155 research outputs found
Temporal proteomic analysis of IGF-1R signalling in MCF-7 breast adenocarcinoma cells
No full textDysregulation of the insulin‐like growth factor 1 receptor signalling network is implicated in tumour growth and resistance to chemotherapy. We explored proteomic changes resulting from insulin‐like growth factor 1 stimulation of MCF‐7 adenocarcinoma cells as a function of time. Quantitative analysis using iTRAQ™ reagents and 2‐D LC‐MS/MS analysis of three biological replicates resulted in the identification of 899 proteins (p≤0.05) with an estimated mean false‐positive rate of 2.6%. Quantitative protein expression was obtained from 681 proteins. Further analysis by supervised k‐means clustering identified five temporal clusters, which were submitted to the FuncAssociate server to assign overrepresented gene ontology terms. Proteins associated with vesicle transport were significantly overrepresented. We further analyzed our data set for proteins showing temporal significance using the software, extraction and analysis of differential gene expression, resulting in 20 significantly and temporally changing proteins (p≤0.1). These significant proteins play roles in, among others, altered glucose metabolism (lactate dehydrogenase A and pyruvate kinase M1/M2) and cellular stress (nascent polypeptide‐associated complex subunit α and heat shock (HSC70) proteins). We used multiple reaction monitoring to validate these interesting proteins and have revealed several differences in relative peptide expression corresponding to protein isoforms and variants
Targeted proteomic analysis of glycolysis in cancer cells
No full textAltered expression of glycolysis proteins is an important yet poorly understood characteristic of cancer. To better understand the glycolytic changes during tumorigenesis, we designed a liquid chromatography multiple reaction monitoring (LC−MRM) assay targeting the “glycolysis proteome” in MCF-7 breast cancer cells, using isotope-coded dimethylation of peptides for relative quantification. In silico, dimethyl labeled tryptic peptides [M + 2H]2+ (of length n) and their yn-1 fragment ions were determined based on UniprotKB database sequence entries for glycolysis proteins, related branching pathways, and reference proteins. Using predicted transitions ([M + 2H]2+ → yn-1), MRM-initiated detection and sequencing (MIDAS) was performed on a dimethyl-labeled, tryptic digest from MCF-7 cells, using two-dimensional liquid chromatography mass spectrometry analysis. Three transitions for each peptide were selected from identified spectra and assessed using 1D-LC−MRM-MS. Collision energy (CE) and dwell times were optimized and matching transitions for “heavy” isotope-coded dimethylated peptides were calculated. Resulting LC−MRM transitions were then used to measure changes in the glycolytic proteome in insulin-like growth factor-1 (IGF-1)-stimulated MCF-7 cells and other breast cell lines. Increases in the expression of glycolysis proteins leading to lactic acid production were observed common to IGF-1-stimulated MCF-7 cells and the invasive MDA-MB-231 cell line. Preliminary analysis of lung tumors with varied states of differentiation demonstrated the clinical applicability of LC−MRM and showed decreased levels of PGK1 in poorly differentiated tumors
Relative quantitative proteomic analysis reveals wound response proteins correlated with after-cooking darkening
No full textMany common potato tuber defects are difficult to elicidate because of the degree of genetic complexity involved, making systems biology approaches necessary. Interaction between chlorogenic acid and iron is responsible for the darkening of potato tuber tissues upon heating – termed after‐cooking darkening (ACD). To explore mechanisms of darkening severity in tuber tissues, we have employed relative quantitative proteomics to discover differentially expressed proteins involved in ACD. Tuber tissue samples were collected from a family of diploid clones which possess a highly segregated degree of the darkening. Exploiting this segregation, as well as the observation that darkening is more prevalent in the stem end of the tuber than the apical end, three sample groups were formed: (i) stem ends of three high‐ACD clones, (ii) stem ends of three low‐ACD clones, and (iii) apical ends of three low‐ACD clones. Protein samples were digested and differentially labeled using isotopic reductive methylation, allowing for an orthogonal two‐way comparison of protein profiles of the sample groups using 2‐D‐LC‐MS/MS. Using a cutoff fold change of 2 between the high‐ and the low‐ACD sample groups, 30 proteins showed a correlation with tissue darkening. Overall, we observed changes in relative protein abundance that showed an enhanced wound‐response program in high‐ACD tissues. Among these proteins, five proteins were further validated at the transcript level using qRT‐PCR. These proteins may be incorporated into design strategies to create potato cultivars with low levels of ACD
Cerebral atrophy in mild cognitive impairment and Alzheimer disease: rates and acceleration.
Get PDFOBJECTIVE: To quantify the regional and global cerebral atrophy rates and assess acceleration rates in healthy controls, subjects with mild cognitive impairment (MCI), and subjects with mild Alzheimer disease (AD). METHODS: Using 0-, 6-, 12-, 18-, 24-, and 36-month MRI scans of controls and subjects with MCI and AD from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database, we calculated volume change of whole brain, hippocampus, and ventricles between all pairs of scans using the boundary shift integral. RESULTS: We found no evidence of acceleration in whole-brain atrophy rates in any group. There was evidence that hippocampal atrophy rates in MCI subjects accelerate by 0.22%/year2 on average (p = 0.037). There was evidence of acceleration in rates of ventricular enlargement in subjects with MCI (p = 0.001) and AD (p < 0.001), with rates estimated to increase by 0.27 mL/year2 (95% confidence interval 0.12, 0.43) and 0.88 mL/year2 (95% confidence interval 0.47, 1.29), respectively. A post hoc analysis suggested that the acceleration of hippocampal loss in MCI subjects was mainly driven by the MCI subjects that were observed to progress to clinical AD within 3 years of baseline, with this group showing hippocampal atrophy rate acceleration of 0.50%/year2 (p = 0.003). CONCLUSIONS: The small acceleration rates suggest a long period of transition to the pathologic losses seen in clinical AD. The acceleration in hippocampal atrophy rates in MCI subjects in the ADNI seems to be driven by those MCI subjects who concurrently progressed to a clinical diagnosis of AD
High Sensitivity C Reactive Protien (HSCRP) Levels and Correlation with Lipid Profile in Hypertension
Get PDFBACKGROUND:
Highly sensitive C reactive protein (HsCRP) levels a risk marker of future cardiovascular events can be elevated in patients with hypertension independent of dyslipidemia.
OBJECTIVE:
To find if any association exists between HsCRP and Lipid levels of patients with hypertension and assess the usefulness of HsCRP as a risk stratification in predicting future coronary artery disease.
Based on the results provide primary prevention strategies for patients with moderate to high risk for CAD.
METHODS AND MATERIALS:
HsCRP and fasting lipid profile were measured in 50 hypertensive patients with a history of HTN for more than 6 months duration, who are on antihypertensive treatment. Serum HsCRP levels were catagorised into 3 groups (3mg/L high risk).
The HsCRP levels and its association with hypertension and correlation with lipid profile was analyzed using SPSS version 20 software.
RESULTS:
In this observational study subjects with hypertension were categorized according to JNC 7 classification of hypertension.
Subjects were grouped into duration of hypertension were compared with HsCRP levels and subjects categorized into 3 risk categories of 3mg/L high risk. There was significant number of patients in the moderate risk category with HsCRP levels between 1-3mg/L (p value < 0.001) but no statistical significance observed when correlated with the duration of hypertension or with the levels of Total cholesterol, LDL-C and HDL-C.
CONCLUSION:
In summary, this study observed that HsCRP levels of > 1-3mg/L were elevated significantly in subjects with hypertension (p value < 0.001) irrespective of their BP levels and duration of hypertension.There was no statistical significance and correlation between levels of HsCRP with levels of LDL-C or HDL-C.
HsCRP levels can be evaluated in hypertensive individuals who do not have symptomatic CAD irrespective of abnormal Lipid profile and can be provided with primary prevention to prevent future cardiovascular events
SFCL and Applications Study for Implementation in Electrical Power System
No full textThe increase in demand and consumption of electricity has led to an increase in system errors. Superconducting Residual Current Limiters (SFCLs) provide ideal performance in the power grid. The concept of superconducting fault current limiters (SFCLs) suggests two types of superconducting materials. First of all Resistive-SFCL (which is inserted directly in series with the circuit to be protected). Second, the inductive SFCL (a transformer shorted by a superconducting tube). We also explore some uses of the proposed SFCLs to limit the fault current that appears in the electrical network. The fault current level has become a major problem in the operation of transmission and distribution systems. Applying the superconducting residual current limiter (SFCL) would not only reduce the load on the equipment in the network, but can also provide a link to improve the reliability of the power system. They also make the electricity grid more efficient and more integrated
A qualitative proteome investigation of the sediment portion of human urine: Implications in the biomarker discovery process
No full textInherent to the biomarker discovery process is a comparative analysis of physiological states. It is therefore critical that the proteome detection protocol does not bias the analysis. With urine, the sediment portion, obtained upon thawing frozen urine, is routinely discarded prior to proteome analysis. However, our results demonstrate that such a practice inadvertently induces bias, having significant implications in the biomarker discovery process. We present the first proteome investigation of human urinary sediments, identifying 60 proteins in this phase by MS. Many sediment proteins were also detected in the urinary supernatant, indicating that several proteins partition between the two phases. This partitioning is dependant on the pH of the sample, as well as the degree of sample agitation. As a consequence of discarding the sediment portion of urine, the concentration of potential candidate biomarkers in the supernatant phase will be altered or, in other instances, may be completely removed from the sample. To minimize this, the pH of all samples should first be normalized, and the samples vigorously vortexed prior to discarding the sediments. For more comprehensive biomarker investigations, we suggest that urinary sediments be analyzed along with the supernatant proteins
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