Associations of a PTPN11 G/A polymorphism at intron 3 with Helicobactor pylori seropositivity, gastric atrophy and gastric cancer in Japanese

<p>Abstract</p> <p>Background</p> <p>Previous studies have revealed the significance of <it>Helicobacter pylori </it>(<it>H. pylori</it>) infection as a risk factor of gastric cancer. Cytotoxin-associated gene A (<it>cagA</it>) positivity has been demonstrated to determine the clinical outcome of <it>H. pylori </it>infection in the presence of SHP-2 (src homology 2 domain-containing protein tyrosine phosphatase-2). This study aimed to examine the formerly reported association of G/A <it>PTPN11 (protein-tyrosine phosphatase, nonreceptor-type 11) </it>polymorphism (rs2301756) with gastric atrophy, as well as the association with gastric cancer in a Japanese population using a large sample size.</p> <p>Methods</p> <p>Study subjects were 583 histologically diagnosed patients with gastric cancer (429 males and 154 females) and age- and sex-frequency-matched 1,636 non-cancer outpatients (1,203 males and 433 females), who visited Aichi Cancer Center Hospital between 2001–2005. Serum anti-<it>H. pylori </it>IgG antibody and pepsinogens were measured to evaluate <it>H. pylori </it>infection and gastric atrophy, respectively. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated by a logistic model.</p> <p>Results</p> <p>Among <it>H. pylori </it>seropositive non-cancer outpatients, the age- and sex-adjusted OR of gastric atrophy was 0.82 (95% CI 0.62–1.10, <it>P </it>= 0.194) for <it>G/A</it>, 0.84 (95% CI 0.39–1.81, <it>P </it>= 0.650) for <it>A/A</it>, and 0.83 (95% CI 0.62–1.09, <it>P </it>= 0.182) for <it>G/A</it>+<it>A/A</it>, relative to <it>G/G </it>genotype, and that of severe gastric atrophy was 0.70 (95% CI 0.47–1.04, <it>P </it>= 0.079), 0.56 (95% CI 0.17–1.91, <it>P </it>= 0.356), and 0.68 (95% CI 0.46–1.01, <it>P </it>= 0.057), respectively. Among <it>H. pylori </it>infected subjects (<it>H. pylori </it>seropositive subjects and seronegative subjects with gastric atrophy), the adjusted OR of severe gastric atrophy was further reduced; 0.62 (95% CI 0.42–0.90, <it>P </it>= 0.012) for <it>G/A</it>+<it>A/A</it>. The distribution of the genotype in patients with gastric cancer was not significantly different from that for <it>H. pylori </it>infected subjects without gastric atrophy.</p> <p>Conclusion</p> <p>Our study results revealed that those with the <it>A/A </it>genotype of <it>PTPN11 </it>rs2301756 polymorphism are at lower risk of severe gastric atrophy, but are not associated with a decreased risk of gastric cancer, which partially supported our previous finding that the polymorphism in the <it>PTPN11 </it>gene encoding SHP-2 was associated with the gastric atrophy risk in <it>H. pylori </it>infected Japanese. The biological roles of this <it>PTPN11 </it>polymorphism require further investigation.</p

Por Secretion System-Dependent Secretion and Glycosylation of Porphyromonas gingivalis Hemin-Binding Protein 35

The anaerobic Gram-negative bacterium Porphyromonas gingivalis is a major pathogen in severe forms of periodontal disease and refractory periapical perodontitis. We have recently found that P. gingivalis has a novel secretion system named the Por secretion system (PorSS), which is responsible for secretion of major extracellular proteinases, Arg-gingipains (Rgps) and Lys-gingipain. These proteinases contain conserved C-terminal domains (CTDs) in their C-termini. Hemin-binding protein 35 (HBP35), which is one of the outer membrane proteins of P. gingivalis and contributes to its haem utilization, also contains a CTD, suggesting that HBP35 is translocated to the cell surface via the PorSS. In this study, immunoblot analysis of P. gingivalis mutants deficient in the PorSS or in the biosynthesis of anionic polysaccharide-lipopolysaccharide (A-LPS) revealed that HBP35 is translocated to the cell surface via the PorSS and is glycosylated with A-LPS. From deletion analysis with a GFP-CTD[HBP35] green fluorescent protein fusion, the C-terminal 22 amino acid residues of CTD[HBP35] were found to be required for cell surface translocation and glycosylation. The GFP-CTD fusion study also revealed that the CTDs of CPG70, peptidylarginine deiminase, P27 and RgpB play roles in PorSS-dependent translocation and glycosylation. However, CTD-region peptides were not found in samples of glycosylated HBP35 protein by peptide map fingerprinting analysis, and antibodies against CTD-regions peptides did not react with glycosylated HBP35 protein. These results suggest both that the CTD region functions as a recognition signal for the PorSS and that glycosylation of CTD proteins occurs after removal of the CTD region. Rabbits were used for making antisera against bacterial proteins in this study

Genome evolution in the allotetraploid frog Xenopus laevis

To explore the origins and consequences of tetraploidy in the African clawed frog, we sequenced the Xenopus laevis genome and compared it to the related diploid X. tropicalis genome. We characterize the allotetraploid origin of X. laevis by partitioning its genome into two homoeologous subgenomes, marked by distinct families of ???fossil??? transposable elements. On the basis of the activity of these elements and the age of hundreds of unitary pseudogenes, we estimate that the two diploid progenitor species diverged around 34 million years ago (Ma) and combined to form an allotetraploid around 17-18 Ma. More than 56% of all genes were retained in two homoeologous copies. Protein function, gene expression, and the amount of conserved flanking sequence all correlate with retention rates. The subgenomes have evolved asymmetrically, with one chromosome set more often preserving the ancestral state and the other experiencing more gene loss, deletion, rearrangement, and reduced gene expression.ope

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Casting votes of antecedents play a key role in successful sequential decision-making.

Aggregation of opinions often results in high decision-making accuracy, owing to the collective intelligence effect. Studies on group decisions have examined the optimum weights for opinion aggregation to maximise accuracy. In addition to the optimum weights of opinions, the impact of the correlation among opinions on collective intelligence is a major issue in collective decision-making. We investigated how individuals should weigh the opinions of others and their own to maximise their accuracy in sequential decision-making. In our sequential decision-making model, each person makes a primary choice, observes his/her predecessors' opinions, and makes a final choice, which results in the person's answer correlating with those of others. We developed an algorithm to find casting voters whose primary choices are determinative of their answers and revealed that decision accuracy is maximised by considering only the abilities of the preceding casting voters. We also found that for individuals with heterogeneous abilities, the order of decision-making has a significant impact on the correlation between their answers and their accuracies. This could lead to a counter-intuitive phenomenon whereby, in sequential decision-making, respondents are, on average, more accurate when less reliable individuals answer earlier and more reliable individuals answer later

Emergence of opinion leaders in reference networks

<div><p>Individuals often refer to opinions of others when they make decisions in the real world. Our question is how the people’s reference structure self-organizes when people try to provide correct answers by referring to more accurate agents. We constructed an adaptive network model, in which each node represents an agent and each directed link represents a reference. In every iteration round within our model, each agent makes a decision sequentially by following the majority of the reference partners’ opinions and rewires a reference link to a partner if the partner’s performance falls below a given threshold. The value of this threshold is common for all agents and represents the performance assessment severity of the population. We found that the reference network self-organizes into a heterogeneous one with a nearly exponential in-degree (the number of followers) distribution, where reference links concentrate around agents with high intrinsic ability. In this heterogeneous network, the decision-making accuracy of agents improved on average. However, the proportion of agents who provided correct answers showed strong temporal fluctuation compared to that observed in the case in which each agent refers to randomly selected agents. We also found a counterintuitive phenomenon in which reference links concentrate more around high-ability agents and the population became smarter on average when the rewiring threshold was set lower than when it was set higher.</p></div

The distribution of the number of followers (in-degree) in the initial and evolved networks.

<p>(a) The solid line is the initial Poisson distribution with a mean of 5. The markers (the circle and +) denote the in-degree distributions of the evolved network with rewiring thresholds <i>θ</i> = 0.5 and 0.6, respectively, obtained over 500 independent runs of our simulation. The in-degree distributions in the evolved networks are significantly different from the initial condition, showing much higher heterogeneity in in-degrees. (b) The same as (a) except that the vertical axis is logarithmically scaled. We can observe the approximately exponential tails in the evolved networks.</p