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

<p>Abstract</p> <p>Background</p> <p><it>Porphyromonas gingivalis </it>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 <it>P. gingivalis </it>ATCC 33277 were obtained using the genome sequence available at the time, strain W83 [GenBank: <ext-link ext-link-id="AE015924" ext-link-type="gen">AE015924</ext-link>]. We present here a re-processed dataset using the recently published genome annotation specific for strain ATCC 33277 [GenBank: <ext-link ext-link-id="AP009380" ext-link-type="gen">AP009380</ext-link>] and an analysis of differential abundance based on metabolic pathways rather than individual proteins.</p> <p>Results</p> <p>Qualitative detection was observed for 1266 proteins using the strain ATCC 33277 annotation for 18 hour internalized <it>P. gingivalis </it>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.</p> <p>Conclusion</p> <p>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 <it>P. gingivalis </it>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.</p

Quantitative proteomics of nutrient limitation in the hydrogenotrophic methanogen Methanococcus maripaludis

<p>Abstract</p> <p>Background</p> <p>Methanogenic Archaea play key metabolic roles in anaerobic ecosystems, where they use H₂and other substrates to produce methane. <it>Methanococcus maripaludis </it>is a model for studies of the global response to nutrient limitations.</p> <p>Results</p> <p>We used high-coverage quantitative proteomics to determine the response of <it>M. maripaludis </it>to growth-limiting levels of H₂, nitrogen, and phosphate. Six to ten percent of the proteome changed significantly with each nutrient limitation. H₂limitation 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 H₂is 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.</p> <p>Conclusion</p> <p>The global proteomic response of <it>M. maripaludis </it>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.</p

How Social Interaction Affects Purchase Intention in Social Commerce: A Cultural Perspective

In the context of social commerce, the influence of culture on consumers’ behavior and attitude is more significant. This paper empirically analyzes the influence of social interaction (perceived risk, trust, and intimacy) on consumers’ purchase intention in social commerce, and the antecedent effect of cultural dimensions (uncertainty avoidance and individualism/collectivism) on social interaction is also explored. Data were collected in China and France from consumers who had prior online shopping experience on social commerce websites. The results show that the impact of perceived risk on subsequent purchase intention in social commerce will be transferred by trust and intimacy to a certain extent. The intimacy between users contributes to trust-building, and both of their positive impacts on purchase intention would show distinct effects in different cultures. Besides, cultural dimensions are proved to have a significant effect on users’ social interaction. Although high uncertainty avoidance brings perceived risk, it can promote subsequent trust-building. These findings help provide managerial insights for social commerce community to establish effective trust mechanism in a multicultural context

Capillary Isoelectric Focusing-Mass Spectrometry Method for the Separation and Online Characterization of Intact Monoclonal Antibody Charge Variants

We report a new online capillary isoelectric focusing-mass spectrometry (CIEF-MS) method for monoclonal antibody (mAb) charge variant analysis using an electrokinetically pumped sheath-flow nanospray ion source and a time-of-flight MS with pressure-assisted chemical mobilization. To develop a successful, reliable CIEF-MS method for mAb, we have selected and optimized many critical, interrelating reagents and parameters that include (1) MS-friendly anolyte and catholyte; (2) a glycerol enhanced sample mixture that reduced non-CIEF electrophoretic mobility and band broadening; (3) ampholyte selected for balancing resolution and MS sensitivity; (4) sheath liquid composition optimized for efficient focusing, mobilization, and electrospray ionization; (5) judiciously selected CIEF running parameters including injection amount, field strength, and applied pressure. The fundamental premise of CIEF was well maintained as verified by the linear correlation (<i>R</i>² = 0.99) between p<i>I</i> values and migration time using a mixture of p<i>I</i> markers. In addition, the charge variant profiles of trastuzumab, bevacizumab, infliximab, and cetuximab, obtained using this CIEF-MS method, were corroborated by imaged CIEF-UV (iCIEF-UV) analyses. The relative standard deviations (RSD) of absolute migration time of p<i>I</i> markers were all less than 5% (<i>n</i> = 4). Triplicate analyses of bevacizumab showed RSD less than 1% for relative migration time to an internal standard and RSD of 7% for absolute MS peak area. Moreover, the antibody charge variants were characterized using the online intact MS data. To the best of our knowledge, this is the first time that direct online MS detection and characterization were achieved for mAb charge variants resolved by CIEF as indicated by a well-established linear pH gradient and correlated CIEF-UV charge variant profiles