HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in b...HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primeror probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A＊02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A＊02.展开更多
Bacterioplankton play key roles in the biogeochemical cycle and in organic contaminant degradation. The species richness and abundance of bacterial subgroups are generally distinct from each other, and this is attribu...Bacterioplankton play key roles in the biogeochemical cycle and in organic contaminant degradation. The species richness and abundance of bacterial subgroups are generally distinct from each other, and this is attributed to their different functions in aquatic ecosystems. The spatiotemporal variations of eight phylogenetic subgroups （Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomycetes, alpha-, beta-, and gamma-Proteobacteria） derived from Donghu Lake were investigated using PCR-DGGE fingerprinting, to explore their responses to environmental factors. Results indicate that Actinobacteria and beta-Proteobacteria were the two largest bacterial subgroups detected. These two groups and Bacteroidetes showed clear seasonal patterns in composition of the operational taxonomic unit. Results also suggest that the bacterioplankton subgroups in Donghu Lake were significantly correlated with different environmental factors. In brief, the total nitrogen was one of the major factors regulating all the bacterioplankton except for Actinobacteria. However, total phosphorus, another important eutrophication factor, contributed to the two largest bacterial groups （Actinobacteria and beta-Proteobacteria）, as well as to the Cyanobacteria and Firmicutes. Therefore, the responses of bacterioplankton subgroups to environmental factors were different, and this should be attributed to the differences in the fimctions of different groups.展开更多
Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests.However,the presence of high levels of glucosinolates severely diminishes the nutritional value of seed mea...Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests.However,the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed(Brassica napus L.).To identify the loci affecting seed glucosinolate cont ent(SGC),we con ducted genome-wide resequencing in a population of 307 diverse B.napus accessions from the three B.napus ecotype groups,namely,spring,winter,and semi-winter.These resequencing data were used for a genome-wide association study(GWAS)to identify the loci affecting SGC.In the three ecotype groups,four comm on and four ecotype-specific haplotype blocks(HBs)were significantly associated with SGC.To identify candidate genes controlling SGC,transcriptome analysis was carried out in 36 accessions showing extreme SGC values.Analyses of haplotypes,genomic variation,and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs,respectively.Our expression analyses dem on strated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B.napus.展开更多
Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly.In this study,we investigated the food habits of 2 rodents,Rattus ...Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly.In this study,we investigated the food habits of 2 rodents,Rattus rattus(ship rat)and Mus musculus castaneus(house mouse)as well as an insectivore,Suncus murinus(shrew),present in human dwellings.Both a microhistological approach and a DNA barcoding approach were used in the present study.Following DNA extraction,amplification was performed using group-specific primers targeting birds,plants and invertebrates.Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents.The findings from the application of both techniques were in agreement,but the detection of prey type with each technique was different.The DNA barcoding approach gave greater species-level identification when compared to the microhistological method,especially for the invertebrate and avian prey.Overall,with both techniques,23 prey taxa were identified in the gut contents of the 3 species,including 15 plants,7 insects and a single bird species.We conclude that with a selection of suitable“barcode genes”and optimization of polymerase chain reaction protocols,DNA barcoding can provide more accurate and faster results.Prey detection from either technique alone can bias the dietary information.Hence,combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet,especially if the pest is an omnivore or insectivore species.展开更多
基金The authors would like to thank Jueqin Yang for assistance with sample preparation. The authors would also like to thank the Fred Hutchinson Cancer Research Center IHWG Cell and Gene Bank for providing reference genomic DNA samples. This work was supported through grants from the National Natural Science Foundation of China （NSF-30830093） and the National Key Program （973） for Basic Research of China （2009CB522409） to HJ. Supplementary Information accompanies the paper on Cellular ＆ Molecular Immunology website.
文摘HLA-A＊02 is the most prevalent and polymorphic major histocompatibility complex （MHC） allele family in humans. Functional differences have been revealed among subtypes, demanding further subtyping of HLA-A＊02 in basic and clinical settings. However, the fast growing polymorphisms render traditional primeror probe-based typing methods impractical and result in increasing ambiguities in direct sequence-based typing. In this study, we combined group-specific amplification and mono-allelic sequencing to design and validate a simple scheme for the complete screening and accurate subtyping of all 540 reported HLA-A＊02 alleles. This scheme could be performed in routine labs to facilitate studies with an interest in HLA-A＊02.
基金Supported by the National Natural Science Foundation of China(No.31071896)the National Basic Research Program of China(973 Program)(No.2008CB418105)+2 种基金the Knowledge Innovation Program of Chinese Academy of Sciences(No.Y15E04)the Youth Innovation Promotion Association,Chinese Academy of Sciences(No.Y22Z07)the Key Laboratory of Marine and Estuarine Fisheries Resources and Ecology,Ministry of Agriculture(No.201007)
文摘Bacterioplankton play key roles in the biogeochemical cycle and in organic contaminant degradation. The species richness and abundance of bacterial subgroups are generally distinct from each other, and this is attributed to their different functions in aquatic ecosystems. The spatiotemporal variations of eight phylogenetic subgroups （Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Planctomycetes, alpha-, beta-, and gamma-Proteobacteria） derived from Donghu Lake were investigated using PCR-DGGE fingerprinting, to explore their responses to environmental factors. Results indicate that Actinobacteria and beta-Proteobacteria were the two largest bacterial subgroups detected. These two groups and Bacteroidetes showed clear seasonal patterns in composition of the operational taxonomic unit. Results also suggest that the bacterioplankton subgroups in Donghu Lake were significantly correlated with different environmental factors. In brief, the total nitrogen was one of the major factors regulating all the bacterioplankton except for Actinobacteria. However, total phosphorus, another important eutrophication factor, contributed to the two largest bacterial groups （Actinobacteria and beta-Proteobacteria）, as well as to the Cyanobacteria and Firmicutes. Therefore, the responses of bacterioplankton subgroups to environmental factors were different, and this should be attributed to the differences in the fimctions of different groups.
基金supported by the National Natural Science Foundation of China (31601333)the Doctoral Fund Southwest University (SWU118010)+1 种基金the National Program on Key Basic Research Project of China (973 Program: 2015CB150201)the Fundamental Research Funds for the Central Universities (XDJK2017B036)
文摘Glucosinolates are amino acid-derived secondary metabolites that act as chemical defense agents against pests.However,the presence of high levels of glucosinolates severely diminishes the nutritional value of seed meals made from rapeseed(Brassica napus L.).To identify the loci affecting seed glucosinolate cont ent(SGC),we con ducted genome-wide resequencing in a population of 307 diverse B.napus accessions from the three B.napus ecotype groups,namely,spring,winter,and semi-winter.These resequencing data were used for a genome-wide association study(GWAS)to identify the loci affecting SGC.In the three ecotype groups,four comm on and four ecotype-specific haplotype blocks(HBs)were significantly associated with SGC.To identify candidate genes controlling SGC,transcriptome analysis was carried out in 36 accessions showing extreme SGC values.Analyses of haplotypes,genomic variation,and candidate gene expression pointed to five and three candidate genes in the common and spring group-specific HBs,respectively.Our expression analyses dem on strated that additive effects of the three candidate genes in the spring group-specific HB play important roles in the SGC of B.napus.
文摘Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly.In this study,we investigated the food habits of 2 rodents,Rattus rattus(ship rat)and Mus musculus castaneus(house mouse)as well as an insectivore,Suncus murinus(shrew),present in human dwellings.Both a microhistological approach and a DNA barcoding approach were used in the present study.Following DNA extraction,amplification was performed using group-specific primers targeting birds,plants and invertebrates.Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents.The findings from the application of both techniques were in agreement,but the detection of prey type with each technique was different.The DNA barcoding approach gave greater species-level identification when compared to the microhistological method,especially for the invertebrate and avian prey.Overall,with both techniques,23 prey taxa were identified in the gut contents of the 3 species,including 15 plants,7 insects and a single bird species.We conclude that with a selection of suitable“barcode genes”and optimization of polymerase chain reaction protocols,DNA barcoding can provide more accurate and faster results.Prey detection from either technique alone can bias the dietary information.Hence,combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet,especially if the pest is an omnivore or insectivore species.
