Genistein binding protein targets in dental pathogens

Oral pathogens have created a menace in recent years due to biofilm formation and antimicrobial drug resistance. The current treatment strategy works well with antibiotics. However, constant use of antibiotics creates a selective pressure, which increases adaptability of the pathogens. Therefore, it is of interest to analyze the potential targets of genistein in dental pathogens using computer aided prediction tools.     

Analysis of superfamily specific profile-profile recognition accuracy

Background  

Annotation of sequences that share little similarity to sequences of known function remains a major obstacle in genome annotation. Some of the best methods of detecting remote relationships between protein sequences are based on matching sequence profiles. We analyse the superfamily specific performance of sequence profile-profile matching. Our benchmark consists of a set of 16 protein superfamilies that are highly diverse at the sequence level. We relate the performance to the number of sequences in the profiles, the profile diversity and the extent of structural conservation in the superfamily.     

Enteropathogens associated with acute diarrhea in community and hospital patients in Jakarta,Indonesia

The prevalence of bacteria, parasite and viral pathogens in 3875 patients with diarrhea in community and hospital settings from March 1997 through August 1999 in Jakarta, Indonesia was determined using routine bacteriology and molecular assay techniques. Bacterial pathogens isolated from hospital patients were, in decreasing frequency, Vibrio cholerae O1, Shigella flexneri, Salmonella spp. and Campylobacter jejuni, while S. flexneri, V. cholerae O1, Salmonella spp. and C. jejuni were isolated from the community patients. V. cholerae O1 was isolated more frequently (P<0.005) from the hospital patients than the community patients. Overall, bacterial pathogens were isolated from 538 of 3875 (14%) enrolled cases of diarrhea. Enterotoxigenic Escherichia coli were detected in 218 (18%) of 1244 rectal swabs. A small percentage of enterohemorrhagic E. coli (1%) and of Clostridium difficile (1.3%) was detected. Parasitic examination of 389 samples resulted in 43 (11%) positives comprising Ascaris lumbricoides (1.5%), Blastocystis hominis (5.7%), Giardia lamblia (0.8%), Trichuris trichiura (2.1%) and Endolimax nana (0.5%). Rotavirus (37.5%), adenovirus (3.3%) and Norwalk-like virus (17.6%) were also detected. Antimicrobial resistance was observed among some isolates. Bacterial isolates were susceptible to quinolones, with the exception of some isolates of C. jejuni which were resistant to ciprofloxacin, nalidixic acid and norfloxacin. Data obtained from this community- and hospital-based study will enable the Indonesian Ministry of Health to plan relevant studies on diarrheal diseases in the archipelago.     

Diagnostic criteria for diabetes revisited: making use of combined criteria

Background  

Existing cut-offs for fasting plasma glucose (FPG) and post-load glucose (2hPG) criteria are not equivalent in the diagnosis of diabetes and glucose intolerance. Adjusting cut-offs of single measurements have not helped so we undertook this project to see if they could be complementary.     

Isolation and characterization of highly pathogenic avian influenza virus subtype H5N1 from donkeys

Background  

The highly pathogenic H5N1 is a major avian pathogen that crosses species barriers and seriously affects humans as well as some mammals. It mutates in an intensified manner and is considered a potential candidate for the possible next pandemic with all the catastrophic consequences.     

<Emphasis Type="Italic">TRAF1/C5</Emphasis>polymorphism is not associated with increased mortality in rheumatoid arthritis: two large longitudinal studies

Introduction  

Recently an association between a genetic variation in TRAF1/C5 and mortality from sepsis or cancer was found in rheumatoid arthritis (RA). The most prevalent cause of death, cardiovascular disease, may have been missed in that study, since patients were enrolled at an advanced disease stage. Therefore, we used an inception cohort of RA patients to investigate the association between TRAF1/C5 and cardiovascular mortality, and replicate the findings on all-cause mortality. As TRAF1/C5 associated mortality may not be restricted to RA, we also studied a large cohort of non-RA patients.     

A theoretical treatment of interval mapping of a disease gene using transmission disequilibrium tests

The genetic basis of the transmission disequilibrium test (TDT) for two-marker loci is explored from first principles. In this case, parents doubly heterozygous for a given haplotype at the pair of marker loci that are each in linkage disequilibrium with the disease gene with the further possibility of a second-order linkage disequilibrium are considered. The number of times such parents transmit the given haplotype to their affected offspring is counted and compared with the frequencies of haplotypes that are not transmitted. This is done separately for the coupling and repulsion phases of doubly heterozygous genotypes. Expectations of the counts for each of the sixteen cells possible with four-marker gametic types (transmitted vs not transmitted) are derived. Based on a test of symmetry in a square 4 x 4 contingency table, chi-square tests are proposed for the null hypothesis of no linkage between the markers and the disease gene. The power of the tests is discussed in terms of the corresponding non-centrality parameters for the alternative hypothesis that both the markers are linked with the disease locus. The results indicate that the power increases with the decrease in recombination probability and that it is higher for a lower frequency of the disease gene. Taking a pair of markers in an interval for exploring the linkage with the disease gene seems to be more informative than the single-marker case since the values of the non-centrality parameters tend to be consistently higher than their counterparts in the single-marker case. Limitations of the proposed test are also discussed.     

The accuracy of several multiple sequence alignment programs for proteins

Background  

There have been many algorithms and software programs implemented for the inference of multiple sequence alignments of protein and DNA sequences. The "true" alignment is usually unknown due to the incomplete knowledge of the evolutionary history of the sequences, making it difficult to gauge the relative accuracy of the programs.