Sequence polymorphisms of the mitochondrial DNA control region and phylogenetic analysis of mtDNA lineages in the Japanese population

Sequence polymorphisms of the hypervariable mitochondrial DNA (mtDNA) regions HVI and HVII, and coding region polymorphisms were investigated in 211 unrelated individuals from the Japanese population. Sequence comparison of the HVI and HVII regions led to the identification of 169 mitochondrial haplotypes defined by 147 variable positions. Among them 145 types were observed in only 1 individual; the other 24 types were shared by 2 or more individuals. The gene diversity was estimated at 0.9961, and the probability of two randomly selected individuals from the population having identical mtDNA types was 0.86%. We also established phylogenetic haplogroups in the Japanese population based on the coding and control region polymorphisms and compared the haplotypes with those in other Japanese, Korean and Chinese populations. As a result, three new subhaplogroups, G4a, G4b, and N9b, and several haplotypes specific for the Japanese and Korean populations were identified. The present database can be used not only for personal identification but also as an aid for geographic or phenotype (race) estimation in forensic casework in Japan.Electronic Supplementary Material Supplementary material is available for this article if you access the article at     

克拉玛依地区HBV基因分型及进化分析

目的：研究克拉玛依地区乙肝病毒（HBV）的基因分型，并且进行进化分析。方法：利用限制性片段多态性分析的方法对272例慢性乙型肝炎患者血清进行基因分型，采用限制性内切酶MboI、Earl酶切扩增产物，以A、B、c、D基因参照品作为对照，12例扩增产物进行测序证实其基因型。结果：272例样品有241例成功分型。C型44．8％，B型36．9％，D型4．2％，B／C型10．8％，B／D型3．3％。少数民族c型40．4％，B型30．8％，D型9．6％，B／C型11．5％，B／D型7．7％，未检测到A型。12例测序结果与39例GenBank中已发表的B、C、D型的同源性在97．8％～98．7％，96．9％～99．3％，97．5％～99．0％。结论：克拉玛依地区HBV基因型主要是C型和B型，其次是D型和混合型，未见A型。进化树分析图显示12例B、C、D型毒株与GenBank序列毒株分别属于同一分支。克拉玛依地区2例D型与新疆哈密地区D型进化距离最近。     

Genomic characterization of swine caliciviruses representing a new genus of Caliciviridae

This study reports the molecular characterization of novel caliciviruses, the St-Valérien-like viruses, which were isolated from pig feces in the province of Quebec, Canada between 2005 and 2007. The genomes of St-Valérien-like viruses contain 6409 nucleotides and include two main open reading frames (ORFs). ORF1 encodes the non structural (NS) polyprotein and the major capsid protein (VP1) while ORF2 encodes the putative basic minor capsid protein. Typical conserved amino acid motifs predict a gene order reminiscent of calicivirus genomes. Phylogenetic, pairwise homology, and distance analyses performed on complete genomic sequences and partial amino acid sequences from the NTPase, polymerase, and major capsid protein segregated the St-Valérien-like viruses in a unique cluster sharing a common root with the Tulane virus and the noroviruses. Based on the genomic analyses presented, the St-Valérien-like viruses are members of a new genus of Caliciviridae for which we propose the name Valovirus.     

比较基因组学在细菌分子进化领域的研究进展

在后基因组时代，比较基因组学已经成为诠释遗传信息生物学意义的重要方法。运用生物信息学的手段，比较分析不同细菌的基因组，我们逐步揭示了细菌染色体物理结构的保守性和基因内容多样性的产生机制。进化生物学家们正试图从基因组数据库中挖掘能够代表物种进化关系的具有普遍适用性的分子线索，重建生命进化树。     

Analysis of HIV-1 pol sequences from Panama: Identification of phylogenetic clusters within subtype B and detection of antiretroviral drug resistance mutations

We report the first study to examine phylogenetic relationships and drug resistance mutations in HIV-1 pol sequences from Panama. For this study, we used plasma RNA samples from 135 HIV-1-infected subjects from Panama, of which 82 (61%) had AIDS and 53 (39%) were asymptomatic drug-naïve individuals. Phylogenetic analyses revealed that 133 (98%) subjects were infected with subtype B viruses and 2 AIDS patients harboured recombinant viruses, CRF02_AG/A3 and CRF12_BF/B, respectively. Using a Bayesian phylogeny inference method, 5 strongly supported clusters of ≥5 sequences, designated B-PA1 to B-PA5, were identified within subtype B, together comprising 87 (65.4%) subtype B viruses. Cluster B-PA1 (n = 42) was significantly associated with East Panama and clusters B-PA2 (n = 15) and B-PA4 (n = 10) were associated with West Panama. A Bayesian coalescent analysis indicated that the most recent common ancestors of the four largest clusters were dated in the 1980s and that of the fifth in the early 1990s. The analysis of antiretroviral drug resistance-associated mutations revealed that 8 (9.7%) AIDS patients, all of them antiretroviral drug-experienced, harboured mutations conferring high or intermediate resistance levels to antiretroviral drugs. No drug resistance mutations were detected among the asymptomatic drug-naïve individuals. In conclusion, the phylogenetic analysis of HIV-1 pol sequences from Panama reveals that a majority of subtype B viruses, which are predominant in Panama, branch within well supported intrasubtype phylogenetic clusters, most of them originating in the 1980s, and some with geographical associations, which may reflect either multiple HIV-1 subtype B introductions or the existence of local transmission networks originating in the early epidemic in Panama.     

Characterization of antimicrobial peptides from the skin secretions of the Malaysian frogs, Odorrana hosii and Hylarana picturata (Anura:Ranidae)

Peptidomic analysis of norepinephrine-stimulated skin secretions from Hose's rock frog Odorrana hosii (Boulenger, 1891) led to the isolation of 8 peptides with differential antibacterial activities. Structural characterization demonstrated that the peptides belonged to the esculentin-1 (1 peptide), esculentin-2 (1 peptide), brevinin-1 (2 peptides), brevinin-2 (2 peptides), and nigrocin-2 (2 peptides) families of antimicrobial peptides. Similar analysis of skin secretions from the Malaysian fire frog Hylarana picturata (Boulenger, 1920) led to the isolation and characterization of peptides belonging to the brevinin-1 (2 peptides), brevinin-2 (5 peptides), and temporin (1 peptide) families. The differences in antimicrobial activities of paralogous peptides provide insight into structure-activity relationships, emphasizing the importance of cationicity in determining potency. The substitution Lys(11)-->Gln in brevinin-1HSa (FLPAVLRVAAKIVPTVFCAISKKC) from O. hosii abolishes growth inhibitory activity against Escherichia coli but has no effect on the high potency (MIC=8mug/ml) against Staphylococcus aureus. In contrast, the substitution (Gly(4)-->Asp) in brevinin-2PTb (GFKGAFKNVMFGIAKSAGKSALNALACKIDKSC) from H. picturata reduces activity against both E. coli and S. aureus. Cladistic analysis based upon the amino acid sequences of the brevinin-2 peptides from Asian frogs provides evidence for sister taxon relationships between O. hosii and O. livida and between H. picturata and H. güntheri.     

The little brown bat, M. lucifugus, displays a highly diverse VH, DH and JH repertoire but little evidence of somatic hypermutation

Myotis lucifugus populations in Northeastern US are being decimated by a fungal disease. Since almost nothing is known about the immune system of bats, we are characterizing the immunoglobulin genes of bats. We show that M. lucifugus has a diverse V_H gene repertoire comprised of five of the seven human V_H gene families and an estimated 236 V_H3 genes. 95% of these germline VH3 genes differ in FR3. A comparison of 67 expressed V_H3 genes with 75 germline V_H3 genes revealed a mutation frequency similar to fetal piglets never exposed to environmental antigens. Analysis of CDR3 regions identified at least 13 putative J_H segments and a large D_H repertoire. The low mutation frequency, highly diverse V_H, D_H, and J_H germline repertoire suggests that this species may rely more on combinatorial and junctional diversity than on somatic hypermutation raising questions about the ability of M. lucifugus to respond rapidly to emerging pathogens.     

2007年山西省部分地区虫媒病毒调查

目的 调查山西省部分地区的虫媒病毒,在当地采集蚊虫标本进行病毒的分离与鉴定.方法 2007年7月和8月在当地采集蚊虫标本,通过组织细胞培养进行病毒分离,利用分子生物学和生物信息学技术对病毒分离物进行鉴定与分析.结果 分离到10株病毒分离物,鉴定结果显示分离株SX0765、SX0766、SX0767、SX0771、SX0789、SX0790、SX0793、SX0794、SX0795、SX0796均为版纳病毒;此外,分离株SX0771和SX0794还同时存在辽宁病毒基因.进一步分析显示版纳病毒新分离株与此前在北京、云南和辽宁分离到的病毒株之间存在明显差异,同源性在89.7%～94.1%之间.结论 在山西省分离到10株版纳病毒和两株辽宁病毒,版纳病毒与我国其他地区分离株有明显差异,在进化上相对独立.     

Molecular evolution of hepatitis A virus in a human diploid cell line

AIM: To investigate the hotspots, direction, and the time course of evolution of hepatitis A virus in the process of consecutive cell culture passage in human KMB17 diploid cells. METHODS: Wild type hepatitis A virus H2w was serially propagated in KMB17 cells until passage 30, and the full-length genomes of H2w and its six chosen progenies were determined by directly sequencing RT-PCR products amplified from viral genomic RNA. Alignment comparison of sequences from H2w with its six progenies and phylogenetic analysis of the whole VP1 region from H2w, progenies of H2w, and other cell culture adapted hepatitis A virus were then carried out to obtain data on the molecular evolution of hepatitis A virus in the process of consecutive passage in KMB17 cells. RESULTS: Most of the mutations occurred by passage 5 and several hotspots related to adaptation of the virus during cell growth were observed. After that stage, few additional mutations occurred through the remaining duration of passage in KMB17 cells except for mutation in the virulence determinants, which occurred in the vicinity of passage 15. The phylogenetic analysis of the whole VP1 region suggested that the progenies of H2w evolved closely to other cell culture adapted hepatitis A virus, i.e. MBB, L-A-1, other than its progenitor H2w. CONCLUSION: Hepatitis A virus served as a useful model for studying molecular evolution of viruses in a given environment. The information obtained in this study may provide assistance in cultivating the next generation of a seed virus for live hepatitis A vaccine production.     

Validation of a DNA-based method for identifying Chrysomyinae (Diptera: Calliphoridae) used in a death investigation

Many authors have proposed DNA-based methods for identifying an insect specimen associated with human remains. However, almost no attempt has been made to validate these methods using additional observations. We tested a protocol for identifying insects in the blow fly subfamily Chrysomyinae (Diptera: Calliphoridae) often found to be associated with a human corpse in Canada or the USA. This method uses phylogenetic analysis of DNA sequence from a short segment of the mitochondrial gene for cytochrome oxidase one (COI). Test chrysomyine COI sequences were obtained from 245 newly sequenced specimens and 51 specimens from the published literature. Published sequences from representatives of nonchrysomyine genera were also included to check for the possibility of a false positive identification. All of the chrysomyine test haplotypes were correctly identified with strong statistical support, and there were no false positives. This method appears to be an accurate and robust technique for identifying chrysomyine species from a death investigation in this geographic region. The far northern species Protophormia atriceps was not evaluated; therefore, caution is required in applying this method at very high latitudes in North America.