Application of serum SELDI proteomic patterns in diagnosis of lung cancer

BACKGROUND: Currently, no satisfactory biomarkers are available to screen for lung cancer. Surface-Enhanced Laser Desorption/ionization Time-of- Flight Mass Spectrometry ProteinChip system (SELDI-TOF-MS) is one of the currently used techniques to identify biomarkers for cancers. The aim of this study is to explore the application of serum SELDI proteomic patterns to distinguish lung cancer patients from healthy individuals. METHODS: A total of 208 serum samples, including 158 lung cancer patients and 50 healthy individuals, were randomly divided into a training set (including 11 sera from patients with stages I/II lung cancer, 63 from patients with stages III/IV lung cancer and 20 from healthy controls) and a blinded test set (including 43 sera from patients with stages I/II lung cancer, 41 from patients with stages III/IV lung cancer and 30 from healthy controls). All samples were analyzed by SELDI technology. The spectra were generated on weak cation exchange (WCX2) chips, and protein peaks clustering and classification analyses were made using Ciphergen Biomarker Wizard and Biomarker Pattern software, respectively. We additionally determined Cyfra21-1 and NSE in the 208 serum samples included in this study using an electrochemiluminescent immunoassay. RESULTS: Five protein peaks at 11493, 6429, 8245, 5335 and 2538 Da were automatically chosen as a biomarker pattern in the training set. When the SELDI marker pattern was tested with the blinded test set, it yielded a sensitivity of 86.9%, a specificity of 80.0% and a positive predictive value of 92.4%. The sensitivities provided by Cyfra21-1 and NSE used individually or in combination were significantly lower than that of the SELDI marker pattern (P < 0.005 or 0.05, respectively). Based on the results of the test set, we found that the SELDI marker pattern showed a sensitivity of 91.4% in the detection of non-small cell lung cancers (NSCLC), which was significantly higher than that in the detection of small cell lung cancers (P < 0.05); The pattern also had a sensitivity of 79.1% in the detection of lung cancers in stages I/II. CONCLUSION: These results suggest that serum SELDI protein profiling can distinguish lung cancer patients, especially NSCLC patients, from normal subjects with relatively high sensitivity and specificity, and the SELDI-TOF-MS is a potential tool for the screening of lung cancer

A data analysis method for isochronous mass spectrometry using two time-of-flight detectors at CSRe

The concept of isochronous mass spectrometry (IMS) applying two time-of-flight (TOF) detectors originated many years ago at GSI. However, the corresponding method for data analysis has never been discussed in detail. Recently, two TOF detectors have been installed at CSRe and the new working mode of the ring is under test. In this paper, a data analysis method for this mode is introduced and tested with a series of simulations. The results show that the new IMS method can significantly improve mass resolving power via the additional velocity information of stored ions. This improvement is especially important for nuclides with Lorentz factor $\gamma$-value far away from the transition point $\gamma _t$ of the storage ring CSRe.Comment: published in Chinese Physics C Vol. 39, No. 10 (2015) 10620

Detection and identification of enterohemorrhagic Escherichia coli O157:H7 and Vibrio cholerae O139 using oligonucleotide microarray

<p>Abstract</p> <p>Background</p> <p>The rapid and accurate detection and identification of the new subtype of the pathogens is crucial for diagnosis, treatment and control of the contagious disease outbreak. Here, in this study, an approach to detect and identify <it>Escherichia coli </it>O157:H7 and <it>Vibrio cholerae </it>O139 was established using oligonucleotide microarray. We coupled multiplex PCR with oligonucleotide microarray to construct an assay suitable for simultaneous identification of two subtypes of the pathogens.</p> <p>Results</p> <p>The <it>stx</it>1, <it>stx</it>2 gene and <it>uid</it>A gene having the specific mutant spot were chosen as the targets for <it>Escherichia coli </it>O157:H7, and meanwhile the <it>ctx</it>A, <it>tcp</it>A, and <it>LPSgt </it>gene for <it>Vibrio cholerae </it>O139. The oligonucleotide microarray was composed of eight probes including negative control and positive control from 16S rDNA gene. The six primers were designed to amplify target fragments in two triplex PCR, and then hybridized with oligonucleotide microarray. An internal control would be to run a PCR reaction in parallel. Multiplex PCR did not produce any non-specific amplicons when 149 related species or genera of standard bacteria were tested (100% specificity). In addition, <it>Escherichia coli </it>O157:H7 and <it>Escherichia coli </it>O157:non-H7, <it>Vibrio cholerae </it>O139 and <it>Vibrio cholerae </it>O1 had been discriminated respectively. Using recombinant plasmid and target pathogens, we were able to detect positive hybridization signals with 10²copies/μL and 10³cfu/mL per reaction.</p> <p>Conclusion</p> <p>The DNA microarray assay reported here could detect and identify <it>Escherichia coli </it>O157:H7 and <it>Vibrio cholerae </it>O139, and furthermore the subtype was distinguished. This assay was a specific and sensitive tool for simultaneous detection and identification of the new subtype of two pathogens causing diarrhea in human.</p

The Other Press, January 5, 1990

<p>The crude earthworm extract catalysed domino reactions for the synthesis of coumarin derivatives.</p

Screening Quality Evaluation Factors of Freeze-Dried Peach ( Prunus Persica

The quality evaluation of processed products is complex. To simplify the quality evaluation process and improve the efficiency, fourteen evaluation factors of freeze-dried powders of seventeen cultivars of peach at different ripening times were analyzed. The most important evaluation indicators and criteria were obtained by analysis of variance (ANOVA), correlation analysis (CA), principal component analysis (PCA), system cluster analysis (SCA), and analytic hierarchy process (AHP). Results showed that the peach powders had the significant differences in quality (P<0.05), and some processing factors were related with some physicochemical and nutritional factors. Five principle components were extracted by PCA and the cumulative contribution achieved was 84.46%. Through the score plot of the first two principal components, a clear differentiation among ripening times was found and three distinct groups were separated according to ripening time. Five characteristic factors were obtained as titratable acid, browning index, hemicellulose, hygroscopicity, and vitamin C by SCA. Their weights of 0.1249, 0.3007, 0.0514, 0.4916, and 0.0315 were obtained by AHP, respectively. The peach cultivars were divided into four evaluation grades by the comprehensive quality score

Proteomic Response to Rising Temperature in the Marine Cyanobacterium Synechococcus Grown in Different Nitrogen Sources.

Synechococcus is one of the most important contributors to global primary productivity, and ocean warming is predicted to increase abundance and distribution of Synechococcus in the ocean. Here, we investigated molecular response of an oceanic Synechococcus strain WH8102 grown in two nitrogen sources (nitrate and urea) under present (25°C) and predicted future (28°C) temperature conditions using an isobaric tag (IBT)-based quantitative proteomic approach. Rising temperature decreased growth rate, contents of chlorophyll a, protein and sugar in the nitrate-grown cells, but only decreased protein content and significantly increased zeaxanthin content of the urea-grown cells. Expressions of CsoS2 protein involved in carboxysome formation and ribosomal subunits in both nitrate- and urea-grown cells were significantly decreased in rising temperature, whereas carbohydrate selective porin and sucrose-phosphate synthase (SPS) were remarkably up-regulated, and carbohydrate degradation associated proteins, i.e., glycogen phosphorylase kinase, fructokinase and glucose-6-phosphate dehydrogenase, were down-regulated in the urea-grown cells. Rising temperature also increased expressions of three redox-sensitive enzymes (peroxiredoxin, thioredoxin, and CP12) in both nitrate- and urea-grown cells. Our results indicated that rising temperature did not enhance cell growth of Synechococcus ; on the contrary, it impaired cell functions, and this might influence cell abundance and distribution of Synechococcus in a future ocean