Proteomic response and molecular regulatory mechanisms of Bacillus cereus spores under ultrasound treatment

This study was aimed at providing new insights on the proteomic response of bacterial spores to ultrasound. Data-independent-acquisition method was used to quantify the proteome change of Bacillus cereus spores after ultrasound treatment (200 W). This study revealed that 2485 proteins were extracted from Bacillus cereus spores, most of them were related to metabolism. After ultrasound treatment, the expression of 340 proteins were significantly changed (the fold change ≥ 2 and p < 0.05), of which 207 proteins were significantly down-regulated. KEGG pathway analysis showed that differentially expressed proteins mainly distributed in metabolism pathway, cell process pathway and genetic information processing pathway after ultrasound treatment. Furthermore, this study analyzed the differentially expressed proteins in significant enrichment pathways. In particular, the expression of key proteins in the phosphorylation reaction of spores was significantly decreased after ultrasound treatment. Thus, ATP synthesis rate decreased and the phosphorylation reaction inhibited. Also, the decrease of the expression of key proteins related to the tricarboxylic acid cycle led to the decrease of nutrients metabolism of spores. Ultrasound treatment induced the down-regulation of fatty acid synthetase expression and promoted fatty acid metabolism at the same time. The content of fatty acids decreased in spores consequently.     

Proteomic characterization of plasma‐derived clotting factor VIII–von Willebrand factor concentrates

Proteomic methods were used to identify the levels of impurities in three commercial plasma‐derived clotting factor VIII‐von Willebrand factor (FVIII/VWF) concentrates. In all three concentrates, significant amounts of other plasma proteins were found. In Octanate and Haemoctin, two concentrates developed in the 1990s, the major impurities identified were inter‐α inhibitor proteins, fibrinogen and fibronectin. These two concentrates were also found to contain additional components such as clotting factor II (prothrombin) that are known activators of FVIII. In Wilate, a recently developed FVIII/VWF concentrate, the amount of these impurities was significantly reduced. Batch‐to‐batch variations and differences between three investigated products were detected using iTRAQ, an isotope labeling technique for comparative MS, demonstrating the potential value of this technique for quality control analysis. The importance of thorough proteomic investigations of therapeutic FVIII/VWF preparations from human plasma is also discussed.     

Proteomic investigation of anti-tumor activities exerted by sinularin against A2058 melanoma cells

The extracts from soft corals have been increasingly investigated for biomedical and therapeutic purposes. The aim of this study is to examine and analyze the anti-tumor effects of the genus Sinularia extract sinularin on A2058 melanoma cells using MTT assay, cell migration assay, wound healing assay, flow cytometric analysis, and proteomic analysis. Sinularin dose-dependently (1-5 μg/mL) inhibited melanoma cell proliferation while the treatment at identical concentrations suppressed cell migration. Sinularin dose-dependently enhanced apoptotic melanoma cells and caused tumor cell accumulation at G2/M phase, indicating that sinularin exerts apoptosis-induced and cell cycle-delayed activities in A2058 melanoma cells. Comparative proteomic analysis was conducted to investigate the effects of sinularin at the molecular level by comparison between the protein profiling of melanoma cells treated with sinularin and without the treatment. Thirty-five differential proteins (13 upregulated and 22 downregulated) concerning the treatment were identified by liquid chromatography-tandem mass spectrometry. Proteomic data and Western blot displayed the levels of several tumor inhibitory or apoptosis-associated proteins including annexin A1, voltage-dependent anion-selective channel protein 1 and prohibitin (upregulated), heat shock protein 60, heat shock protein beta-1, and peroxiredoxin-2 (downregulated) in A2058 melanoma cells exposed to sinularin. Increased expression of p53, cleaved-caspase-3, cleaved-caspase-8, cleaved-caspase-9, p21, and Bax and decreased expression of Bcl-2 in sinularin-treated melanoma cells suggest that the anti-tumor activities of sinularin against melanoma cells are particularly correlated with these pro-apoptotic factors. These data provide important information for the mechanisms of anti-tumor effects of sinularin on melanoma cells and may be helpful for drug development and progression monitoring of human melanoma.     

Comparison of in-gel protein separation techniques commonly used for fractionation in mass spectrometry-based proteomic profiling

Fractionation of complex samples at the cellular, subcellular, protein, or peptide level is an indispensable strategy to improve the sensitivity in mass spectrometry-based proteomic profiling. This study revisits, evaluates, and compares the most common gel-based protein separation techniques i.e. 1D SDS-PAGE, 1D preparative SDS-PAGE, IEF-IPG, and 2D-PAGE in their performance as fractionation approaches in nano LC-ESI-MS/MS analysis of a mixture of protein standards and mitochondrial extracts isolated from rat liver. This work demonstrates that all the above techniques provide complementary protein identification results, but 1D SDS-PAGE and IEF-IPG had the highest number of identifications. The IEF-IPG technique resulted in the highest average number of detected peptides per protein. The 2D-PAGE was evaluated as a protein fractionation approach. This work shows that the recovery of proteins and resulting proteolytic digests is highly dependent on the total volume of the gel matrix. The performed comparison of the fractionation techniques demonstrates the potential of a combination of orthogonal 1D SDS-PAGE and IEF-IPG for the improved sensitivity of profiling without significant decrease in throughput.     

Gerbils of a seizure-sensitive strain have a mitochondrial inner membrane protein with different isoelectric points from those of a seizure-resistant strain

The distribution of proteins in the cerebral cortex of a seizure-sensitive (SS) strain of gerbil and its seizure-resistant (SR) counterpart was profiled using two-dimensional gel electrophoresis. A series of proteins of similar molecular weight (around 83 kDa) showed small but consistent differences in their isoelectric point (pI) with indistinguishable profiles of distribution between the two strains. Amino acid sequences of peptides produced by limited proteolysis of each protein in the spots from the strains were identical or highly homologous to those of mitofilin, a mitochondrial inner membrane protein (IMMT) in humans. Analysis of cDNA sequences revealed the proteins of these spots to be gerbil mitofilin-like proteins (gIMMT), with a few base substitutions between SS and SR strains, in particular within a region near a putative transmembrane domain that is highly conserved in humans and gerbils. The amino acid at the site was acidic, Glu in humans and Asp in the strain SR of gerbil and a neutral, Asn in strain SS. In addition to these base substitutions, production of multiple species of mRNA for gIMMT by alternative splicing was observed.     

Implications of column peak capacity on the separation of complex peptide mixtures in single- and two-dimensional high-performance liquid chromatography

Column peak capacity was utilized as a measure of column efficiency for gradient elution conditions. Peak capacity was evaluated experimentally for reversed-phase (RP) and cation-exchange high-performance liquid chromatography (HPLC) columns, and compared to the values predicted from RP-HPLC gradient theory. The model was found to be useful for the prediction of peak capacity and productivity in single- and two-dimensional (2D) chromatography. Both theoretical prediction and experimental data suggest that the number of peaks separated in HPLC reaches an upper limit, despite using highly efficient columns or very shallow gradients. The practical peak capacity value is about several hundred for state-of-the-art RP-HPLC columns. Doubling the column length (efficiency) improves the peak capacity by only 40%, and proportionally increases both the separation time and the backpressure. Similarly, extremely shallow gradients have a positive effect on the peak capacity, but analysis becomes unacceptably long. The model predicts that a 2D-HPLC peak capacity of 15,000 can be achieved in 8 h using multiple fraction collection in the first dimension followed by fast RP-HPLC gradients employing short, but efficient columns in the second dimension.     

Interdisciplinary study for the evaluation of biochemical alterations on mussel <Emphasis Type="Italic">Mytilus galloprovincialis</Emphasis> exposed to a tributyltin-polluted area

An interdisciplinary approach was employed to monitor the concentration and the effects of butyltin compounds in mussels (Mytilus galloprovincialis). Tissues from animals exposed to a marine area (Vado Ligure harbour) with a high concentration of tributyltin (TBT) were analysed and compared with control samples. TBT concentrations were measured by gas chromatography–mass spectrometry and the protein pattern in gill tissues was studied by proteomic analysis. Several proteomic signatures associated with contaminant exposure were observed; spots that were significantly increased in all contaminated samples were identified by mass spectrometry as fragments of β-tubulin. The degradation of β-tubulin was then confirmed by western blot analysis with specific anti-β-tubulin antibody. The effects observed on mussel gills after exposure in the TBT-polluted area are discussed.