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841.
Xiaohui Lin Quancai Wang Peiyuan Yin Liang Tang Yexiong Tan Hong Li Kang Yan Guowang Xu 《Metabolomics : Official journal of the Metabolomic Society》2011,7(4):549-558
Metabolic markers are the core of metabonomic surveys. Hence selection of differential metabolites is of great importance
for either biological or clinical purpose. Here, a feature selection method was developed for complex metabonomic data set.
As an effective tool for metabonomics data analysis, support vector machine (SVM) was employed as the basic classifier. To
find out meaningful features effectively, support vector machine recursive feature elimination (SVM-RFE) was firstly applied.
Then, genetic algorithm (GA) and random forest (RF) which consider the interaction among the metabolites and independent performance
of each metabolite in all samples, respectively, were used to obtain more informative metabolic difference and avoid the risk
of false positive. A data set from plasma metabonomics study of rat liver diseases developed from hepatitis, cirrhosis to
hepatocellular carcinoma was applied for the validation of the method. Besides the good classification results for 3 kinds
of liver diseases, 31 important metabolites including lysophosphatidylethanolamine (LPE) C16:0, palmitoylcarnitine, lysophosphatidylethanolamine
(LPC) C18:0 were also selected for further studies. A better complementary effect of the three feature selection methods could
be seen from the current results. The combinational method also represented more differential metabolites and provided more
metabolic information for a “global” understanding of diseases than any single method. Further more, this method is also suitable
for other complex biological data sets. 相似文献
842.
Tian L Wang Y Ling Y Yin J Chen J Huang J 《Journal of chromatography. B, Analytical technologies in the biomedical and life sciences》2011,879(31):3688-3693
A sensitive and specific high performance liquid chromatography-electrospray ionization-tandem mass spectrometry (HPLC-ESI-MS/MS) method has been developed and validated for the determination of isoforskolin in canine plasma. Liquid-liquid extraction was used to extract isoforskolin and the internal standard (I.S.) eplerenone from canine plasma. The chromatographic separation was performed on an Agela Venusil XBP Phenyl column with an isocratic mobile phase consisting of methanol-2mM ammonium acetate-formic acid (62:38:0.1, v/v/v), pumped at 0.35 mL/min. Isoforskolin and I.S. were detected at m/z 433.4→373.3 and m/z 415.3→163.5 in positive ion and multiple reaction monitoring (MRM) mode, respectively. The standard curves were linear over the concentration range of 0.1-200 ng/mL (r>0.99). The intra- and inter-batch accuracy values for isoforskolin at four concentrations were 90.2-108.3% and 97.8-106.6%, respectively. The RSDs were less than 6.0%. The mean extraction recoveries of isoforskolin and I.S. were 97.0 and 88.4%, respectively. The method was successfully applied to the pharmacokinetic study after an intravenous administration of isoforskolin in beagle dogs. 相似文献
843.
Cytoglobin, generated using genetic engineering method, is a kind of recombinant human stellate cell activation-associated
protein. We speculate that it could influence the development of hepatic fibrosis like Sellate cell activation-associated
protein which was discovered by Kawada et al. Therefore, we investigated its anti-fibrosis effect on liver both in vivo and
in vitro. During our research, we found that cytoglobin showed obvious effect compared with the control group on Thioacetamide-induced
liver fibrosis in SD rats, including significantly decrease in aspartate aminotransferase, Hyaluronic acid, laminin and collagen
I(Col I) levels in serum and hydroxyproline in livers, which are the important indices reflecting the degree of hepatic fibrosis.
Meanwhile, the viability of rat hepatic stellate cell line T6 (HSC-T6) cells was inhibited by cytoglobin and the apoptosis
induced by cytoglobin in HSC-T6 cells was detected by Annexin V/PI double staining. Activation of the caspase cascade including
caspase-3 for the intrinsic pathways was demonstrated. The results also showed that the expression of Bcl-2 protein decreased
whereas that of Bax protein increased, leading to an increase of the Bax/Bcl-2 ratio. Our results demonstrated that cytoglobin
exhibited anti-fibrosis activity on livers in vivo and in vitro, involving apoptosis induction. 相似文献
844.
Background: Long‐term Helicobacter pylori infection leads to chronic gastritis, peptic ulcer, and gastric malignancies. Indigenous microflora in alimentary tract maintains a colonization barrier against pathogenic microorganisms. This study is aimed to observe the gastric and duodenum microflora alteration after H. pylori infection in Mongolian Gerbils model. Materials and Methods: A total of 18 Mongolian gerbils were randomly divided into two groups: control group and H. pylori group that were given H. pylori NCTC J99 strain intragastrically. After 12 weeks, H. pylori colonization was identified by rapid urease tests and bacterial culture. Indigenous microorganisms in stomach and duodenum were analyzed by culture method. Histopathologic examination of gastric and duodenum mucosa was also performed. Results: Three of eight gerbils had positive H. pylori colonization. After H. pylori infection, Enterococcus spp. and Staphylococcus aureus showed occurrences in stomach and duodenum. Lactobacillus spp. showed a down trend in stomach. The levels and localizations of Bifidobacterium spp., Bacteroides spp., and total aerobes were also modified. Bacteroides spp. significantly increased in H. pylori positive gerbils. No Enterobacteriaceae were detected. Positive colonization gerbils showed a higher histopathologic score of gastritis and a similar score of duodenitis. Conclusions: Long‐term H. pylori colonization affected the distribution and numbers of indigenous microflora in stomach and duodenum. Successful colonization caused a more severe gastritis. Gastric microenvironment may be unfit for lactobacilli fertility after long‐term H. pylori infection, while enterococci, S. aureus, bifidobacteria, and bacteroides showed their adaptations. 相似文献
845.
Historically, small proteins (sproteins) of less than 50 amino acids, in their final processed forms or genetically encoded as such, have been understudied. However, both serendipity and more recent focused efforts have led to the identification of a number of new sproteins in both Gram-negative and Gram-positive bacteria. Increasing evidence demonstrates that sproteins participate in a wide array of cellular processes and exhibit great diversity in their mechanisms of action, yet general principles of sprotein function are emerging. This review highlights examples of sproteins that participate in cell signaling, act as antibiotics and toxins, and serve as structural proteins. We also describe roles for sproteins in detecting and altering membrane features, acting as chaperones, and regulating the functions of larger proteins. 相似文献
846.
847.
A "lewisi-like" Trypanosoma parasite was isolated from the blood of Chinese striped field mice (Apodemus agrarius) trapped in the fields in the Gannan Tibet area, Gansu province, China. The parasite was successfully cultivated in vitro in HL-1 medium supplemented 20% fetal bovine serum (FBS). Full formed spheromastigote, metacyclic trypomastigote and trypomastigote structures were all visible in films made from the culture. A nucleotide fragment of 2159-bp length was amplified from genomic DNA of the parasite using specific primers for the 18S rRNA gene of trypanosomes. The alignment indicated that this parasite had higher identities with T. (Herpetosoma) grosi (more than 99.6%) than other Herpetosoma species (less than 98.5%), which suggest that the parasite should be classified as T. (Herpetosoma) grosi. This is the first time in China that an isolation of T. (Herpetosoma) grosi is reported although several strains of T. (Herpetosoma) lewisi have been isolated from rodents of family Muridae in various provinces. Thus, it was designated as T. (Herpetosoma) grosi Cha1 and deposited in the center of parasite strain collection and preservation in our laboratory for future study. In addition, this culture method will be used to isolate, maintain and study the long-term development of this parasite in vitro. 相似文献
848.
Increasing evidence shows that protein phosphorylation on serine (Ser), threonine (Thr) and tyrosine (Tyr) residues is a major regulatory post-translational modification in the bacteria. To reveal the phosphorylation state in the Gram-negative pathogenic bacterium Helicobacter pylori, we carried out a global and site-specific phosphoproteomic analysis based on TiO(2) -phosphopeptide enrichment and high-accuracy LC-MS/MS determination. Eighty-two phosphopeptides from 67 proteins were identified with 126 phosphorylation sites, among which 79 class I sites were determined to have a distribution of 42.8:38.7:18.5% for the Ser/Thr/Tyr phosphorylation, respectively. The H. pylori phosphoproteome is characterized by comparably big size, high ratio of Tyr phosphorylation, high abundance of multiple phosphorylation sites in individual phosphopeptides and over-representation of membrane proteins. An interaction network covering 28 phosphoproteins was constructed with a total of 163 proteins centering on the major H. pylori virulence factor VacA, indicating that protein phosphorylation in H. pylori may be delicately controlled to regulate many aspects of the metabolic pathways and bacterial virulence. 相似文献
849.
The aim of metalloproteomics is to identify and characterize putative metal-binding proteins and metal-binding motifs. In this study, we performed a systematical metalloproteomic analysis on Streptococcus pneumoniae through the combined use of efficient immobilized metal affinity chromatography enrichment and high-accuracy linear ion trap-Orbitrap MS to identify metal-binding proteins and metal-binding peptides. In total, 232 and 166 putative metal-binding proteins were respectively isolated by Cu- and Zn-immobilized metal affinity chromatography columns, in which 133 proteins were present in both preparations. The putative metalloproteins are mainly involved in protein, nucleotide and carbon metabolisms, oxidation and cell cycle regulation. Based on the sequence of the putative Cu- and Zn-binding peptides, putative Cu-binding motifs were identified: H(X)mH (m=0-11), C(X)(2) C, C(X)nH (n=2-4, 6, 9), H(X)iM (i=0-10) and M(X)tM (t=8 or 12), while putative Zn-binding motifs were identified as follows: H(X)mH (m=1-12), H(X)iM (i=0-12), M(X)tM (t=0, 3 and 4), C(X)nH (n=1, 2, 7, 10 and 11). Equilibrium dialysis and inductively coupled plasma-MS experiments confirmed that the artificially synthesized peptides harboring differential identified metal-binding motifs interacted directly with the metal ions. The metalloproteomic study presented here suggests that the comparably large size and diverse functions of the S. pneumoniae metalloproteome may play important roles in various biological processes and thus contribute to the bacterial pathologies. 相似文献
850.
Firnhaber C Azzoni L Foulkes AS Gross R Yin X Van Amsterdam D Schulze D Glencross DK Stevens W Hunt G Morris L Fox L Sanne I Montaner LJ 《PloS one》2011,6(6):e21450