Association of plasma apolipoprotein CIII, high sensitivity C-reactive protein and tumor necrosis factor-α contributes to the clinical features of coronary heart disease in Li and Han ethnic groups in China.

BACKGROUND: Apolipoprotein CIII (apoCIII) is an independent risk for coronary heart disease (CHD). In this study, we investigated the associations among plasma apoCIII, hs-CRP and TNF-α levels and their roles in the clinical features of CHD in the Li and Han ethnic groups in China. METHODS: A cohort of 474 participants was recruited (238 atherosclerotic patients and 236 healthy controls) from the Li and Han ethnic groups. Blood samples were obtained to evaluate apoCIII, TNF-α, hs-CRP and lipid profiles. Chi-squared, t-tests, and Kruskal-Wallis or Wilcoxon-Mann-Whitney tests, Pearson or Spearman correlation tests and multiple unconditional logistic regression were employed to analyze lipid profiles and variations in plasma apoCIII, TNF-α, hs-CRP in subgroups of CHD and their contributions to CHD using SPSS version 20.0 software. RESULTS: Compared to healthy participants, unfavorable lipid profiles were identified in CHD patients with enhanced systolic pressure, diastolic pressure, fasting blood sugar (FBS), TG, TC, LDL-C, apoB, Lp(a) (P < 0.05, TC and Lp(a); P < 0.01, FBS, TG, LDL-C, apoB); and lower HDL-C and apoAI (P < 0.05). Plasma apoCIII, TNF-α and hs-CRP levels were higher in CHD individuals (16.77 ± 5.98 mg/dL vs. 10.91 ± 4.97 mg/dL; 17.23 ± 6.34 pg/mL vs. 9.49 ± 3.88 pg/mL; 9.55 ± 7.32 mg/L vs. 2.14 ± 1.56 mg/L; P < 0.01 vs. healthy participants). Identical patterns were obtained in the Li and Han groups (16.46 ± 6.08 mg/dL vs. 11.72 ± 5.16 mg/dL; 15.71 ± 5.52 pg/mL vs. 9.74 ± 4.31 pg/mL; 8.21 ± 7.09 mg/L vs. 2.15 ± 1.51 mg/L in Li people; 17.05 ± 5.90 mg/dL vs. 10.07 ± 4.63 mg/dL; 18.59 ± 6.73 pg/mL vs. 9.23 ± 3.38 pg/mL; 10.75 ± 7.44 mg/L vs. 2.12 ± 1.63 mg/L in Han people; P < 0.01). Paired comparisons of subgroups with stable angina, unstable angina, and acute myocardial infarction (AMI) revealed significant variation in plasma levels of apoCIII, TNF-α and hs-CRP (P < 0.01), but not among subgroups with mild, moderate and severe stenosis (P > 0.05). Plasma apoCIII, TNF-α and hs-CRP contributed to the development of CHD (OR = 2.554, 7.252, 6.035, P < 0.01) with paired correlations in CHD patients (apoCIII vs. TNF-α, r = 0.425; apoCIII vs. hs-CRP, r = 0.319; TNF-α vs. hs-CRP, r = 0.400, P < 0.01). CONCLUSIONS: Association among plasma apoCIII, hs-CRP and TNF-α interacts with unfavorable lipid profiles to contribute to the clinical features of CHD with stable angina, unstable angina, and AMI in the Li and Han ethnic groups in China.

Association of the S2 allele of the SstI polymorphism in the apoC3 gene with plasma apoCIII interacts with unfavorable lipid profiles to contribute to atherosclerosis in the Li ethnic group in China.

BACKGROUND: The SstI polymorphism in the apolipoprotein 3 gene (apoC3) has been identified in many ethnic groups. In addition, the S2 allele of the SstI polymorphism is shown to be associated with increased plasma triglyceride (TG) levels. Plasma apoCIII is an important atherogenic factor, which interrupts lipid metabolism and is positively associated with plasma TG levels. However, the existence of the SstI polymorphism in the Li ethnic group in China remains to be confirmed. The relationship between the S2 allele of the SstI polymorphism and plasma apoCIII or TG and their roles in atherosclerosis are also unknown. METHODS: A cohort of 628 participants was recruited (316 atherosclerotic patients and 312 healthy controls) from both the Li and Han ethnic groups. Blood samples were obtained to evaluate the SstI polymorphism in the apoC3 and lipid profiles. Chi-squared and t-tests and multiple unconditional logistic regression were employed to analyze the genotypic and allelic frequencies and lipid profiles using SPSS version 20.0 software. RESULTS: The SstI polymorphism in the apoC3 was identified in the Li ethnic group. The S2 allele and plasma apoCIII and TG levels were associated with the development of atherosclerosis (P < 0.01, S2 allele and apoCIII; P < 0.05, TG) in the Li ethnic group. The S2 allele was associated with increased plasma apoCIII levels in the atherosclerotic group (P < 0.01), but with increased plasma apoCIII and TG levels in control group (both P < 0.01). In addition to the increases in the S2 allele frequency and plasma TG and apoCIII levels, atherosclerotic patients in the Li ethnic group also exhibited increased apoB, decreased HDL-C and apoAI and a lower apoAI:apoB ratio (all P < 0.01). CONCLUSIONS: Our results indicate that the S2 allele of the SstI polymorphism in the apoC3 gene is associated with plasma apoCIII levels in the Li population. In combination with unfavorable lipid profiles, this might contribute to susceptibility to atherosclerosis.

Metabolomics analysis of the yolk of Zhijin white goose during the embryogenesis based on LC-MS/MS.

The egg yolk of the goose is rich in lipids, proteins and minerals, which is the main source of nutrition during the goose embryogenesis. Actually, the magnitude and variety of nutrients in yolk are dynamically changed to satisfy the nutritional requirements of different growth and development periods. The yolk sac membrane (YSM) plays a role in metabolizing and absorbing nutrients from the yolk, which are then consumed by the embryo or extra-fetal tissues. Therefore, identification of metabolites in egg yolk can help to reveal nutrient requirement in goose embryo. In this research, to explore the metabolite changes in egg yolk at embryonic day (E) 7, E12, E18, E23, and E28, we performed the assay using ultra-high performance liquid chromatography/tandem mass spectrometry (UHPLC-MS/MS). The findings showed that E7 and E12, E23 and E28 were grouped together, while E18 was significantly separated from other groups, indicating the changes of egg yolk development and metabolism. In total, 1472 metabolites were identified in the egg yolk of Zhijin white goose, and 636 differential metabolites (DMs) were screened, among which 264 were upregulated and 372 were downregulated. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the DMs were enriched in the biosynthesis and metabolism of amino acids, digestion and absorption of protein, citrate cycle (TCA cycle), aminoacyl-tRNA biosynthesis, phosphotransferase system (PTS), mineral absorption, cholesterol metabolism and pyrimidine metabolism. Our study may provide new ideas for improving prehatch embryonic health and nutrition.

Membrane protein complex of APS reductase and Qmo is present in Desulfovibrio vulgaris and Desulfovibrio alaskensis.

Due to their adjacent location in the genomes of Desulfovibrio species and their potential for formation of an electron transfer pathway in sulfate-reducing prokaryotes, adenosyl phosphosulfate (APS) reductase (Apr) and quinone-interacting membrane-bound oxidoreductase (Qmo) have been thought to interact together during the reduction of APS. This interaction was recently verified in Desulfovibrio desulfuricans. Membrane proteins of Desulfovibrio vulgaris Hildenborough ΔqmoABCD JW9021, a deletion mutant, were compared to the parent strain using blue-native PAGE to determine whether Qmo formed a complex with Apr or other proteins. In the parent strain of D. vulgaris, a unique band was observed that contained all four Qmo subunits, and another band contained three subunits of Qmo, as well as subunits of AprA and AprB. Similar results were observed with bands excised from membrane preparations of Desulfovibrio alaskensis strain G20. These results are in support of the formation of a physical complex between the two proteins; a result that was further confirmed by the co-purification of QmoA/B and AprA/B from affinity-tagged D. vulgaris Hildenborough strains (AprA, QmoA and QmoB) regardless of which subunit had been tagged. This provides clear evidence for the presence of a Qmo-Apr complex that is at least partially stable in protein extracts of D. vulgaris and D. alaskensis.

Protein complexing in a methanogen suggests electron bifurcation and electron delivery from formate to heterodisulfide reductase.

In methanogenic Archaea, the final step of methanogenesis generates methane and a heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB). Reduction of this heterodisulfide by heterodisulfide reductase to regenerate HS-CoM and HS-CoB is an exergonic process. Thauer et al. [Thauer, et al. 2008 Nat Rev Microbiol 6:579-591] recently suggested that in hydrogenotrophic methanogens the energy of heterodisulfide reduction powers the most endergonic reaction in the pathway, catalyzed by the formylmethanofuran dehydrogenase, via flavin-based electron bifurcation. Here we present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehydrogenase. In addition to establishing a physical basis for the electron-bifurcation model of energy conservation, the composition of the complex also suggests that either H(2) or formate (two alternative electron donors for methanogenesis) can donate electrons to the heterodisulfide-H(2) via F(420)-nonreducing hydrogenase or formate via formate dehydrogenase. Electron flow from formate to the heterodisulfide rather than the use of H(2) as an intermediate represents a previously unknown path of electron flow in methanogenesis. We further tested whether this path occurs by constructing a mutant lacking F(420)-nonreducing hydrogenase. The mutant displayed growth equal to wild-type with formate but markedly slower growth with hydrogen. The results support the model of electron bifurcation and suggest that formate, like H(2), is closely integrated into the methanogenic pathway.

Wearable Hydrogel-Based Epidermal Sensor with Thermal Compatibility and Long Term Stability for Smart Colorimetric Multi-Signals Monitoring.

Hydrogel-based wearable epidermal sensors (HWESs) have attracted widespread attention in health monitoring, especially considering their colorimetric readout capability. However, it remains challenging for HWESs to work at extreme temperatures with long term stability due to the existence of water. Herein, a wearable transparent epidermal sensor with thermal compatibility and long term stability for smart colorimetric multi-signals monitoring is developed, based on an anti-freezing and anti-drying hydrogel with high transparency (over 90% transmittance), high stretchability (up to 1500%) and desirable adhesiveness to various kinds of substrates. The hydrogel consists of polyacrylic acid, polyacrylamide, and tannic acid-coated cellulose nanocrystals in glycerin/water binary solvents. When glycerin readily forms strong hydrogen bonds with water, the hydrogel exhibits outstanding thermal compatibility. Furthermore, the hydrogel maintains excellent adhesion, stretchability, and transparency after long term storage (45 days) or at subzero temperatures (-20 °C). For smart colorimetric multi-signals monitoring, the freestanding smart colorimetric HWESs are utilized for simultaneously monitoring the pH, T and light, where colorimetric signals can be read and stored by artificial intelligence strategies in a real time manner. In summary, the developed wearable transparent epidermal sensor holds great potential for monitoring multi-signals with visible readouts in long term health monitoring.

Bioinformatics analysis of ceRNA regulatory network of baicalin in alleviating pathological joint alterations in CIA rats.

Rheumatoid arthritis (RA) is an autoimmune disease characterized by chronic inflammation of synovium, leading to cartilage damage, bone erosion, even joint destruction and deformity. The conventional treatment modalities in RA are associated with side effects, emphasizing the need for alternative therapeutic remedies. Baicalin possesses multiple pharmacological effects and the advantage of low toxicity. This study aimed to reveal the potential gene regulatory mechanisms underlying the alleviating effects of baicalin in joint pathological alterations in Collagen-Induced Arthritis (CIA) rat models. At 28 days after the primary immunization, 60 mg/kg/d of baicalin was administered via intraperitoneal injection once daily for 40 days, and the pathological alterations of hind paw joints were examined with X-ray imaging. Subsequently, the synovial tissue of knee joints was isolated, from which total RNA was extracted, and mRNA and miRNA sequencing libraries were established. Finally, High-throughput transcriptome sequencing(RNA-seq) technology was performed, and the lncRNAs/miRNAs/mRNAs competing endogenous RNA(ceRNA) regulatory network was analyzed. The CIA model was successfully established, and baicalin treatment significantly alleviated the destruction of distal joints of CIA rat models (p < 0.01). We found that 3 potential ceRNA regulatory networks of baicalin were established, including lncRNA ENSRNOT00000076420/miR-144-3p/Fosb, lncRNA MSTRG.1448.13/miR-144-3p/Atp2b2 and lncRNA MSTRG.1448.13/miR-144-3p/Shanks. The validation results from synovial tissue of CIA rats were consistent with the RNA-Seq results. Overall, this study revealed potentially important genes and ceRNA regulatory network that mediate the alleviating effects of baicalin on joint pathological alterations in CIA rats.

Proteomics of Streptococcus gordonii within a model developing oral microbial community.

BACKGROUND: Streptococcus gordonii is one of several species that can initiate the formation of oral biofilms that develop into the complex multispecies microbial communities referred to as dental plaque. It is in the context of dental plaque that periodontal pathogens such as Porphyromonas gingivalis cause disease. We have previously reported a whole cell quantitative proteomics investigation of P. gingivalis in a model dental plaque community of S. gordonii, P. gingivalis, and Fusobacterium nucleatum. Here we report the adaptation of S. gordonii to the same model. RESULTS: 1122 S. gordonii proteins were detected in S. gordonii control samples, 915 in communities with F. nucleatum, 849 with P. gingivalis, and 649 with all three organisms. Quantitative comparisons showed extensive proteome changes in association with F. nucleatum or P. gingivalis individually or both P. gingivalis and F. nucleatum together. The changes were species specific, though the P. gingivalis interaction may be dominant, indicated by large differences between the proteomes with F. nucleatum or P. gingivalis but limited changes between communities with P. gingivalis or both P. gingivalis and F. nucleatum. The results were inspected manually and an ontology analysis conducted using DAVID. Extensive changes were seen in nutrition pathways with increases in energy metabolism and changes in the resulting byproducts, while the acid and sugar repressed PTS (phosphoenolpyruvate dependent phosphotransferase system) sugar transport systems showed decreases. These results were seen across all the multispecies samples, though with different profiles according to the partner species. F. nucleatum association decreased proteins for the metabolic end products acetate and ethanol but increased lactate, the primary source of acidity from streptococcal cultures. P. gingivalis containing samples had a reduction in levels of proteins for ethanol and formate but increased proteins for both acetate and lactate production. The communities also showed increases in exopolysaccharide synthesis, amino acid biosynthesis, and oxidative stress protection and decreases in adhesion and transporter proteins. CONCLUSION: This study showed that S. gordonii demonstrates species specific responses during interactions with F. nucleatum or P. gingivalis. Extensive changes were seen in energy metabolism and byproduct production implicating nutrient transfer as an important community interaction.

Effects of Purple Corn Anthocyanin on Growth Performance, Meat Quality, Muscle Antioxidant Status, and Fatty Acid Profiles in Goats.

This study was conducted to examine the effect of purple corn anthocyanin on performance, meat quality, muscle antioxidant activity, antioxidant gene expression, and fatty acid profiles in goats. The feeding trial period lasted 74 d. The adaptation period was 14 d, and the formal experimental period was 60 d. Eighteen Qianbei-pockmarked goats (Guizhou native goat breed; body weight, 21.38 ± 1.61 kg; mean ± standard deviation) were randomly allotted into three equal groups, including a control with no purple corn pigment (PCP) and groups receiving either 0.5 g/d PCP or 1.0 g/d PCP. The inclusion of PCP did not affect (p > 0.05) the dry matter intake, average daily gain, or feed conversion ratio compared to the control group. The addition of PCP reduced (p < 0.05) shear force in the longissimus thoracis et lumborum muscle (LTL) during the growth phase of the goats. Goats receiving PCP showed higher (p < 0.05) levels of reduced glutathione, 2,2-diphenyl-1-picrylhydrazyl scavenging activity and peroxidase in LTL compared to the control. Moreover, compared to the control, the PCP group displayed lower (p < 0.05) concentrations of 12:0, C16:0, and total saturated fatty acids, but increased (p < 0.05) concentrations of various unsaturated fatty acids, including C18:1n9, C20:3n6, C20:4n6, C18:2n6 cis, C20:3n6, C22:5n3, C22:6n3, and total polyunsaturated fatty acids (PUFAs). The abundance of nuclear factor, erythroid 2 like 2, superoxide dismutase 1, glutathione peroxidase 1, and catalase was upregulated (p < 0.05) in the LTL of goats receiving 0.5 g/d PCP in comparison to the other groups. Collectively, result of the current study indicated that PCP anthocyanin could be used as a source of natural functional additive because anthocyanin-rich PCP has the potential to improve meat quality and enhance muscle antioxidant status as well as improve the proportions of PUFAs in goat muscle.

Materials with Tunable Optical Properties for Wearable Epidermal Sensing in Health Monitoring.

Advances in wearable epidermal sensors have revolutionized the way that physiological signals are captured and measured for health monitoring. One major challenge is to convert physiological signals to easily readable signals in a convenient way. One possibility for wearable epidermal sensors is based on visible readouts. There are a range of materials whose optical properties can be tuned by parameters such as temperature, pH, light, and electric fields. Herein, this review covers and highlights a set of materials with tunable optical properties and their integration into wearable epidermal sensors for health monitoring. Specifically, the recent progress, fabrication, and applications of these materials for wearable epidermal sensors are summarized and discussed. Finally, the challenges and perspectives for the next generation wearable devices are proposed.

An integrated proteomics/transcriptomics approach points to oxygen as the main electron sink for methanol metabolism in Methylotenera mobilis.

Methylotenera species, unlike their close relatives in the genera Methylophilus, Methylobacillus, and Methylovorus, neither exhibit the activity of methanol dehydrogenase nor possess mxaFI genes encoding this enzyme, yet they are able to grow on methanol. In this work, we integrated a genome-wide proteomics approach, shotgun proteomics, and a genome-wide transcriptomics approach, shotgun transcriptome sequencing (RNA-seq), of Methylotenera mobilis JLW8 to identify genes and enzymes potentially involved in methanol oxidation, with special attention to alternative nitrogen sources, to address the question of whether nitrate could play a role as an electron acceptor in place of oxygen. Both proteomics and transcriptomics identified a limited number of genes and enzymes specifically responding to methanol. This set includes genes involved in oxidative stress response systems, a number of oxidoreductases, including XoxF-type alcohol dehydrogenases, a type II secretion system, and proteins without a predicted function. Nitrate stimulated expression of some genes in assimilatory nitrate reduction and denitrification pathways, while ammonium downregulated some of the nitrogen metabolism genes. However, none of these genes appeared to respond to methanol, which suggests that oxygen may be the main electron sink during growth on methanol. This study identifies initial targets for future focused physiological studies, including mutant analysis, which will provide further details into this novel process.

Genetics of the glutamate-mediated methylamine utilization pathway in the facultative methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5.

The ability of some microbial species to oxidize monomethylamine via glutamate-mediated pathways was proposed in the 1960s; however, genetic determinants of the pathways have never been described. In the present study we describe a gene cluster essential for operation of the N-methylglutamate pathway in the methylotrophic beta-proteobacterium Methyloversatilis universalis FAM5. Four major polypeptides from protein fractions displaying high activities of N-methylglutamate synthetase, N-methylglutamate dehydrogenase and gamma-glutamylmethylamide synthetase were selected for mass spectrometry-based identification. The activities of enzymes were associated with the presence of peptides identified as ferredoxin-dependent glutamate synthase (GltB2), large subunit of putative heterotetrameric sarcosine oxidase (SoxA) and glutamine synthetase type III (GSIII) respectively. A gene cluster (8.3 kb) harbouring gltB2, soxA and gsIII-like genes was amplified from M. universalis FAM5, sequenced and assembled. Two partial and six complete open reading frames arranged in the order soxBDAG-gsIII-gltB132 were identified and subjected to mutational analysis, functional and metabolic profiling. We demonstrated that gltB-like and sox-like genes play a key role in methylamine utilization and encode N-methylglutamate synthetase and N-methylglutamate dehydrogenase respectively. Metabolic, enzymatic and mutational analyses showed that the gsIII-like gene encodes gamma-glutamylmethylamide synthetase; however, this enzyme is not essential for oxidation of methylamine.

Phosphorylation of major Porphyromonas gingivalis virulence factors is crucial for their processing and secretion.

The main etiological agent of periodontitis is the anaerobic bacterium Porphyromonas gingivalis. Virulence of this pathogen is controlled by various mechanisms and executed by major virulence factors including the gingipain proteases, peptidylarginine deiminase (PPAD), and RagB, an outer membrane macromolecular transport component. Although the structures and functions of these proteins are well characterized, little is known about their posttranslational maturation. Here, we determined the phosphoproteome of P. gingivalis in which phosphorylated tyrosine residues constitute over 80% of all phosphoresidues. Multiple phosphotyrosines were found in gingipains, PPAD, and RagB. Although mutation of phosphorylated residues in PPAD and RagB had no effect on secretion or activity, site-directed mutagenesis showed that phosphorylation in hemagglutinin/adhesin domains of RgpA and Kgp, and in the catalytic domain of RgpB, had a strong influence on secretion, processing, and enzymatic activity. Moreover, preventing phosphorylation of one gingipain influenced the others, suggesting multiple phosphorylation-dependent pathways of gingipain maturation in P. gingivalis. Various candidate kinases including Ptk1 BY kinase and ubiquitous bacterial kinase 1 (UbK1) may be involved, but their contribution to gingipain processing and activation remains to be confirmed.

RNA-sequence reveals differentially expressed genes affecting the crested trait of Wumeng crested chicken.

Wumeng crested chicken has a cluster of slender feathers on its head, and the underlying skull region exhibits an obvious tumor-like protrusion. This is the typical skull structure of crested chickens. The associated regulatory genes are located on autosomes and are incompletely dominant. This trait is related to brain herniation, but the genetic mechanisms of its formation and development are unclear. In this study, RNA sequencing (RNA-Seq) analysis was conducted on 6 skull tissue samples from 3 Wumeng crested chickens with prominent skull protrusions and 3 without a prominent skull protrusion phenotype. A total of 46,376,934 to 43,729,046 clean reads were obtained, the percentage of uniquely mapped reads compared with the reference genome was between 89.73%-91.00%, and 39,795,458-41,836,502 unique reads were obtained. Among different genomic regions, the highest frequency of sequencing reads occurred in exon regions (85.44-88.28%). Additionally, a total of 423 new transcripts and 26,999 alternative splicings (AS) events were discovered in this sequencing analysis. This study identified 1,089 differentially expressed genes (DEGs), among which 485 were upregulated and 604 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that the DEGs were enriched in terms related to signal transduction, cell development, cell differentiation, the lysosome, serine, and threonine metabolism, and the interaction of cytokines with cytokine receptors. Based on the comprehensive analysis of DEGs combined with reported quantitative trait loci (QTLs), the expression of BMP2, EPHA3, EPHB1, HOXC6, SCN2B, BMP7, and HOXC10 was verified by real-time quantitative polymerase chain reaction (qRT-PCR). The qRT-PCR results were consistent with the RNA-Seq results, indicating that these 7 genes may be candidates genes regulating the crested trait.

Expressed genome of Methylobacillus flagellatus as defined through comprehensive proteomics and new insights into methylotrophy.

In recent years, techniques have been developed and perfected for high-throughput identification of proteins and their accurate partial sequencing by shotgun nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS), making it feasible to assess global protein expression profiles in organisms with sequenced genomes. We implemented comprehensive proteomics to assess the expressed portion of the genome of Methylobacillus flagellatus during methylotrophic growth. We detected a total of 1,671 proteins (64% of the inferred proteome), including all the predicted essential proteins. Nonrandom patterns observed with the nondetectable proteins appeared to correspond to silent genomic islands, as inferred through functional profiling and genome localization. The protein contents in methylamine- and methanol-grown cells showed a significant overlap, confirming the commonality of methylotrophic metabolism downstream of the primary oxidation reactions. The new insights into methylotrophy include detection of proteins for the N-methylglutamate methylamine oxidation pathway that appears to be auxiliary and detection of two alternative enzymes for both the 6-phosphogluconate dehydrogenase reaction (GndA and GndB) and the formate dehydrogenase reaction (FDH1 and FDH4). Mutant analysis revealed that GndA and FDH4 are crucial for the organism's fitness, while GndB and FDH1 are auxiliary.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

BACKGROUND: Porphyromonas gingivalis is a Gram-negative intracellular pathogen associated with periodontal disease. We have previously reported on whole-cell quantitative proteomic analyses to investigate the differential expression of virulence factors as the organism transitions from an extracellular to intracellular lifestyle. The original results with the invasive strain P. gingivalis ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: AE015924]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: AP009380] and an analysis of differential abundance based on metabolic pathways rather than individual proteins. RESULTS: Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized P. gingivalis within human gingival epithelial cells and controls exposed to gingival cell culture medium, an improvement of 7% over the W83 annotation. Internalized cells showed increased abundance of proteins in the energy pathway from asparagine/aspartate amino acids to ATP. The pathway producing one short chain fatty acid, propionate, showed increased abundance, while that of another, butyrate, trended towards decreased abundance. The translational machinery, including ribosomal proteins and tRNA synthetases, showed a significant increase in protein relative abundance, as did proteins responsible for transcription. CONCLUSION: Use of the ATCC 33277 specific genome annotation resulted in improved proteome coverage with respect to the number of proteins observed both qualitatively in terms of protein identifications and quantitatively in terms of the number of calculated abundance ratios. Pathway analysis showed a significant increase in overall protein synthetic and transcriptional machinery in the absence of significant growth. These results suggest that the interior of host cells provides a more energy rich environment compared to the extracellular milieu. Shifts in the production of cytotoxic fatty acids by intracellular P. gingivalis may play a role in virulence. Moreover, despite extensive genomic re-arrangements between strains W83 and 33277, there is sufficient sequence similarity at the peptide level for proteomic abundance trends to be largely accurate when using the heterologous strain annotated genome as the reference for database searching.

Proteomics of Porphyromonas gingivalis within a model oral microbial community.

BACKGROUND: Porphyromonas gingivalis is a periodontal pathogen that resides in a complex multispecies microbial biofilm community known as dental plaque. Confocal laser scanning microscopy showed that P. gingivalis can assemble into communities in vitro with Streptococcus gordonii and Fusobacterium nucleatum, common constituents of dental plaque. Whole cell quantitative proteomics, along with mutant construction and analysis, were conducted to investigate how P. gingivalis adapts to this three species community. RESULTS: 1156 P. gingivalis proteins were detected qualitatively during comparison of the three species model community with P. gingivalis incubated alone under the same conditions. Integration of spectral counting and summed signal intensity analyses of the dataset showed that 403 proteins were down-regulated and 89 proteins up-regulated. The proteomics results were inspected manually and an ontology analysis conducted using DAVID. Significant decreases were seen in proteins involved in cell shape and the formation of the cell envelope, as well as thiamine, cobalamin, and pyrimidine synthesis and DNA repair. An overall increase was seen in proteins involved in protein synthesis. HmuR, a TonB dependent outer membrane receptor, was up-regulated in the community and an hmuR deficient mutant was deficient in three species community formation, but was unimpaired in its ability to form mono- or dual-species biofilms. CONCLUSION: Collectively, these results indicate that P. gingivalis can assemble into a heterotypic community with F. nucleatum and S. gordonii, and that a community lifestyle provides physiologic support for P. gingivalis. Proteins such as HmuR, that are up-regulated, can be necessary for community structure.

Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis.

BACKGROUND: Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H2 and other substrates to produce methane. Methanococcus maripaludis is a model for studies of the global response to nutrient limitations. RESULTS: We used high-coverage quantitative proteomics to determine the response of M. maripaludis to growth-limiting levels of H2, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H2 limitation increased the abundance of a wide variety of proteins involved in methanogenesis. However, one protein involved in methanogenesis decreased: a low-affinity [Fe] hydrogenase, which may dominate over a higher-affinity mechanism when H2 is abundant. Nitrogen limitation increased known nitrogen assimilation proteins. In addition, the increased abundance of molybdate transport proteins suggested they function for nitrogen fixation. An apparent regulon governed by the euryarchaeal nitrogen regulator NrpR is discussed. Phosphate limitation increased the abundance of three different sets of proteins, suggesting that all three function in phosphate transport. CONCLUSION: The global proteomic response of M. maripaludis to each nutrient limitation suggests a wider response than previously appreciated. The results give new insight into the function of several proteins, as well as providing information that should contribute to the formulation of a regulatory network model.

Comprehensive proteomics of Methylobacterium extorquens AM1 metabolism under single carbon and nonmethylotrophic conditions.

In order to validate a gel free quantitative proteomics assay for the model methylotrophic bacterium Methylobacterium extorquens AM1, we examined the M. extorquens AM1 proteome under single carbon (methanol) and multicarbon (succinate) growth, conditions that have been studied for decades and for which extensive corroborative data have been compiled. In total, 4447 proteins from a database containing 7556 putative ORFs from M. extorquens AM1 could be identified with two or more peptide sequences, corresponding to a qualitative proteome coverage of 58%. Statistically significant nonzero (log(2) scale) differential abundance ratios of methanol/succinate could be detected for 317 proteins using summed ion intensity measurements and 585 proteins using spectral counting, at a q-value cut-off of 0.01, a measure of false discovery rate. The results were compared to recent microarray studies performed under equivalent chemostat conditions. The M. extorquens AM1 studies demonstrated the feasibility of scaling up the multidimensional capillary HPLC MS/MS approach to a prokaryotic organism with a proteome more than three times the size of microbes we have investigated previously, while maintaining a high degree of proteome coverage and reliable quantitative abundance ratios.

Comparison of coronary plaque composition among patients with acute coronary syndrome and stable coronary artery disease.

BACKGROUND: The identification of vulnerable plaques before rupture is an important clinical goal. The purpose of the present study was to assess the difference in plaque composition among patients with acute coronary syndrome (ACS) and stable coronary artery disease (SCAD) by intravascular ultrasound virtual histologic analysis. METHODS: One hundred and thirty-nine patients were divided into ACS group and SCAD group according to clinical presentation. A total of 229 de novo lesions with >50% stenosis in native coronary arteries with diameters >2.5 mm were studied with intravascular ultrasonography. Geometric and compositional data were obtained using intravascular ultrasound virtual histology software. RESULTS: There were no significant differences in overall lesions for fibrous ((52.0+/-11.9)% vs (54.3+/-8.5)%, P>0.05), fibrolipidic ((12.3+/-10.1)% vs (13.8+/-9.5)%, P > 0.05), calcium ((14.0+/-9.1)% vs (19.3+/-13.1)%, P>0.05), or necrotic core ((22.0+/-11.1)% vs (19.7 +/- 5.4)%, P > 0.05) percentages in ACS and SCAD patients, respectively. There were also no significant differences in culprit lesions for fibrous ((46.4+/-12.0)% vs (53.6+/-8.8)%, P>0.05), fibrolipidic ((9.1+/-9.0)% vs (12.9+/-9.7)%, P>0.05), calcium ((16.6+/-9.7)% vs (21.8+/-26.3)%, P>0.05), or necrotic core ((28.0+/-12.6)% vs (20.6+/-5.2)%, P>0.05) percentages in ACS and SCAD patients, respectively. High density lipoprotein-cholesterol levels >1.04 mmol/L were associated with more fibrolipidic ((14.5+/-10.4)% vs (7.1+/-6.5)%, P<0.05) and less necrotic core ((20.6+/-9.7)% vs (27.9+/-12.6)%, P<0.05) percentages in the cohort with ACS. CONCLUSIONS: In this study, coronary plaque composition assessed by intravascular ultrasound virtual histologic analysis was not significantly different between ACS and SCAD patients. The anatomic relationship of the specific plaque components to the lumen of the vessel was more important than the quantitative information of plaque composition for plaque stability.