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Cakmak-Arslan G, Kaya Y, Mamuk S, Akarsu ES, Severcan F. The investigation of the molecular changes during lipopolysaccharide-induced systemic inflammation on rat hippocampus by using FTIR spectroscopy. J Biophotonics 2024:e202300541. [PMID: 38531619 DOI: 10.1002/jbio.202300541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/12/2024] [Accepted: 03/13/2024] [Indexed: 03/28/2024]
Abstract
The aim of this study is to reveal the molecular changes accompanying the neuronal hyper-excitability during lipopolysaccharide (LPS)-induced systemic inflammation on rat hippocampus using Fourier transform infrared (FTIR) spectroscopy. For this aim, the body temperature of Wistar albino rats administered LPS or saline was recorded by radiotelemetry. The animals were decapitated when their body temperature began to decrease by 0.5°C after LPS treatment and the hippocampi of them were examined by FTIR spectroscopy. The results indicated that systemic inflammation caused lipid peroxidation, an increase in the amounts of lipids, proteins and nucleic acids, a decrease in membrane order, an increase in membrane dynamics and changes in the secondary structure of proteins. Principal component analysis successfully separated control and LPS-treated groups. In conclusion, significant structural, compositional and functional alterations occur in the hippocampus during systemic inflammation and these changes may have specific characteristics which can lead to neuronal hyper-excitability.
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Affiliation(s)
- Gulgun Cakmak-Arslan
- Department of Biology, Faculty of Arts and Sciences, Duzce University, Duzce, Turkey
| | - Yildiray Kaya
- Department of Biology, Faculty of Arts and Sciences, Duzce University, Duzce, Turkey
| | - Soner Mamuk
- Department of Medical Pharmacology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Eyup Sabri Akarsu
- Department of Medical Pharmacology, Faculty of Medicine, Ankara University, Ankara, Turkey
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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Dogan A, Sen I, Severcan M, Brockmann G, Severcan F. Strain and Depot-specific Differences in Adipose Tissues of Obese BFMI Mice. In Vivo 2023; 37:1672-1679. [PMID: 37369466 DOI: 10.21873/invivo.13253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND/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.
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Affiliation(s)
- Ayca Dogan
- Department of Physiology, Faculty of Medicine, Altinbas University, Istanbul, Turkey
| | - Ilke Sen
- Department of Physiology and Pharmacology, Karolinska Institute, Stockholm, Sweden
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, Faculty of Engineering and Natural Sciences, Altinbas University, Istanbul, Turkey
| | - Gudrun Brockmann
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University, Berlin, Germany
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey;
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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Kucuk Baloglu F, Guldag Tas D, Yilmaz O, Severcan F. The recovery effect of Vitamin C on structural alterations due to Streptozotocin-Induced diabetes in rat testicular tissues. Spectrochim Acta A Mol Biomol Spectrosc 2023; 288:122149. [PMID: 36470089 DOI: 10.1016/j.saa.2022.122149] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 10/31/2022] [Accepted: 11/21/2022] [Indexed: 06/17/2023]
Abstract
Type I Diabetes is a multisystem disease that causes alterations in carbohydrate, protein, and fat metabolisms due to hyperglycemia. It has an extensive pathology, especially the mechanism involving oxidative stress is still complex. Type I diabetes is correlated with increased formation of free radicals and decreased levels of antioxidant potential. Vitamin C (Vit C) is a powerful antioxidant that participates in antioxidant defense, protecting lipid membranes and proteins from oxidative damage by donating electrons to free radicals. The effect of type I diabetes and the recovery role of Vit C on the structure and composition of the biomolecular content of testicular tissue is still unknown. Therefore, the current study aimed to investigate the alterations in the biomolecules of rat testes due to Streptozotocin (STZ)-induced type I diabetes using Attenuated Total Reflectance (ATR)-Fourier Transform Infrared (FTIR) spectroscopy and histological staining. The results revealed that the biomolecular structure and composition of testicular tissue are highly affected due to the development of diabetes. We obtained decreased saturation levels and increased unsaturation index in the lipids indicating the presence of lipid peroxidation in the diabetic state. The elevated lipid peroxidation levels have been implicated in the pathogenesis of naturally occurring and chemically induced diabetes. On the other hand, the protein content of diabetic rat testicular tissue was shown to decrease considerably, indicating an increase in proteolysis processes. Supporting the ratio of protein structural and conformational change, protein secondary structural components were also found to alter substantially in the diabetic state. Diabetes was also shown to lead to a decrease in the content of nucleic acids compared to proteins. These diabetes-induced alterations were found to be substantially recovered with the administration of Vit C. Although different doses and administration types of Vit C have been reported in the literature, there is no consensus yet. Therefore, we used three different doses of Vit C in our study as high (100 mg/kg/day), medium (50 mg/kg/day) and low (15 mg/kg/day) doses intraperitoneally in the present study, and the medium dose was found to be the most effective in the recovery from the diabetes-induced structural damages on rat testicular tissue. Vit C may have a therapeutic effect to be used as a complementary therapy in the treatment of diabetes.
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Affiliation(s)
- Fatma Kucuk Baloglu
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Giresun University, Department of Biology, Giresun, Turkey
| | - Damla Guldag Tas
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
| | - Okkes Yilmaz
- Firat University, Department of Biology, Elazig, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Altinbas University, Department of Biophysics, Faculty of Medicine, Istanbul, Turkey.
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Elibol B, Severcan M, Jakubowska-Dogru E, Dursun I, Severcan F. The structural effects of Vitamin A deficiency on biological macromolecules due to ethanol consumption and withdrawal: An FTIR study with chemometrics. J Biophotonics 2022; 15:e202100377. [PMID: 35333440 DOI: 10.1002/jbio.202100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The 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.
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Affiliation(s)
- Birsen Elibol
- Faculty of Medicine, Department of Medical Biology, Bezmialem Vakif University, Istanbul, Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara, Turkey
| | - Ewa Jakubowska-Dogru
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ilknur Dursun
- Faculty of Medicine, Department of Physiology, Istinye University, Istanbul, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Faculty of Medicine, Department of Biophysics, Altinbas University, Istanbul, Turkey
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Yonar D, Severcan M, Gurbanov R, Sandal A, Yilmaz U, Emri S, Severcan F. Rapid diagnosis of malignant pleural mesothelioma and its discrimination from lung cancer and benign exudative effusions using blood serum. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166473. [PMID: 35753541 DOI: 10.1016/j.bbadis.2022.166473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023]
Abstract
Malignant 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.
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Affiliation(s)
- Dilek Yonar
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Yuksek Ihtisas University, Faculty of Medicine, Biophysics Department, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronics Engineering, Ankara, Turkey
| | - Rafig Gurbanov
- Bilecik Seyh Edebali University, Department of Bioengineering, Bilecik, Turkey
| | - Abdulsamet Sandal
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Ankara Occupational and Environmental Diseases Hospital, Ankara, Turkey
| | - Ulku Yilmaz
- Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Salih Emri
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Medicana Hospital, Department of Chest Diseases, Kadikoy, Istanbul, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Altinbas University, Faculty of Medicine, Biophysics Department, Istanbul, Turkey.
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Dogan A, Gurbanov R, Severcan M, Severcan F. CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics. Turk J Biol 2021; 45:549-558. [PMID: 34803453 PMCID: PMC8573849 DOI: 10.3906/biy-2105-65] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
From 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.
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Affiliation(s)
- Ayca Dogan
- Department of Physiology, Faculty of Medicine, Altinbaş University, İstanbul Turkey
| | - Rafig Gurbanov
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, Bilecik Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, Faculty of Engineering and Natural Sciences, Altınbaş University, İstanbul Turkey
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altınbaş University, İstanbul Turkey
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Ustaoglu SG, Ali MHM, Rakib F, Blezer ELA, Van Heijningen CL, Dijkhuizen RM, Severcan F. Biomolecular changes and subsequent time-dependent recovery in hippocampal tissue after experimental mild traumatic brain injury. Sci Rep 2021; 11:12468. [PMID: 34127773 PMCID: PMC8203626 DOI: 10.1038/s41598-021-92015-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/27/2021] [Indexed: 12/25/2022] Open
Abstract
Traumatic brain injury (TBI) is the main cause of disability and mortality in individuals under the age of 45 years. Elucidation of the molecular and structural alterations in brain tissue due to TBI is crucial to understand secondary and long-term effects after traumatic brain injury, and to develop and apply the correct therapies. In the current study, the molecular effects of TBI were investigated in rat brain at 24 h and 1 month after the injury to determine acute and chronic effects, respectively by Fourier transform infrared imaging. This study reports the time-dependent contextual and structural effects of TBI on hippocampal brain tissue. A mild form of TBI was induced in 11-week old male Sprague Dawley rats by weight drop. Band area and intensity ratios, band frequency and bandwidth values of specific spectral bands showed that TBI causes significant structural and contextual global changes including decrease in carbonyl content, unsaturated lipid content, lipid acyl chain length, membrane lipid order, total protein content, lipid/protein ratio, besides increase in membrane fluidity with an altered protein secondary structure and metabolic activity in hippocampus 24 h after injury. However, improvement and/or recovery effects in these parameters were observed at one month after TBI.
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Affiliation(s)
- Sebnem Garip Ustaoglu
- Department of Medical Biochemistry, Faculty of Medicine, Altinbas University, Bakirkoy, Istanbul, Turkey.
| | - Mohamed H M Ali
- Diabetes Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), P.O. Box 34110, Doha, Qatar.
| | - Fazle Rakib
- Department of Chemistry and Earth Sciences, Qatar University, Doha, Qatar
| | - Erwin L A Blezer
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Caroline L Van Heijningen
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rick M Dijkhuizen
- Biomedical MR Imaging and Spectroscopy Group, Center for Image Sciences, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altinbas University, Bakirkoy, Istanbul, Turkey.,Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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Gok S, Kuzmenko O, Babinskyi A, Severcan F. Vitamin E Derivative with Modified Side Chain Induced Apoptosis by Modulating the Cellular Lipids and Membrane Dynamics in MCF7 Cells. Cell Biochem Biophys 2021; 79:271-287. [PMID: 33442824 DOI: 10.1007/s12013-020-00961-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 12/04/2020] [Indexed: 10/22/2022]
Abstract
The vitamin E derivative with side chain modification (TC6OAc) has been shown to possess anticancer activity in our earlier in vivo studies. It was hypothesized that, as Vitamin E (VE) and VE derivative are fat soluble lipophilic molecules, they exert their function by modulating the lipid metabolism and related pathways. This study aimed to evaluate the cellular impact of this VE derivative (2,5,7,8-Tetramethyl-2-(4'-Methyl-3'-Pentenyl)-6-Acetoxy Chromane-TC6OH), using α-tocopherol as a reference compound throughout the experiments. Their effects on the cellular metabolism, the biophysical properties of cellular lipids and the functional characteristics of cells were monitored in human estrogen receptor (ER) positive breast cancer cells. It has been documented that TC6OH treatment induces tumor cell apoptosis by dissipating the mitochondrial membrane potential, modulating the lipid, transportation and degradation as well as downregulating certain anti-apoptotic and growth factor related proteins. Due to resistance of ER positive cells to the established therapies, the findings of this study are of translational value.
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Affiliation(s)
- Seher Gok
- The Scientific and Technological Research Council of Turkey, Ankara, Turkey
| | - Oleksandr Kuzmenko
- Department of Vitamins and Coenzymes Biochemistry, Palladin Institute of Biochemistry, Kiev, Ukraine
| | - Andrii Babinskyi
- Department of Vitamins and Coenzymes Biochemistry, Palladin Institute of Biochemistry, Kiev, Ukraine
| | - Feride Severcan
- Faculty of Medicine, Department of Biophysics, Altinbas University, Istanbul, Turkey. .,Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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Kepenek ES, Severcan M, Gozen AG, Severcan F. Discrimination of heavy metal acclimated environmental strains by chemometric analysis of FTIR spectra. Ecotoxicol Environ Saf 2020; 202:110953. [PMID: 32800227 DOI: 10.1016/j.ecoenv.2020.110953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 06/24/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Heavy 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 μg/ml) or Pb (90 μg/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.
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Affiliation(s)
- Eda Seyma Kepenek
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, School of Engineering and Natural Sciences, Altinbas University, Istanbul, Turkey.
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
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Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. Journal of Photochemistry and Photobiology B: Biology 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
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Cakmak Arslan G, Severcan F. The effects of radioprotectant and potential antioxidant agent amifostine on the structure and dynamics of DPPC and DPPG liposomes. Biochimica et Biophysica Acta (BBA) - Biomembranes 2019; 1861:1240-1251. [DOI: 10.1016/j.bbamem.2019.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/17/2019] [Accepted: 04/23/2019] [Indexed: 12/30/2022]
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12
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Kepenek ES, Gozen AG, Severcan F. Molecular characterization of acutely and gradually heavy metal acclimated aquatic bacteria by FTIR spectraoscopy. J Biophotonics 2019; 12:e201800301. [PMID: 30578608 DOI: 10.1002/jbio.201800301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/11/2018] [Accepted: 12/19/2018] [Indexed: 05/28/2023]
Abstract
In the environment, bacteria can be exposed to the concentration gradient of toxic heavy metals (gradual) or sudden high concentration of them (acute). In both situations, bacteria get acclimated to toxic heavy metal concentrations. Acclimation causes metabolic and molecular changes in bacteria. In this study, we aimed to understand whether there are differences between molecular profiles of the bacteria (Brevundimonas, Gordonia and Microbacterium) which are under acute or gradual exposure to cadmium or lead by using ATR-FTIR spectroscopy. Our results revealed the differences between the acclimation groups in membrane dynamics including changes in the structure and composition of the membrane lipids and proteins. Furthermore, protein concentrations decreased in acclimated bacterial groups. Also, a remarkable increase in exopolymer production occurred in acclimated groups. Interestingly, bacteria under acute cadmium exposure produced the significantly higher amount of exopolymer than they did under gradual exposure. On the contrary, under lead exposure gradually acclimate strains produced significantly higher amounts of exopolymer than those of acutely acclimated ones. This information can be used in bioremediation studies to obtain bacterial strains producing a higher amount of exopolymer.
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Affiliation(s)
- Eda S Kepenek
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ayse G Gozen
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Istanbul Altınbas University, Istanbul, Turkey
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Severcan F, Abbas S, Yonar D, Emri S. Infrared Spectroscopy Offers Tremendous Potential in Cancer Diagnosis. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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14
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Ozyurt I, Garip S, Kucuk Baloglu F, Zorlu F, Severcan F. Investigation of the Structural Effects of Radiotherapy Dose Rate on Rat Lung Tissue: An FTIR Imaging Study. Biophys J 2019. [DOI: 10.1016/j.bpj.2018.11.3040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Abbas S, Simsek Ozek N, Emri S, Koksal D, Severcan M, Severcan F. Diagnosis of malignant pleural mesothelioma from pleural fluid by Fourier transform-infrared spectroscopy coupled with chemometrics. J Biomed Opt 2018; 23:1-14. [PMID: 30317725 DOI: 10.1117/1.jbo.23.10.105003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
This 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.
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Affiliation(s)
- Sherif Abbas
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Ain Shams University, Physics Department, Cairo, Egypt
| | - Nihal Simsek Ozek
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Ataturk University, Department of Biology, Erzurum, Turkey
- Ataturk University, East Anatolian High Technology Research and Application Center (DAYTAM), Erzurum, Turkey
| | - Salih Emri
- Hacettepe University, Department of Chest Diseases, Ankara, Turkey
- Altinbas University, Department of Chest Diseases, Faculty of Medicine, Istanbul, Turkey
| | - Deniz Koksal
- Hacettepe University, Department of Chest Diseases, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronic Engineering, Ankara, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Altinbas University, Department of Biophysics, Faculty of Medicine, Istanbul, Turkey
- Altinbas University, Graduate Program of Biomedical Sciences, Institute of Health Sciences, Istanbul, Turkey
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16
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Garip Ustaoglu S, Evis Z, Ilbay G, Boskey AL, Severcan F. Side-Effects of Convulsive Seizures and Anti-Seizure Therapy on Bone in a Rat Model of Epilepsy. Appl Spectrosc 2018; 72:689-705. [PMID: 28905646 DOI: 10.1177/0003702817734617] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The severe sole effects of seizures on the cortical part of bone were reported in our previous study. However, the side effects of anti-epileptic drug therapy on bones has not been differentiated from the effects of the convulsive seizures, yet. This study provides the first report on differentiation of the effects of seizures and carbamazepine (a widely used antiepileptic drug) therapy on bones; 50 mg/kg/day drug was given to genetically induced absence epileptic rats for five weeks. Distinct bone regions including cortical, trabecular, and growth plate in each of tibia, femur, and spine tissues were studied using Fourier transform infrared (FT-IR) imaging and Vickers microhardness test. Blood levels of vitamin D and bone turnover biomarkers were also measured. According to the FT-IR imaging results, both seizure and carbamazepine-treated groups, more dominantly the drug-treated group, had lower mineral content with altered collagen crosslinks and higher crystallinity, implying reduced bone strength. Lower microhardness values also supported lower mechanical strength in bones. The most affected bone tissue and region from seizures and treatment was found as the spine and cortical, respectively. While there was a reduction in vitamin D and calcium levels in both seizure and carbamazepin-treated groups, significantly elevated PTH and bone turnover biomarkers were only seen in the drug-treated group.
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Affiliation(s)
- Sebnem Garip Ustaoglu
- 1 Department of Biochemistry, 187458 Middle East Technical University , Ankara, Turkey
- 2 Department of Medical Biochemistry, 187458 Faculty of Medicine, Altinbas University, Istanbul, Turkey
| | - Zafer Evis
- 3 Department of Engineering Sciences, Middle East Technical University, Ankara, Turkey
| | - Gul Ilbay
- 4 Department of Physiology, Faculty of Medicine, Kocaeli University, Kocaeli, Turkey
| | - Adele Ludin Boskey
- 5 25062 Mineralized Tissue Laboratory, Hospital for Special Surgery, New York, NY, USA
| | - Feride Severcan
- 6 Department of Biological Sciences, 187458 Middle East Technical University , Ankara, Turkey
- 7 Department of Biophysics, 187458 Faculty of Medicine, Altinbas University, Istanbul, Turkey
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17
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Gurbanov R, S Ozek N, Tunçer S, Severcan F, Gozen AG. Aspects of silver tolerance in bacteria: infrared spectral changes and epigenetic clues. J Biophotonics 2018; 11:e201700252. [PMID: 29243883 DOI: 10.1002/jbio.201700252] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/13/2017] [Indexed: 06/07/2023]
Abstract
In this study, the molecular profile changes leading to the adaptation of bacteria to survive and grow at inhibitory silver concentration were explored. The profile obtained through infrared (IR)-based measurements indicated extensive changes in all biomolecular components, which were supported by chemometric techniques. The changes in biomolecular profile were prominent, including nucleic acids. The changes in nucleic acid region (1350-950 cm-1 ) were encountered as a clue for conformational change in DNA. Further analysis of DNA by IR spectroscopy revealed changes in the backbone and sugar conformations. Moreover, Enzyme-Linked Immunosorbent Assay-based measurements of DNA methylation levels were performed to see if epigenetic mechanisms are in operation during bacterial adaptation to this environmental challenge. The results indicated a notable demethylation in Escherichia coli and methylation in Staphylococcus aureus likely to be associated with their elaborate adaptation process to sustain survival and growth.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik Şeyh Edebali University, Bilecik, Turkey
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Nihal S Ozek
- Department of Biology, Ataturk University, Erzurum, Turkey
| | - Sinem Tunçer
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Turkey
| | - Ayse G Gozen
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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18
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Gurbanov R, Gozen AG, Severcan F. Rapid classification of heavy metal-exposed freshwater bacteria by infrared spectroscopy coupled with chemometrics using supervised method. Spectrochim Acta A Mol Biomol Spectrosc 2018; 189:282-290. [PMID: 28823969 DOI: 10.1016/j.saa.2017.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/08/2017] [Accepted: 08/13/2017] [Indexed: 05/21/2023]
Abstract
Rapid, cost-effective, sensitive and accurate methodologies to classify bacteria are still in the process of development. The major drawbacks of standard microbiological, molecular and immunological techniques call for the possible usage of infrared (IR) spectroscopy based supervised chemometric techniques. Previous applications of IR based chemometric methods have demonstrated outstanding findings in the classification of bacteria. Therefore, we have exploited an IR spectroscopy based chemometrics using supervised method namely Soft Independent Modeling of Class Analogy (SIMCA) technique for the first time to classify heavy metal-exposed bacteria to be used in the selection of suitable bacteria to evaluate their potential for environmental cleanup applications. Herein, we present the powerful differentiation and classification of laboratory strains (Escherichia coli and Staphylococcus aureus) and environmental isolates (Gordonia sp. and Microbacterium oxydans) of bacteria exposed to growth inhibitory concentrations of silver (Ag), cadmium (Cd) and lead (Pb). Our results demonstrated that SIMCA was able to differentiate all heavy metal-exposed and control groups from each other with 95% confidence level. Correct identification of randomly chosen test samples in their corresponding groups and high model distances between the classes were also achieved. We report, for the first time, the success of IR spectroscopy coupled with supervised chemometric technique SIMCA in classification of different bacteria under a given treatment.
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Affiliation(s)
- Rafig Gurbanov
- Department of Molecular Biology and Genetics, Bilecik S.E. University, 11230 Bilecik, Turkey; Department of Biochemistry, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayse Gul Gozen
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey; Department of Biophysics, Faculty of Medicine, Altinbas University, 34217 Istanbul, Turkey.
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19
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Abstract
The effect of aging process on stem cell function is crucial because of their critical role in tissue regeneration and repair. The impact of aging on stem cells needs to be understood clearly for the success of clinical application and obtaining desired therapeutic outcome throughout the novel stem cell based therapies. The existing methods used to monitor and characterize the stem cells have some unwanted effects on the properties of stem cells and these methods also do not provide real-time information about cellular conditions. These challenges enforce the usage of nondestructive, rapid, sensitive, high-quality, label-free, cheep, and innovative chemical monitoring methods. In this context, vibrational spectroscopy provides promising alternative to get new information into the field of stem cell biology for chemical analysis, quantification, and imaging of stem cells. Infrared spectroscopy and imaging coupled with chemometric methods can be used as novel and complimentary methods to obtain new insight into stem cell studies for future therapeutic and regenerative medicine.
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Affiliation(s)
- Ceren Aksoy
- Research Coordination Department, Middle East Technical University, Ankara, Turkey
| | - Feride Severcan
- Department of Biophysics, Altınbaş University School of Medicine, İstanbul, Turkey.
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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20
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Kucuk Baloglu F, Baloglu O, Heise S, Brockmann G, Severcan F. Triglyceride dependent differentiation of obesity in adipose tissues by FTIR spectroscopy coupled with chemometrics. J Biophotonics 2017; 10:1345-1355. [PMID: 28128535 DOI: 10.1002/jbio.201600223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/28/2016] [Accepted: 12/23/2016] [Indexed: 06/06/2023]
Abstract
The excess deposition of triglycerides in adipose tissue is the main reason of obesity and causes excess release of fatty acids to the circulatory system resulting in obesity and insulin resistance. Body mass index and waist circumference are not precise measure of obesity and obesity related metabolic diseases. Therefore, in the current study, it was aimed to propose triglyceride bands located at 1770-1720 cm-1 spectral region as a more sensitive obesity related biomarker using the diagnostic potential of Fourier Transform Infrared (FTIR) spectroscopy in subcutaneous (SCAT) and visceral (VAT) adipose tissues. The adipose tissue samples were obtained from 10 weeks old male control (DBA/2J) (n = 6) and four different obese BFMI mice lines (n = 6 per group). FTIR spectroscopy coupled with hierarchical cluster analysis (HCA) and principal component analysis (PCA) was applied to the spectra of triglyceride bands as a diagnostic tool in the discrimination of the samples. Successful discrimination of the obese, obesity related insulin resistant and control groups were achieved with high sensitivity and specificity. The results revealed the power of FTIR spectroscopy coupled with chemometric approaches in internal diagnosis of abdominal obesity based on the spectral differences in the triglyceride region that can be used as a spectral marker.
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Affiliation(s)
- Fatma Kucuk Baloglu
- Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey
| | - Onur Baloglu
- Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey
| | - Sebastian Heise
- Department of Breeding Biology and Molecular Genetics, Humboldt Universitatzu Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Department of Breeding Biology and Molecular Genetics, Humboldt Universitatzu Berlin, Berlin, Germany
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06531, Ankara, Turkey
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21
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Inan Genç A, Gok S, Banerjee S, Severcan F. Valdecoxib Recovers the Lipid Composition, Order and Dynamics in Colon Cancer Cell Lines Independent of COX-2 Expression: An ATR-FTIR Spectroscopy Study. Appl Spectrosc 2017; 71:105-117. [PMID: 27354402 DOI: 10.1177/0003702816654164] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Prostanoids play an important role in a variety of physiological and pathophysiological processes including inflammation and cancer. The rate-limiting step in the prostanoid biosynthesis pathway is catalyzed by cyclooxygenases (COXs). Aberrant expression of the inducible isoform COX-2 plays a significant role in colon cancer initiation and progression. In this study, we have hypothesized that COX-2 specific inhibitors such as Valdecoxib (VLX), being highly hydrophobic, may alter biophysical properties of cellular lipids. In this study, COX-2 expressing (HT29) and COX-2 non-expressing (SW620) colon cancer cell lines were treated with VLX and examined using attenuated total reflection infrared spectroscopy. The results revealed that VLX treatment decreased lipid fluidity in the cells irrespective of COX-2 expression status and affected order parameters of the lipids in both cell lines. Cluster analysis also indicated that the spectral differences between the two cell lines are profound and could be successfully differentiated. Valdecoxib treatment could enhance the composition, order and dynamics of the lipids of colon cancer cells independently of its COX-2 inhibitory mechanism. Valdecoxib has therapeutic effects upon colon cancer, therefore it can be used as an adjuvant and/or chemopreventive agent for colon cancer.
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Affiliation(s)
- Aysun Inan Genç
- Department of Biological Sciences, Middle East Technical University, Turkey
| | - Seher Gok
- Department of Biological Sciences, Middle East Technical University, Turkey
| | - Sreeparna Banerjee
- Department of Biological Sciences, Middle East Technical University, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Turkey
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22
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Baltacıoğlu H, Bayındırlı A, Severcan F. Secondary structure and conformational change of mushroom polyphenol oxidase during thermosonication treatment by using FTIR spectroscopy. Food Chem 2017; 214:507-514. [DOI: 10.1016/j.foodchem.2016.07.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Revised: 05/10/2016] [Accepted: 07/05/2016] [Indexed: 01/23/2023]
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23
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Bozkurt O, Bilgin MD, Evis Z, Pleshko N, Severcan F. Early Alterations in Bone Characteristics of Type I Diabetic Rat Femur: A Fourier Transform Infrared (FT-IR) Imaging Study. Appl Spectrosc 2016; 70:2005-2015. [PMID: 27680083 DOI: 10.1177/0003702816671059] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 08/08/2016] [Indexed: 06/06/2023]
Abstract
Alterations in microstructure and mineral features can affect the mechanical and chemical properties of bones and their capacity to resist mechanical forces. Controversial results on diabetic bone mineral content have been reported and little is known about the structural alterations in collagen, maturation of apatite crystals, and carbonate content in diabetic bone. This current study is the first to report the mineral and organic properties of cortical, trabecular, and growth plate regions of diabetic rat femurs using Fourier transform infrared (FT-IR) microspectroscopy and the Vickers microhardness test. Femurs of type I diabetic rats were embedded into polymethylmethacrylate blocks, which were used for FT-IR imaging and microhardness studies. A lower mineral content and microhardness, a higher carbonate content especially labile type carbonate content, and an increase in size and maturation of hydroxyapatite crystals were observed in diabetic femurs, which indicate that diabetes has detrimental effects on bone just like osteoporosis. There was a decrease in the level of collagen maturity in diabetic femurs, implying a decrease in bone collagen quality that may contribute to the decrease in tensile strength and bone fragility. Taken together, the findings revealed alterations in structure and composition of mineral and matrix components, and an altered quality and mechanical strength of rat femurs in an early stage of type I diabetes. The results contribute to the knowledge of structure-function relationship of mineral and matrix components in diabetic bone disorder and can further be used for diagnostic or therapeutic purposes.
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Affiliation(s)
- Ozlem Bozkurt
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Biophysics, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Mehmet Dincer Bilgin
- Department of Biophysics, Faculty of Medicine, Adnan Menderes University, Aydın, Turkey
| | - Zafer Evis
- Department of Engineering Sciences, Middle East Technical University, Ankara, Turkey
| | - Nancy Pleshko
- Department of Bioengineering, Temple University, Philadelphia, Pennsylvania, USA
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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24
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Cakmak G, Severcan M, Zorlu F, Severcan F. Structural and functional damages of whole body ionizing radiation on rat brain homogenate membranes and protective effect of amifostine. Int J Radiat Biol 2016; 92:837-848. [PMID: 27585945 DOI: 10.1080/09553002.2016.1230237] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
PURPOSE To investigate the effects of whole body ionizing radiation at a sublethal dose on rat brain homogenate membranes and the protective effects of amifostine on these systems at molecular level. MATERIALS AND METHODS Sprague-Dawley rats, in the absence and presence of amifostine, were whole-body irradiated at a single dose of 8 Gy and decapitated after 24 h. The brain homogenate membranes of these rats were analyzed using Fourier Transform Infrared (FTIR) spectroscopy. RESULTS Ionizing radiation caused a significant increase in the lipid to protein ratio and significant decreases in the ratios of olefinic = CH/lipid, CH2/lipid, carbonyl ester/lipid and CH3/lipid suggesting, respectively, a more excessive decrease in the protein content and the degradation of lipids as a result of lipid peroxidation. In addition, radiation changed the secondary structure of proteins and the status of packing of membrane lipid head groups. Furthermore, it caused a decrease in lipid order and an increase in membrane fluidity. The administration of amifostine before ionizing radiation inhibited all the radiation-induced alterations in brain homogenate membranes. CONCLUSIONS The results revealed that whole body ionizing radiation at a sublethal dose causes significant alterations in the structure, composition and dynamics of brain homogenate membranes and amifostine has a protective effect on these membranes.
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Affiliation(s)
- Gulgun Cakmak
- a Department of Biology, Faculty of Arts and Sciences , Duzce University , Duzce , Turkey
| | - Mete Severcan
- b Department of Electrical and Electronic Engineering , Middle East Technical University , Ankara , Turkey
| | - Faruk Zorlu
- c Department of Radiation Oncology, Faculty of Medicine , Hacettepe University , Ankara , Turkey
| | - Feride Severcan
- d Department of Biological Sciences , Middle East Technical University , Ankara , Turkey
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25
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Simsek Ozek N, Zeller I, Renaud DE, Gümüş P, Nizam N, Severcan F, Buduneli N, Scott DA. Differentiation of Chronic and Aggressive Periodontitis by FTIR Spectroscopy. J Dent Res 2016; 95:1472-1478. [PMID: 27608648 DOI: 10.1177/0022034516663696] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Without longitudinal clinical data, it is difficult to differentiate some cases of chronic periodontitis (CP) and aggressive periodontitis (AgP). Furthermore, both forms of disease are exacerbated by tobacco use. Therefore, this cross-sectional study was planned, primarily, to determine the ability of Fourier-transform infrared (FTIR) spectroscopy to distinguish CP and AgP patients by analysis of human saliva samples and, secondarily, to assess the potential confounding influence of smoking on discriminating disease-specific spectral signatures. FTIR spectra were collected from patients with a clinical diagnosis of CP (n = 18; 7 smokers) or AgP (n = 23; 9 smokers). Self-reported smoking status, which may be unreliable, was confirmed by salivary cotinine analysis. Spectral band area analysis and hierarchical cluster analyses were performed to clarify if the 2 periodontitis groups as well as smoker and nonsmoker patients could be differentiated from each other. Significant variations in lipid, amino acid, lactic acid, and nucleic acid content were found between nonsmoker CP and AgP groups. Although significantly lower lipid, phospholipid, protein, amino acid, lactic acid, and nucleic acid content was noted in the smoker AgP group compared with the nonsmoker AgP group, in the CP group, phospholipid, protein, amino acid, and lactic acid content was significantly lower for smokers compared with the nonsmokers. Based on these variations, nonsmoker CP and AgP patients were discriminated from each other with high sensitivity and specificity. Successful differentiation was also obtained for the smoker CP and AgP groups. Thiocyanate levels successfully differentiated smokers from nonsmokers, irrespective of periodontal status, with 100% accuracy. Differentiation of AgP and CP forms, concomitant with determination of smoking status, may allow the dental health professional to tailor treatment accordingly.
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Affiliation(s)
- N Simsek Ozek
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.,Department of Biology, Atatürk University, Erzurum, Turkey
| | - I Zeller
- Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - D E Renaud
- Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
| | - P Gümüş
- Department of Periodontology, School of Dentistry, Ege University, Bornova, İzmir, Turkey
| | - N Nizam
- Department of Periodontology, School of Dentistry, Ege University, Bornova, İzmir, Turkey
| | - F Severcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - N Buduneli
- Department of Periodontology, School of Dentistry, Ege University, Bornova, İzmir, Turkey
| | - D A Scott
- Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, USA
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26
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Gok S, Aydin OZ, Sural YS, Zorlu F, Bayol U, Severcan F. Bladder cancer diagnosis from bladder wash by Fourier transform infrared spectroscopy as a novel test for tumor recurrence. J Biophotonics 2016; 9:967-75. [PMID: 27041149 DOI: 10.1002/jbio.201500322] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/10/2016] [Accepted: 03/14/2016] [Indexed: 05/13/2023]
Abstract
This study proposes Fourier Transform Infrared (FTIR) spectroscopy as a more sensitive, rapid, non-destructive and operator-independent analytical diagnostic method for bladder cancer recurrence from bladder wash than other routinely used urine cytology and cystoscopy methods. A total of 136 patients were recruited. FTIR spectroscopic experiments were carried out as a blind study, the classification results of which were then compared with those of cytology and cystoscopy. Firstly, 71 samples (n = 37; bladder cancer and n = 34; control) were studied with transmittance FTIR spectroscopy. After achieving successful differentiation of the groups, to develop a more rapid diagnostic tool and check the reproducibility of the results, the work was continued with different samples (n = 65 as n = 44; bladder cancer and n = 21; control), using the reflection mode (ATR) of FTIR spectroscopy by a different operator. The results revealed significant alterations in moleculer content in the cancer group. Based on the spectral differences, using transmittance FTIR spectroscopy coupled with chemometrics, the diseased group was successfully differentiated from the control. When only carcinoma group was taken into consideration a sensitivity value of 100% was achieved. Similar results were also obtained by ATR-FTIR spectroscopy. This study shows the power of infrared spectroscopy in the diagnosis of bladder cancer.
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Affiliation(s)
- Seher Gok
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Ozge Z Aydin
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey
| | - Yavuz S Sural
- Department of Urology, Tepecik Research and Training Hospital, 35110, İzmir, Turkey
| | - Ferruh Zorlu
- Department of Urology, Tepecik Research and Training Hospital, 35110, İzmir, Turkey
| | - Umit Bayol
- Department of Urology, Tepecik Research and Training Hospital, 35110, İzmir, Turkey
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06800, Ankara, Turkey.
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27
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Garip S, Ceyhan ST, Korkmaz C, Atis M, Guney E, Bal EM, Severcan F. PP-018 - Embryo quality assessment in in vitro fertilization (IVF) using metabolite footprints secreted to human embryo culture media by ATR-FTIR spectroscopy and multivariate analysis. Reprod Biomed Online 2016. [DOI: 10.1016/s1472-6483(16)30153-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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Gurbanov R, Bilgin M, Severcan F. Restoring effect of selenium on the molecular content, structure and fluidity of diabetic rat kidney brush border cell membrane. Biochimica et Biophysica Acta (BBA) - Biomembranes 2016; 1858:845-54. [DOI: 10.1016/j.bbamem.2016.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 02/02/2023]
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29
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Garip S, Bayari SH, Severcan M, Abbas S, Lednev IK, Severcan F. Structural effects of simvastatin on liver rat [corrected] tissue: Fourier transform infrared and Raman microspectroscopic studies. J Biomed Opt 2016; 21:25008. [PMID: 26891599 DOI: 10.1117/1.jbo.21.2.025008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/21/2016] [Indexed: 06/05/2023]
Abstract
Simvastatin 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 α-helix and increase in random coil, while native β-sheet decreases and aggregated β-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.
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Affiliation(s)
- Sebnem Garip
- Istanbul Kemerburgaz University, Department of Medical Biochemistry, Faculty of Medicine, Mahmutbey Dilmenler Caddesi, No: 26, Istanbul 34217, Turkey
| | - Sevgi Haman Bayari
- Hacettepe University, Department of Physics Engineering, Faculty of Engineering, Beytepe Campus, Ankara 06800, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronics Engineering, Faculty of Engineering, Dumlupinar Bulvari, No: 1, Ankara 06800, Turkey
| | - Sherif Abbas
- Middle East Technical University, Department of Biological Sciences, Faculty of Arts and Sciences, Dumlupinar Bulvari, No: 1, Ankara 06800, Turkey
| | - Igor K Lednev
- University at Albany, Department of Chemistry, State University of New York, Albany, New York 12222, United States
| | - Feride Severcan
- University at Albany, Department of Chemistry, State University of New York, Albany, New York 12222, United States
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30
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Ozek NS, Zelle I, Renaud D, Gümüs P, Nizam N, Severcan F, Buduneli N, Scott D. Differentiation of chronic and aggressive forms of periodontitis and of smokers and non-smokers by Fourier-transform infrared spectroscopy. Tob Prev Cessat 2016. [DOI: 10.18332/tpc/62416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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31
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Baltacıoğlu H, Bayındırlı A, Severcan M, Severcan F. Effect of thermal treatment on secondary structure and conformational change of mushroom polyphenol oxidase (PPO) as food quality related enzyme: A FTIR study. Food Chem 2015; 187:263-9. [DOI: 10.1016/j.foodchem.2015.04.097] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/25/2015] [Accepted: 04/21/2015] [Indexed: 11/25/2022]
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32
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Gurbanov R, Simsek Ozek N, Gozen AG, Severcan F. Quick Discrimination of Heavy Metal Resistant Bacterial Populations Using Infrared Spectroscopy Coupled with Chemometrics. Anal Chem 2015; 87:9653-61. [DOI: 10.1021/acs.analchem.5b01659] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rafig Gurbanov
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Nihal Simsek Ozek
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayse Gul Gozen
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Feride Severcan
- Department of Biochemistry and ‡Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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Sen I, Bozkurt O, Aras E, Heise S, Brockmann GA, Severcan F. Lipid profiles of adipose and muscle tissues in mouse models of juvenile onset of obesity without high fat diet induction: a Fourier transform infrared (FT-IR) spectroscopic study. Appl Spectrosc 2015; 69:679-688. [PMID: 26054332 DOI: 10.1366/14-07443] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The current study aims to determine lipid profiles in terms of the content and structure of skeletal muscle and adipose tissues to better understand the characteristics of juvenile-onset spontaneous obesity without high fat diet induction. For the purposes of this study, muscle (longissimus, quadriceps) and adipose (inguinal, gonadal) tissues of 10-week-old male DBA/2J and Berlin fat mouse inbred (BFMI) lines (BFMI856, BFMI860, BFMI861) fed with a standard breeding diet were used. Biomolecular structure and composition was determined using attenuated total reflection Fourier transform (ATR FT-IR) spectroscopy, and muscle triglyceride content was further quantified using high-performance liquid chromatography (HPLC) coupled with an evaporative light scattering detector (ELSD). The results revealed a loss of unsaturation in BFMI860 and BFMI861 lines in both muscles and inguinal adipose tissue, together with a decrease in the hydrocarbon chain length of lipids, especially in the BFMI860 line in muscles, suggesting an increased lipid peroxidation. There was an increase in saturated lipid and triglyceride content in all tissues of BFMI lines, more profoundly in longissimus muscle, where the increased triglyceride content was quantitatively confirmed by HPLC-ELSD. Moreover, an increase in the metabolic turnover of carbohydrates in muscles of the BFMI860 line was observed. The results demonstrated that subcutaneous (inguinal) fat also displayed considerable obesity-induced alterations. Taken together, the results revealed differences in lipid structure and content of BFMI lines, which may originate from different insulin sensitivity levels of the lines, making them promising animal models for spontaneous obesity. The results will contribute to the understanding of the generation of insulin resistance in obesity without high fat diet induction.
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Affiliation(s)
- Ilke Sen
- Middle East Technical University, Department of Biological Sciences, 06800 Ankara, Turkey
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Gok S, Severcan M, Goormaghtigh E, Kandemir I, Severcan F. Differentiation of Anatolian honey samples from different botanical origins by ATR-FTIR spectroscopy using multivariate analysis. Food Chem 2015; 170:234-40. [DOI: 10.1016/j.foodchem.2014.08.040] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 08/08/2014] [Accepted: 08/10/2014] [Indexed: 11/30/2022]
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35
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Demir P, Onde S, Severcan F. Phylogeny of cultivated and wild wheat species using ATR-FTIR spectroscopy. Spectrochim Acta A Mol Biomol Spectrosc 2015; 135:757-763. [PMID: 25145919 DOI: 10.1016/j.saa.2014.07.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 07/02/2014] [Accepted: 07/15/2014] [Indexed: 06/03/2023]
Abstract
Within the last decade, an increasing amount of genetic data has been used to clarify the problems inherent in wheat taxonomy. The techniques for obtaining and analyzing these data are not only cumbersome, but also expensive and technically demanding. In the present study, we introduce infrared spectroscopy as a method for a sensitive, rapid and low cost phylogenetic analysis tool for wheat seed samples. For this purpose, 12 Triticum and Aegilops species were studied by Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopy. Hierarchical cluster analysis and principal component analysis clearly revealed that the lignin band (1525-1505 cm(-1)) discriminated the species at the genus level. However, the species were clustered according to their genome commonalities when the whole spectra were used (4000-650 cm(-1)). The successful differentiation of Triticum and its closely related genus Aegilops clearly demonstrated the power of ATR-FTIR spectroscopy as a suitable tool for phylogenetic research.
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Affiliation(s)
- Pinar Demir
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey
| | - Sertac Onde
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey.
| | - Feride Severcan
- Department of Biology, Middle East Technical University, 06800 Ankara, Turkey
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36
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Yonar D, Sandal A, Emri S, Severcan F. A Novel Method for Early Diagnosis of Malignant Pleural Mesothelioma from Human Serum Samples: ATR-FTIR Spectroscopy. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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37
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Kucuk Baloglu F, Garip S, Heise S, Brockmann G, Severcan F. FTIR imaging of structural changes in visceral and subcutaneous adiposity and brown to white adipocyte transdifferentiation. Analyst 2015; 140:2205-2214. [DOI: 10.1039/c4an02008a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
FTIR microspectroscopy coupled with UCP1 immunohistological staining enables the detection of obesity-related molecular alterations and transdifferentiations in visceral and subcutaneous adipose tissues in spontaneously obese mice lines.
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Affiliation(s)
- Fatma Kucuk Baloglu
- Department of Biological Sciences
- Middle East Technical University
- Ankara
- Turkey
| | - Sebnem Garip
- Department of Medical Biochemistry
- Faculty of Medicine
- Istanbul Kemerburgaz University
- Istanbul
- Turkey
| | - Sebastian Heise
- Department of Breeding Biology and Molecular Genetics
- Humboldt Universitatzu Berlin
- Berlin
- Germany
| | - Gudrun Brockmann
- Department of Breeding Biology and Molecular Genetics
- Humboldt Universitatzu Berlin
- Berlin
- Germany
| | - Feride Severcan
- Department of Biological Sciences
- Middle East Technical University
- Ankara
- Turkey
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Baloglu FK, Brockmann G, Heise S, Garip S, Severcan F. Investigation of Gender Effect on Obesity using a Model of Inbreed Obese Mouse Lines by Fourier Transform Infrared Imaging. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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39
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Demir P, Akkas SB, Severcan M, Zorlu F, Severcan F. Ionizing radiation induces structural and functional damage on the molecules of rat brain homogenate membranes: a Fourier transform infrared (FT-IR) spectroscopic study. Appl Spectrosc 2015; 69:154-164. [PMID: 25588232 DOI: 10.1366/13-07154] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Humans can be exposed to ionizing radiation, due to various reasons, whose structural effects on biological membranes are not well defined. The current study aims to understand the ionizing radiation-induced structural and functional alterations in biomolecules of brain membranes using Fourier transform infrared (FT-IR) spectroscopy using rat animal models. For this purpose, 1000 cGy of ionizing radiation was specifically directed to the head of Sprague Dawley rats. The rats were decapitated after 24 h. The results revealed that the lipid-to-protein ratio decreased and that irradiation caused lipid peroxidation and increases in the amounts of olefinic =CH, carbonyl, and methylene groups of lipids. In addition, ionizing radiation induced a decrease in membrane fluidity, disordering of membrane lipids, strengthening of the hydrogen bonding of the phosphate groups of lipid head-groups, and weakening in the hydrogen bonding of the interfacial carbonyl groups of lipids. Radiation further caused significant decrements in the α-helix and turns, and significant increments in the β-sheet and random coil contents in the protein structure. Hierarchical cluster analyses, performed in the whole region (3030-1000 cm(-1)), lipid (3030-2800 cm(-1)), and protein (1700-1600 cm(-1)) regions separately, successfully differentiated the control and irradiated groups of rat brain membranes and showed that proteins in the membranes are affected more than lipids from the damages induced with ionizing radiation. As a result, the current study showed that FT-IR spectroscopy can be used successfully as a novel method to monitor radiation-induced alterations on biological membranes.
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Affiliation(s)
- Pinar Demir
- Department of Biological Sciences, Middle East Technical University, Dumlupınar Bulvarı No. 1, 06800, Ankara, Turkey
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Gurbanov R, Abbas S, Bilgin M, Severcan F. The Effect of Selenium Treatment On-Diabetic-Induced Structural Variations in the Molecules of Rat Kidney Plasma Membrane. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.3402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Turker S, Severcan M, Ilbay G, Severcan F. Epileptic seizures induce structural and functional alterations on brain tissue membranes. Biochimica et Biophysica Acta (BBA) - Biomembranes 2014; 1838:3088-96. [DOI: 10.1016/j.bbamem.2014.08.025] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 08/09/2014] [Accepted: 08/23/2014] [Indexed: 10/24/2022]
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Kardas M, Gozen AG, Severcan F. FTIR spectroscopy offers hints towards widespread molecular changes in cobalt-acclimated freshwater bacteria. Aquat Toxicol 2014; 155:15-23. [PMID: 24964200 DOI: 10.1016/j.aquatox.2014.05.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/22/2014] [Accepted: 05/22/2014] [Indexed: 06/03/2023]
Abstract
High concentrations of heavy metals can be toxic for bacteria. However, after prolonged exposure, bacteria can become acclimated and begin to be able to grow in the presence of heavy metals. Acclimation can involve alterations of metabolism and molecular structures. Our aim was to examine these alterations in cobalt-acclimated bacteria via attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy on viable samples. Bacillus sp. and Pseudomonas sp. isolated from a temperate shallow lake and a well-established strain of E. coli were investigated. Our results revealed consistent, wide-spread changes in cell membrane and cell wall dynamics of Bacillus sp. and E. coli, including a decrease in peptidoglycan content of Bacillus sp. and increased lipid ordering of the membrane in both bacteria. Furthermore, a decrease in RNA and protein concentrations of Bacillus sp. was measured. All three bacteria studied showed a decrease in conformational freedom of proteins following cobalt acclimation. Interestingly, both Bacillus sp. and E. coli showed slight but significant alterations in their DNA conformations which might imply a methylation-mediated memory formation leading to epigenetic modulation for cobalt adaptation.
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Affiliation(s)
- Mehmet Kardas
- Middle East Technical University, Biological Sciences, Microbial Ecology Laboratory and Biophysics Laboratory, Ankara 06800, Turkey
| | - Ayse Gul Gozen
- Middle East Technical University, Biological Sciences, Microbial Ecology Laboratory and Biophysics Laboratory, Ankara 06800, Turkey.
| | - Feride Severcan
- Middle East Technical University, Biological Sciences, Microbial Ecology Laboratory and Biophysics Laboratory, Ankara 06800, Turkey
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Bilge D, Sahin I, Kazanci N, Severcan F. Interactions of tamoxifen with distearoyl phosphatidylcholine multilamellar vesicles: FTIR and DSC studies. Spectrochim Acta A Mol Biomol Spectrosc 2014; 130:250-256. [PMID: 24792199 DOI: 10.1016/j.saa.2014.04.027] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/06/2014] [Accepted: 04/06/2014] [Indexed: 06/03/2023]
Abstract
Interactions of a non-steroidal antiestrogen drug, tamoxifen (TAM), with distearoyl-sn-glycero-3-phosphatidylcholine (DSPC) multilamellar liposomes (MLVs) were investigated as a function of drug concentration (1-15 mol%) by using two noninvasive techniques, namely Fourier transform infrared (FTIR) spectroscopy and differential scanning calorimetry (DSC). FTIR spectroscopy results show that increasing TAM concentrations (except 1 mol%) increased the wavenumbers of the CH2 stretching modes, implying an disordering effect for DSPC MLVs both in the gel and liquid crystalline phases. The bandwidth values of the CH2 stretchings except for 1 mol% increased when TAM concentrations increased for DSPC liposomes, indicating an increase in the dynamics of liposomes. The CO stretching and PO2- antisymmetric double bond stretching bands were analyzed to study interactions of TAM with head groups of lipids. As the concentrations of TAM increased, dehydration occurred around these functional groups in the polar part of the lipids. The DSC studies on thermal properties of DSPC lipids indicate that TAM eliminated the pre transition, shifted the main phase transition to lower temperatures and broadened the phase transition curve of the liposomes.
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Affiliation(s)
- Duygu Bilge
- Department of Physics, Faculty of Science, Ege University, 35100 İzmir, Turkey
| | - Ipek Sahin
- Department of Physics, Faculty of Science, Ege University, 35100 İzmir, Turkey
| | - Nadide Kazanci
- Department of Physics, Faculty of Science, Ege University, 35100 İzmir, Turkey.
| | - Feride Severcan
- Department of Biological Sciences, Middle East Technical University, 06531 Ankara, Turkey
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Aksoy C, Kaya FA, Kuşkonmaz BB, Uçkan D, Severcan F. Structural investigation of donor age effect on human bone marrow mesenchymal stem cells: FTIR spectroscopy and imaging. Age (Dordr) 2014; 36:9691. [PMID: 25081108 PMCID: PMC4150902 DOI: 10.1007/s11357-014-9691-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2013] [Accepted: 07/17/2014] [Indexed: 06/03/2023]
Abstract
Stem cell studies hold enormous potential for development of new therapies for tissue regeneration and repair. Bone marrow mesenchymal stem cells (BM-MSCs) can differentiate into a variety of non-hematopoietic tissues and contribute maintenance of healthy hematopoiesis by providing supportive cellular microenvironment into BM. Here, we investigated age-related differences in BM-MSCs by using attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy and FTIR imaging together with hierarchical clustering as a novel methods to clarify global alterations in the structure and function of macromolecules in characterized BM-MSCs of different aged donors. The results may contribute to identification of age-related new molecular marker(s) to determine the effects of donor age on MSCs. The spectral results reflected that there were significant increases in the concentration of saturated lipids, proteins, glycogen, and nucleic acids in children and adolescent group BM-MSCs when compared to the infants and early and mid adults. The concentration of mentioned macromolecules in adult (early and mid) BM-MSCs were significantly lower than the concentrations in the children and adolescents. These results were attributed to the increase in the proliferation activity in younger BM-MSCs. The distribution of macromolecules into the cells was shown as in the form of chemical maps by FTIR imaging, and the results are in agreement with the ATR-FTIR spectroscopy results. The cellular activity degree was determined by the thiazolyl blue tetrazolium bromide (MTT) proliferation assay to support ATR-FTIR spectroscopy results. BM-MSCs of five different age groups were discriminated by making the hierarchical cluster analysis where the spectral data according to alterations in structure and composition of macromolecules were considered.
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Affiliation(s)
- Ceren Aksoy
- />Department of Biotechnology, Middle East Technical University, 06800 Ankara, Turkey
| | - Fatima Aerts Kaya
- />Pedi-Stem Center for Stem Cell Research and Development, Hacettepe University, 06100 Ankara, Turkey
| | - Bülent Barış Kuşkonmaz
- />Divison of Hematology, Department of Pediatrics, Hacettepe University, 06100 Ankara, Turkey
| | - Duygu Uçkan
- />Pedi-Stem Center for Stem Cell Research and Development, Hacettepe University, 06100 Ankara, Turkey
- />Divison of Hematology, Department of Pediatrics, Hacettepe University, 06100 Ankara, Turkey
| | - Feride Severcan
- />Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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Turker S, Ilbay G, Severcan M, Severcan F. Investigation of Compositional, Structural, and Dynamical Changes of Pentylenetetrazol-Induced Seizures on a Rat Brain by FT-IR Spectroscopy. Anal Chem 2014; 86:1395-403. [DOI: 10.1021/ac402992j] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sevgi Turker
- Department
of Biological Sciences, Middle East Technical University, Ankara, 06531, Turkey
- Department
of Biology, Kocaeli University, Kocaeli, 41900, Turkey
| | - Gul Ilbay
- Department
of Physiology, Faculty of Medicine, Kocaeli University, Kocaeli, 41900, Turkey
| | - Mete Severcan
- Department
of Electrical and Electronic Engineering, Middle East Technical University, Ankara, 06531, Turkey
| | - Feride Severcan
- Department
of Biological Sciences, Middle East Technical University, Ankara, 06531, Turkey
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47
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Özer Z, Gök S, Altan H, Severcan F. Concentration-based measurement studies of L-tryptophan using terahertz time-domain spectroscopy (THz-TDS). Appl Spectrosc 2014; 68:95-100. [PMID: 24405959 DOI: 10.1366/13-07165] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
L-Tryptophan is an extremely important amino acid for a variety of biological functions in living organisms. In this study we were able to measure changes in the concentration of L-tryptophan when incorporated into pellets with polyethylene as a host. The changes were measured both through the characteristic absorption bands of the C11 and C12 bonds in the low terahertz frequency range and using changes in the refractive index where pellets with higher concentrations of L-tryptophan showed higher refractive indices. The volumetric concentration of L-tryptophan in the polyethylene pellet was accurately determined with a simple model that explains the contribution to the complex refractive index for the resultant sample due to the two constituent materials. These measurements show that terahertz time-domain techniques can be applied to detect variation in concentration of certain amino acids rapidly by examining the relative phase delay and amplitude change of the terahertz transients.
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Affiliation(s)
- Zeynep Özer
- Department of Physics, Middle East Technical University, 06800 Cankaya Ankara, Turkey
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Simsek Ozek N, Bal IB, Sara Y, Onur R, Severcan F. Structural and functional characterization of simvastatin-induced myotoxicity in different skeletal muscles. Biochim Biophys Acta Gen Subj 2014; 1840:406-15. [DOI: 10.1016/j.bbagen.2013.09.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Revised: 07/20/2013] [Accepted: 09/06/2013] [Indexed: 01/05/2023]
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Garip S, Sahin D, Severcan F. Epileptic seizure-induced structural and functional changes in rat femur and tibia bone tissues: a Fourier transform infrared imaging study. J Biomed Opt 2013; 18:111409. [PMID: 23887385 DOI: 10.1117/1.jbo.18.11.111409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The disease- and drug-related bone disorders are rapidly increasing in the population. It is previously reported that anti-epileptic drugs (AEDs) may cause osteopenia, osteoporosis, and fractures in epilepsy patients. However, it cannot be determined whether the bone disorders in epileptic patients are due to AED therapy and/or to epilepsy and epileptic seizures. There is no study in the literature which investigates the sole effects of epilepsy and epileptic seizures on bone tissues. The current study provides the first report on determination of the possible effects of epilepsy and epileptic seizures on long bone tissues. Wistar Albino Glaxo/Rijswijk rats, which are accepted as genetic rat models for human absence epilepsy, were compared with the healthy Wistar rats to get information about the sole effects of epilepsy and epileptic seizures on bones. Cortical regions of tibia and femur bones were studied by Fourier transform infrared microspectroscopy (FTIRM). According to FTIRM parameters, variation on bone mineral and matrix composition, including decreased mineral content, decreased collagen cross-links, increased carbonate substitution, and larger crystals in epileptic group compared to the healthy one, show severe effects of epilepsy and seizures on bone tissues for the first time.
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Affiliation(s)
- Sebnem Garip
- Middle East Technical University, Department of Biochemistry, 06531 Ankara, Turkey
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50
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Severcan F, Gocmen SU, Ozek NS, Severcan M. Characterization of simvastatin‐induced structural and functional alterations in the molecules of kidney brush border membrane by ATR‐FTIR spectroscopy and chemometric approaches. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.1033.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Feride Severcan
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTurkey
| | - Semire Uzun Gocmen
- Department of BiophysicsMustafa Kemal UniversityFaculty of MedicineHatayTurkey
| | - Nihal Simsek Ozek
- Department of Biological SciencesMiddle East Technical UniversityAnkaraTurkey
| | - Mete Severcan
- Department of Electrical and Electronics EngineeringMiddle East Technical UniversityAnkaraTurkey
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