Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation,gene expression,and trait variation

The identification of true causal loci to unravel the statistical evidence of genotype-phenotype correlations and the biological relevance of selected single-nucleotide polymorphisms (SNPs) is a challenging issue in genome-wide association studies (GWAS). Here, we introduced a novel method for the prioritization of SNPs based on p-values from GWAS. The method uses functional evidence from populations, including phenotype-associated gene expressions. Based on the concept of genetic interactions, such as perturbation of gene expression by genetic variation, phenotype and gene expression related SNPs were prioritized by adjusting the p-values of SNPs. We applied our method to GWAS data related to drug-induced cytotoxicity. Then, we prioritized loci that potentially play a role in druginduced cytotoxicity. By generating an interaction model, our approach allowed us not only to identify causal loci, but also to find intermediate nodes that regulate the flow of information among causal loci, perturbed gene expression, and resulting phenotypic variation.     

Functional trade‐offs increase species diversity in experimental plant communities

Functional trade‐offs have long been recognised as important mechanisms of species coexistence, but direct experimental evidence for such mechanisms is extremely rare. Here, we test the effect of one classical trade‐off – a negative correlation between seed size and seed number – by establishing microcosm plant communities with positive, negative and no correlation between seed size and seed number and analysing the effect of the seed size/number correlation on species richness. Consistent with theory, a negative correlation between seed size and seed number led to a higher number of species in the communities and a corresponding wider range of seed size (a measure of functional richness) by promoting coexistence of large‐ and small‐seeded species. Our study provides the first direct evidence that a seed size/number trade‐off may contribute to species coexistence, and at a wider context, demonstrates the potential role of functional trade‐offs in maintaining species diversity.     

The First Outbreak of Chorioptes texanus (Acari: Psoroptidae) Infestation in a Cattle Farm in Korea

Mites in the genus Chorioptes cause a mild form of skin disease in both domestic and wild ruminants. In July 2006, dermatitis characterized by alopecia, marked lichenification, accumulation of crust, and fissuring was recognized in 14 out of 200 Holstein dairy cattle raised in the cattle farm of the National Institute of Animal Science in Cheonan, Republic of Korea. Skin lesions were distributed mainly over the tail base, and sacral and perineal regions. Microscopic examinations of skin scraping samples from severely affected areas revealed numerous mites of all developmental stages. Morphologically, pedicels of the mites were short and unjointed. The tarsal suckers occurred on the pedicels of all the legs in the male worm and on the first, second, and fourth pair of legs in the adult female worm. A single long seta at the tarsus of legs III and the length of legs II being about twice as long as legs IV in adult male mites were observed. Arising anterior to the inner-most spatulate seta was a short seta with an average of 26.4 ± 5.8 µm in length. Also, the length of setae #4 on the opisthosomal lobes was relatively short. Based on these observations, the mites were identified as Choriptes texanus. Although the chorioptic mange may not influence the mortality rate in the affected farm, reports indicate that a decline in milk production can be observed. This is the first report of chorioptic infestation in a cattle farm from Korea.     

Diversity of the lichenized fungi in King George Island, Antarctica, revealed by phylogenetic analysis of partial large subunit rDNA sequences

Lichens are predominant and important components of flora in the terrestrial ecosystem of Antarctica. However, relatively few researches on the phylogenetic position of Antarctic lichen-forming fungi have been accomplished. In this study, partial sequences of nuclear large subunit rDNAs from 50 Antarctic specimens were obtained and the phylogeny was reconstructed. Antarctic lichen species were distributed among 4 orders, including the monophyletic order Agyrales, paraphyletic orders Pertusariales and Teloschistales, and polyphyletic order Lecanorales. Species diversity was highest in the order Lecanorales, followed by Teloschistales and Pertusariales. Based on the phylogeny and sequence similarity analyses, it is proposed that the taxonomy of Stereocaulon alpinum, Physcia caesia, Usnea aurantiacoatra, and Cladonia species should be revised by careful examination of their phenotypic and molecular characteristics. Six species known to be endemic to Antarctica, Catillaria corymbosa, Himantormia lugubris, Leptogium puberulum, Pertusaria pertusa, Rhizoplaca aspidophora, and Umbilicaria antarctica, formed unique lineages, implying independent origins in the Antarctic area.     

Human papillomavirus (HPV) type distribution in Korean women: a meta-analysis

The aim of the present study is to estimate the overall prevalence and type distribution of human papillomavirus (HPV) in Korean women, through literature review and meta-analysis. We searched published data for the period between 1995 and 2007 using the following inclusion criteria; (1) studies using type-specific HPV tests, (2) data from Korean female, (3) with cytologic or pathologic results, (4) having more than 20 cases for each subgroup classified by cytologic results, and (5) HPV detection including types 16, 18, and at least one other type. In total, 18 studies (13,842 cases) published up to April 2007 were identified and selected. Adjusted overall HPV prevalence was 23.9% (95% CI: 23.8-24.1%) in women with normal cytology and 95.8% (95% CI: 95.4-96.2%) in women with cervical cancer. Type 16 was predominant regardless of cervical disease status, and type 58 occupied a significantly larger proportion in high-grade cervical intraepithelial lesions and cervical cancer in Korean women. HPV types 58, 33, and 52 together accounted for about 20% of infections in cervical cancer and high-grade intraepithelial lesions. After introduction of HPV prophylactic vaccines, extended protection, especially against types 58, 33, and 52, will be an important issue for cervical cancer prevention in Korea. The future dominant genotypes will require follow-up epidemiological studies with a large-scale, multicentered, and prospective design.     

Regulation of 3-phosphoinositide-dependent protein kinase-1 (PDK1) by Src involves tyrosine phosphorylation of PDK1 and Src homology 2 domain binding

3-Phosphoinositide-dependent protein kinase-1 (PDK1) appears to play a central regulatory role in many cell signalings between phosphoinositide-3 kinase and various intracellular serine/threonine kinases. In resting cells, PDK1 is known to be constitutively active and is further activated by tyrosine phosphorylation (Tyr(9) and Tyr(373/376)) following the treatment of the cell with insulin or pervanadate. However, little is known about the mechanisms for this additional activation of PDK1. Here, we report that the SH2 domain of Src, Crk, and GAP recognized tyrosine-phosphorylated PDK1 in vitro. Destabilization of PDK1 induced by geldanamycin (a Hsp90 inhibitor) was partially blocked in HEK 293 cells expressing PDK1-Y9F. Co-expression of Hsp90 enhanced PDK1-Src complex formation and led to further increased PDK1 activity toward PKB and SGK. Immunohistochemical analysis with anti-phospho-Tyr(9) antibodies showed that the level of Tyr(9) phosphorylation was markedly increased in tumor samples compared with normal. Taken together, these data suggest that phosphorylation of PDK1 on Tyr(9), distinct from Tyr(373/376), is important for PDK1/Src complex formation, leading to PDK1 activation. Furthermore, Tyr(9) phosphorylation is critical for the stabilization of both PDK1 and the PDK1/Src complex via Hsp90-mediated protection of PDK1 degradation.     

Importance of the degree of antigen polymerization by detoxification in modulating the immunogenicity of acellular pertussis vaccine

For the acellular pertussis vaccine with a high immunogenicity, the concentration, composition and characteristics of acellular pertussis antigens are the crucial points to be considered. Nevertheless, it has not been proved yet whether or not the polymerization degree, one of the characteristics of formalin-detoxified acellular pertussis antigens, has an influence on vaccine potency. Thus, in the present study, the correlations among detoxification conditions of acellular pertussis bulks, their polymerization degrees and their immunogenicities were examined. In addition, the relative importance of pertussis toxoid in vaccine immunogenicity was also investigated. Results show that a lower lysine concentration during detoxification induces highly-polymerized antigens, the immunogenicity has a great dependency on the polymerization degree of antigens, and also pertussis toxoid has a relatively stronger influence on the immunogenicity than other antigens. Accordingly, in the aspect of the potency of detoxified acellular pertussis vaccine, it can be demonstrated that the polymerization of antigens and its degree are the major factors affecting the immunogenicity along with a relatively high content of pertussis toxoid.