Application of Fourier transform infrared spectroscopy to biomolecular profiling of cultured fibroblast cells from Gaucher disease patients: A preliminary investigation.

BACKGROUND: Gaucher disease (GD) is defined as an autosomal recessive disorder resulting from the deficiency of glucocerebrosidase (E.C. 3.2.1.45). Glucocerebrosidase is responsible for the degradation of glucosylceramide into ceramide and glucose. The deficiency of this enzyme results in the accumulation of undegraded glucosylceramide, almost exclusively in macrophages. With Fourier transform infrared (FTIR) spectroscopy, the complete molecular diversity of the samples can be studied comparatively and the amount of the particular materials can be determined. Also, the secondary structure ratios of proteins can be determined by analysing the amide peaks. OBJECTIVES: The primary aim of this study is to introduce FTIR-ATR spectroscopy technique to GD research for the first time in the literature and to assess its potential as a new molecular method. MATERIAL AND METHODS: Primary fibroblast cell cultures obtained from biopsy samples were used, since this material is widely used for the diagnosis of GD. Intact cells were placed onto a FTIR-ATR crystal and dried by purging nitrogen gas. Spectra were recorded in the mid-infrared region between 4500-850 cm-1 wavenumbers. Each peak in the spectra was assigned to as organic biomolecules according to their chemical bond information. A quantitative analysis was performed using peak areas and we also used a hierarchical cluster analysis as a multivariate spectral analysis. RESULTS: We obtained FTIR spectra of fibroblast samples and assigned the biomolecule origins of the peaks. We observed individual heterogeneity in FTIR spectra of GD fibroblast samples, confirming the well-known phenotypic heterogeneity in GD at the molecular level. Significant alterations in protein, lipid and carbohydrate levels related to the enzyme replacement therapy were also observed, which is also supported by cluster analysis. CONCLUSIONS: Our results showed that the application of FTIR spectroscopy to GD research deserves more attention and detailed studies with an increased sample size in order to evaluate its potential in the diagnosis and follow-up of GD patients.

Comparative proteomic approach in rat model of absence epilepsy.

The aim of this study was to investigate cellular proteins in the pathogenesis of the genetic rat model of absence epilepsy. Protein spots were identified with peptide mass fingerprinting analysis using matrix-assisted laser desorption ionization time of flight mass spectrometry. Data were gathered from the frontoparietal cortex and thalamus of Wistar Albino Glaxo/Rij (WAG/Rij) and Wistar by using two-dimensional gel electrophoresis (2D-PAGE). Six proteins (Clathrin light chain-A protein, Transmembrane EMP24 Domain-Containing Protein, Stathmin-4, Myosin Light Chain4, Rheb, phosphoserine phosphatase) were found to be differentially expressed in the frontoparietal cortex of WAG/Rij and Wistar rats in both age groups. Another set of six proteins (Protein FAM89A and Oasl1, Gemin2, NuDEL1, Pur-beta, 3-alpha HSD) were found to be differentially expressed in the thalamus of WAG/Rij and Wistar rats. Findings from the frontoparietal cortex suggest the presence of altered serine metabolism and increased vesicular trafficking in the frontoparietal cortex of WAG/Rij rats compared with Wistar rats. These differences in the protein levels might reflect the crucial role of these proteins and related pathways in the generation of absence seizures. In the thalamic specimens, age-dependent changes in protein expression were remarkable, suggesting that this phenomenon may be a precursor or a consequence of absence seizures. Our findings further highlight the potential role of the mTOR signaling pathway in absence epilepsy.

Purification and mass spectrometry based characterization of a pediocin produced by Pediococcus acidilactici 13.

Bacteriocins are antimicrobial peptides produced by several bacterial species. Among the bacteriocins pediocin-like bacteriocins have a significant inhibitory activity on the foodborne pathogens especially on Listeria monocytogenes. This study aims to select a simple and usable purification method to purify/concentrate the antimicrobial peptide and characterization of the bacteriocin produced by Pediococcus acidilactici 13 by using proteomic approaches which is a recent omic technology. For purification dialysis, ultrafiltration method was used, and as a result of this study the bacteriocin activity reached 819,200 AU/mL from 102,400 AU/mL initially. Two dimensional gel electrophoresis and then matrix-assisted laser desorption ionization/time of flight mass spectrometry (MALDI-TOF MS) analysis were carried out to identify the current bacteriocin and related proteins. Obtained data revealed similarity to pediocin PA-1 transport/processing ATP-binding protein PedD (accession number: P36497), pediocin operon PedC (accession number: Q68GC4) and bacteriocin pediocin PA-1 (accession number: P29430) from UniProtKB/Swiss-Prot databank, thus the bacteriocin produced by P. acidilactici 13 is considered similar to pediocin PA-1.

Comprehensive identification of erythrocyte membrane protein deficiency by 2D gel electrophoresis based proteomic analysis in hereditary elliptocytosis and spherocytosis.

PURPOSE: Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (1DE) may reveal qualitative or quantitative defects in red blood cell (RBC) membrane proteins, two-dimensional gel electrophoresis (2DE) can be used for determination of the protein changes caused by the disease process in a relatively high-throughput manner, because it permits an analysis of thousands of modified or unmodified proteins simultaneously. The principal aim of this study was to compare hereditary elliptocytosis (HE), hereditary spherocytosis (HS), and control RBC membrane protein profiles and identify proteins as a clinical marker by the sensitive methods. EXPERIMENTAL DESIGN: RBC membrane proteins of HE, HS, and control groups were compared by 2DE and matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) MS analysis was obtained using peptide mass fingerprint for protein identification. RESULTS: Twenty proteins were identified with peptide mass fingerprint analysis and different expression levels were found in HE, HS, and controls for some proteins that includes three biomarker proteins (ankyrin, spectrin, band 3) that may have prognostic or predictive importance. CONCLUSIONS AND CLINICAL RELEVANCE: 2DE of RBC proteins is a potentially valuable method for studying heritable disorders such as HE and HS. By identifying a deficiency in membrane proteins associated with the RBC cytoskeleton, the diagnosis of HE and HS can be confirmed.

Proteomic identification of erythrocyte membrane protein deficiency in hereditary spherocytosis.

Hereditary spherocytosis (HS) is the most common congenital hemolytic anemia in Caucasians, with an estimated prevalence ranging from 1:2000 to 1:5000. The molecular defect in one of the erythrocytes (RBC) membrane proteins underlying HS like; spectrin-α, spectrin-ß, ankyrin, band 3 and protein 4.2 that lead to membrane destabilization and vesiculation, may change the RBCs into denser and more rigid cells (spherocytes), which are removed by the spleen, leading to the development of hemolytic anemia. It is classified as mild, moderate and severe, according to the degree of the hemolytic anemia and the associated symptoms. Two-dimensional gel electrophoresis (2-DE) is potentially valuable method for studying heritable disorders as HS that involve membrane proteins. This separation technique of proteins based upon two biophysically unrelated parameters; molecular weight and charge, is a good option in clinical proteomics in terms of ability to separate complex mixtures, display post-translational modifications and changes after phosphorylation. In this study, we have used contemporary methods with some modifications for the solubilisation, separation and identification of erythrocyte membrane proteins in normal and in HS RBCs. Spectrin alpha and beta chain, ankyrin and band 3 proteins expression differences were found with PDQuest software 8.0.1. and peptide mass fingerprinting (PMF) analysis performed for identification of proteins in this study.

A preliminary investigation into the venom proteome of Macrovipera lebetina obtusa (Dwigubsky, 1832) from Southeastern Anatolia by MALDI-TOF mass spectrometry and comparison of venom protein profiles with Macrovipera lebetina lebetina (Linnaeus, 1758) from Cyprus by 2D-PAGE.

We compared venoms of two subspecies of blunt-nosed viper Macrovipera lebetina (Linnaeus, 1758) from Southeastern Anatolia and Cyprus by two-dimensional gel electrophoresis (2D-PAGE). Additionally, peptide mass fingerprinting analysis was carried out using matrix-assisted laser desorption ionization/time of flight (MALDI-TOF) mass spectrometry in order to achieve preliminary protein identification from M. lebetina obtusa venom from Turkey. As a result of 2D-PAGE, statistical tests revealed some significant differences that can be considered as subspecies-specific biomarker candidates between two subspecies. Using bioinformatic analyses, proteins belonging to 11 families were identified from the venom of M. l. obtusa: phospholipase A(2), metalloproteinase, serin proteinase, disintegrin, cysteine-rich secretory protein, C-type lectin, vascular endothelial growth factor, nerve growth factor, hyaluronidase, L: -amino acid oxidase, and trypsin inhibitor. Venom of M. lebetina was studied by 2D-PAGE for the first time in the literature, and also this is the first work aiming to determine regional variations of snake venoms by this method in Turkey and Cyprus. Our preliminary results show that snake venom research deserves more attention in Turkey as well as in the toxinology field in general.

Melanocortin-4 receptor polymorphisms in Turkish pediatric obese patients.

The most common Melanocortin-4 receptor (MC4R) missense variant Val103Ileu (rs2229616) is related to obesity. In this study, we examined the distribution of MC4R polymorphisms both in the clinical pediatric obese group and in the high/lowsocioeconomic school group. 24 probable exogene obese children without family history (group I), 66 probable familial obese children (group II), and 111 complicated obese children (group III) were included. Groups I and II obese participants were gathered in a school-based epidemiologic study and compared with 49 apparently healthy non-obese controls. Significant difference in genotype distribution was observed between the groups I and II. Val 103 Ile polymorphism was more common among group III (4.5%). Furthermore, we detected Glu 42 Lys (18.18%) polymorphism in our population, which was not previously reported. Frequency of Val 103 Ile (A) allele polymorphism was 0.75 and 2.25; Glu 42 Lys A allele polymorphism was 9.0 and 1.5, in groups II and III, respectively. None of the MC4R mutations were found in high-socioeconomic school and in control groups. Our data indicated that MC4R polymorphisms were more frequent both in clinical pediatric obese group and in low-socioeconomic school group. In addition, our data revealed that carrying the polymorphism may increase the hereditary form of obesity.

Biology of stem cells in human umbilical cord stroma: in situ and in vitro surveys.

Cells in the umbilical cord stroma have gained attention in recent years; however, differentiation to certain lineages in humans has been demonstrated in few studies. Unlike bone marrow MSCs, human umbilical cord stroma cells (HUCSCs) are far from being well characterized. This study attempts to describe proliferation, structural, and differentiation properties of these cells to account for their exceptional nature in many aspects. Cellular dynamics, cellular structure, and the degree of transformations during expansion and differentiation into mesenchymal and neuronal lineages were examined in vitro over a 10-month period. Comparisons with human bone marrow MSCs regarding differentiation were performed. HUCSCs in culture revealed two distinct cell populations, type 1 and type 2 cells, that possessed differential vimentin and cytokeratin filaments. Corresponding cells were encountered in cord sections displaying region-specific localization. alpha-Smooth muscle actin and desmin filaments, which were evident in cord sections, diminished through passages. No difference was noted regarding type 1 and type 2 cells in differentiation to chondrogenic, adipogenic, and osteogenic lineages, whereas a preferential differentiation was noted in neuronal lineage. Relative success was achieved by production of chondrocytic spheres and osteogenic monolayers, whereas adipocytes were immature compared with bone marrow MSCs. The presence of neuronal markers suggests that they transform into a certain state of maturity under neurogenic induction. Conclusively, HUCSCs retain their original phenotype in culture without spontaneous differentiation, have a limited lifespan, and bear multipotent stem cell characteristics. Given these characteristics, they may be generally considered progenitor cells if manipulated under appropriate conditions and deserve further study to be potentially used in cell-based therapies.