Journal of Integrated -OMICS
Not a member yet
215 research outputs found
Sort by
Proteomic identification of plasma biomarkers in type 2 diabetic nephropathy: DOI: 10.5584/jiomics.v1i1.44
No full textRecent advances in quantitative proteomics have offered opportunities to discover plasma proteins as biomarkers for tracking the progression and for understanding the molecular mechanisms of diabetes. We used quantitative proteomic analysis to identify novel biomarkers of nephropathy in plasma from type 2 diabetic patients. Plasma samples were analyzed by fluorescence two-dimensional differential gel electrophoresis (2D-DIGE), and differentially expressed proteins identification was performed by matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Proteomics analysis of the plasma proteome in type 2 diabetes mellitus with nephropathy identified 34 protein spots representing 31 unique proteins. These proteins mainly belonged to metabolic (such as 5'-AMP-activated protein kinase subunit beta-1) and growth regulatory (such as LIM homeobox protein 6) proteins. Additionally, our quantitative proteomic approach has identified numerous previous reported plasma markers of type 2 diabetes mellitus such as apolipoprotein A-I and ficolin-3. On the contrary, we have presented several putative type 2 diabetes mellitus biomarkers including calpain-7 and choline/ethanolamine kinase which have not been reported and may be associated with the progression and development of the disease. The potential of utilizing these markers for screening and treating type 2 diabetes mellitus warrants further investigation. Collectively, our results show that the proteins identified in this study may constitute potential biomarkers for the diagnosis of type 2 diabetics with nephropathy
Proteomic analysis of Chinese kale (B. alboglabra) leaves during growth: DOI: 10.5584/jiomics.v1i1.25
No full textBrassica alboglabra (Chinese kale) is a vegetable extensively grown in Thailand, which has high nutritional value and useful phytochemicals. Farmers generally harvest B. alboglabra starting from the fifth week of growth to sell in the market. In this study, changes in protein expression during growth and development of B. alboglabra were investigated. Proteins were extracted from two to eight-week leaves, and a total of 334 protein spots separated by two-dimensional gel electrophoresis and selected 103 spots were digested and analyzed by using LC-MS/MS. The identified proteins could be classified into nine classes, namely proteins involved in photosynthesis and photorespiration, amino acid metabolism, carbon-compound and carbohydrate metabolism, protein metabolism, stress response, cellular communication and signal transduction, glycolysis and gluconeogenesis, unidentified and others. The highest number of proteins was the proteins involved in photosynthesis and photorespiration, presumably because leaves are the primary sites for photosynthesis and photorespiration, so there is an induction of proteins such as ribulose bisphosphate carboxylase and ribulose bisphosphate carboxylase activase. This is the first study to investigate protein expression in B. alboglabra leaves during growth and development. The studies provide information for protein database in this plant species
Differential expression of Outer membrane proteins in early stages of meropenem-resistance in Acinetobacter baumannii: DOI: 10.5584/jiomics.v1i2.67
No full textAcinetobacter baumannii has emerged as one of the six most important drug-resistant microbes in the world. Resistance by A. baumannii to β-lactams and in particular to meropenem is a serious concern. In this connection, it is essential to understand the changes in the outer membrane proteome of A. baumannii in the initial stages of resistance. For this we have chosen one low resistant strain with MIC of 32 μg/ml and one intermediate strain with very low MIC of 0.8 μg/ml of meropenem and compared their outer membrane profiles with that of sensitive strain, ATCC 19606 of A. baumannii. Decreased expression of porins, transporters and increased production of metabolic enzymes like Succinyl-CoA synthetase, enoyl-CoA hydratase is a common feature in both intermediate strain and low resistant strains. Interestingly, the differential protein expression levels showed a direct relationship with increasing meropenem resistance. It is clear that initial exposure to meropenem resistance drives A. baumannii to restrict the production of OmpAb, CarO, transporters, while the upregulation of genes of altered CarO, metabolic enzymes, peroxidines and antioxidant protein assist in the survival of the bacterium. Because of these unique features of adaptation combined with high metabolic changes in response to antibiotic pressure, A. baumannii poses challenges in therapeutic strategies
Large-scale 2-D DIGE studies - guidelines to overcome pitfalls and challenges along the experimental procedure: DOI: 10.5584/jiomics.v1i1.50
No full textIn large 2-D DIGE proteomic studies with a large number of samples, it is essential to design the experimental setup to detect statistically significant protein changes under consideration of experimental variances. Here we present some guidelines and general remarks on how to extract protein expression data by following protein spots on their way from first spot synchronization, detection, quantification and statistical analysis until excision and identification. Furthermore, common difficulties and potential pitfalls are discussed which might not be obvious to novices and even more experienced users of DIGE technology
Cell fractionation - an important tool for compartment proteomics: DOI: 10.5584/jiomics.v1i1.52
No full textIn order to maximize coverage in proteome studies, a successful approach is the fractionation of cellular compartments. For providing evidence for the most reliable and efficient separation technique, we compared four different procedures for subcellular fractionation of Jurkat cells. The analysis of fractions by LTQ-Orbitrap yielded between 559 and 1195 unambiguously identified unique proteins. The assumed correct localisation of the proteins was defined using Scaffold3 according to GO annotations, with the highestreliability (~80%) for the cytoplasmic fraction and the lowest (~20%) for the cytoskeletal fraction. This comparison revealed evidence for the efficiencies of separating subcellular fractions and will thereby facilitate the decision on which procedure might be the best match to a specific research question and contribute to the emerging field of compartment proteomics
Quantitative Proteomic Analysis of Retina in Oxygen-Induced Retinopathy Mice using iTRAQ with 2D NanoLC-nanoESI-MS/MS: DOI: 10.5584/jiomics.v1i2.36
No full textAnalysis of retina proteome during the hypoxia-induced retinal neovascularization (RN) process may be helpful to elucidate pathogenesis of the related diseases, such as diabetic retinopathy (DR) and retinopathy of prematurity (ROP). RN model was induced in C57BL/6 mice by exposing 7-day-old mice to 75% oxygen for 5 days followed by 5 days in room air. Retina tissues at postnatal day 17 from both control and oxygen-induced retinopathy (OIR) mice were used for proteomic analysis. We have employed a quantitative proteomic approach, iTRAQ coupled with 2D nanoLC-nanoESI-MS/MS to quantitatively compare the relative changes in the retinal proteome from control and OIR mice. In total, 264 proteins from mouse retina were identified at a 95% confidence level. Among them, OIR induced significant changes in 28 proteins (14 up-regulated and 14 down-regulated). Obvious changes include the up-regulation of a few plasma proteins (indicating the breakdown of the blood-retina barrier) vimentin, ribosomal proteins, some proteases, neural cell adhesion molecule (NCAM) 180, retinoschisin and down-regulation of several crystallins such as isoform 1 of α crystallin A chain, isoform 2 of α crystallin A chain, a crystallin B chain, g crystallin D and b-A3/A1 crystallin. The iTRAQ result of a crystallin B chain was also confirmed by Western blot analysis. The proteomic results showed in this study should provide new avenues for understanding the pathogenesis of retinal neovascularization and its related retina diseases
Extraction and purification of the lectin found in the tubers of Eranthis hyemalis (winter aconite): DOI: 10.5584/jiomics.v1i2.72
No full text
Lectin are proteins which play an important role in the defence mechanisms of plants against the attack of microorganisms and insects: this role has provoked particular interest in the fields of biotechnology and agriculture. This paper describes the extraction and purification of the lectin found in tubers of the winter aconite (Eranthis hyemalis), with the aim of improving and modernising the existing extraction protocol. The Eranthis hyemalis lectin (EHL) is a member of the type-2 Ribosome Inactivating Proteins (RIP) family, proteins which have the ability to inhibit in vitro protein synthesis. RIPs have been linked to plant defence by their antiviral, antifungal and insecticidal properties, and some have been found to be potent inhibitors of the Human Immunodeficiency Virus-1 (HIV-1) virus. EHL was purified using affinity column chromatography and ammonium sulphate precipitation; thiourea was used as antioxidant in order to prevent EHL denaturing during the extraction process. The presence of EHL in the extract was verified using a blood agglutination test with rabbit erythrocytes. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis was employed to determine the lectin size; EHL was found to be formed of two chains with molecular weights of approximately 31 kDa; the size of the whole protein was estimated as approximately 60 kDa. The concentration of the EHL in the post-column eluent, determined using the Bradford Assay, was 380.1 μg.cm-3. This improved extraction protocol is the first step which will enable future research on the potential use of EHL in crop protection, by studying its insecticidal, fungicidal and bactericidal properties
Hemoglobin subunit beta (HBB) is a potential biomarker for predicting response to Gefitinib in NSCLC patients: DOI: 10.5584/jiomics.v1i2.74
No full textEGFR mutation status has been reported to correlate well with the response of NSCLC patients to Ge9tinib. However, EGFR mutation analysis is invasive in nature and recent studies supported the notion that EGFR mutation was unable to predict response to Ge9tinib in somepatients. We therefore conducted plasma proteomics to identify potential biomarkers that are less invasive and whose expressions correlatemore signi9cantly to response to Ge9tinib. To identify protein candidates that correlate with response to Ge9tinib, we pro9led the relativeexpression levels of plasma proteins between responders and non-responders prior to Ge9tinib treatment. Relative quanti9cation of plasmaproteins were analysed using Isobaric Tags for Relative and Absolute Quanti9cation (iTRAQ) and liquid chromatography-electrospray ionization (ESI) tandem mass spectrometry. Proteins that were commonly upregulated or downregulated amongst responders but not the nonresponders were selected for validation via immunoblotting. HBB protein was found to be signi9cantly under-expressed in the plasma samples from 6 out of 7 ge9tinib-responsive patients but over-expressed in a majority of the non-responders. Our 9nding showed that HBB is apotential biomarker for predicting response to Ge9tinib that may be subject to a larger study to examine its role as a companion biomarkerfor Ge9tinib therap
Transcriptomic responses in Japanese medaka (Oryzias latipes) exposed to 17β-estradiol: DOI: 10.5584/jiomics.v1i1.29
No full textThe effects of 17b-estradiol (E2) were evaluated using the medaka DNA microarray representing 36,398 genes. We first evaluated chronic effects on medaka exposed to E2 at different concentrations for 60 days posthatch. At ≥ 30 ng/L of E2 severe reproductive impairments such as sex reversal were observed. Larval medaka, Oryzias latipes, (within 24 hrs posthatch) were then exposed to E2 at various concentrations (3, 30, 100 ng/L) for up to 7 days. Microarray analyses of the E2-exposed larvae revealed that exposure to E2 up-regulated and down-regulated 339 and 105 genes, respectively. The up-regulated genes included ones involved in the p53 signaling pathway, apoptosis, and growth and development, in addition to well-known biomarkers such as vitellogenin and choriogenins. Down-regulated genes included heat shock proteins and estrogen receptors. Most of the up-regulated genes encoding the p53 signaling pathway, apoptosis, and growth and development exhibited a dose-dependent increase in gene expression, whereas the down-regulated genes in the heat shock protein category showed a dose-dependent decrease in gene expression. Time course experiments suggested that the E2 treatment attenuated the time-dependent changes in gene expressions of these genes. Among the genes related to oocyte maturation, estrogen-regulated genes such as choriogenins and vitellogenins were dramatically induced in response to E2 exposure, whereas other steroid-regulated genes such as zona pellucida-domain proteins did not change in gene expression by the E2 treatment. Results suggest that transcriptomic studies on larval medaka help elucidate the effects caused by endocrine disruptors on various biological pathways in vertebrate development
Quantitative Analysis of Histone Exchange during Chromatin Purification: DOI: 10.5584/jiomics.v1i1.26
No full textCentral to the study of chromosome biology are techniques that permit the purification of small chromatin sections for analysis of associated DNA and proteins, including histones. Chromatin purification protocols vary greatly in the extent of chemical cross-linking used to prevent protein dissociation/re-association during isolation. Particularly for genome-wide analyses, chromatin purification requires a balanced level of fixation trapping native protein-protein and protein/DNA interactions, yet leaving chromatin sections soluble and accessible to affinity reagents. We have devised a quantitative methodology for optimizing levels of chemical cross-linking for affinity purification of chromatin sections using isotopically labeled media. We show that fine-tuning of chemical cross-linking is necessary for efficient isolation of chromatin sections when minimal histone/protein exchange is required