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Food preservatives especially used to prevent microbiological spoilage in nutritional products are among the most indispensable additives. Here, the biochemical effects of three commonly used preservatives, sodium benzoate (SB), potassium sorbate (PS) and sodium nitrite (SN), on Saccharomyces cerevisiae were investigated. 5-100 mM SB, 300 ppm PS and 25-100 mM SN significantly inhibited early exponential yeast cell proliferation compared to the control after 12 h exposure. Cell metabolic activity percentages were also significantly inhibited at the studied highest three concentrations. While glutathione S-transferase activity generally increased after SB and PS treatments, superoxide dismutase activity increased only after 50 mM SB treatment. Although the lipid peroxidation marker malondialdehyde levels generally increased as a result of treatments with food additives, significant increases were determined in 300 ppm PS, and 50 and 100 mM SN groups. According to the principal component and hierarchical cluster analysis, food additive treated groups clearly discriminated from control. Finally, the principal component analysis (PCA) loading plots showed that higher doses of food additives altered lipid concentration, disrupted proteins and increased the concentrations of mannans and beta-glucans. These findings are significant in terms of better understanding the underlying mechanism of food additive induced toxicity for the control of yeast cell proliferation.

Ischemia reperfusion (I/R) injury which causes kidney dysfunction is one of the most studied diseases directly linked to oxidative stress. In this regard, it is important to protect cells against damage by inducing antioxidant response. Herein, we aimed to evaluate the therapeutic roles and possible mechanisms of propolis and boric acid in kidney I/R injury based on relevant basic research and clinical studies. Sprague-Dawley rats were subjected to 50 min of ischemia followed by 3 h of reperfusion. Animals were randomly divided into a control group (the abdominal wall was just opened and closed), an I/R injury group, the propolis intervention group (200 mg/kg, intragastric administration, 1 h before ischemia), boric acid intervention group (14 mg/kg, intragastric administration 1 h before ischemia), and the propolis + boric acid intervention group (intragastric administration 1 h before ischemia). Kidney function, the antioxidant defensive system, and renal damage were assessed. In addition, the oxidative stress and inflammatory status were estimated in renal tissue. Furthermore, DNA damageand apoptosis were detected by immunohistochemistry. When compared with I/R group, propolis alone and especially propolis + boric acid groups significantly improved functional parameters. While the antioxidant response was increased, renal injury size and apoptosis were significantly decreased in both groups. Also, the MDA and TNF-alpha levels besides the 8-OHdG formation were downregulated. According to these outcomes, it can be said that especially propolis together with boric acid ameliorates kidney injury caused by I/R through acting as an antioxidant, anti-inflammatory, and antiapoptotic agent. In conclusion, propolis alone and its combination with boric acid could be developed as therapeutic agents against serious renal I/R injuries.

This study reports the development of a highly sensitive antibiotic-based discrimination and sensor platform for the detection of Gram-positive bacteria through surface-enhanced Raman spectroscopy (SERS). Herein, a combination of gold nanorod arrays (GNAs) and colloidal gold nanoparticles (AuNPs) was used as a SERS platform. To specifically capture Gram-positive bacteria, both GNAs and AuNPs were functionalized with thiol-modified vancomycin (HS-Van) molecules. Three different strains of bacteria (Bacillus subtilis and Staphylococcus aureus as Gram-positive, and Escherichia coli as Gram-negative) were employed to test the proposed system. HS-Van functionalized GNAs (GNA@Van) captured Gram-positive bacteria with high specificity. Also, the bacteria captured by GNA@Van (GNA@Van@Bct) systems showed high signal-to-noise SERS signals with high reproducibility. Addition of AuNP@Van to GNA@Van@Bct resulted in the emergence of a sandwich system (GNA@Van@Bct@Van@AuNP). This system led to a further enhanced SERS signal. The chemometric analysis of GNA@Van@Bct@Van@AuNP enabled the obvious discrimination and detection of Gram-positive bacteria. For comparison, we also tested a smooth gold surface with the same procedure and a similar trend was observed with lower SERS activity.

Cisplatin-based chemotherapy is responsible for a large number of renal failures, and it is still associated with high rates of mortality today. Oleuropein (OLE) presents a plethora of pharmacological beneficial properties. In this study we investigated whether OLE could provide sufficient protection against cisplatin-induced nephrotoxicity. With this aim, Sprague-Dawley rats were divided into eight groups: control; 7 mg/kg/d cisplatin, 50 mg/kg, 100 mg/kg, and 200 mg/kg OLE; and treatment with OLE for 3 days starting at 24 hours following cisplatin injection. After exposure to the chemotherapy agent and OLE, oxidative DNA damage was quantitated in the renal tissue of experimental animals by measuring the amount of 8-hydroxy-2′-deoxyguanosine (8-OHdG) adducts. Malondialdehyde (MDA) level, total oxidative stress (TOS), and total antioxidant status (TAS) were assessed to determine the oxidative injury in kidney cells. The histology of the kidney was examined using four different staining methods: hematoxylin-eosin (H&E), periodic acid Schiff (PAS), Masson trichrome, and amyloid. In addition, the blood urea nitrogen (BUN), uric acid (UA), and creatinine (CRE) levels were established. Our experimental data showed that tissue 8-OHdG levels were significantly higher in the cisplatin group when compared to the control group. The glomerular cells were sensitive to cisplatin as tubular cells. In addition, treatment with cisplatin elevated the levels of BUN, UA, CRE, and TOS, but lowered the level of TAS compared to the control group. The OLE therapy modulated oxidative stress in order to restore normal kidney function and reduced the formation of 8-OHdG induced by cisplatin. Furthermore, the OLE treatment significantly reduced pathological findings in renal tissue. We demonstrate for the first time that OLE presents significant cytoprotective properties against cisplatin-induced genotoxicity by restoring the antioxidant system of the renal tissue. According to our findings, OLE is a promising novel natural source for the prevention of serious kidney damage in current chemotherapies.

Building on our previous work that discovered chalcone as a promising pharmacophore for anticancer activity, we have various other chalcone derivatives and have synthesized a series of novel bischalcone to explore their anticancer activity. Among all tested compounds, compounds 6a, 6b, and 6c showed the highest antiproliferative activity against A-549 cancer cell lines with the average IC50 values of 4.18, 4.52, and 5.05 µM, respectively. Moreover, compound 6c showed high antiproliferative activity against the Caco-2 cell line; thus, it was 2- and 4-fold more active than the reference compounds, i.e., methotrexate and capecitabine. Compound 6a also induced cell-cycle arrest in the S phase, whereas compounds 6b and 6c were observed to stop at the G0/G1 phase. Thereafter, we evaluated that compound 6c also had the highest apoptosis/necrosis ratio than other compounds and the standard compound. The anticancer property of the 6c was also supported by molecular docking studies carried out on the EGFR and HER2 receptors. Overall, we expect that these compounds can be further developed for the potential treatment of lung cancer.

Background Statins are the most commonly used drugs for the treatment of hypercholesterolemia. Their most frequent side effect is myotoxicity. To date, it remains unclear whether statins preferentially induce myotoxicity in fast- or in slow-twitch muscles. Therefore, we investigated these effects on fast- (extensor digitorum longus; EDL), slow- (soleus; SOL), and mixed-twitch muscles (diaphragm; DIA) in rats by comparing their contractile and molecular structural properties. Methods Simvastatin-induced functional changes were determined by muscle contraction measurements, and drug-induced molecular changes were investigated using Fourier transform infrared (FTIR) and attenuated total reflectance (ATR) FTIR spectroscopy. Results With simvastatin administration (30 days, 50 mg/kg), a depression in the force–frequency curves in all muscles was observed, indicating the impairment of muscle contractility; however, the EDL and DIA muscles were affected more severely than the SOL muscle. Spectroscopic findings also showed a decrease in protein, glycogen, nucleic acid, lipid content and an increase in lipid order and lipid dynamics in the simvastatin-treated muscles. The lipid order and dynamics directly affect membrane thickness. Therefore, the kinetics and functions of membrane ion channels were also affected, contributing to the statin-induced impairment of muscle contractility. Furthermore, a reduction in α-helix and β-sheet and an increase in random coil, aggregated and antiparallel β-sheet were observed, indicating the protein denaturation. Spectral studies showed that the extent of molecular structural alterations in the muscles following simvastatin administration was in the order EDL > DIA > SOL. Conclusions Simvastatin-induced structural and functional alterations are more profound in the fast-twitch than in the slow-twitch muscles. General significance Myotoxic effects of simvastatin are primarily observed in the fast-twitch muscles.

Statins are commonly used drugs in the treatment of hypercholesterolaemia. There are many adverse effects of statins on skeletal muscle, but the underlying mechanisms remain unclear. In the present study, the effects of low dose (20 mg/kg) simvastatin, a lipophilic statin, on rat EDL muscle (extensor digitorum longus muscle) were investigated at the molecular level using FTIR (Fourier-transform infrared) spectroscopy. FTIR spectroscopy allows us rapid and sensitive determination of functional groups belonging to proteins, lipids, carbohydrates and nucleic acids simultaneously. The results revealed that simvastatin treatment induces a significant decrease in lipid, nucleic acid, protein and glycogen content. A significant increase in the lipid/protein and nucleic acid/protein ratios was also obtained with simvastatin treatment. Furthermore, an increase in lipid order and membrane fluidity was detected. A decrease in the bandwidth of the amide I band and shifting of the position of this band to higher frequency values in treated muscle indicates structural changes in proteins. Detailed secondary structure analysis of the amide I band revealed a significant increase in antiparallel and aggregated β-sheet, random coil structure and a significant decrease in β-sheet structure, which indicates protein denaturation.

Gozen, Ayse Gul/0000-0001-5479-051X; Tuncer, Sinem/0000-0002-8947-8646; WOS:000432008800009 PubMed: 29243883 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. TubitakTurkiye Bilimsel ve Teknolojik Arastirma Kurumu (TUBITAK) [113Y515] Tubitak, Grant/Award number: 113Y515

To date, no structural study has been carried out on the effects of vitamin A deficiency (VAD) on hippocampal macromolecules. Therefore, in the present study, the effect of dietary VAD on the structure, content and function of rat hippocampal molecules was investigated using Fourier transform IF spectroscopy. Male Wistar rats were randomly divided into three groups: an experimental group maintained on a vitamin A-deficient liquid diet (VAD,n7); a control group maintained on a vitamin A-supplemented liquid diet (CON,n9); a pure control group maintained on standard solid laboratory chow (PC,n7). The PC group was included in the study to ensure that the usage of liquid diet did not influence the outcomes of VAD. Both the CON and PC groups were successfully discriminated from the VAD group by principal component analysis and hierarchical cluster analysis. The spectral analysis indicated a significant decrease in the contents of saturated and unsaturated lipids, cholesteryl esters, TAG and nucleic acids in the VAD group when compared with the CON group (P≤ 0·05). In addition, a significant decrease in membrane fluidity and a significant increase in lipid order (e.g. acyl chain flexibility) were observed in the VAD group (P≤ 0·001). The results of the artificial neural network analysis revealed a significant decrease in the α-helix structure content and a significant increase in the turn and random coil structure contents, indicating protein denaturation, in the VAD group when compared with the CON and PC groups (P≤ 0·05). Dietary exclusion of vitamin A for 3 months apparently had an adverse impact on compositional, structural and dynamical parameters. These changes can be due to increased oxidative stress, confirming the antioxidant protection provided by vitamin A when used as a dietary supplement at low-to-moderate doses.

Fourier Transform Infrared (FTIR) spectroscopy and imaging techniques are formidable, novel, rapid and non-destructive tools for characterization of different biological systems from molecules to membranes, cells and tissues. These techniques with multivariate analysis tools can be used in the diagnosis/follow-up of diseases including cancer, and in monitoring drug or chemical induced alterations in tissues and cells. In the current study, Attenuated Total Reflectance FTIR spectroscopy together with chemometric (cluster and principal component) analysis were utilized as a diagnostic tool for urinary bladder cancer while FTIR imaging technique was used in the clarification of sodium butyrate (NaB) induced-differentiation in colon cancer cells since butyrate has an anti-proliferative effect in colon cancer. For bladder cancer studies, bladder wash samples of bladder cancer and control groups were used directly for spectra collection. ATR-FTIR studies revealed significant alterations in lipid, protein, and nucleic acid content of bladder wash samples of cancer groups as compared to the control ones. Based on these spectral variations, bladder cancer group can be successfully differentiated from control via chemometric analysis with a higher sensitivity and specificity than many other methods used currently in bladder cancer diagnosis. In colon cancer study, aggressive CaCo2 cell lines were treated with 3mM NaB and cultured for 48h for complete differentiation. Specific band ratio analysis such as lipid/protein, glycogen/phosphate and RNA/DNA were calculated from the chemical maps of control and NaB-treated cells. Imaging results indicated the reconstruction of cancer induced changes in response to NaB treatment by modulating the saturated, unsaturated, triglyceride, protein and nucleic acid content in the treated cells. The findings of this study supported that FTIR spectroscopic and imaging techniques are valuable, label-free and sensitive bio-analytical tools for cancer diagnostics and investigating the global roles of drugs on cancer treatment.

Statins are commonly used to control hypercholesterolemia and to prevent cardiovascular diseases. Among the statins, Simvastatin is one of the most frequently prescribed statins because of its efficacy in reducing LDL lipoprotein cholesterol levels, its tolerability, and its reduction of cardiovascular risk and mortality. Conflicting results have been reported with regard to benefits (pleiotropic effects) as well as risks (adverse effects) of simvastatin on different soft and hard tissues. In the current study, Attenuated Total Reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy was used to obtain detailed information about protein conformational changes due to simvastatin therapy of soft tissues namely liver, testis, sciatic nerve and hard tissues such as femur and tibia. Protein secondary structural changes were predicted by intensity calculations from second derivative spectra and neural network (NN) analysis, using the amide I band (1700-1600 cm(-1)) of FTIR spectra. Moreover, based on protein secondary structural differences, hierarchical cluster analysis was carried out in the 1700-1600 cm(-1) region. The results of our study in liver, testis and sciatic nerve tissues revealed that simvastatin treatment significantly decreased alpha helix structure and beta sheet structure at 1638 cm(-1), while increased the anti-parallel and aggregated beta sheet and random coil structures implying a simvastatin-induced protein denaturation in treated groups. Different to soft tissues, the results of hard tissue studies on femur and tibia bones revealed increased alpha helix structure and decreased anti-parallel beta sheet, aggregated beta sheet and random coil structures implying more strengthened bone tissues in simvastatin-treated groups. Finally, the simvastatin-treated and control groups for all soft and bone tissues were successfully differentiated using cluster analysis. According to the heterogeneity values in the cluster analysis of these tissues, the sciatic nerve tissue was found to be the most affected tissue from simvastatin treatment among the studied soft tissues. In addition, the high heterogeneity value implied high secondary structural difference between control and simvastatin-treated groups in tibia bone tissues. These findings reveal that FTIR spectroscopy with bioinformatic analyses such as neural network and hierarchical clustering, allowed us to determine the simvastatin-induced protein conformational changes as adverse and pleiotropic effects of the drug on different soft and hard tissues.

MicroRNAs (miRNAs), are ∼22 nucleotides long, non-coding RNAs that control gene expression post-transcriptionally by binding to their target mRNA's 3′UTRs (untranslated regions). Due to their roles in various important regulatory processes and pathways, miRNAs have been implicated in disease mechanisms such as tumorigenesis when their expression is deregulated. To date, a significant number of miRNAs and their target messenger RNAs (mRNAs) have been identified and verified. It is generally accepted that miRNAs can potentially bind to many mRNAs, which brings the requirement of validation of these interactions. While understanding that such individual interactions is crucial to delineate the role of a specific miRNA, we took a holistic approach and analyzed global changes in the cell due to expression of a miRNA in a model cell line system. Our model consisted of MCF7 cells stably transfected with miR-125b (MCF7-125b) and empty vector (MCF7-EV). MiR-125b is one of the known down-regulated miRNAs in breast cancers. In this study we examined the global structural changes in MCF7 cells lacking and expressing miR-125b by Attenuated Total Reflectance Fourier Transform Infrared (ATR-FTIR) Spectroscopy and investigated the dynamic changes by more sensitive spin-labelling Electron Spin Resonance (ESR) spectroscopy. Our results revealed less RNA, protein, lipid, and glycogen content in MCF7-125b compared to MCF7-EV cells. Membrane fluidity and proliferation rate were shown to be lower in MCF7-125b cells. Based on these changes, MCF7-125b and MCF7-EV cells were discriminated successfully by cluster analysis. Here, we provide a novel means to understand the global effects of miRNAs in cells. Potential applications of this approach are not only limited to research purposes. Such a strategy is also promising to pioneer the development of future diagnostic tools for deregulated miRNA expression in patient samples.

Simvastatin, a lipophilic statin derived drug, is commonly used drug for treating lipid and cardiovascular disorders. It is well known that the long term usage of this drug leads to peripheral neuropathy, mononeuropathy and memory problems. Moreover a possible treating agent in central nervous system disease like Alzheimer has been reported. The results that were obtained from simvastatin and nervous system are clinically unclear and controversial. Therefore the current study was aimed to clarify the possible effects of simvastatin on the content, composition, dynamics and conformation of macromolecules in rat sciatic nerve using ATR-FTIR Spectroscopy. Experimental male adult rats were divided two groups as control (n=10) and simvastatin-treated group (n=10). 50 mg simvastatin/ kg was given to treated group by oral gavage for 1 month. In the FTIR spectra, the shift in peak positions, the change in bandwidths and the intensity/area values of the bands were determined and compared in between control and treated groups. The results revealed that there is a significant decrease in amount of unsaturated lipid in simvastatin treated sciatic nerve, which indicates an increase in lipid peroxidation. Moreover, with simvastatin treatment a reduction in the saturated lipid, protein, glycogen and nucleic acid content was found showing degradation or decrease in the synthesis of these molecules. Protein secondary structure was found to be changed as a decrease in α-helix and β-sheet content and an increase aggregated β-sheet and random coil content in treated samples implying protein denaturation. The outcomes of this study show that high dose simvastatin application leads to structural and molecular variations in sciatic nerve by affecting its macromolecular composition.Keywords: sciatic nerve, simvastatin, statin, ATR-FTIR spectroscopy, protein secondary structure.

Colon cancer is a major cause of morbidity and mortality throughout the world.The pathogenesis of colon cancer with respect to loss of cellular differentiation has not been clearly understood. To understand this loss in colon cancer and to differentiate the cancer cells, sodium butyrate (NaB), one of the differentiation inducer, is commonly used. NaB is produced in the colonic lumen as a consequence of bacterial fermentation of complex carbohydrates and it alters colon cancer cell morphology and reduces the cell growth and motility. Although, the differentiation process of colon cancers, which are stimulated with NaB, has been resolved at genetic level, the underlying mechanisms regarding structural and functional alterations regulating the differentiation of colon cancer cells have not been well characterized. Therefore, in this study, it was aimed to explore the NaB-induced macromolecular structural and functional changes in differentiation of colon cancer cells by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy and FTIR microspectroscopy. These changes were determined from the spectral analysis of control and NaB treated colon cancer cell spectra and their chemical maps. Based on the spectral differences, cluster analysis was applied to discriminate the groups. The spectral analysis indicated the differences in saturated and unsaturated lipids, protein and nucleic acid content between the control and NaB treated cancer cells. The variation in membrane fluidity and lipid order was also determined in the NaB treated cells. Moreover, the successful discrimination between control and treated cells was obtained. The results of this study not only shed light on better understanding the loss of differentiation mechanisms in colon cancers but also strongly support the power of ATR-FTIR spectroscopy and FTIR microscopy as novel, simple, reagent-free methods for the identification of differentiated cancer cells.