Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations.

SUMMARY: We developed web-based applications that encourage the exploration of the literature on human genetic associations by using a database that is continuously updated from PubMed. These applications provide user-friendly interfaces for searching summarized information on human genetic associations, using either genes or diseases as the starting point. AVAILABILITY: Phenopedia and Genopedia can be freely accessed at http://www.hugenavigator.net/HuGENavigator/startPagePhenoPedia.do and http://www.hugenavigator.net/HuGENavigator/startPagePedia.do, respectively.

Campylobacter jejuni cocultured with epithelial cells reduces surface capsular polysaccharide expression.

The host cell environment can alter bacterial pathogenicity. We employed a combination of cellular and molecular techniques to study the expression of Campylobacter jejuni polysaccharides cocultured with HCT-8 epithelial cells. After two passages, the amount of membrane-bound high-molecular-weight polysaccharide was considerably reduced. Microarray profiling confirmed significant downregulation of capsular polysaccharide (CPS) locus genes. Experiments using conditioned media showed that sugar depletion occurred only when the bacterial and epithelial cells were cocultured. CPS depletion occurred when C. jejuni organisms were exposed to conditioned media from a different C. jejuni strain but not when exposed to conditioned media from other bacterial species. Proteinase K or heat treatment of conditioned media under coculture conditions abrogated the effect on the sugars, as did formaldehyde fixation and cycloheximide treatment of host cells or chloramphenicol treatment of the bacteria. However, sugar depletion was not affected in flagellar export (fliQ) and quorum-sensing (luxS) gene mutants. Passaged C. jejuni showed reduced invasiveness and increased serum sensitivity in vitro. C. jejuni alters its surface polysaccharides when cocultured with epithelial cells, suggesting the existence of a cross talk mechanism that modulates CPS expression during infection.

The G67E mutation in hMLH1 is associated with an unusual presentation of Lynch syndrome.

Germline mutations in the mismatch repair (MMR) genes are associated with Lynch syndrome, also known as hereditary non-polyposis colorectal cancer (HNPCC) syndrome. Here, we characterise a variant of hMLH1 that confers a loss-of-function MMR phenotype. The mutation changes the highly conserved Gly67 residue to a glutamate (G67E) and is reminiscent of the hMLH1-p.Gly67Arg mutation, which is present in several Lynch syndrome cohorts. hMLH1-Gly67Arg has previously been shown to confer loss-of-function (Shimodaira et al, 1998), and two functional assays suggest that the hMLH1-Gly67Glu protein fails to sustain normal MMR functions. In the first assay, hMLH1-Gly67Glu abolishes the protein's ability to interfere with MMR in yeast. In the second assay, mutation of the analogous residue in yMLH1 (yMLH1-Gly64Glu) causes a loss-of-function mutator phenotype similar to yMLH1-Gly64Arg. Despite these molecular similarities, an unusual spectrum of tumours is associated with hMLH1-Gly67Glu, which is not typical of those associated with Lynch syndrome and differs from those found in families carrying the hMLH1-Gly67Arg allele. This suggests that hMLH1 may have different functions in certain tissues and/or that additional factors may modify the influence of hMLH1 mutations in causing Lynch syndrome.

Long-term follow-up of the incidence of Helicobacter pylori.

OBJECTIVES: Helicobacter pylori causes peptic ulcer disease and gastric cancer. Understanding the incidence of H. pylori could help guide research on potential infection prevention strategies. Previous studies indicate infection occurs in young children, but the risk of infection in older children and adolescents is unclear. Our hypothesis was that H. pylori infection is rare in adolescence or adulthood. Our aim was to determine the incidence of H. pylori over a prolonged follow-up in a cohort of 626 noninfected individuals. METHODS: Participants, including index children, mothers, fathers and siblings, from a previous study (1997-2002) were traced, and 883 of 946 participated in this extended follow-up. We used the 13C urea breath test (13C-UBT) to determine the incidence of H. pylori among 626 family members not infected in 2002, including 75 younger siblings who were not born or too young for testing in 2002. RESULTS: Eight (3.8%) of 210 index participants (mean ± standard deviation age 17.92 ± 0.77 years) became infected during 11.07 ± 0.56 years of follow-up (incidence, 3.42 per 1000 person-years; 95% confidence interval (CI), 1.48-6.74). Only one (0.6%) of 165 older siblings became infected (incidence, 0.57 per 1000 person-years; 95% CI, 0.007-3.16) and one of 176 parents became infected (incidence, 0.63 per 1000 person-years; 95% CI, 0.01-3.5). Of 75 younger siblings (age 10.9 ± 2.85 years) who were too young for testing or not yet born in 2002, nine (12%) became infected (incidence, 11.32 per 1000 person-years; 95% CI, 5.27-21.49). The highest incidence of H. pylori infection was in those born after 2005. CONCLUSIONS: The incidence of H. pylori was extremely low in older children and adults in developed countries. Spontaneous clearance of infection was uncommon in our study population.

Cell envelope characteristics of Helicobacter pylori: their role in adherence to mucosal surfaces and virulence.

Helicobacter pylori colonises the gastric mucosa of humans and causes both antral gastritis and duodenal ulcer disease. Exactly how H. pylori causes disease is not known but several pathogenic determinants have been proposed for the organism. These include adhesins, cytotoxins and a range of different enzymes including urease, catalase and superoxide dismutase. Surface molecules of H. pylori such as flagella, lipopolysaccharide, the urease enzyme and outer membrane proteins are putative adhesin molecules. While phosphatidylethanolamine and the Lewis(b) blood group antigen have been proposed as receptor molecules for the organism the exact mechanism by which H. pylori adheres to the gastric mucosa has still to be identified. Characterisation of the adhesins of H. pylori could lead to the development of adhesin analogues for use in the inhibition of colonisation and improved therapy for ulcer disease. In vivo studies with isogenic mutants which are incapable of adhering to the gastric mucosa would greatly clarify the significance of adherence. Such mutants could possibly be useful as a vaccine against infection with wild-type organisms.

Adherence of Helicobacter pylori to the gastric mucosa.

Bacterial adhesion to the intestinal epithelium is a critical initial step in the pathogenesis of many enteric diseases. Helicobacter pylori is a duodenal pathogen that adheres to the gastric epithelium and causes gastritis and peptic ulceration. The mechanism by which H pylori causes disease has not been elucidated but adherence to the gastric mucosa is thought to be an important virulence determinant of the organism. What is known about adherence of H pylori to the gastric mucosa is summarized. Topics discussed are the mechanism of H pylori adherence; in vitro and in vivo models of H pylori infection; and adherence and potential adhesins and receptors for H pylori.

Pathogenesis of degenerative joint disease.

Proteoglycan degradation is central to the development of degenerative joint disease. Proteoglycans may be degraded by lysosomal enzymes from chondrocytes, synoviocytes or leucocytes. Collagen and matrix degradation occurs either by direct damage or due to degrading enzymes released into synovial fluid. Once the pathological sequence has begun it continues in a cyclic manner unless arrested by the ability of chondrocytes to synthesise sufficient matrix components. Treatment should ideally be directed to this end.

Prioritizing genomic applications for action by level of evidence: a horizon-scanning method.

As evidence accumulates on the use of genomic tests and other health-related applications of genomic technologies, decision makers may increasingly seek support in identifying which applications have sufficiently robust evidence to suggest they might be considered for action. As an interim working process to provide such support, we developed a horizon-scanning method that assigns genomic applications to tiers defined by availability of synthesized evidence. We illustrate an application of the method to pharmacogenomics tests.

Trends in pharmacogenomic epidemiology: 2001-2007.

BACKGROUND: Pharmacogenomic epidemiology (PGxE) assesses the range of responses to pharmacologic agents in relation to genetic variation in population groups. We analyzed publication trends to describe the emerging field of PGxE. METHODS: We analyzed PGxE literature published from 2001 to 2007 by using the HuGE Navigator, a curated database of abstracts on human genome epidemiology extracted from PubMed. We summarized trends by gene and study design and, for the 4 most cited genes, by associated health outcomes and drugs. RESULTS: In all, 1,855 PGxE articles were indexed from 2001 through 2007, with annual publications increasing more than 15-fold during this period. Observational studies outnumbered clinical trials by a ratio of 10 to 1 (1,660 vs. 178). Just 4 genes together accounted for nearly one-fifth of all publications: ABCB1, CYP2C9, CYP2C19, and CYP2D6. For these 4 genes, the most frequently cited therapeutic category was antineoplastic agent, followed by anticoagulant, antiulcer, and antidepressant. Warfarin was the single most frequently cited drug. CONCLUSIONS: The field of PGxE is growing rapidly, encompassing a large spectrum of diseases and drugs important in clinical practice. Systematic tracking and synthesis of the published literature in PGxE can help identify promising applications and guide translation research.

Problems of adolescence.

The family physician's attention is directed towards the problems of adolescents, which problems are the results of conduct disturbances and diseases. The latter are generally the result of drug abuse, delinquency, suicide, considered as major deviations; disturbances caused by sexual conflicts, family problems as well as problems encountered in their studies and their work. Possibilities of preventive and therapeutic care are briefly presented.

Absence of effect of Lewis A and Lewis B expression on adherence of Helicobacter pylori to human gastric cells.

BACKGROUND & AIMS: Lewis b blood group antigen and antibodies to Lewis b inhibit the binding of stationary-phase Helicobacter pylori organisms to fixed sections of gastric tissue. The aim of this study was to determine the effect of expression of Lewis a and Lewis b on binding of H. pylori to primary gastric cells. METHODS: ABO and Lewis blood types were determined for 13 individuals. Cells were isolated from gastric biopsy specimens by collagenase digestion. Lewis antigen expression and adherence of H. pylori to the cells were quantitated using flow cytometry. RESULTS: Two of the three nonsecretors were found to express Lewis b on their cells. Nineteen of 19 individuals expressed Lewis a on their cells and 18 of 19 expressed Lewis b. The percentage of cells expressing Lewis antigens varied from individual to individual. H. pylori binding was independent of expression of Lewis antigens. Preincubation of cells with antibodies to Lewis antigens did not inhibit the adherence. CONCLUSIONS: H. pylori adheres to isolated human gastric cells in a manner that is not dependent on Lewis antigen expression on these cells, and expression of Lewis antigens on the surface of gastric cells is not dependent on Lewis antigen expression on erythrocytes.

The urease enzyme of Helicobacter pylori does not function as an adhesin.

Helicobacter pylori urease is essential for colonization of the gastric mucosa irrespective of whether the stomach is acidic or hypochlorhydric. It has therefore been speculated that the enzyme functions as an adhesin. The aim of this study was to compare the adherence of H. pylori N6 with the adherence of an isogenic urease-negative mutant, strain N6(ureB::TnKm), to gastric cells. Strain N6 originated from a patient with gastritis. Strain N6(ureB::TnKm) is specifically modified in the gene which encodes the large subunit of urease, UreB, and hence does not form a UreA-UreB enzyme complex. We have used flow cytometry to assess the adherence of H. pylori to the cells. We have also used phase-contrast microscopy to assess the adherence of the organism to Kato III cells. In the absence of urea both strains bound to Kato III cells and to primary gastric cells. Binding of both strains to the cells occurred rapidly. The presence of urea in the incubation medium decreased the binding of strain N6 to the cells. This was due to a rise in the pH of the incubation medium, which caused loss of viability of the organism. Urea had no effect on the adherence of strain N6(ureB::TnKm). We conclude that the urease of H. pylori does not play a role in the adherence of the organism to gastric cells.

Linguistic diversity in Australia.

"This paper explores the changing patterns of language diversity in Australia, Sydney and Melbourne between 1991 and 1996. It shows that there has been a great increasing linguistic diversity, accompanied by an overall decline in the use of ¿older' community languages in favour of ¿newer' languages from Asia and the Middle East."

Language maintenance and language shift: community languages in Australia, 1996.

"There is a continuing significant shift to English spoken in the home among Australia's established community language groups. There are also success stories in language maintenance. Factors influencing language use include the distribution of speakers, the age profile of the community, intermarriage patterns and cultural distance from Anglo-Australians. Australia-wide, the shift rates to English spoken at home range between three percent from Macedonian and 62 percent from Dutch in the first generation, and 15 percent from Macedonian and 95 percent from Dutch in the second generation."