The aim of this study was to develop a simple method using universal primers for species identification based on direct PCR sequencing. Two primer sets were designed based on the conserved regions of the 12S and 16S rRNA loci detected by the comprehensive sequence comparison among 30 mammalian whole mitochondrial genomes. In humans, the expected sizes of PCR products of the 12S and 16S rRNAs were 215 and 244 bp, respectively. Both primer sets successfully amplified the expected PCR products from various kinds of vertebrates including mammals, birds, reptiles, amphibians, and fish, and the sequenced segments contained sufficient nucleotide differences to identify each animal species. A case example of the identification of a piece of buried bone of unknown species is presented, and the species was identified as a pig by this method.

Numerous studies have demonstrated that plant species diversity enhances ecosystem functioning in terrestrial ecosystems, including diversity effects on insect arthropods (herbivores, predators and parasitoids) and plants. Yet, the effects of increased plant diversity across trophic levels in different ecosystems and biomes have not yet been explored on a global scale. Through a global meta-analysis of 2914 observations from 351 studies, we found that increased plant species richness reduced herbivore abundance and damage but increased predator and parasitoid abundance, predation, parasitism, and overall plant performance. Moreover, increased predator/parasitoid performance was correlated with reduced herbivore abundance and enhanced plant performance. We

In this study, we investigated the five polymorphic Alu loci located within human major histocompatibility complex (MHC) class I region in 445 individuals from four distinct Chinese populations: Hunan Han, Inner Mongolia Han, Inner Mongolia Mongol and Guangdong Han populations, with an emphasis on the linkage disequilibrium (LD) between Alu insertions and human leukocyte antigen (HLA)-A, Cw and B loci in a southern (Hunan Province) and a northern (Inner Mongolia Autonomous Region) Chinese Han population. Our data showed that (a) the allele and haplotype frequencies of Alu and HLA-A loci did not differ significantly between the two southern Chinese Han populations and showed remarkable homogeneity in the two northern Chinese populations; (b) AluyHG had the highest insertion rate and HLA-A*02 harboring the single AluyHG insertion was most frequent among Alu insertion-bearing haplotypes in all four populations; (c) haplotypes AluyHF insertion-HLA-A*26, AluyHG insertion-HLA-A*02 and AluyHJ insertion-HLA-A*24 were in significant LD across the four groups and (d) haplotype AluyMICB insertion-HLA-Cw*06 was in significant LD in both populations, while significant LD of haplotypes AluyMICB insertion-HLA-B*54 and AluyMICB insertion-HLA-B*48 was only observed in the Hunan Han population and the Inner Mongolia Han population, respectively. Haplotype HLA-B*48-MICA gene deletion-AluyMICB insertion was observed at a frequency of about 3.85% in the latter population. Our data, together with previous reports on several Asian-Oceanian populations suggest the identity by descent of several common HLA-A allelic lineages in these modern human populations. The novel population-specific LD patterns uncovered in this study also shed new insight into HLA evolution and haplotype origin.

Isocitrate dehydrogenase 1 (IDH1) mutations have recently been identified as early and frequent genetic alterations in astrocytomas, oligodendrogliomas, and oligoastrocytomas, as well as secondary glioblastomas, whereas primary glioblastomas very rarely contain IDH1 mutations. Furthermore, a specific monoclonal antibody, IMab-1, which recognizes IDH1-R132H-the most frequent IDH1 mutation-has been generated. IMab-1 has been reported to react with the IDH1-R132H protein, but not the wild-type IDH1 or the other IDH1 mutant proteins in Western-blot analysis. However, the importance of immunohistochemistry using IMab-1 has not yet been elucidated. In this study, we compared the findings from IMab-1 immunohistochemistry and direct DNA sequencing using 49 glioma samples. IMab-1 detected 12 out of 49 cases; however, only nine cases were found to be IDH1-R132H by direct DNA sequencing because of a small population of IDH1-R132H mutation-possessing tumor cells, indicating that IMab-1 immunohistochemistry is useful for detecting IDH1-R132H. We conducted immunohistochemical detection in 52 cases of grade III astrocytomas. The median time to progression (TTP) was significantly longer in the cases with the IDH1 mutation (86.7 months) compared to the cases without the IDH1 mutation (wild type, 10.4 months) (p < 0.01). In conclusion, the anti-IDH1-R132H-specific monoclonal antibody IMab-1 is very useful for detecting IDH1-R132H in immunohistochemistry, and predicting the time to progression in grade III anaplastic astrocytomas. Therefore, IMab-1 is likely to be useful for the diagnosis of mutation-bearing gliomas and for determining the treatment strategy of grade III gliomas.

No abstract

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a devastating disease of wheat (Triticum aestivum) worldwide. Wheat high-temperature seedling plant (HTSP) resistance to Pst is non-race-specific and durable. WRKY transcription factors have been proven to play important roles in plant defence responses to attacks by several pathogens. However, there is no direct evidence as to whether WRKY transcription factors play a role in HTSP resistance to Pst. We isolated a WRKY gene, named TaWRKY70, from wheat cultivar Xiaoyan 6. The expression level of TaWRKY70 was increased significantly when exposed to high temperatures (HTs) during the initial symptom expression stage of Pst infection. The expression of this gene increased in plants treated with ethylene (ET), salicylic acid (SA) and cold (4°C) stresses, but decreased in plants treated with methyl jasmonate (MeJA) and heat (40°C) stresses. Silencing of TaWRKY70 led to greater susceptibility to Pst (in terms of the increase in length of uredinial pustules and the decrease in the number of necrotic cells) compared with non-silenced plants when exposed to HT during the initial symptom expression stage of Pst infection, coinciding with expression changes of the ET- and SA-responsive genes TaPIE1 and TaPR1.1. In contrast, the expression level of the jasmonic acid (JA)-responsive gene TaAOS was not affected by TaWRKY70. These results indicate that TaWRKY70 is positively involved in HTSP resistance, during which SA and ET signalling are probably activated.

Background The objectives of this study were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis. Results We analyzed the metabolomics and transcriptomics data of S. miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of S. miltiorrhiza . Integrated analysis of transcriptomics and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of S. miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in S. miltiorrhiza flowers. Low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in S. miltiorrhiza flowers. Conclusions Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in S. miltiorrhiza .

Previous studies have identified several HLA-B specificities that are associated with nasopharyngeal carcinoma (NPC) in populations of Chinese descent, in particular HLA-B35, -B38, -B46, and -B58. Perhaps except for HLA-B46, other associations cannot be simply accounted for by the linkage disequilibrium between HLA-A and B loci. The human major histocompatibility complex (MHC) class I chain-related gene A (MICA) maps 46 kb centromeric to HLA-B and is highly polymorphic; it encodes a stress-inducible protein which functions as a ligand for the NKG2D/DAP10 complex to activate natural killer (NK) cells, gammadelta T cells, and CD8(+) T cells. We postulated MICA gene as a susceptibility factor for nasopharyngeal carcinoma, an Epstein-Barr virus-associated malignancy. In this study, 218 unrelated patients newly diagnosed with NPC and 196 randomly selected healthy controls from southern China mainland were analyzed for the short tandem repeat polymorphism of exon 5 of MICA gene (MICA-STR) and MICA gene deletion, using fluorescent polymerase chain reaction-gene scanning (PCR/size-sequencing) and polymerase chain reaction-sequence-specific priming (PCR/SSP) technology. MICA*A9 was present at significantly increased frequency in the patient group (P (C)=0.0001002, OR=2.528, 95% CI=1.636-3.907), whereas the frequency of MICA*A5.1 was significantly decreased (P (C)=0.006, OR=0.594, 95% CI=0.437-0.806). Gender-based stratification revealed a significant increase of MICA*A9 frequency (P (C)=0.000072, OR=3.255, 95% CI=1.855-5.709) and a significant decrease of MICA*A5.1 frequency (P (C)=0.000737, OR=0.486, 95% CI=0.337-0.702) in male patients with NPC (N=166), compared with male normal controls (N=120). A significant interaction between MICA*A9 and gender was observed ([see text]=41.58, P=0.0001). Statistics also revealed heterogeneity of effects among MICA*A5.1/MICA*A9-bearing phenotypes and a dose-dependent effect of MICA*A5.1 and MICA*A9 on NPC risk in male subgroup. This constitutes the first demonstration of a gender-specific association between MICA-STR polymorphism and NPC, which could largely be attributable to the underlying gender-related mechanisms that modulate MICA gene expression. The results provide strong supporting evidence suggesting that MICA*A9 may be a genetic risk factor for NPC in male individuals in this population. The potential interaction between MICA and other non-HLA host factors and environmental exposures remains to be further studied.