The TGM2 gene is associated with schizophrenia in a British population.

Several lines of evidence have suggested an interesting link between gluten ingestion and schizophrenia. Increased levels of gliadin antibodies have been observed in patients with schizophrenia. Tissue transglutaminase (transglutaminase 2, TGM2) is involved in the production of gliadin antibodies. To investigate genetic association of the TGM2 gene with schizophrenia, we detected eight single nucleotide polymorphisms (SNPs) present in the gene among 131 family trios composed of fathers, mothers and affected offspring with schizophrenia. Data analysis with the UNPHASED program showed allelic association for rs2076380 (chi(2) = 5.51, P = 0.019), rs7270785 (chi(2) = 8.13, P = 0.004), rs4811528 (chi(2) = 6.13, P = 0.013) and rs6023526 (chi(2) = 6.13, P = 0.013). The global P-value was 0.029 for 10,000 permutations with the TDT analysis. The strongest association was observed for the rs7270785-rs4811528 haplotypes (chi(2) = 16.18, df = 3, P = 0.001), and the global P-value was 0.008 for 10,000 permutations with the 2-SNP haplotype analysis. The 8-SNP haplotype analysis also revealed a strong haplotypic association (chi(2) = 44.82, df = 18, P = 0.0004) and the 1-df test showed that the A-T-A-A-T-G-A-G haplotype was excessively transmitted (chi(2) = 16.98, corrected P = 0.0007). The present results suggest that the TGM2 gene may be involved in the development of schizophrenia.

Molecular phylogenetic analysis of Candida tropicalis isolates by multi-locus sequence typing.

Multi-locus sequencing data for 242 different isolates of Candida tropicalis generated a dendrogram showing 235 strains assigned to a single large recently evolved group which contained several small clonal clusters. Haplotype analysis of a representative strain subset revealed a high level of recombination events in an otherwise clonal population. Pairs of isolates from single sources showed non-identity attributable to loss of heterozygosity in some genes in a manner similar to that established for C. albicans.

Comparison of Candida albicans strain types among isolates from three countries.

Multi-locus sequence typing data for 217 Candida albicans isolates cultured since 1990 from blood and vaginal samples in Japan, England/Wales and the USA were analysed for geographically related variations. While no significant differences were found between distributions of diploid sequence types (DSTs) in blood vs. vaginal isolates, there were highly significant differences in the clade distributions of isolates from the three geographical sources. Clade 2 strains were predominantly isolates from England/Wales, while clade 3 strains came mainly from the USA. The isolates from Japan were highly prevalent among strains in clades 5-17, and provided the first example seen so far in C. albicans of an amino acid encoded by three separate codons. Within clade 1, the most commonly encountered clade for isolates from all three regions, 15 Japanese isolates and 1 English isolate formed a separate clonal cluster in eBURST analysis. A similarly well demarcated clonal cluster rich in isolates from Japan was also found among the clade 4 strains. The data suggest C. albicans undergoes localized evolution, but human movements and person-to-person spread considerably blur the boundaries of such evolution.

Genetic association of the AKT1 gene with schizophrenia in a British population.

OBJECTIVES: A number of studies have reported a genetic association of the AKT1 gene with schizophrenia, although some have failed to replicate the AKT1 association. This study was undertaken to further explore the AKT1 association with more single nucleotide polymorphisms in a British sample. METHODS: A total of 221 families, consisting of 148 fathers, 204 mothers and 222 offspring affected with schizophrenia, were recruited for genetic analysis. Analysis for allelic and haplotypic associations was performed with the UNPHASED program, using likelihood-based association analysis for nuclear families with missing parental genotype data. RESULTS: Allelic association was detected at rs1130214 (chi(2)=6.28, P=0.012) and at rs11847866 (chi(2)=4.64, P=0.031), although the remaining single nucleotide polymorphisms did not show allelic association with schizophrenia. The global P value of overall associations was 0.059 after 10000 permutations. Assessment using the Haploview program revealed rs1130214, rs2494746 and rs11847866 in the same linkage disequilibrium block and haplotype analysis showed disease association for the rs1130214-rs2494746-rs11847866 haplotypes (chi(2)=10.18, d.f.=4, P=0.037), of which the T-G-A haplotype was excessively transmitted (chi(2)=6.93, uncorrected P=0.008) and this haplotypic association survived Bonferroni correction (P=0.04). CONCLUSION: The present results provide further evidence to support the AKT1 association with schizophrenia.

No association between the PPARG gene and schizophrenia in a British population.

It has consistently been reported that patients with schizophrenia have an increased risk of type-2 diabetes. To investigate a genetic link between these two diseases, the combined effects of the PLA2G4A, PTGS2 and PPARG genes were tested among 221 British nuclear families consisting of fathers, mothers and affected offspring with schizophrenia. A total of 10 single nucleotide polymorphisms (SNPs) were tested and the likelihood-based association analysis for nuclear families was used to analyse the genotyping data. Eight SNPs detected across the PPARG gene did not show allelic association with schizophrenia; a weak association was detected at rs2745557 in the PTGS2 locus (chi2=4.19, p=0.041) and rs10798059 in the PLA2G4A locus (chi2=4.28, p=0.039) but these associations did not survive after 10,000 permutations to correct the p-value (global p=0.246). The gene-gene interaction test did not show any evidence of either cis-phase interactions for the PLA2G4A and PTGS2 combinations or a trans-phase interaction for the PLA2G4A and PPARG combinations. The PPARG gene has been reported to be strongly associated with type-2 diabetes, but the present study did not support the hypothesis that the PPARG gene may also play an important role in the development of schizophrenia.

Mitochondrial haplotypes and recombination in Candida albicans.

Candida albicans is a common commensal and opportunistic pathogenic fungus. Although it normally reproduces clonally, several lines of evidence exist for genetic recombination and some form of sexual reproduction. We have sequenced seven regions of its mitochondrial genome in 36 strains and constructed haplotypes for the 66 polymorphic sites, which include single-nucleotide polymorphisms and insertion/deletions. Nineteen different haplotypes were observed. Strains with the same mitochondrial haplotype were found in different clades defined by nuclear multilocus sequence typing (MLST) and the UPGMA dendrograms constructed using either set of data were different in topology. There was no apparent correlation between mitochondrial haplotype and the source of the strain (geographical or anatomical). Examination of the mitochondrial haplotypes revealed substantial evidence for recombination between polymorphic sites. This suggests that the use of mitochondrial haplotypes in phylogenetic studies should be approached with caution. These results provide further evidence for recombination and genetic exchange in the biology of C. albicans.

Mixed Candida albicans strain populations in colonized and infected mucosal tissues.

Multilocus sequence typing of six Candida albicans colonies from primary isolation plates revealed instances of colony-to-colony microvariation and carriage of two strain types in single oropharyngeal and vaginal samples. Higher rates of colony variation in commensal samples suggest selection of types from mixed populations either in the shift to pathogenicity or the response to antifungal treatment.

Strain typing and determination of population structure of Candida krusei by multilocus sequence typing.

A multilocus sequence typing (MLST) scheme for Candida krusei was devised, based on sequencing of six gene fragments of the species. The existence of heterozygous results for each of the six fragments sequenced confirms that C. krusei is diploid for at least part of its genome. The C. krusei MLST scheme had a discriminatory index of 0.998, making this system ideal for strain typing of C. krusei clinical isolates. MLST data for 122 independent C. krusei isolates from a range of geographical sources were analyzed by eBURST, structure, and the unweighted-pair group method using average linkages to derive a population structure comprising four subtype strain clusters. There was no evidence of geographical associations with particular subtypes. Data for pairs of isolates from seven patients showed that each patient was colonized and/or infected with strain types that were indistinguishable by MLST. The C. krusei MLST database can be accessed online at http://pubmlst.org/ckrusei/.

Molecular phylogenetics of Candida albicans.

We analyzed data on multilocus sequence typing (MLST), ABC typing, mating type-like locus (MAT) status, and antifungal susceptibility for a panel of 1,391 Candida albicans isolates. Almost all (96.7%) of the isolates could be assigned by MLST to one of 17 clades. eBURST analysis revealed 53 clonal clusters. Diploid sequence type 69 was the most common MLST strain type and the founder of the largest clonal cluster, and examples were found among isolates from all parts of the world. ABC types and geographical origins showed statistically significant variations among clades by univariate analysis of variance, but anatomical source and antifungal susceptibility data were not significantly associated. A separate analysis limited to European isolates, thereby minimizing geographical effects, showed significant differences in the proportions of isolates from blood, commensal carriage, and superficial infections among the five most populous clades. The proportion of isolates with low antifungal susceptibility was highest for MAT homozygous a/a types and then alpha/alpha types and was lowest for heterozygous a/alpha types. The tree of clades defined by MLST was not congruent with trees generated from the individual gene fragments sequenced, implying a separate evolutionary history for each fragment. Analysis of nucleic acid variation among loci and within loci supported recombination. Computational haplotype analysis showed a high frequency of recombination events, suggesting that isolates had mixed evolutionary histories resembling those of a sexually reproducing species.

Multilocus sequence typing for differentiation of strains of Candida tropicalis.

A system is described for typing isolates of the pathogenic fungus Candida tropicalis, based on sequence polymorphisms in fragments of six genes: ICL1, MDR1, SAPT2, SAPT4, XYR1, and ZWF1a. The system differentiated 87 diploid sequence types (DSTs) among a total of 106 isolates tested or 80 DSTs among 88 isolates from unique sources. Replicate isolates from the same source clustered together with high statistical similarity, with the exception of one isolate. However, a clade of very closely related isolates included replicate isolates from three different patients, as well as single isolates from eight other patients. This clade, provisionally designated clade 1, was one of three clusters of isolates with high statistical similarity. Five of six isolates in one cluster that may acquire clade status were resistant to flucytosine. This study adds C. tropicalis to Candida albicans and Candida glabrata as Candida species for which a multilocus sequence typing (MLST) system has been set up. The C. tropicalis MLST database can be accessed at http://pubmlst.org/ctropicalis/.

Genetic evidence for recombination in Candida albicans based on haplotype analysis.

The possibility of sexual reproduction in the human pathogenic fungus Candida albicans is a question of great interest in medical mycology. Not only is it a fundamental biological issue, but it is also a potential mechanism for contributing to the phenotypic plasticity (and hence the virulence) of the organism. Molecular genotyping methods such as multi-locus sequence typing (MLST) are generating data that can shed light on this question. In the present study we have used MLST information to generate haplotypes that identify many different homologues of a chromosome within a collection of strains. Particular combinations of these haplotypes provide evidence for chromosomal segregation and intra-chromosome recombination. All of our observations of haplotype diversity could also be explained by other mechanisms, such as gene conversion or mitotic recombination, and the resolution of these issues will require a denser map of accurately localised markers. A common event observed in strain evolution is loss of heterozygosity at a particular marker. Our results contribute to the emerging picture of C. albicans as an organism whose primary means of reproduction is clonal, but with a small but important contribution from sexual reproduction, occurring in nature but not under commonly used laboratory conditions.