducted upon oncology department (45 colon cancer, 45 gastric cancer and 43 control individuals). The obtained spectroscopic results and biochemical assays showed significant reduction in the amount of functional groups in cancer groups contrary with total protein measurements and structure of protein differences between colon and gastric cancers. Differentiations were visible in serum levels of CEA, CA-125, CA-15-3, CA-19-9 AFP (Alpha fetoprotein) of gastric and colon cancer patients as well as in amide III and secondly described amide I regions. Our findings suggest that amide I bonds in colon cancer cells can be helpful in diagnosis of colon cancer. Indeed, our results showed that metabolic processes were higher in gastric cancer group than in colon cancer. Hence, FTIR spectroscopy and curve-fitting analysis of amide I profile can be successfully applied as tools for identifying quantitative and qualitative changes of proteins in human cancerous blood serum. However, what is very important, in PCA analysis we see, that the scatter plot of PC1 (variability 80%) and PC2 (variability 15%) show that the data related to the control and two cancer groups are clustered together with different magnitudes and directions.Öğe Assessment of the effect of endocrine abnormalities on biomacromolecules and lipids by FT-IR and biochemical assays as biomarker of metabolites in early Polycystic ovary syndrome women(Elsevier, 2021) Güleken, Zozan; Bulut, Huri; Bulut, Berk; Depciuch, JoannaPolycystic ovary syndrome (PCOS) is a common endocrinopathy associated with metabolic disturbances.Both in the development and improvement of the disease, the structure of phospholipids and proteinsin the blood serum plays important role in the treatment of these disease. Herein, to investigate themetabolic process and the variations of biomacromolecules and lipids between young PCOS women andhealthy subjects, biochemistry and Fourier Transform InfraRed spectroscopy (FTIR) methods, were used.Moreover, partial least squares regression (PLS) and Principal component analysis (PCA) to researchdifferentiation of biomacromolecules, were performed. We obtained blood serum of of 100 individ-uals including 57 with PCOS and 43 healthy controls. The biochemical blood profile of PCOS womenwas presented by spectroscopic measurements, which is an analytical technique, as well as by labora-tory indexes and oxidative stress status measurements. There was a significant structural differentiationbetween studied groups in the number of functional groups and biomolecules differentiation dependingon the protein expression and oxidative stress status. Hence, FTIR spectroscopy and oxidative load can beeffectively utilized as tools for classifying quantitative and qualitative changes of biomolecules in PCOSsamples. PCOS samples did not correlate with luteinizing hormone (LH) level and proteins but had anegative correlation between carbohydrates and fatty acids, compared with control group.Öğe Characterization of Covid-19 infected pregnant women sera using laboratory indexes, vibrational spectroscopy, and machine learning classifications(Elsevier B.V., 2022) Güleken, Zozan; Jakubczyk, Pawe?; Paja, W.; Krzysztof, Pancerz; Bulut, Huri; Öten, Esra; Depciuch, Joanna; Tarhan, Nevzat K.Herein, we show differences in blood serum of asymptomatic and symptomatic pregnant women infected with COVID-19 and correlate them with laboratory indexes, ATR FTIR and multivariate machine learning methods. We collected the sera of COVID-19 diagnosed pregnant women, in the second trimester (n = 12), third-trimester (n = 7), and second-trimester with severe symptoms (n = 7) compared to the healthy pregnant (n = 11) women, which makes a total of 37 participants. To assign the accuracy of FTIR spectra regions where peak shifts occurred, the Random Forest algorithm, traditional C5.0 single decision tree algorithm and deep neural network approach were used. We verified the correspondence between the FTIR results and the laboratory indexes such as: the count of peripheral blood cells, biochemical parameters, and coagulation indicators of pregnant women. CH2 scissoring, amide II, amide I vibrations could be used to differentiate the groups. The accuracy calculated by machine learning methods was higher than 90%. We also developed a method based on the dynamics of the absorbance spectra allowing to determine the differences between the spectra of healthy and COVID-19 patients. Laboratory indexes of biochemical parameters associated with COVID-19 validate changes in the total amount of proteins, albumin and lipase.Öğe ÇUHA ÇİÇEĞİ VE SARI KANTARON YAĞLARININ MULTİPLE SKLEROZ MODELİ OLUŞTURULMUŞ FARELERDEKİ JAK/STAT SİNYAL YOLAKLARI ÜZERİNE ETKİSİ(2022) Bulut, Huri; Şentürk, Hilal; Güleken, Zozan; Selek, Şahabettin; Teloğlu, Emine Şeyda; Üstünova, SavaşAmaç: Multipl Skleroz, merkezi sinir sisteminde inflamatuar infiltrasyonlarla ilerleyen otoimmün demiyelinizan bir hastalıktır. JAK-STAT sinyal yolunun düzensizliği, otoimmün ensefalomiyelit ile indüklenmiş Multipl Skleroz modellerinin patogenezinde önemli bir rol oynar. Bu çalışmanın amacı, sarı kantaron ve çuha çiçeği yağlarının tüketiminin, JAK-STAT sinyal yolu üzerindeki terapötik etkilerini ortaya çıkarmaktır.Gereç ve Yöntemler: Çalışmamızda 42 adet dokuz haftalık C57bl/6 J fareler kullanıldı. Fareler, Multipl Skleroz (MS) (n=32) ve kontrol grubu (n=10) olmak üzere iki ana gruba ayrıldıktan sonra MS grubundaki tüm farelere deneysel otoimmün ensefalomiyelit yöntemi ile Multipl Skleroz hastalığı oluşturuldu. Multipl Skleroz grubu kendi içinde MS (n=7), MS + Çuha çiçeği (n=10) ve MS + Sarı Kantaron (n=15) olacak şekilde üç gruba ayrıldı. Tedavi grupları, 6 hafta boyunca sarı kantaron (20 g/kg) ve çuha çiçeği (20 g/kg) yağları içeren özel üretim yemler ile beslendi. Multipl Skleroz indüksiyonundan iki hafta sonra, hastalığın klinik belirtileri her fare için günlük olarak puanlandı. Çalışmamızın sonunda beyin dokusu örneklerini elde etmek için tüm gruplardaki fareler sakrifiye edildi. Beyin doku homojenatlarında Western Blot yöntemi ile JAK2, p-JAK2, STAT1 ve p-STAT1 protein ekspresyon seviyeleri ölçüldü.Bulgular: Çalışmamızda Multipl Skleroz hastalığı patogenezi ile ilişkili JAK/STAT yolağındaki p-JAK2, JAK2, p-STAT1 ve STAT1 ekspresyon düzeylerinin MS grubunda kontrollere göre anlamlı olarak arttığını, sarı kantaron ve çuha çiçeği yağı ile beslenen gruplarda ise anlamlı olarak azaldığını gösterdik (p<0.05).Sonuç: Bu çalışmada elde ettiğimiz veriler ışığında, özellikle çuha çiçeği ve sarı kantaron yağlarının besin takviyesi olarak tüketilmesinin, Multipl Skleroz hastalığının moleküler patogenezinin iyileşmesine katkı sağlayacağı söylenebilir.Öğe Diagnosis of endometriosis using endometrioma volume and vibrational spectroscopy with multivariate methods as a noninvasive method(Elsevier Science, 2022) Güleken, Zozan; Bulut, Huri; Depciuch, Joanna; Tarhan, NevzatEndometriomas are typically an advanced form of endometriosis that leads to the formation of scar tissue, adhesions, and an inflammatory reaction. There is no certain serum marker for the diagnosis of endometriosis. This study aims to research the correlation between the amount of peaks corresponding to proteins and lipids with the volume of endometrioma and determine the chemical structure of blood serum collected from women suffering from endometriosis patients with endometrioma and healthy subjects using Fourier Transform Infrared (FTIR) spectroscopy. FTIR spectroscopy is used as a non-invasive diagnostic technique for the discrimination of endometriosis women with endometrioma and control blood sera. The FTIR spectra of 100 serum samples acquired from 50 patients and 50 healthy individuals were used for this study. For this purpose, multivariate analyses such as Principal Component Analysis (PCA), Partial Last Square analysis (PLS) with Variables Importance in Projection (VIP), and probability models, were performed. Our results showed that FTIR range 1500 cm-1 and 1700 cm-1 and around 2700 cm-1 - 3000 cm-1, regions may be used for the diagnosis of endometriosis. Also, we find that proteins and lipids fraction increase with the volume of endometrioma. Moreover, PLS and VIP analysis suggested that lipids could be helpful in the diagnosis of endometriosis women with endometrioma.Öğe Differential of cholangiocarcinoma disease using Raman spectroscopy combined with multivariate analysis(2022) Depciuch, Joanna; Parlinska-Wojtan, Magdalena; Serin, Kürşat Rahmi; Bulut, Huri; Ulukaya, Engin; Tarhan, Nevzat; Güleken, ZozanCholangiocarcinoma (CCA) is a type of cancer, which 5-year survival is lower than 20 %, and which is detected mostly in advanced stage of the disease. Unfortunately, there are no diagnostic tools, which could show changes in the body indicating the development of the disease. Therefore, in this study, we investigate Raman spectroscopy as a promising analytical tool in medical diagnostics and as a method, which would allow to distinguish between healthy patients and patients suffering from cholangiocarcinoma. The obtained Raman spectra showed, that lower intensities of peaks corresponding to amino acids and proteins, as well as higher intensities of peaks originating from lipids vibrations were observed in healthy individuals in comparison with cancer patients. Moreover, Partial Last Square (PLS), Principal Component Analysis (PCA) and Hierarchical Component Analysis (HCA) of Raman spectra indicate that the ranges between 800 cm-1 and 1800 cm-1, 3477 cm-1 -3322 cm-1 and 1394 cm-1 -1297 cm-1 allow to distinguish cancer patients from healthy ones. The obtained results showed, that Raman spectroscopy is a good candidate, to become in future one of the diagnostic tools of Cholangiocarcinoma.Öğe Investigation of the effects of transcranial direct current stimulation and neurofeedback by continuous performance test(Elsevier Ireland Ltd, 2020) Güleken, Zozan; Eskikurt, Gökçer; Karamürsel, SacitTranscranial direct current stimulation (tDCS) is a noninvasive neuromodulation technique based on weak direct current stimulation through the scalp. Neurofeedback (NFB) is a learning strategy that may help alter to brain wave parameters, by monitoring electroencephalography (EEG) feedback via special programs. We aimed to investigate the supportive effects of tDCS in addition to NFB training. 16 healthy volunteers were divided equally into two groups. One of the groups was trained by NFB with the sensorimotor rhythm (SMR) protocol; 2 days per week, 10 sessions of 30 min, the other group received 10 min of tDCS before each NFB sessions. Continuous Performance Test (CPT) was used to measure, response time and suppression and to determine selective attention condition. Also, Beck Depression and Anxiety Inventories were used to exclude people with depression and anxiety. Depression scores of NFB + tDCS group were decreased significantly. CPT scores were better at last sessions for both groups compared to the first sessions. Sessions were analyzed by comparing 1st, 2nd, 5th and 10th sessions. While the NFB + tDCS group had statistically significant changes at theta/beta ratios with SMR and alpha band amplitudes, NFB group statistics had changed at theta/SMR ratios. NFB training shows its effects at the end of 10 sessions. Despite an increase in the latencies of correct and commission responses on the task of CPT, additional use of tDCS improves cognitive performance. Also, tDCS has a supportive effect on the healthy participants who have mild anxiety and depression; also inhibition deficits of subjects were clear.Öğe Spectrochemical and biochemical assay comparison study of the healing effect of the aloe vera and hypericum perforatum loaded nanofiber dressings on diabetic wound(Elsevier, 2021) Güleken, Zozan; Depciuch, Joanna; Ege, Hasan; İlbay, Gül; Kalkandelen, Cevriye; Özbeyli, Dilek; Bulut, Huri; Tarhan, Nevzat; Erdem Kuruca, SerapDiabetic wounds have a slow healing process and easy to be infected. In addition to current drug treatments, supportive approaches are needed for diabetic wound treatment. In this study, we aimed to load Aloe Vera (AV) and Hypericum perforatum oil (HPO) with PCL/Ge (Poly (?-caprolactone)/Gelatine) polymeric biodegradable by electrospinning method into nanofiber dressings on an experimental diabetic wound model to compare the diabetic wound healing effect. Changes in the amount and chemical structure of phospholipids, proteins, and lipids were investigated in the blood and serum samples of the animals using Fourier transform infrared (FTIR) analysis. To evaluate biological events associated with the wound repair process in inflammatory phase we used oxidant and antioxidant status to determine the healing status of wounds such as Total antioxidant status (TAS), Total oxidant level (TOS) and tumor necrosis factor alpha (TNF-?) levels. TOS level increased in DM groups and decreased in the AV and HPO group. Oxidative stress index decreased and TNF-? level increased in the HPO group. FTIR spectra showed changes in the phospholipids, proteins, and carbon chain of lipids in the whole blood as well as serum of DM rats. FTIR spectra combined with Principal component analysis (PCA) showed, that treated DM rats by AV and HPO caused return chemical structure of blood and serum to this observed in control group. Higher similarity with control group for HPO rats was observed. HPO is better than AV in the alternative for healing on diabetic wound. Thus, we have demonstrated that IR spectroscopy and multivariate data analysis and biochemical assays are consistent and correlative with each other.
