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Analysis of follicular fluid and serum markers of oxidative stress in women with unexplained infertility by Raman and machine learning methods
(Wiley, 2023) Depciuch, Joanna; Paja, Wieslaw; Pancerz, Krzysztof; Uzun, Ozgur; Bulut, Huri; Tarhan, Nevzat; Guleken, Zozan
Oocytes are surrounded by a fluid called follicular fluid, which provides an essential microenvironment for developing oocytes in human fertility. Various molecules exist in antral follicles, including proteins, steroid hormones, polysaccharides, metabolites, reactive oxygen species, and antioxidants. Oxidative stress is involved in the etiology of defective oocyte development or poor oocyte and embryo quality. Raman spectroscopy, a noninvasive method, can be used for biological diagnostics and direct chemical identification of follicular fluid. Therefore, we measured the oxidative index of follicular fluids and then attempted Raman spectroscopy on the follicular fluids combined with machine learning techniques to identify, detect, and quantify follicular fluid of unexplained infertility-diagnosed women as a safe and effective tool to use as adjacent for clinical studies. This was a retrospective study set in an academic hospital where the patients were selected from an unexplained infertility-diagnosed population in the in vitro fertilization (IVF) center. Raman spectra of 128 follicular fluid samples (n = 63 control; and 65 unexplained infertility) were obtained. To profile Raman-based results of follicular fluid, oxidative load measurements, multivariate analysis, correlation tests, and six machine learning methods were used. Raman bands associated with oxidative load and amide III and lipids differed significantly. Classification using stacks of Raman signals was applied by random forest, C5.0 decision tree algorithm, k-nearest neighbors, deep neural networks, support vector machine, and XGBoost trees algorithms achieved an overall accuracy of 92.04% to 99.17% in assigned correctly. Group has an oxidative load in their follicle fluids consistent with clinical results and biochemical measurements and performing testing based on Raman spectra validated by kNN clustering and SVM object vector separation machine learning methods. The study suggests that Raman spectroscopy can detect changes in follicle fluid in unexplained infertility.
Angiotensin IV improves spatial memory in streptozotocin?induced diabetic rats by reducing oxidative stress and altering BDNF levels
(NCI CPTAC, 2021) Kılıç, Aysu; Üstunova, Savaş; Elibol, Birsen; Bulut, Huri; Meral, İsmail; Şahin, Gülderen
In this study, we investigated the protective effects of angiotensin IV (Ang IV) on cognitive function in streptozotocin (STZ)?induced diabetic rats. Male Wistar albino rats, were randomly divided into four groups; control (C), diabetes (Dia, 60 mg/kg, STZ, i.p.), Ang IV (5 ?g/kg, s.c.) and Dia+Ang IV. The passive avoidance and Morris water maze (MWM) tests were used to evaluate learning and memory performance. Behavioral tests were carried out between 21 and 30 days after the initial Ang IV injection. Hippocampi were dissected and retained for biochemical and Western blot analysis. The Dia group exhibited the poorest behavioral results, while the Dia+Ang IV group performed highest on the MWM task. Superoxide dismutase, glutathione peroxidase, and malondialdehyde levels increased significantly in the Dia group compared to Dia+Ang IV. Brain?derived neurotrophic factor (BDNF) and N?methyl?D?aspartate levels were significantly elevated, while levels of GABAA significantly decreased, in the Dia+Ang IV group compared to the Dia group. These findings suggest that peripheral administration of Ang IV ameliorated spatial memory in diabetic rats by decreasing hippocampal oxidative stress and BDNF levels.
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, Zozan
Cholangiocarcinoma (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.
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, Joanna
Colon 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.
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, Joanna
Polycystic 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.
Association between Serum Galectin-3 and Growth Differentiation Factor-15 Levels and Coronary Slow Flow Phenomenon
(Taiwan Soc Cardiology, 2023) Yuksel, Yasin; Yildiz, Cennet; Bulut, Huri
Background: Coronary slow flow phenomenon (CSFP) is characterized by delay in the progression of contrast material in the coronary tree that is not accompanied by significant coronary artery narrowing. Pathophysiologic pathways underpinning CSFP still remain poorly understood. Objectives: To evaluate the relationship between serum galectin-3 (GAL-3) and growth differentiation factor-15 Methods: Fifty CSFP patients and 40 subjects with normal coronary arteries were included in this retrospective study. The patients' serum GDF-15 and GAL-3 concentration levels were measured using relevant kits. Thrombolysis in myocardial infarction frame count (TFC) of each patients was determined. Results: We did not find any differences with respect to clinical and demographic features between the two groups. GDF-15 and GAL-3 concentration levels were significantly higher in the patients with CSFP. Moreover GDF-15 and GAL-3 concentration levels were positively correlated with TFC (GDF-15; r = 0.448, GAL-3; r = 0.642, p < 0.001 for both). Multivariate logistic regression showed that GAL-3 and GDF-15 were predictors of the CSFP. Similarly, GDF15 and GAL-3 were the only predictors of TFC. More specifically, GDF-15 and GAL-3 concentration levels of 182.18 pg/mL and 8.58 ng/mL predicted CSFP with sensitivities of 76% and 87.5%, respectively, and specificities of 84% and 75%, respectively. Conclusions: GDF-15 and GAL-3 levels were increased in the CSFP patients and predicted the presence and severity of CSFP. Thus, these two biomarkers might prove useful in relation to the diagnosis of CSFP.
Blood serum lipid profiling may improve the management of recurrent miscarriage: a combination of machine learning of mid-infrared spectra and biochemical assays
(SPRINGER HEIDELBERG, 2022) Guleken, Zozan; Bahat, Pınar Yalçın; Toto, Ömer Faruk; Bulut, Huri; Jakubczyk, Pawel; Cebulski, Jozef; Paja, Wieslaw; Pancerz, Krzysztof; Wosiak, Agnieszka; Depciuch, Joanna
The present article is focused on developing and validating an efficient, credible, minimally invasive technique based on spectral signatures of blood samples of women with recurrent miscarriage vs. those of healthy individuals who were followed in the Department of Obstetrics and Gynecology for 2 years. For this purpose, blood samples from a total of 120 participants, including healthy women (n=60) and women with diagnosed recurrent miscarriage (n=60), were obtained. The lipid profile (high-density lipoprotein, low-density lipoprotein, triglyceride, and total cholesterol levels) and lipid peroxidation (malondialdehyde and glutathione levels) were evaluated with a Beckman Coulter analyzer system for chemical analysis. Biomolecular structure and composition were determined using an attenuated total reflectance sampling methodology with Fourier transform infrared spectroscopy alongside machine learning technology to advance toward clinical translation. Here, we developed and validated instrumentation for the analysis of recurrent miscarriage patient serum that was able to differentiate recurrent miscarriage and control patients with an accuracy of 100% using a Fourier transform infrared region corresponding to lipids. We found that predictors of lipid profile abnormalities in maternal serum could significantly improve this patient pathway. The study also presents preliminary results from the first prospective clinical validation study of its kind.
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.
Conserved amino acid residues that affect structural stability of candida boidinii formate dehydrogenase
(Springer, 2021) Bulut, Huri; Yüksel, Büşra; Gül, Mehmet; Eren, Meryem; Karataş, Ersin; Kara, Nazlı; Yılmazer, Berin; Koçyiğit, Abdurrahim; Labrou, Nikolaos E.; Bi?nay, Barış
The NAD+-dependent formate dehydrogenase (FDH; EC 1.2.1.2) from Candida boidinii (CboFDH) has been extensively used in NAD(H)-dependent industrial biocatalysis as well as in the production of renewable fuels and chemicals from carbon dioxide. In the present work, the effect of amino acid residues Phe285, Gln287, and His311 on structural stability was investigated by site-directed mutagenesis. The wild-type and mutant enzymes (Gln287Glu, His311Gln, and Phe285Thr/His311Gln) were cloned and expressed in Escherichia coli. Circular dichroism (CD) spectroscopy was used to determine the effect of each mutation on thermostability. The results showed the decisive roles of Phe285, Gln287, and His311 on enhancing the enzyme’s thermostability. The melting temperatures for the wild-type and the mutant enzymes Gln287Glu, His311Gln, and Phe285Thr/His311Gln were 64, 70, 77, and 73 °C, respectively. The effects of pH and temperature on catalytic activity of the wild-type and mutant enzymes were also investigated. Interestingly, the mutant enzyme His311Gln exhibits a large shift of pH optimum at the basic pH range (1 pH unit) and substantial increase of the optimum temperature (25 °C). The present work supports the multifunctional role of the conserved residues Phe285, Gln287, and His311 and further underlines their pivotal roles as targets in protein engineering studies.
Correction: Serum Vasostatin-1 level is increased in women with preeclampsia
(Georg Thieme Verlag Stuttgard, 2022) Hamzaoğlu, Kübra; Bulut, Huri; Malik, Eduard; Güralp, Onur; Tüten, Abdullah; Tüten, Nevin; Gök, Koray
No Abstract Available
Correlation between endometriomas volume and Raman spectra. Attempting to use Raman spectroscopy in the diagnosis of endometrioma
(Elsevier B.V., 2022) Güleken, Z.; Bulut, Huri; Bulut, Berk; Paja, W.; Parlinska-Wojtan, M.; Depciuch, J.
The formation of the uterus lining, i.e. the endometrium, outside the uterus (ex. in the abdominal cavity, ovaries, or anywhere in the body) is called endometriosis. The presence of endometrial tissue present in the ovaries, thickens after menstruation, leading to menstrual-like bleeding and to the formation of chocolate cyst (Endometrioma) because of the accumulation of old, brown blood in the ovary. It is still unknown, what triggers the development of endometrioma. However, it leads to excessive bleeding during menstrual periods or abnormal bleeding between periods and infertility. Endometriosis is often first diagnosed in those who seek medical attention for infertility. Therefore, new markers of endometrioma as well as new methods of its diagnosis are sought. In this study we used Raman spectra of serum collected from 50 healthy women and 50 women suffering from endometriosis. The obtained Raman data were used in multivariate analysis to determine the Raman range, which can be used for endometrioma diagnostics. Partial Least Square (PLS), Principal Component Analysis (PCA) and Hierarchical Component Analysis (HCA) showed, that it is possible to distinguish between the serum collected from healthy and un-healthy women using the Raman range between 800 cm?1 and 1800 cm?1 and between 2956 cm?1 and 2840 cm?1, while the first range corresponds to the fingerprint region and the second one to lipids vibrations. Consequently, the Pearson correlation test showed a significant positive correlation between values of lipid intensity in Raman spectra and volume of endometriomas. Summarizing, Raman spectroscopy can be a helpful tool in endometrioma diagnosis and the lipid vibrations are candidates for being a spectroscopic marker of the disease being studied. © 2022 Elsevier B.V.
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, Savaş
Amaç: 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.
Cuscuta campestris tedavisi ile mide kanseri hücrelerinde apoptozun indüklenmesi ve reaktif oksijen türlerinin oluşumu yoluyla proliferasyonun engellenmesi
(DergiPark, 2021) Bulut, Huri; Durmuş, Ezgi; Hacıosmanoğlu, Ebru; Bozalı, Kübra; Şentürk, Hilal; Koçyiğit, Abdurrahim
Amaç: Kanser tahrip edici, ölümcül bir hastalıktır ve dünya çapındaki ölüm nedenleri arasında ikinci sırada yer almaktadır. Mide kanseri gibi kanser türleri için farklı tedavi yöntemleri mevcut olsa da çoğu tedavi yöntemleri birçok yan etkiye sahiptir. Çeşitli iyileştirici özelliklere sahip Cuscuta campestris' in kanser hücreleri üzerindeki etkilerinin araştırılması yeni bir alandır ve etkileri tam olarak çalışılmamış ve aydınlatılmamıştır. Bu çalışmada, C. campestris özütünün farklı konsantrasyonlarının mide kanseri hücreleri üzerindeki sitotoksik, genotoksik, apoptotik ve reaktif oksijen türlerinin üretimindeki etkilerini araştırdık. Gereç ve yöntem: Araştırmamızda, C. campestris için antioksidan, pro-oksidan ve radikal temizleyici aktiviteleri değerlendirildi ve miktar tayini LC-MS / MS yöntemi ile analiz edildi. C. Campestris’ in normal hücrelere kıyasla mide kanseri (AGC) hücreleri üzerindeki seçiciliğini göstermek için insan normal deri fibroblastik (CCD-1079Sk) hücre hattı kullanıldı. Apoptoz belirteçlerinin tayininde akridin oranj / etidyum bromür çift boyama, akış sitometrisi ve western blot metotlarından faydalanıldı. Genotoksik aktivite tayini, Comet analizi ile gerçekleştirildi. Bulgular: Sonuçlarımız, C. Campestris etanolik özütünün doza bağlı bir şekilde, mide kanseri hücre hattı üzerinde normal hücrelere kıyasla önemli ölçüde daha yüksek sitotoksik etkilere sahip olduğunu göstermiştir. Ayrıca, elde ettiğimiz veriler C. campestris'in mide kanseri hücre hatlarında reaktif oksijen türlerinin oluşumunu arttırdığını ve DNA hasarına neden olduğunu açıkça göstermiştir. Yapılan apoptoz tayin ölçümleri C. campestris' in bölünmüş kaspaz-3, bölünmüş kaspaz-9, bölünmüş PARP ve P-53'ü aktive etmesiyle kanser hücreleri üzerinde apoptotik bir etkiye sahip olduğunu da doğrulamıştır. Sonuç: Bu çalışmanın sonucu olarak, C. Campestris’in mide karsinomu tedavisinde umut vadeden bir antikanser ajanı olabileceği düşünülmektedir.
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, Nevzat
Endometriomas 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.
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, Zozan
Cholangiocarcinoma (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.
Effect of metal Ions on the activity of ten NAD-dependent formate dehydrogenases
(2020) Bulut, Huri; Valjakka, Jarkko; Yüksel, Büşra; Yılmazer, Berin; Turunen, Ossi; Binay, Barış
NAD-dependent formate dehydrogenase (FDH) enzymes are frequently used in industrial and scientific applications. FDH is a reversible enzyme that reduces the NAD molecule to NADH and produces CO2 by oxidation of the formate ion, whereas it causes CO2 reduction in the reverse reaction. Some transition metal elements - Fe3+, Mo6+ and W6 + - can be found in the FDH structure of anaerobic and archaeal microorganisms, and these enzymes require cations and other redox-active cofactors for their FDH activity. While NAD-dependent FDHs do not necessarily require any metal cations, the presence of various metal cations can still affect FDH activities. To study the effect of 11 different metal ions, NAD-dependent FDH enzymes from ten different microorganisms were tested: Ancylobacter aquaticus (AaFDH), Candida boidinii (CboFDH), Candida methylica (CmFDH), Ceriporiopsis subvermispora (CsFDH), Chaetomium thermophilum (CtFDH), Moraxella sp. (MsFDH), Myceliophthora thermophila (MtFDH), Paracoccus sp. (PsFDH), Saccharomyces cerevisiae (ScFDH) and Thiobacillus sp. (TsFDH). It was found that metal ions (mainly Cu2+ and Zn2+) could have quite strong inhibition effects on several enzymes in the forward reaction, whereas several cations (Li+, Mg2+, Mn2+, Fe3+ and W6+) could increase the forward reaction of two FDHs. The highest activity increase (1.97 fold) was caused by Fe3+ in AaFDH. The effect on the reverse reaction was minimal. The modelled structures of ten FDHs showed that the active site is formed by 15 highly conserved amino acid residues spatially settling around the formate binding site in a conserved way. However, the residue differences at some of the sites close to the substrate do not explain the activity differences. The active site space is very tight, excluding water molecules, as observed in earlier studies. Structural examination indicated that smaller metal ions might be spaced close to the active site to affect the reaction. Metal ion size showed partial correlation to the effect on inhibition or activation. Affinity of the substrate may also affect the sensitivity to the metal's effect. In addition, amino acid differences on the protein surface may also be important for the metal ion effect.
The effect of omentectomy on the blood levels of adipokines in obese patients with endometrial cancer
(Elsevier Science, 2022) Comba, Cihan; Özdemir, İsa Aykut; Demirayak, Gökhan; Erdoğan, Şakir Volkan; Demir, Ömer; Özlem Yıldız, Güneş; Bulut, Huri; Karakaş, Sema; Gülseren, Varol; Afşar, Selim; Güngördük, Kemal
Objective To investigate the blood levels of adipokines in obese patients with endometrial cancer who have and have not undergone omentectomy. Methods Between September 2017 and September 2019, the study recruited 54 patients with endometrial cancer. Measurements were taken of blood levels of human leptin, perilipin-1, adiponectin, adipolin, resistin, visfatin, and estrone preoperatively and postoperatively before adjuvant therapy or at the end of one month. The serum samples were separated by centrifugation for 10 mins at 3,000 revolutions/min, then stored at ?80 °C until assay. Results In this prospective study, a total of 54 endometrial cancer patients were analyzed in two separate groups according to the omentectomy status. Comprehensive staging surgery with omentectomy and without omentectomy was performed in 26 patients and 28 patients, respectively. The age, body mass index, body fat index, waist circumference, and skin thickness values of the patients with and without omentectomy were found to be similar. No statistically significant difference was determined between the patients with and without omentectomy in respect of the blood level of the adipokines measured preoperatively. A strong statistically significant correlation was determined between the pre and postoperative levels of Human Leptin (p = 0.002), perilipin-1(p = 0.001), adipolin (p < 0.001), adiponectin (p < 0.001), resistin (p = 0.001), visfatin (p < 0.001), and estrone (p = 0.004) (r = ?0.43, ?0.47, 0.75, 0.84, ?0.47, - 0.58, ?0.41, respectively) Conclusions Omentectomy affected the postoperative blood levels of adipokines in obese patients with endometrial cancer. As omentectomy may have some positive effects on metabolism in these patients, it may be considered during endometrial cancer surgery due to the possible positive metabolic effects.
Effects of combined administration of doxorubicin and chloroquine on lung pathology in mice with solid Ehrlich ascites carcinoma
(2022) Utkusavas, Ayfer; Gurel Gurevin, Ebru; Yilmazer, Nadim; Uvez, Ayca; Oztay, Fusun; Bulut, Huri
Combined use of a chemotherapeutic agent and an autophagy inhibitor is a novel cancer treatment strategy. We investigated the effects of chloroquine (CQ) on lung pathology caused by both solid Ehrlich ascites carcinoma (EAC) and doxorubicin (DXR). A control group and eight experimental groups of adult female mice were inoculated subcutaneously with 2.5 × 106 EAC cells. DXR (1.5 mg/kg and 3 mg/kg) and CQ (25 mg/kg and 50 mg/kg) alone or in combination were injected intraperitoneally on days 2, 7 and 12 following inoculation with EAC cells. Lung tissue samples were examined using immunohistochemistry (IHC) for endothelial (eNOS), inducible nitric oxide synthase (iNOS) and neutrophil gelatinase-associated lipocalin (NGAL). Serum catalase (CAT), glutathione peroxidase (GPx), superoxide dismutase (SOD) and malondialdehyde (MDA) levels were measured using ELISA. We found decreased levels of iNOS and eNOS in the groups that received 1.5 mg/kg DXR alone and in combination with 25 mg/kg and 50 mg/kg CQ. Combined administration of DXR and CQ partially prevented disruption of alveolar structure. Levels of antioxidant enzymes and MDA were lower in all treated groups; the greatest reduction was observed in mice that received the combination of 25 mg/kg CQ + 1.5 mg/kg DXR. Levels of NGAL were elevated in all treated groups. We found that CQ ameliorated both EAC and DOX induced lung pathology in female mice with solid EAC by reducing oxidative stress.
Effects of TNF inhibitors and an IL12/23 inhibitor on changes in body weight and adipokine levels in psoriasis patients: a 48-week comparative study
(Taylor and Francis, 2021) Onsun, Nahide; Akaslan, Tahsin Cagdas; Sallahoglu, Kadriye; Gulcan, Aliye Sevdem; Bulut, Huri; Yabaci, Aysegul
Background: Psoriasis is a chronic inflammatory disease associated with obesity and metabolic syndrome. Adipokines are thought to be a link between psoriasis and obesity. Leptin, adiponectin, and omentin are bioactive adipokines thought to play a role in both metabolic comorbidities and inflammation. Anti-tumour necrosis factor alfa (anti-TNF-?) agents are effective for psoriasis treatment, although significant weight gain has been reported during anti-TNF-? therapy. The interleukin 12/23 (IL 12/23) inhibitor ustekinumab is also effective for psoriasis treatment. We compared the effects of three anti-TNF-? drugs and an IL-12/23 inhibitor on adipokines and weight gain during treatment. Patients and methods: This prospective study included 80 patients (37 women, 43 men) with moderate to severe plaque psoriasis whose age and weight were matched. The patients were divided into four equal groups: etanercept, infliximab, adalimumab, and ustekinumab treatment groups. Psoriasis Area Severity Index (PASI) score, body weight (muscle and fat compartments), and leptin, adiponectin, and omentin levels were evaluated at baseline and weeks 4, 12, 24, and 48 of treatment. Results: There were no differences between drug groups in terms of weight parameters or biochemical parameters at baseline. At the end of 48 weeks, there was significant weight gain in the adalimumab group. Patients who received infliximab showed significant weight gain by week 12, but in the following weeks they returned to their initial weight. Body weight reached a maximum level by week 12 in patients using etanercept, but they lost weight in the following weeks and finished the study below their initial weight. Patients using ustekinumab did not demonstrate significant weight change during the 48 weeks except at week 12. At the end of week 48, PASI75 (improvement in PASI ?75%) response rates were approximately 85% for the ustekinumab group, 80% for the adalimumab group, 75% for the infliximab group, and 50% for the etanercept group. Leptin, adiponectin, and omentin levels were higher in the ustekinumab group at all weeks except baseline. The lowest levels were observed in the etanercept group. The treatment response rate was also lower in the etanercept group. Limitations: We did not evaluate visfatin and resistin levels, insulin sensitivity, and cardiovascular risk that may be associated with weight gain and adipokine levels. Conclusions: Unlike TNF inhibitors, ustekinumab does not cause significant weight changes and it increases adipokine levels more than TNF inhibitors. Adipokine levels seem to be related to the treatment response.
FTIR, RAMAN and biochemical tools to detect reveal of oxidative Stress-Related lipid and protein changes in fibromyalgia
(Elsevier, 2023) Guleken, Zozan; Suna, Gizem; Karaca, Sahika Burcu; Bulut, Huri; Ayada, Ceylan; Pancerz, Krzysztof; Paja, Wieslaw
In this study, our aim was to investigate the pathogenesis and diagnosis of fibromyalgia (FM), a complex disorder with poorly understood causes. We focused on examining the role of oxidative stress and associated lipid and protein alterations in FM patients. To achieve this, we conducted a comprehensive analysis of serum samples obtained from 60 FM patients and 40 healthy individuals. In our analysis, we employed various biochemical assays and spectroscopic techniques including Fourier Transform Infra-Red (FTIR) and Raman spectroscopy. Moreover, we applied advanced statistical methods such as chemometrics and machine learning algorithms to analyze the collected data.The obtained results showed higher levels of oxidative stress, around 113% on the visual analogue scale score and around 5800% higher when C = O vibrations from lipids visible in FTIR spectra were analyzed. Also, lower levels of total antioxidants and oxidants in FM patients were observed compared with the healthy group.Moreover, FTIR spectra of serum collected from FM patients showed significantly higher absorbance of bands corresponding to polysaccharides, proteins, and lipids, while differences were not found in the Raman spectra. The principal component analysis (PCA) of the obtained spectroscopic data showed that it is possible to distinguish patients suffering from FM and healthy control groups with 100% accuracy using FTIR spectroscopy. PLS analysis showed significance in the differentiation of lipid vibrations among groups. In summary, FTIR coupled with chemometrics has the potential for fibromyalgia diagnosis.

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