Genome analysis of dengue type-1 virus isolated between 1990 and 2001 in Brazil reveals a remarkable conservation of the structural proteins but amino acid differences in the non-structural proteins

We have investigated the genetic diversity of dengue type-1 (DEN-1) virus in Brazil. The full nucleotide sequences of three DEN-1 virus isolated from DEN fever (DF) and DEN hemorrhagic fever patients in northeastern Brazil in 1997 (BR/97) and one from a DF patient in the south of Brazil in 2001 (BR/01) were compared to that of the reference strain BR/90 obtained in the city of Rio de Janeiro in 1990. Sequence analysis showed that the structural proteins were remarkably conserved between all isolates. A total of 27 amino acid changes occurred throughout the non-structural proteins. Among them, nine amino acid substitutions were specific of BR/97 and BR/01 isolates, indicating that in situ evolution of these strains had occurred. Within the BR/97 and BR/01 samples, some amino acid substitutions have been previously identified in DEN-1 virus strains sequenced so far, suggesting that recombination events might have occurred.     

Identification of HLA-A*0224: implications for PCR-SSP HLA typing

We describe a novel HLA-A*02 allele, A*0224, that was identified after a comparison of DNA and serological typing revealed a discrepancy in the HLA-A types: HLA-A2 was defined by serology but was not detected by the polymerase chain reaction using sequence-specific primers (PCR-SSP). DNA sequencing indicated the presence of a variant HLA-A*02 allele that differed from A*0201 by a single base (C/A) at position 453. This base substitution corresponded to the annealing site of a primer common to the two A*02-amplifying PCR-SSP mixtures used in the method. This provides an explanation for the results and highlights a limitation of PCR-SSP methods even where two PCR mixtures are used to detect alleles. Serological titration studies suggested that A*0201, A*0205 and A*0224 are unlikely to be differentiated during routine serological typing.     

Identification of an HLA-DQ2 peptide binding motif and HLA-DPw3-bound self-peptide by pool sequencing

Molecules of the major histocompatibility complex (MHC) present antigenic peptides to T cells. Sequencing peptide pools eluted from MHC class I molecules has established allele-specific peptide binding motifs. We applied pool sequencing to analyze human MHC class II-bound peptides and found that HLA-DQ2-eluted peptides predominantly contained lysine, isoleucine, and phenylalanine at relative position i, i + 3 and i + 8, respectively. These residues putatively represent anchor residues for MHC binding. Analysis of a heterogeneous HLA-DPw3/DPw4-eluted peptide pool yielded a sequence matching an epitope from the endogeneous enzyme glyceraldehyde-3-phosphate dehydrogenase. This self-peptide and a partially identical, known allo-epitope bound specifically to DPw3 and DR13 molecules, suggesting the sharing of a binding motif. In particular, the presence of an arginine at relative position 4 appeared important for binding to these HLA class II specificities. Thus, pool sequencing is applicable for the analysis of MHC class II-eluted peptides.     

IL-4–BATF signaling directly modulates IL-9 producing mucosal mast cell (MMC9) function in experimental food allergy

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9.1C3单克隆抗体轻,重链可变区基因克隆及序列分析

９．１Ｃ３分子是一种参与ＮＫ、巨噬细胞及ＬＡＫ细胞杀伤过程的重要细胞表面分子，主要表达于外周血单个核细胞表面。本文运用分子生物学技术，从分泌９．１Ｃ３ＭＣＡｂ的杂交瘤细胞中提取总ＲＮＡ，经反转录、ＰＣＲ分另１１分离了９．１Ｃ３ＭｃＡｂ轻链可变区（ＶＬ）基因及重链可变区（ＶＨ）基因，并用全自动荧光ＤＮＡ序列分析仪对９．１Ｃ３ＶＨ、ＶＬ基因序列进行了分析。结果表明：９．１Ｃ３ＶＨ基因为３５１ｂＰ，编码１１７ａａ残基，９．１３ＶＬ为３２４ｂＰ，编码１０８ａａ残基；从推导出的氨基酸序列分析证实９．１Ｃ３ＶＨ、ＶＬ序列均符合小鼠ｌｇ可变区的氨基酸序列特征；根据Ｋａｂｂａｔ分类体系，９．１Ｃ３ＶＨ隶属Ｉｇ重链第Ⅱ（Ｃ）亚组，９．１Ｃ３ＶＬ隶属小鼠ＩｇＫ链第Ⅴ亚组。９．１Ｃ３ＶＨ、ＶＬ基因的克隆成功为其单链抗体的构建、表达奠定了良好的物质基础。     

The DQA1*0104 allele is carried by DRB1*1001- and DRB1*1401-positive haplotypes in Caucasians, Africans and Orientals

Abstract: The DQA1*0104 allele is known to differ from DQA1*0101 by a single nucleotide in the sequenced part of the first exon. DQA1*0104 has a guanine in the second position of the second expressed codon, whereas DQA1*0101 and all other sequenced DQA1 alleles have an adenine in that position, changing aspartic acid to glycine. The DQA1*0104 allele was originally described in African Americans with the DRB1*12, DRB3*0101, DQA1*0104, DQB1*0501, DRB1*12, DRB3*0202, DQA1*0104, DQB1*0605 or DRB1*14, DQA1*0104, DQB1*0503 haplotypes. When developing DQA1 typing by PCR amplification with sequence-specific primers (PCR-SSP), we observed that all DR10- and DR14-positive samples carried the DQA1*0104 allele, wheres all DRB1*01 -positive DNAs carried the closely related DQA1*0101 allele. In the present study, samples representing the major ethnic groups with DR-DQ haplotypes known to carry the DQA1*0104 allele or the very similar DQA1*0101 allele were investigated by Taq I RFLP analysis, PCR-SSP typing and nucleotide sequencing. The DQA1*0104 allele was found to differ from DQA1*0101 not only in the second expressed codon, but also by a productive mutation in the signal peptide. All investigated DRB1*1001 -(n = 24) and DRB1*1401 -positive (n = 25) haplotypes, defined by homozygosity or association, of Caucasian, African or Oriental origin carried the DQA1*0104 allele, whereas the DQA1*0101 allele was found on all DRB1*01 -positive (n = 32) haplotypes. These findings demonstrate that in the assignment of HLA class II alleles, polymorphism outside the second exon sometimes must be considered. The maintenance of the DQA1*0104 allele on a few distinct haplotypes indicates that the allele is old and might also be compatible with a functional difference between the DQA1*0101 and DQA1*0104 alleles.     

DNA polymerase gene locus of <Emphasis Type="Italic">Cercopithecine herpesvirus 1</Emphasis> is a suitable target for specific and rapid identification of viral infection by PCR technology

The family Herpesviridae comprises at least 100 herpesviruses. Numerous human and animal pathogenic herpesviruses have been identified so far, including Cercopithecine herpesvirus 1 (CeHV-1). This virus is a member of the subfamily Alphaherpesvirinae and is the most hazardous herpesvirus to man. CeHV-1 is also known as B-virus or monkey B virus and as Herpesvirus simiae. In order to gain more genetic information, the viral DNA polymerase (DPOL) gene was identified using polymerase chain reaction (PCR) and DNA nucleotide sequence analysis. The deduced amino acid sequence contains the motifs and signatures that are typical for the B-family of DPOLs. The DPOL gene of CeHV-1 was found to be a suitable target for the specific and rapid identification of the Cercopithecine herpesvirus 1 infection by PCR technology. Comparative analysis of the DNA sequences of the DPOL gene loci of CeHV-1, Human herpesvirus 1 and 2 (HHV-1 and HHV-2), and other herpesviruses was carried out for determination of unique genomic regions of the individual DPOL genes. A primer set of 12 primers was used for screening the DNA of CeHV-1, HHV-1, and HHV-2 by detailed PCR. It was found that six out of twelve primer combinations are able to detect specifically the CeHV-1 genome without cross reactivity with the genome of HHV-1 and/or HHV-2. The specificity of the individual amplified DNA fragments was confirmed by DNA nucleotide sequence analysis. The results of these studies indicate that the six primer combinations of the specific CeHV-1 DPOL primer set is the method of choice for a rapid, precise and specific identification of a CeHV-1 infection by PCR. Due to the fact that this specific CeHV-1 DPOL primer set does not amplify any DNAs of HHV-1 or HHV-2 genome this technology is stressing and can be successfully used unlimited and more credible in all laboratories with PCR technical facility routinely for detection of a CeHV-1 infection in vivo or in vitro.The GenBank Accession No. of the sequence of DNA polymerase gene of Cercopithecine herpesvirus 1 (CeHV-1) reported in this study is AY568415, DPOL protein ID AAT67222; nuclear phosphoprotein ID AAT67223     

Ten novel HLA-DRB1 alleles and one novel DRB3 allele

Ten novel HLA-DRB1 and one DRB3 alleles are described. Eight of the variants are single-nucleotide substitutions, four resulting in an amino acid change (DRB1*1145, *1148, *0828 and *1514) and four with silent substitutions (DRB1*040504, *130103, *160502 and DRB3*020204). Two alleles differ by two nucleotide changes altering one (DRB1*1447 and *1361) amino acid and one allele alters three nucleotides and two amino acids.     

Seven new HLA-B alleles associated with antigens in the B7 CREG

This paper describes seven novel HLA-B alleles. Five of these new alleles contain polymorphic motifs previously reported in HLA-B alleles, suggesting an origin resultant from a gene conversion mechanism. B*0723 contains a polymorphism previously unreported in class I HLA molecules. B*4105 contains a nucleotide substitution previously unreported in class I HLA molecules, which encodes a protein sequence previously reported only in HLA-C locus alleles.