Novel Rhizobium lineages isolated from root nodules of the common bean (Phaseolus vulgaris L.) in Andean and Mesoamerican areas

The taxonomic affiliations of nineteen root-nodule bacteria isolated from the common bean (Phaseolus vulgaris L.) in Mexico, Ecuador and Brazil were investigated by analyses of 16S rRNA and of four protein-coding housekeeping genes. One strain from Mexico could be assigned to Rhizobium etli and two from Brazil to Rhizobium leucaenae, whereas another from Mexico corresponded to a recently described bean-nodulating species-level lineage related to R. etli and Rhizobium phaseoli. Ten strains isolated in Ecuador and Mexico corresponded to three novel Rhizobium lineages that fall into the R. phaseoli/R. etli/Rhizobium leguminosarum clade. One of those lineages, with representatives isolated mostly from Ecuador, seems to be dominant in beans from that Andean region. Only one of the Mexican strains clustered within the Rhizobium tropici clade, but as an independent lineage. Interestingly, four strains were affiliated with species within the Rhizobium radiobacter clade. The existence of yet non-described native Rhizobium lineages in both the Andean and Mesoamerican areas is discussed in relation to common-bean diversity and environmental conditions.     

2009年深圳地区肠道病毒71型毒株VP4基因进化分析

目的 对深圳地区手足口病(hand,foot and mouth disease,HFMD)肠道病毒71型分离株(enterovirus 71,EV71)的VP4基因遗传进化进行分析.方法 2009年采集深圳市儿童医院就诊的HFMD患者的粪便标本491份,选取其中8份经细胞培养鉴定为阳性的EV71毒株用RT-PCR扩增VP4基因,利用MEGA4.0软件进行遗传进化分析.结果 2009年深圳地区8株EV71 VP4基因全长207 bp,编码69个氨基酸;8株EV71 VP4基因核苷酸同源性为94.2％ ～98.1％,与深圳2001至2004年分离的17株EV71毒株核苷酸同源性在89.9％ ～98.1％,与GenBank中其他EV71病毒株VP4的核苷酸同源性为79.2％～100％;其中与亚洲流行株阜阳株(EU703812)核苷酸的同源性最高(100％),其次是C4代表株及2004年深圳株(AY895144)为94.2％ ～97.1％.除了印度株和其中1株EV71的VP4编码的氨基酸在第54位(ACA)不同之外,其余7株EV71 VP4编码的氨基酸序列之间以及与GenBank报道的其他序列同源性达100％.8株EV71 VP4基因核苷酸与C4代表株相比有17处不同,除1处以外其余全在简并密码位点上;轻重症病例毒株之间VP4基因序列未见明显改变.进化树显示8株EV71均属于C4基因亚型.结论 2009年深圳市流行的EV71属于C4基因亚型,流行的EV71 VP4基因非常保守,不属于变异区段,绝大部分核苷酸的变异属无义突变,VP4基因编码的氨基酸变异几乎为0.     

Influenza A and B in a cohort of outpatient children and adolescent with influenza like-illness during two consecutive influenza seasons

IntroductionInfluenza is an important cause of morbimortality worldwide. Although people at the extremes of age have a greater risk of complications, influenza has been more frequently investigated in the elderly than in children, and inpatients than outpatients. Yearly vaccination with trivalent or quadrivalent vaccines is the main strategy to control influenza.ObjectivesDetermine the clinical and molecular characteristics of influenza A and B infections in children and adolescents with influenza-like illness (ILI).MethodsA cohort of outpatient children and adolescents with ILI was followed for 20 months. Influenza was diagnosed with commercial multiplex PCR platforms.Results179 patients had 277 episodes of ILI, being 79 episodes of influenza A and 20 episodes of influenza B. Influenza A and B cases were mild and had similar presentation. Phylogenetic tree of influenza B viruses showed that 91.6% belonged to the B/Yamagata lineage, which is not included in trivalent vaccines.ConclusionsInfluenza A and B are often detected in children and adolescents with ILI episodes, with similar and mild presentation in outpatients. The mismatch between the circulating influenza viruses and the trivalent vaccine offered in Brazil may have contributed to the high frequency of influenza A and B in this population.     

Accessory extensor pollicis longus

Phylogenetically the accessory extensor pollicis longus in man seems to find its origin in the deep extensor layer, and this has largely been described in primates. I describe a case and present a comprehensive review of other publications on the subject.     

Forensic characteristics and phylogenetic analysis of both Y-STR and Y-SNP in the Li and Han ethnic groups from Hainan Island of China

Hainan Island is the southernmost and smallest Chinese province, isolated from the mainland. The Li and Han ethnic groups account for over 98% of the population on the island. However, the Li ethnic group is an indigenous community of Hainan Island, with great differences in culture, language and origin with respect to the Han, the largest ethnic group. Here, we studied these two ethnic groups from the perspective of the Y-chromosome single nucleotide polymorphisms (Y-SNPs) and short tandem repeats (Y-STRs) to unravel their forensic and phylogenetic characteristics. A total of 302 unrelated male samples from the Li and Han ethnic groups in Hainan Island were genotyped by a combination of three separate typing systems (next-generation sequencing and pyrosequencing for the Y-SNPs and capillary electrophoresis for the Y-STRs), a previously developed high-resolution panel containing 141 Y-SNPs and 27 Y-STRs. The haplotype diversity of the Li ethnic group reached 0.9997, and 49 terminal haplogroups were observed in the Li and Han ethnic groups. Haplogroup O1b1a1a1a1a1b-CTS5854 was the most predominant haplogroup, including 44.12% of Li individuals. Median-joining trees showed little gene flow between the Li and Han individuals, as well as between the Li and other ethnic groups in Hainan Island. Our results indicated that 1) in contrast with the Han ethnic group, a low degree of genetic diversity was observed in the Li ethnic group; 2) there was limited gene flow between the Li and Han ethnic groups; and 3) founder effect was identified in the Li ethnic group in Hainan Island.     

The polyvagal perspective

The polyvagal theory introduced a new perspective relating autonomic function to behavior, that included an appreciation of the autonomic nervous system as a "system," the identification of neural circuits involved in the regulation of autonomic state, and an interpretation of autonomic reactivity as adaptive within the context of the phylogeny of the vertebrate autonomic nervous system. The paper has two objectives: first, to provide an explicit statement of the theory; and second, to introduce the features of a polyvagal perspective. The polyvagal perspective emphasizes how an understanding of neurophysiological mechanisms and phylogenetic shifts in neural regulation leads to different questions, paradigms, explanations, and conclusions regarding autonomic function in biobehavioral processes than peripheral models. Foremost, the polyvagal perspective emphasizes the importance of phylogenetic changes in the neural structures regulating the autonomic nervous system and how these phylogenetic shifts provide insights into the adaptive function and the neural regulation of the two vagal systems.     

Genetic characterization of tick-borne flaviviruses: new insights into evolution, pathogenetic determinants and taxonomy

Here, we analyze the complete coding sequences of all recognized tick-borne flavivirus species, including Gadgets Gully, Royal Farm and Karshi virus, seabird-associated flaviviruses, Kadam virus and previously uncharacterized isolates of Kyasanur Forest disease virus and Omsk hemorrhagic fever virus. Significant taxonomic improvements are proposed, e.g. the identification of three major groups (mammalian, seabird and Kadam tick-borne flavivirus groups), the creation of a new species (Karshi virus) and the assignment of Tick-borne encephalitis and Louping ill viruses to a unique species (Tick-borne encephalitis virus) including four viral types (i.e. Western Tick-borne encephalitis virus, Eastern Tick-borne encephalitis virus, Turkish sheep Tick-borne encephalitis virus and Louping ill Tick-borne encephalitis virus). The analyses also suggest a complex relationship between viruses infecting birds and those infecting mammals. Ticks that feed on both categories of vertebrates may constitute the evolutionary bridge between the three distinct identified lineages.     

Multiple lines of evidence on the genetic relatedness of the parthenogenetic and bisexual Haemaphysalis longicornis (Acari: Ixodidae)

As an obligate hematophagous ectoparasite, the hard tick Haemaphysalis longicornis exhibits two reproductive strategies, bisexual reproduction, and obligate parthenogenesis, which have attracted a widespread attention. However, the speciation of parthenogenetic population remained ambiguous due to its similarity in morphology but the remarkable differences in cytogenetics as compared with those of the bisexual ones. In the present study, we explored several new lines of genetic evidence to resolve this controversial issue. The number of the chromosomes in two lineages was checked by classical methods and their total DNA levels were determined utilizing flowcytometry. In addition, the sequences of 12S rDNA, 16S rDNA, cytochrome c oxidase I and II (COI, COII) and internal transcribed spacer-2 (ITS-2) genes were used to assess their phylogenetic relationship. We observed that the chromosome ploidy of bisexual and parthenogenetic H. longicornis collected by our laboratory was diploid and triploid, respectively. Flowcytometry analysis indicated a ratio close to 2:3 in the DNA contents of bisexual to parthenogenetic H. longicornis. Although the chromosome ploidy is different, their gene sequences are extremely similar. Analogous to the intra-species genetic difference of other invertebrates, sequence differences of all loci examined are below 2%. Phylogenetic trees constructed from 12S rDNA, 16S rDNA, COI, and ITS-2 genes revealed that they were all in the same monophyletic clade instead of splitting independently into evolutional branches. Moreover, according to 4× Rule, the K/θ ratio of two reproductive populations calculated based on COI was much smaller than four, strongly supporting that they belong to the same species. Therefore, we conclude that the evolutionary process just disturbs the chromosome ploidy and the sexual determination of parthenogenetic population and that it would be better to consider parthenogenetic H. longicornis as a metapopulation rather than a cryptic species.     

Genome insights of mercury methylation among Desulfovibrio and Pseudodesulfovibrio strains

Mercury methylation converts inorganic mercury into the toxic methylmercury, and the consequences of this transformation are worrisome for human health and the environment. This process is performed by anaerobic microorganisms, such as several strains related to Pseudodesulfovibrio and Desulfovibrio genera. In order to provide new insights into the molecular mechanisms of mercury methylation, we performed a comparative genomic analysis on mercury methylators and non-methylators from (Pseudo)Desulfovibrio strains. Our results showed that (Pseudo)Desulfovibrio species are phylogenetically and metabolically distant and consequently, these genera should be divided into various genera. Strains able to perform methylation are affiliated with one branch of the phylogenetic tree, but, except for hgcA and hgcB genes, no other specific genetic markers were found among methylating strains. hgcA and hgcB genes can be found adjacent or separated, but proximity between those genes does not promote higher mercury methylation. In addition, close examination of the non-methylator Pseudodesulfovibrio piezophilus C1TLV30 strain, showed a syntenic structure that suggests a recombination event and may have led to hgcB depletion. The genomic analyses identify also arsR gene coding for a putative regulator upstream hgcA. Both genes are cotranscribed suggesting a role of ArsR in hgcA expression and probably a role in mercury methylation.