Desorption Ionization-time Of Flight Mass Spectrometry Research Articles

Drug Resistance in Biofilm and Planktonic Cells of Achromobacter spp., Burkholderia spp., and Stenotrophomonas maltophilia Clinical Isolates.

Background: Biofilm production in nonfermenting Gram-negative bacteria influences drug resistance. The aim of this work was to evaluate the effect of different antibiotics on biofilm eradication of clinical isolates of Achromobacter, Burkholderia, and Stenotrophomonas maltophilia. Methods: Clinical isolates were identified by matrix-assisted laser desorption ionization-time of flightmass spectrometry in a third-level hospital in Monterrey, Mexico. Crystal violet staining was used to determine biofilm production. Drug susceptibility testing was determined by broth microdilution in planktonic cells and biofilm cells. Results: Resistance in planktonic cells was moderate to trimethoprim-sulfamethoxazole, and low to chloramphenicol, minocycline, levofloxacin (S. maltophilia and Burkholderia), ceftazidime, and meropenem (Burkholderia and Achromobacter). Biofilm eradication required higher drug concentrations of ceftazidime, chloramphenicol, levofloxacin, and trimethoprim-sulfamethoxazole than planktonic cells (p < 0.05). Levofloxacin showed biofilm eradication activity in S. maltophilia, minocycline and meropenem in Burkholderia, and meropenem in Achromobacter. Conclusions: Drug resistance increased due to biofilm production for some antibiotics, particularly ceftazidime and trimethoprim-sulfamethoxazole for all three pathogens, chloramphenicol for S. maltophilia and Burkholderia, and levofloxacin for Burkholderia. Some antibiotics could be used for the treatment of biofilm-associated infections in our population, such as levofloxacin for S. maltophilia, minocycline and meropenem for Burkholderia, and meropenem for Achromobacter.

Identification of Autoantigens in Pediatric Gastric Juices.

This study aimed to investigate the presence of autoantigens in the gastric juices of children. Gastric juice and serum samples were obtained from 53 children <15 years of age who underwent gastric endoscopy. Among these, 8, 22, and 23 participants were in the age groups 0-5, 6-10, and 11-15 years, respectively. These samples were analyzed using two-dimensional electrophoresis (2-DE), immunoblot analysis, and matrix-assisted laser desorption ionization-time of-flight mass spectrometry. Furthermore, we reviewed the histopathological findings and urease test results and compared them with the results of 2-DE and immunoblot analysis. There were no statistically significant differences in urease test positivity, grades of chronic gastritis, active gastritis, or Helicobacter pylori infiltration of the antrum and body among the three age groups. Three distinct patterns of gastric juice were observed on 2-DE. Pattern I was the most common, and pattern III was not observed below the age of 5 years. Histopathological findings were significantly different among active gastritis (p=0.037) and H. pylori infiltration (p=0.060) in the gastric body. The immunoblots showed large spots at an approximate pH of 3-4 and molecular weights of 31-45 kDa. These distinct, large positive spots were identified as gastric lipase and pepsin A and C. Three enzymes, which are normally secreted under acidic conditions were identified as autoantigens. Further investigation of the pathophysiology and function of autoantigens in the stomach is required.

Identification and analysis of a clinically isolated strain of Halomonas based on whole-genome sequencing and comparative genomics.

The aim of this study was to identify the species of a Halomonas strain isolated from a neonatal blood sample and to understand the potential pathogenicity and characteristic genes of the strain. The genomic DNA of strain 18071143 (identified as Halomonas by matrix-assisted laser desorption-ionization time of flight-mass spectrometry and the 16S ribosomal RNA (rRNA) gene sequence) was sequenced using Nanopore PromethION platforms. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) were calculated using the complete genome sequences of the strain. Comparative genomic analyses were performed on strain 18071143 and 3 strains of Halomonas (Halomonas stevensii S18214, Halomonas hamiltonii KCTC 22154, and Halomonas johnsoniae KCTC 22157) that were associated with human infections and had high genomic similarity to strain 18071143. Phylogenetic, ANI, and dDDH similarity analyses based on genome sequence indicated that strain 18071143 belonged to the species H stevensii. Similarities exist between strain 18071143 and the other 3 Halomonas strains in terms of gene structure and protein function. Nonetheless, strain 18071143 has greater potential for DNA replication, recombination, repair, and horizontal transfer. Whole-genome sequencing holds great promise for accurate strain identification in clinical microbiology. In addition, the results of this study provide data for understanding Halomonas from the perspective of pathogenic bacteria.

The use of matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI TOF-MS) to characterize bulk-tank milk isolated bacteria in Mangaung, South Africa

The use of matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI TOF-MS) to characterize bulk-tank milk isolated bacteria in Mangaung, South Africa

Isolation and Characterization of Rare Flavone Tetraglycosides from the Seeds of the Bioactive Plant: Peganum harmala L.

The phytochemical investigation of Peganum harmala L. seeds yielded two rare flavone tetraglycosides following isolation, purification, and analyses. The compound determined to be diosmetin-7-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyl-(1→2)-[α-L-rhamnopyranosyl-(1→6)]-β-D-glucopyranoside (1) was first isolated from the species while the other compound characterized to be acacetin-7-O-β-D-glucopyranosyl-(1→2)-β-D-glucopyranosyl-(1→2)-[α-L-rhamnopyranosyl-(1→6)]-β-D-glucopyranoside (2) was isolated from the genus Peganum for the first time. Their structures were primarily elucidated by one-dimensional (1D) and two-dimensional (2D) nuclear magnetic resonance (NMR) (1H, 13C NMR, DEPT, COSY, HSQC and HMBC) and supported by matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and MALDI-TOF-MS/MS analyses.

Polyphenol Profiling of Chestnut Pericarp, Integument and Curing Water Extracts to Qualify These Food By-Products as a Source of Antioxidants.

Plant polyphenols have beneficial antioxidant effects on human health; practices aimed at preserving their content in foods and/or reusing food by-products are encouraged. The impact of the traditional practice of the water curing procedure of chestnuts, which prevents insect/mould damage during storage, was studied to assess the release of polyphenols from the fruit. Metabolites extracted from pericarp and integument tissues or released in the medium from the water curing process were analyzed by matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) and electrospray-quadrupole-time of flight-mass spectrometry (ESI-qTOF-MS). This identified: (i) condensed and hydrolyzable tannins made of (epi)catechin (procyanidins) and acid ellagic units in pericarp tissues; (ii) polyphenols made of gallocatechin and catechin units condensed with gallate (prodelphinidins) in integument counterparts; (iii) metabolites resembling those reported above in the wastewater from the chestnut curing process. Comparative experiments were also performed on aqueous media recovered from fruits treated with processes involving: (i) tap water; (ii) tap water containing an antifungal Lb. pentosus strain; (iii) wastewater from a previous curing treatment. These analyses indicated that the former treatment determines a 6–7-fold higher release of polyphenols in the curing water with respect to the other ones. This event has a negative impact on the luster of treated fruits but qualifies the corresponding wastes as a source of antioxidants. Such a phenomenon does not occur in wastewater from the other curing processes, where the release of polyphenols was reduced, thus preserving the chestnut’s appearance. Polyphenol profiling measurements demonstrated that bacterial presence in water hampered the release of pericarp metabolites. This study provides a rationale to traditional processing practices on fruit appearance and qualifies the corresponding wastes as a source of bioactive compounds for other nutraceutical applications.

Clinical relevance, Speciation, and Antibiogram of Non -Diphtherial Corynebacteria isolated from various clinical samples in a tertiary care hospital in Zagazig, Egypt

Background: The non-diphtherial Corynebacteria, also called “Coryneforms” bacteria are a diversified group of gram positive non sporing bacilli belonging to the genus Corynebacteria. Such bacteria are considered members of human microbiota (skin, respiratory and genital mucus membranes). Coryneform bacteria's pathogenic capacity has been undervalued until recently. Despite of frequently deemed as contaminants, these bacteria have been correlated to diverse clinical infections recently. Objectives: To isolate, speciate, and determine antimicrobial susceptibility pattern of clinically relevant non-diphtherial Corynebacteria from various clinical samples. Methodology: Different clinical samples (blood, urine, sputum, wound swabs, pus) collected from hospitalized patients attending at Zagazig University Hospital. The samples were processed and cultured as per conventional bacteriological methods. A total of 75 clinically relevant corynebacterial isolates exhibited speciation utilizing matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) analysis and their antibiogram was done by disc diffusion method by means of combined guidelines of Clinical and Laboratory Standards Institute (CLSI) as well as British Society for Antimicrobial Chemotherapy (BSAC) because of lack of definite CLSI guidelines. Results: The mean age of the studied patients was 64.6 ± 14.9 years, 60% were male and 40% female. A total 75 clinically relevant Corynebacteria species were obtained from different clinical samples, including wound swabs and pus (53%), sputum (20%), and blood (17%). Forty two percent were isolated from ICUs. The most prevalent isolated species was C.amycolatum (27%), C. striatum (20%), and C.jeikieum (16%). Beta lactam antibiotics showed least activity against Corynebacteria species with resistance rate against penicillin 76% and ceftriaxone 72%, while all isolates exhibited uniform sensitivity (100%) against vancomycin as well as linezolid. Conclusion: This study showed isolation of different clinically relevant non-diaphterial Corynebacteria from different clinical samples with pus and wound swabs as the most common samples from which Corynebacteria were isolated. In particular, C.amycolatum was the most common isolated species. Beta lactam antibiotics (penicillin, ceftriaxone) showed the least activity while vancomycin and linezolid were the most active agents against nondiapdhterial Corynebacteria isolates. Herein, we confirm diphtheroids’ clinical importance among different infections that necessitate evaluating their susceptibility patterns to some common antibacterial agents for guide the best antibiotic to treat infections caused by these species.

Quantitative clinical glycomics strategies: A guide for selecting the best analysis approach.

Glycans introduce complexity to the proteins to which they are attached. These modifications vary during the progression of many diseases; thus, they serve as potential biomarkers for disease diagnosis and prognosis. The immense structural diversity of glycans makes glycosylation analysis and quantitation difficult. Fortunately, recent advances in analytical techniques provide the opportunity to quantify even low-abundant glycopeptides and glycans derived from complex biological mixtures, allowing for the identification of glycosylation differences between healthy samples and those derived from disease states. Understanding the strengths and weaknesses of different quantitative glycomics analysis methods is important for selecting the best strategy to analyze glycosylation changes in any given set of clinical samples. To provide guidance towards selecting the proper approach, we discuss four widely used quantitative glycomics analysis platforms, including fluorescence-based analysis of released N-linked glycans and three different varieties of MS-based analysis: liquid chromatography (LC)-mass spectrometry (MS) analysis of glycopeptides, matrix-assisted laser desorption ionization-time of flight MS, and LC-ESI-MS analysis of released N-linked glycans. These methods' strengths and weaknesses are compared, particularly associated with the figures of merit that are important for clinical biomarker studies, including: the initial sample requirements, the methods' throughput, sample preparation time, the number of species identified, the methods' utility for isomer separation and structural characterization, method-related challenges associated with quantitation, repeatability, the expertise required, and the cost for each analysis. This review, therefore, provides unique guidance to researchers who endeavor to undertake a clinical glycomics analysis by offering insights on the available analysis technologies.

Description of a Clinical Strain of Mycobacterium cambodiensis sp. nov., a New Member of the Mycobacterium simiae Complex

A bronchoalveolar lavage sample was collected by bronchoscopy from a 25-year-old Cambodian male patient with suspected clinical tuberculosis and was inoculated in Lowenstein-Jensen medium. Colonies of a rapidly growing, non-chromogenic Gram-positive and acid-fast bacterium were investigated. Scanning electron microscopy showed 1.2 ± 0.29 μm-long and 0.58 ± 0.07 μm-large bacilli that could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic tests (API® ZYM, API® Coryne and Biolog® Phenotype MicroArray assays). In vitro, the isolate was susceptible to isoniazid, amikacin and trimethoprim- sulfamethoxazole. Whole-genome sequencing yielded a 5,703,981-bp draft genome that displayed 69.3% of GC content with 5,207 coding-protein genes and 56 predicted RNA genes, including 3 rRNAs. The rpoB sequence showed 93% sequence similarity with that of Mycobacterium parascrofulaceum in the Mycobacterium simiae complex. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pan-genomic analyses confirmed that this isolate represented an undescribed species within the M. simiae complex. This species was named Mycobacterium cambodiensis after its source of isolation. The isolate was deposited in the Collection de Souches de l’Unite des Rickettsies (CSUR) with the number CSURP9652.

Recombinant expression of lytic polysaccharide monooxygenase and its functional characterization

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes that can act on crystalline polysaccharides directly, which plays a critical role in cellulose degradation. In addition to reports on its structure and mechanism of action, it is important to study the auxiliary activity 9 (AA9) characteristics from different resources to support the mechanism research. The gene encoded ToLPMO9A was cloned from Trichoderma orientalis EU7-22 and first heterologously expressed in Pichia pastoris GS115. Both metal ions and reducing agent concentrations showed an important effect on ToLPMO9A. The ToLPMO9A exhibited maximal activity at 60 °C and a 6.0 pH. In addition, ToLPMO9A showed substrate specificity. The matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis showed that ToLPMO9A cleaved the glycosidic bonds at C1 and C4/C6 position via oxidation. Concerning the synergistic effects on enzymic activity, ToLPMO9A exhibited promotion with endo-glucanase or exo-glucanase, but inhibition with β-glucosidases. In conclusion, ToLPMO9A could be a good choice for enzyme cocktails and provide theoretical support for subsequent action mechanisms and broader applications.

Peptidome profiles in melamine diet-induced bladder stones in C57BL/6 mice

The aim of this research was to detect potential serum biomarkers of melamine diet-induced bladder stones in C57BL/6 mice. Magnetic bead-based weak cationexchange chromatography (MB-WCX) and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) were employed to detect serum biomarkers in 10 mice fed a melamine diet and 10 control mice. Seventeen peaks (fold change>1.5) with a mass to charge (m/z) value of 1000–10,000 Da were detected in the two groups. Among the significant peaks, five were upregulated and the other 12 were downregulated in the model group. Among the upregulated peaks, 2954.49 and 1710.49 were found to correspond to the peptide regions of NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 8(Ndufα8) and basigin, respectively, by liquid chromatography with electrospray ionization and tandem triple quadrupole mass spectrometry(LC-ESI-MS/MS). Western blot analysis was used to detect the expression of Ndufα8 and basigin in another 10 model mice and 10 control mice. The western blot results confirmed the LC-ESI-MS/MS data. The expression of serum basigin and Ndufα8 was partly dependent the concentration of melamine, but no time dependence. In conclusion, Ndufα8 and basigin may be potential serum biomarkers for the detection of melamine diet-induced bladder stones in C57BL/6 mice

\u201cMycobacterium mephinesia\u201d, a Mycobacterium terrae complex species of clinical interest isolated in French Polynesia

A 59-year-old tobacco smoker male with chronic bronchitis living in Taravao, French Polynesia, Pacific, presented with a two-year growing nodule in the middle lobe of the right lung. A guided bronchoalveolar lavage inoculated onto Löwenstein-Jensen medium yielded colonies of a rapidly-growing non-chromogenic mycobacterium designed as isolate P7213. The isolate could not be identified using routine matrix-assisted laser desorption ionization-time of flight-mass spectrometry and phenotypic and probe-hybridization techniques and yielded 100% and 97% sequence similarity with the respective 16S rRNA and rpoB gene sequences of Mycobacterium virginiense in the Mycobacterium terrae complex. Electron microscopy showed a 1.15 µm long and 0.38 µm large bacillus which was in vitro susceptible to rifampicin, rifabutin, ethambutol, isoniazid, doxycycline and kanamycin. Its 4,511,948-bp draft genome exhibited a 67.6% G + C content with 4,153 coding-protein genes and 87 predicted RNA genes. Genome sequence-derived DNA-DNA hybridization, OrthoANI and pangenome analysis confirmed isolate P7213 was representative of a new species in the M. terrae complex. We named this species “Mycobacterium mephinesia”.

Characterization of nutrient status of Halamphora luciae (Bacillariophyceae) using matrix-assisted ultraviolet laser-desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS)

ABSTRACTThe effects of N and P depletion on the production and structural characterization of the cellular carbohydrate polymers of the estuarine diatom Halamphora luciae in batch culture were examined using matrix-assisted laser desorption-ionization time-of flight mass spectrometry (MALDI-TOF MS) complemented with monosaccharide composition determination and structural analyses by methylation of aqueous extracted product. The MALDI MS analysis of the cells showed a similar profile in control and N- and P-depleted media, with a displacement to higher molecular weight for cells grown in depleted media. In the monosaccharide analyses, both nutrient depletion and culture ageing led to an increase in glucose content, indicating that MALDI-TOF MS in whole cells was detecting the changes in chrysolaminarin. The maxima for the ions from f/2-P and to a lesser extent in f/2-N were displaced to higher m/z values indicating a higher degree of polymerization (DP). Methylation analysis confirmed the presence of chrysolaminarin, a (1→3)-β-d-glucan with branching in C2 and C6, where the glucan backbone had a substitution every four glucose residues. The (1→3)-β-d-glucan was also detected in the cingule by fluorescence with aniline blue.

Leishmania donovani molecules recognized by sera of filaria infected host facilitate filarial infection.

We earlier found that F6 fraction of human filaria Brugia malayi cross-reacted with sera of Leishmania donovani infected hamsters and immunization with F6 inhibited both filarial and leishmanial infections. In the present study, we identified a 52.9-93.6 kDa fraction (Ld1) of L. donovani that cross-reacted with sera of B. malayi infected animals and investigated effect of Ld1 on filarial infection. Immunization of BALB/c mice with Ld1 facilitated B. malayi infection with remarkable increase in parasite burden. Facilitation of filarial infection was associated with downregulated cell proliferation, IL-5, IL-13, IFN-γ, TNF-α, and IL-2 levels and upregulated IL-4 and TGF-β. Ld1 exposure also suppressed MHC class-I, MHC class-II, and FcεR1 expression, and phagocytosis in naive mouse macrophages, and CD4+, CD8+, and CD19+ cell population in mouse spleen. Two-dimensional electrophoresis and matrix-assisted laser desorption ionization-time of flight-mass spectrometry revealed eight proteins in Ld1: putative heat shock protein (HSP) 70-related protein 1, HSP70 mitochondrial precursor, alanine aminotransferase, 2,3-bisphosphoglycerate-independent phosphoglycerate mutase, protein disulfide isomerase, putative ATPase beta subunit, trypanothione reductase, and a hypothetical protein. HSP70 protein mitochondrial precursor and trypanothione reductase showed homology with Trypanosoma cruzi and L. donovani, respectively, and the rest 6 proteins including hypothetical protein bear homology with L. infantum. In conclusion, the present study for the first time shows that immunization with filarial cross-reactive Ld1 fraction of L. donovani facilitates filarial infection by modulating Th1 and Th2 responses. Ld1 molecules may therefore facilitate filarial infection in filaria-leishmania co-infection.

Characteristics of invisible cervical intraepithelial neoplasia Ⅲ under colposcopy

Objective: To explore the human papilomavirus (HPV) genotypes and epithelial thickness of invisible cervical intraepithelial neoplasia Ⅲ (CIN Ⅲ) under colposcopy. Methods: One hundred and sixty-nine biopsies from 93 patients with a final diagnosis of CIN Ⅲ were extracted from the Shenzhen cervical cancer screening trial Ⅱ (SHENCCAST Ⅱ) . The SHENCCAST Ⅱ was conducted from 2009 to 2010. All the cervical blocks from these patients were re-cut and placed on 6 slides, i.e. sandwich model, with the top and bottom sections being stained with HE, the top second be processed for other studies, 3 sections for HPV genotypes by matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) assay. The thickness of squamous epithelium of CIN Ⅲ was measured by a microscope (×10) after re-cut. Colposcope directed CIN Ⅲ biopsies positively was defined as visible CIN Ⅲ, while random CIN Ⅲ biopsies positively was defined as invisible CIN Ⅲ. Results: HPV16 positivity was 37.2% (16/43) and 55.6% (70/126) between invisible and visible CIN Ⅲ biopsies, respectively (χ(2)=4.318, P=0.038) . Forty-nine cases of the 93 CIN Ⅲ patients were HPV16 positive, while 44 of them non-HPV16 positive. The proportion of patients with ≥45 years of age for other non-HPV16 positive 40.9% (18/44) was significantly higher than that HPV16 positive 20.4% (10/49; χ(2)=4.630, P=0.031) . Patients with HPV16 positive were more likely to have lesions ≥1 quadrant (χ(2)=7.786, P=0.005) than other non-HPV16 positive. Compared the average epithelium thickness of invisible CIN Ⅲ tissue (140±12) μm, the average epithelium thickness of visible CIN Ⅲ tissue (161±9) μm was thicker. There was statistical difference between two groups (t=4.383, P=0.038). The mean average epithelial thickness of CIN Ⅲ with HPV16 positive (172±11) μm was thicker than that the mean average epithelial thickness of CIN Ⅲ with non-HPV16 positive (130±10) μm (t=4.784, P=0.031) . Conclusions: Invisible lesions is difficult to identify under colposcopy and is related to non-HPV16 positive, small lesion size and thinner squamous epithelium. For non-HPV16 positive or older women should be performed colposcope directed biopsies and randomly multi-sites biopsies by colopscopy, which may be helpful to improve the detection of CIN Ⅲ and to reduce miss diagnosis.

Peculiarities of Pyrolysis of Hydrolytic Lignin in Dispersed Gas Phase and in Solid State

The unique decomposition pathways of hydrolytic lignin (HL) dissolved in an acetone/water mixture (9:1) and dispersed by a droplet evaporation technique under nitrogen gas flow has been investigated in a conventional reactor at atmospheric condition, a temperature region of 400–550 °C, and a residence time of 0.12 s. The results validate the fact that dispersion of the lignin into the gas phase by decreasing the sample size (as well as “minimizing the char area to avoid catalytic contact” of molecular products/radicals with the surface) may open new perspectives in understanding the chemistry of the depolymerization of lignin. Using Laser Desorption Ionization-Time of Flight-Mass Spectrometry (LDI-TOF-MS) the intrinsic ion m/z = 550, as the major MS peak from fresh HL dissolved in an acetone/water mixture before pyrolysis, was detected. Surprisingly, the expected phenolic compounds after pyrolysis were in trace amounts at less than 15% conversion of lignin. Instead, oligomeric intermediate substances with...

Cell line studies and analytical measurements of three paclitaxel complex variations

The copper(II) cation, sucrose, and hydroxychloroquine were complexed with the chemotherapy agent paclitaxel and studied for medicinal activity. Data (GI50, LD50) from single dose and five dose National Cancer Institute sixty cell line panels are presented. Analytical measurements of different complexes were made using Nuclear Magnetic Resonance (1H NMR), Matrix Assisted Laser Desorption Ionization-Time of Flight-Mass Spectrometry (MALDI-TOF-MS) and Fourier Transform-Ion Cyclotron Resonance (FT-ICR). Molecular modeling is utilized to better understand the impact that species could have on physical parameters associated with Lipinski’s Rule of Five, such as logP and TPSA. On average, Cu(II) and hydroxychloroquine decreased GI50 values, while sucrose increased GI50 values of paclitaxel.

Weak cation exchange magnetic beads coupled with matrix-assisted laser desorption ionization-time of flight-mass spectrometry in screening serum protein markers in osteopenia.

The present study aimed at investigating the weak cation magnetic separation technology and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS) in screening serum protein markers of osteopenia from ten postmenopausal women and ten postmenopausal women without osteopenia as control group, to find a new method for screening biomarkers and establishing a diagnostic model for primary type I osteoporosis. Serum samples were collected from postmenopausal women with osteopenia and postmenopausal women with normal bone mass. Proteins were extracted from serum samples by weak cation exchange magnetic beads technology, and mass spectra acquisition was done by MALDI-TOF-MS. The visualization and comparison of data sets, statistical peak evaluation, model recognition, and discovery of biomarker candidates were handled by the proteinchip data analysis system software(ZJU-PDAS). The diagnostic models were established using genetic arithmetic based support vector machine (SVM). The SVM result with the highest Youden Index was selected as the model. Combinatorial Peaks having the highest accuracy in distinguishing different samples were selected as potential biomarker. From the two group serum samples, a total of 133 differential features were selected. Ten features with significant intensity differences were screened. In the pair-wise comparisons, processing of MALDI-TOF spectra resulted in the identification of ten differential features between postmenopausal women with osteopenia and postmenopausal women with normal bone mass. The difference of features by Youden index showed that the highest features had a mass to charge ratio of 1699 and 3038 Da. A diagnosis model was established with these two peaks as the candidate marker, and the specificity of the model is 100 %, the sensitivity was 90 % by leave-one-out cross validation test. The two groups of specimens in SVM results on the scatter plot could be clearly distinguished. The peak with m/z 3038 in the SVM model was suggested as Secretin by TagIdent tool. To provide further validation, the secretin levels in serum were analyzed using enzyme-linked immunosorbent assays that is a competitive inhibition enzyme immunoassay technique for the in vitro quantitative measurement of secretin in human serum.Electronic supplementary materialThe online version of this article (doi:10.1186/s40064-016-2276-4) contains supplementary material, which is available to authorized users.

A SELDI-TOF approach to ecotoxicology: comparative profiling of low molecular weight proteins from a marine diatom exposed to CdSe/ZnS quantum dots

Quantum dots (QDs), namely semiconductor nanocrystals, due to their particular optical and electronic properties, have growing applications in device technology, biotechnology and biomedical fields. Nevertheless, the possible threat to human health and the environment have attracted increasing attention as the production and applications of QDs increases rapidly while standard evaluation of safety lags.In the present study we performed proteomic analyses, by means of 2D gel electrophoresis and Surface Enhanced Laser Desorption Ionization-Time of Flight-Mass Spectrometry (SELDI-TOF-MS). We aimed to identify potential biomarkers of exposure to CdSe/ZnS quantum dots. The marine diatom Phaeodactylum tricornutum exposed to 2.5nM QDs was used as a model system. Both 2DE and SELDI showed the presence of differentially expressed proteins. By Principal Component Analysis (PCA) we were able to show that the differentially expressed proteins can discriminate between exposed and not exposed cells. Furthermore, a protein profile specific for exposed cells was obtained by SELDI analysis. To our knowledge, this is the first example of the application of SELDI technology to the analysis of microorganisms used as biological sentinel model of marine environmental pollution.

Proteomic pilot study of tuberculosis pleural effusion.

To discuss the differences in protein expression among tuberculosis pleural effusion (TBPE), malignant pleural effusion (MPE) and transudative pleural effusion (TSPE). We recruited 50 patients with pleural effusion, including 20 TBPEs, 17 MPEs and 13 TSPEs. Using the two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption ionization-time of flight-mass spectrometry (MALDI-TOF-MS), we acquired the peptide mass finger printings (PMFs) of featured proteins. Then, we identified characteristic proteins by searching in the protein databank of the National Center of Biotechnology Information (NCBI) and assessed their diagnostic significance. We found five characteristic proteins: C1-inhibitor (C1-INH), transthyretin (TTR), human complement fragment 3b (C3b), human ceruloplasmin (CP), and Z34c protein fragment Fc (Z34c-Fc). C1-INH shows a high expression in TBPE and a low expression in MPE while TTR and C3 show low expression in TBPE and high expressions in MPE. Z34c-Fc and CP have a higher expression in TBPE than in TSPE. No common characteristic protein was found between MPE and TSPE. Statistic analysis consisted of paired t-tests and the difference between them is significance (P<0.05). C1-inhibitor (C1-INH), transthyretin (TTR), human Complement fragment 3b (C3b), human Ceruloplasmin (CP) and Z34c protein fragment Fc (Z34c-Fc) may provide an additional perspective in the differential diagnosis of PE.