Comparative proteome analysis of Actinoplanes utahensis grown on various saccharides based on 2D-DIGE and MALDI-TOF/TOF-MS

Complete genome sequence of Actinoplanes sichuanensis strain 03-723T

A mesophilic bacterium Actinoplanes sichuanensis strain 03-723T was previously isolated from soil by Sun et al. Here, we present a complete and annotated genome sequence of this strain, which has a total size of 12.1 Mbp with a G + C content of 70.1%.

DIGE Analysis Software and Protein Identification Approaches

Two-dimensional difference gel electrophoresis (2D-DIGE) is a high-resolution protein separation technique, with the excellent dynamic range obtained by fluorescent tag labeling of protein samples. Scanned images of 2D-DIGE gels show thousands of protein spots, each spot representing a single or a group of protein isoforms. By using commercially available software, each protein spot is defined by an outline, which is digitized and correlated with the quantity of proteins present in each spot. Software packages include DeCyder, SameSpots, and Dymension 3. In addition, proteins of interest can be excised from post-stained gels and identified with conventional mass spectrometric techniques. High-throughput mass spectrometry is performed using sophisticated instrumentation, including matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF), MALDI-TOF/TOF, and liquid chromatography tandem mass spectrometry (LC-MS/MS). Tandem MS (MALDI-TOF/TOF or LC-MS/MS) analyzes fragmented peptides, resulting in amino acid sequence information, which is especially useful when protein spots are low abundant or where a mixture of proteins is present.

Purification, Identification and Neuroprotective Effects of Proteins from Bombyx batryticatus in Glu-Stimulated PC12 Cells

Bombyx batryticatus (BB) is one of the most commonly used Traditional Chinese Medicines (TCMs) in the treatment of convulsions and epilepsy. The antiepileptic effects of total proteins from BB (BBPs) have been proven in our previous research. In this study, BBPs were further purified, the neuroprotective effects were evaluated in Glu-stimulated PC12 cells, and the structure was identified by Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Six subfractions (PF-1 to PF-6) were obtained by DEAE-52 Sepharose FF ion-exchange chromatography. It was found that PF-1, PF-2, and PF-3, with similar protein compositions, possessed neuroprotective effects in Glu-stimulated PC12 cells by significantly increasing the GABA level, and decreasing the levels of IL-1β and TNF-α. The most active fraction (PF-2) was further separated by Sephadex G-75 gel filtration chromatography, and an effective protein component named PF-2-2 was obtained. Fluorescein isothiocyanate-labeled PF-2-2 (FITC-PF-2-2) was prepared, and the binding of FITC-F-2-2 to the PC12 cells was directly observed with a confocal microscope. PF-2-2 was found to first bind to the surface of PC12 cells and then internalize into the cells. The main band of PF-2-2 was then analyzed by MALDI-TOF/TOF-MS and searched in the MASCOT database; finally a protein named Low molecular mass 30 kDa lipoprotein 21G1 was identified. In conclusion, PF-2-2 and purified proteins isolated from BBPs have potential application prospects in the treatment of epilepsy.

Gene Cascade Shift and Pathway Enrichment in Rat Kidney Induced by Acarbose Through Comparative Analysis

Acarbose is an effective anti-diabetic drug to treat type 2 diabetes mellitus (T2DM), a chronic degenerative metabolic disease caused by insulin resistance. The beneficial effects of acarbose on blood sugar control in T2DM patients have been confirmed by many studies. However, the effect of acarbose on patient kidney has yet to be fully elucidated. In this study, we report in detail the gene expression cascade shift, pathway and module enrichment, and interrelation network in acarbose-treated Rattus norvegicus kidneys based on the in-depth analysis of the GSE59913 microarray dataset. The significantly differentially expressed genes (DEGs) in the kidneys of acarbose-treated rats were initially screened out by comparative analysis. The enriched pathways for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were further identified. The protein-protein interaction (PPI) analysis for DEGs was achieved through the STRING database mining. Pathway interrelation and hub genes for enriched pathways were further examined to uncover key biological effects of acarbose. Results revealed 44 significantly up-regulated genes and 86 significantly down-regulated genes (130 significant differential genes in total) in acarbose-treated rat kidneys. Lipid metabolism pathways were considerably improved by acarbose, and the physical conditions in chronic kidney disease (CKD) patients were improved possibly through the increase of the level of high-density lipoprotein (HDL) by lecithin-cholesterol acyl-transferase (LCAT). These findings suggested that acarbose may serve as an ideal drug for CKD patients, since it not only protects the kidney, but also may relieve the complications caused by CKD.