Evidence of selection pressures of neuraminidase gene (NA) of influenza A virus subtype H5N1 on different hosts in Guangxi Province of China

In the present study, the possible evidence of positive selection was analyzed for the neuraminidase (NA) sequences of Guangxi H5N1 strains of China. Based on an overall site-specific positive selection analysis, it was found that NA gene of H5N1 Guangxi strains underwent purifying selection and no significant positively selected sites were identified. For the branch-specific positive selection analysis, there was no positive selection evidence for the branches leading to different poultry hosts (chicken, duck and goose). Conclusively, positive selection seems not possible (if not rare) for the NA gene in influenza H5N1 subtype, at least for the samples found in Guangxi Province of China.     

Comparison of influenza outbreaks in the Republic of Kazakhstan and Russia induced by 2009 yearly new variant of A(H1N1) influenza virus

The aim of the work is the comparison of the epidemiology of influenza and acute respiratory virus infections(ARVI)in the Republic of Kazakhstan with the corresponding influenza epidemic in Russia induced by influenza pandemic virus A/California/07/2009 in 2009. Data on influenza and ARVI from the Republic of Kazakhstan and Federal Center of influenza was collected and investigated over the course of several weeks from hospitalized patients with the same diagnosis among all population and in age groups on 16 territories of Kazakhstan and in 49 major cities of Russia. The epidemic in Kazakhstan resembled the Russian epidemic in terms of its abnormally early beginning,expression of monoaetiology,the spread of the epidemic into all territories and start of the epidemics among adult population. High percentage of hospitalized people and lethal outcome were registered in this epidemic. Similarity of epidemic process character in corresponding border-line territories of both countries was found out.     

Synonymous codon usage pattern among the S,M, and L segments in Crimean-congo hemorrhagic fever virus

Crimean-Congo hemorrhagic fever (CCHF) virus is one among the major zoonosis viral diseases that use the Hyalomma ticks as their transmission vector to cause viral infection to the human and mammalian community. The fatality of infectious is high across the world especially in Africa, Asia, Middle East, and Europe. This study regarding codon usage bias of S, M, and L segments of the CCHF virus pertaining to the host Homo sapiens, reveals in-depth information about the evolutionary characteristics of CCHFV. Relative Synonymous Codon Usage (RSCU), Effective number of codons (ENC) were calculated, to determine the codon usage pattern in each segment. Correlation analysis between Codon adaptation index (CAI), GRAVY (Hydrophobicity), AROMO (Aromaticity), and nucleotide composition revealed bias in the codon usage pattern. There was no strong codon bias found among any segments of the CCHF virus, indicating both the factors i.e., natural selection and mutational pressure shapes the codon usage bias.     

Genomic signature analysis of the recently emerged highly pathogenic A(H5N8) avian influenza virus: implying an evolutionary trend for bird-to-human transmission

In early 2014, a novel subclade (2.3.4.4) of the highly pathogenic avian influenza (HPAI) A(H5N8) virus caused the first outbreak in domestic ducks and migratory birds in South Korea. Since then, it has spread to 44 countries and regions. To date, no human infections with A(H5N8) virus have been reported, but the possibility cannot be excluded. By analyzing the genomic signatures of A(H5N8) strains, we found that among the 47 species-associated signature positions, three positions exhibited human-like signatures (HLS), including PA-404S, PB2-613I and PB2-702R and that mutation trend of host signatures of avian A(H5N8) is different before and after 2014. About 82% of A(H5N8) isolates collected after January of 2014 carried the 3 HLS (PA-404S/PB2-613I/PB2-702R) in combination, while none of isolates collected before 2014 had this combination. Furthermore, the HA protein had S137A and S227R substitutions in the receptor-binding site and A160T in the glycosylation site, potentially increasing viral ability to bind human-type receptors. Based on these findings, the newly emerged HPAI A(H5N8) isolates show an evolutionary trend toward gaining more HLS and, along with it, the potential for bird-to-human transmissibility. Therefore, more extensive surveillance of this rapidly spreading HPAI A(H5N8) and preparedness against its potential pandemic are urgently needed.     

Characterizing sequence variation in the VP1 capsid proteins of foot and mouth disease virus (serotype 0) with respect to virion structure

The VP1 capsid protein of foot and mouth disease virus (FMDV) is highly polymorphic and contains several of the major immunogenic sites important to effective antibody neutralization and subsequent viral clearance by the immune system. Whether this high level of polymorphism is of adaptive value to the virus remains unknown. In this study we examined sequence data from a set of 55 isolates in order to establish the nature of selective pressures acting on this gene. Using the known molecular structure of VP1, the rates and ratios of different types of nonsynonymous and synonymous changes were compared between different parts of the protein. All parts of the protein are subject to purifying selection, but this is greatest amongst those amino acid residues within β-strands and is significantly reduced at residues exposed on the capsid surface, which include those residues demonstrated by previous mutational analyses to permit the virus to escape from monoclonal antibody binding. The ratios of nonsynonymous substitution resulting in various forms of physicochemically radical and conserved amino acid change were shown to be largely equal throughout these different parts of the protein. There was a consistently higher level of nonsynonymous and charge radical sites in those regions of the gene coding for residues exposed on the outer surface of the capsid and a marked difference in the use of amino acids between surface and nonsurface regions of the protein. However, the analysis is consistent with the hypothesis that the observed sequence variation arises where it is least likely to be disruptive to the higher-order structure of the protein and is not necessarily due to positive Darwinian selection. Received: 8 March 1997 / Accepted: 12 August 1997     

Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan

In order to understand the evolution of the 2009 influenza A (H1N1) pandemic within local regions of Japan, we studied the significance of regional migration between these regions. For this purpose, we have employed an extended SEIR model to describe the immigration of infected people and the stochastic variation of the infectious efficiency. We then applied a data assimilation technique in order to study how the agreement of the simulation results with the observed data depends on the presence/absence of immigration and the degree of variation of the infectious efficiency. Reproducibility is evaluated by log-likelihood values. The log-likelihood does not indicate the significance of immigration. Although there are multiple waves in the time course of the number of reported infected individuals, these waves could be explained by the stochastic nature of infectious events.     

Spatio-temporal variation of natural and sexual selection in breeding populations of the coreid bug,Colpula lativentris (Heteroptera: Coreidae)

Spatio-temporal variations of lifetime reproductive succes (LRS) of both male and female individuals of a coreid bugColpula lativentris were measured and analyzed using the multiple regression method of Arnold and Wade (1984a, b). The standardized variance of LRS was larger in males than that in females as males often to secure mates for a long period whereas females could easily find mates and oviposit simply dependent on ovarial maturation. LRS was partitioned into 4 consecutive fitness components: (1) reproductive lifespan, (2) copulating efficiency, (3) guarding efficiency (for males) or oviposition efficiency (for females), and (4) number of eggs per clutch. In males copulating efficiency was the largest determining factor of LRS, whereas in females reproductive lifespan was the most important factor. Such tendencies were stable on both a yearly and local basis. Patterns of relative contribution of natural selection (reproductive lifespan and number of eggs per clutch) and sexual selection (copulating efficiency and guarding or oviposition efficiency) to LRS were clearly different between males and females. This sexual difference is, at least to some extent, thought to be brought about by sexual selection among males for mating opportunity, though no physical fight was observed among males. Directional selection on body length was found only in relation to the clutch size of females because large females tended to lay larger clutches. No significant directional selection was found in other fitness components.     

Adaptation at specific loci. VII. Natural selection,dispersal and the diversity of molecular-functional variation patterns among butterfly species complexes (Colias: Lepidoptera,Pieridae)

Natural genetic variants at the phosphoglucose isomerase, PGI, gene differ in spatial patterning of their polymorphism among species complexes of Colias butterflies in North America. In both lowland and alpine complexes, molecular-functional properties of the polymorphic genotypes can be used to predict genotype-specific adult flight performances and resulting large genotypic differences in adult fitness components. In the lowland species complex, there is striking uniformity of PGI polymorph frequencies at a number of sites across the American West; this fits with earlier findings of strong, similar differences in fitness components over this range. In an alpine complex, Colias meadii shows similar uniformity of PGI frequencies within habitat types, either montane steppe or alpine tundra, over several hundred kilometres in the absence of dispersal. At the same time, large shifts (10-20%) in frequency of the most common alleles occur between steppe and tundra populations, whether these are isolated or, as in some cases, are in contact and exchange many dispersing adults each generation. Data on male mating success of common C. meadii PGI genotypes in steppe and tundra show heterozygote advantage in both habitat types, with shifts in relative homozygote disadvantage between habitats which are consistent with observed frequency differences. Nonadaptive explanations for this situation are rejected, and alternative, thermal-ecology-based adaptive hypotheses are proposed for later experimental test. These findings show that strong local selection may dominate dispersal as an evolutionary agent, whether or not dispersal is present, and that selection may often be the major force promoting 'cohesion' of species over long distances. This case offers new opportunities for integrating studies of molecular structure and function with ecological aspects of natural selection in the wild, both within and among species.     

Protein profiling of nasopharyngeal aspirates of hospitalized and outpatients revealed cytokines associated with severe influenza A(H1N1)pdm09 virus infections: A pilot study

Influenza A viruses (IAV) mutate rapidly and cause seasonal epidemics and occasional pandemics, which result in substantial number of patient visits to the doctors and even hospitalizations. We aimed here to identify inflammatory proteins, which levels correlated to clinical severity of the disease. For this we analysed 102 cytokines and growth factors in human nasopharyngeal aspirate (NPA) samples of 27 hospitalized and 27 outpatients diagnosed with influenza A(H1N1)pdm09 virus infection. We found that the relative levels of monocyte differentiation antigen CD14, lipocalin-2 (LCN2), C-C-motif chemokine 20 (CCL20), CD147, urokinase plasminogen activator surface receptor (uPAR), pro-epidermal growth factor (EGF), trefoil factor 3 (TFF3), and macrophage migration inhibitory factor (MIF) were significantly lower (p < 0.008), whereas levels of retinol-binding protein 4 (RBP4), C-X-C motif chemokine 5 (CXCL5), interleukin-8 (IL-8), complement factor D (CFD), adiponectin, and chitinase-3-like 1 (CHI3L1) were significantly higher (p < 0.008) in NPA samples of hospitalized than non-hospitalized patients. While changes in CD14, LCN2, CCL20, uPAR, EGF, MIF, CXCL5, IL-8, adiponectin and CHI3L1 levels have already been correlated with severity of IAV infection in mice and humans, our study is the first to describe association of CD147, RBP4, TFF3, and CFD with hospitalization of IAV-infected patients. Thus, we identified local innate immune profiles, which were associated with the clinical severity of influenza infections.     

It's all relative: allometry and variation in the baculum (os penis) of the harp seal, Pagophilus groenlandicus (Carnivora: Phocidae)

We compared allometry and variation in the baculum (os penis), mandible, and humerus of the harp seal, Pagophilus groenlandicus. This species is presumed to have a promiscuous mating system in which choice of mate by females during intromission with different males is likely. The baculum is large and grows throughout life so may be an honest indicator of males' quality (size) or viability (age). We predicted that bacular size would exhibit stronger allometry relative to body size than mandibles or humeri. The baculum is less functionally (mechanically) constrained than mandibles or humeri so we also predicted it would be more variable, though less variable than sexually selected traits which do not function as honest indicators. Our sample (N=67 seals) represented broad ranges of size and age (0–35 yr) so we compared variation using residuals from allometric regressions of skeletal measurements on body length. Bacular size was isometric to body length until ∼ 137 cm (when some seals enter puberty) in body length then was highly positively allometric; mandibular and humeral size were negatively allometric to body length throughout growth. Bacula were more variable than mandibles or humeri. Bacular size in large specimens (>137 cm in body length) was related strongly to body length and weakly to age. We interpret bacular size to be an uncheatable honest indicator of male quality and viability. High bacular variation conforms with theoretical predictions of females' asymmetrical choice of mate and choice of extremes, and may reflect corresponding anatomical variation among females. Some bacular variation may also result incidentally from positive allometry coupled with lifelong bacular growth, which can amplify early differences between reproductive and somatic growth, enabled by weak selection on bacular form in relation to function.     

Minisatellite DNA profiling detects lineages and parentage in the endangered kakapo (Strigops habroptilus) despite low microsatellite DNA variation

An important goal of the conservationmanagement program of the critically endangeredground parrot, the New Zealand kakapo (Strigops habroptilus) is the determination ofparentage and levels of genetic diversitywithin the remaining population. Our previousmicrosatellite DNA studies have shown that allindividuals of this species except one arehomozygous at seven loci examined. Incontrast, we now show that a minisatellite DNAanalysis of kakapo provides sufficientvariation to conduct paternity analyses anddetect heterogeneity within the 86 livingkakapo. The sole remaining Fiordland kakapo,Richard Henry, is shown to be geneticallydivergent from individuals originating from theonly other remaining population on StewartIsland, suggesting that two lineages of kakapoare present in the extant population. This hasparticular significance for the conservationmanagement goal of maintenance of the maximumgenetic diversity in the species as a whole. The example of the kakapo illustrates thatminisatellite DNA markers can be useful incases where microsatellite DNA fails to showsufficient variation.     

温州地区人群对甲型H1N1流感认知情况及其疫苗不良反应的调查

目的了解温州地区居民对甲型H1N1流感(以下简称甲流)的认知情况及其疫苗的不良反应,分析相关调查数据为医务人员加强疾病防控提供依据。方法采用自行设计问卷,随机抽取2010年3月-4月温州地区居民888人为调查对象,对其进行问卷调查。结果温州地区人群对甲流及其疫苗的认知程度平均得分为15.69分,处于中低水平,各年龄段、各职业人群在认知度上差异存在统计学意义(P<0.05),走访的113名70岁以上的老人在甲型H1N1信息上欠缺认识。调查对象中50.5%人群对甲流疫苗的安全性持质疑观望态度。调查对象中共115人已接种疫苗,13人出现不良反应,占11.3%。结论甲流疫苗具有较高的安全性,但温州地区人群对甲型H1N1流感相关知识了解欠缺,而且群众的信任度不高,因此仍应加大宣传力度,尤其加强对老年人的预防宣教。JP     

Different positively selected sites at the gametophytic self-incompatibility pistil S-RNase gene in the Solanaceae and Rosaceae (Prunus, Pyrus, and Malus)

In this work we perform a comparative study on the location of positively selected sites (those likely responsible for defining specificity differences) at the S-RNase gene, the pistil component of the gametophytic self-incompatibility system. For Plantaginaceae and Rosaceae (Prunus and Pyrus/Malus) this is the first study of this kind. A clear sign of positive selection was observed for 13, 17, and 27 amino acid sites in Solanaceae, Prunus, and Pyrus/Malus, respectively, using two different methodologies. In Plantaginaceae no clear positively selected sites were identified. Possible reasons for this result are discussed. Indirect experimental evidence suggests that the identified positively selected amino acid sites play a role in specificity determination. The percentage of positively selected sites is similar in Solanaceae and Rosaceae but the location of those sites is different. Electronic supplementary material The online version of this article (doi: ) contains supplementary material, which is available to authorized users. Reviewing Editor: Dr. Martin Kreitman     

H5N1亚型禽流感病毒血凝素基因的原核表达及间接ELISA方法的初步建立

根据GenBank公布的H5N1亚型禽流感病毒(AIV)血凝素(HA)基因序列设计引物,用PCR方法扩增H5N1亚型禽流感病毒HA1基因, 将该片段定向插入到原核表达载体pET_32a(+)中,构建原核表达载体pET_HA1。阳性质粒转化宿主菌BL21(DE3), 经IPTG诱导, HA1基因获得表达, 重组蛋白以包涵体的形式存在。通过改变IPTG的浓度和诱导时间 , 确定了表达HA1基因的最佳诱导条件: IPTG终浓度为0.8mmol/L,诱导时间为3h。Western blot分析表明表达产物具有良好的免疫学活性。以纯化的表达产物作为诊断抗原建立了检测H5亚型AIV抗体的iHA_ELISA方法。结果表明,抗原的最佳包被浓度为4μg/mL,血清的最佳稀释度为1∶200, 阳性标准初步定为：OD待检血清＞05,且 OD待检血清/OD阴性血清＞2。     

Exploring rate variation among and within sites in a densely sampled tree: species level phylogenetics of north american tiger beetles (genus cicindela)

Species-level phylogenetic studies require fast-evolving nucleotide positions to resolve relationships among close relatives, but these sites may be highly homoplastic and perhaps uninformative or even misleading deeper in the tree. Here we describe a species-level analysis of tiger beetles in the genus Cicindela (Coleoptera: Cicindelidae) for 132 terminal taxa and 1897 nucleotide positions from three regions of mtDNA, comprising 75% coverage of species occurring in North America. Evenly weighted parsimony analysis recovered four major clades representing radiations confined to North and Central America. Relationships near the tips were well supported but signal was contradictory at deeper nodes. Two major categories (3rd positions and all others) can be distinguished in likelihood analysis of character variation, of which only the fast-changing 3rd position characters were affected by saturation. However, their downweighting under a variety of criteria did not improve the tree topology at basal nodes. There was weak conflict between 3rd and non-3rd position characters deep in the tree, but support levels declined towards the root for all categories, even on trees that were reconstructed from 3rd and non-3rd positions separately. Statistical analysis of parsimony-based character transitions along branches showed a largely homogeneous distribution of change along the root-to-tip axis. The comparison of character transitions among the four major portions of the tree revealed deviations from stochastic distribution for the non-3rd positions, but not for 3rd positions. Hence, variability of functionally constrained non-3rd positions differs between clades and may be dependent on the character states at other sites, consistent with the covarion model of molecular evolution. The results suggest that some properties of 3rd positions are less problematic for phylogenetic reconstruction than other categories despite their high total homoplasy. In densely sampled data sets of closely related species, the disadvantages of weighting schemes according to homoplasy levels outweigh the benefits, showing the difficulty of devising meaningful weighting schemes that are applicable universally throughout the tree.     

Clinal variation in body size and sexual dimorphism in an Indian fruit bat, Cynopterus sphinx (Chiroptera: Pteropodidae)

Geographic variation in body size and sexual dimorphism of the short‐nosed fruit bat (Cynopterus sphinx) was investigated in peninsular India. Bats were sampled at 12 localities along a 1200 km latitudinal transect that paralleled the eastern flanks of the Western Ghats. The geographic pattern of variation in external morphology of C. sphinx conforms to the predictions of Bergmann's Rule, as indicated by a steep, monotonic cline of increasing body size from south to north. This study represents one of the first conclusively documented examples of Bergmann's Rule in a tropical mammal and confirms that latitudinal clines in body size are not exclusively restricted to temperate zone homeotherms. Body size was indexed by a multivariate axis derived from principal components analysis of linear measurements that summarize body and wing dimensions. Additionally, length of forearm was used as a univariate index of structural size to examine geographic variation in a more inclusive sample of bats across the latitudinal transect. Multivariate and univariate size metrics were strongly and positively correlated with body mass, and exhibited highly concordant patterns of clinal variation. Stepwise multiple regression on climatological variables revealed that increasing size of male and female C. sphinx was associated with decreasing minimum temperature, increasing relative humidity, and increasing seasonality. Although patterns of geographic size variation were highly concordant between the sexes, C. sphinx also exhibited a latitudinal cline in the magnitude and direction of sexual size dimorphism. The size differential reversed direction across the latitudinal gradient, as males averaged larger in the north, and females averaged larger in the south. The degree of female‐biased size dimorphism across the transect was negatively correlated with body size of both sexes. Canonical discriminant analysis revealed that male‐ and female‐biased size dimorphism were based on contrasting sets of external characters. Available data on geographic variation in the degree of polygyny in C. sphinx suggests that sexual selection on male size may play a role in determining the geographic pattern of sexual size dimorphism.     

Crucial role of the influenza virus NS2 (NEP) C-terminal domain in M1 binding and nuclear export of vRNP

The influenza virus genome replicates in the host cell nucleus, and the progeny viral ribonucleoproteins (vRNPs) are exported to the cytoplasm prior to maturation. The influenza virus NS2 protein has a nuclear export signal (NES) and binds to M1. It is therefore postulated that vRNP is exported from the nucleus by binding to NS2 through M1. However, the significance of the association between NS2 and M1 for the nuclear export of vRNP is still poorly understood. We herein demonstrate that the C-terminal domain of NS2 (residues 81–100) is essential for M1 binding and the nuclear export of progeny vRNPs.

Structured summary

MINT-8057301, MINT-8057317: NS2 (uniprotkb:P03508) binds (MI:0407) to M1 (uniprotkb:P03485) by pull down (MI:0096)     

Variation patterns of bilateral characters: variation among characters and among populations in the White Sea herring, Clupea pallasi marisalbi (Berg) (Clupeidae, Teleosti)

Phenotypic variation in two populations of the White Sea herring Clupea pallasi marisalbi (Berg) (spring spawners and summer spawners), based on 21 meristic and 21 morphometric bilateral characters, has been studied. Total phenotypic variance was partitioned into a within-individual or stochastic component (fluctuating asymmetry) and an among-individual or factorial component, reflecting heterogeneity among individuals and resulting from the diversity of genotypes and environments. Both standardized stochastic and factorial components show clear negative correlations with means across characters. Negative correlation of the factorial components with means is in contradiction to the commonly accepted explanation of negative means-standardized variances association. Slopes of regression of standardized stochastic variances on means in meristic characters was significantly higher in summer spawners than in spring spawners, and results in discordance of stochastic variance across characters: it is higher in spring spawners for low and average variability characters and does not differ for both populations for high variability characters. The populations do not show notable differences in variation of morphometric characters. Consideration of other available data on these populations, such as spawning behaviour and salinity resistance of larvae, suggests that the lower slope of regression of stochastic variances on means is associated with the reduced viability of spring spawners     

Female guppies agree to differ: phenotypic and genetic variation in mate-choice behavior and the consequences for sexual selection

Variation among females in mate choice may influence evolution by sexual selection. The genetic basis of this variation is of interest because the elaboration of mating preferences requires additive genetic variation in these traits. Here we measure the repeatability and heritability of two components of female choosiness (responsiveness and discrimination) and of female preference functions for the multiple ornaments borne by male guppies (Poecilia reticulata). We show that there is significant repeatable variation in both components of choosiness and in some preference functions but not in others. There appear to be several male ornaments that females find uniformly attractive and others for which females differ in preference. One consequence is that there is no universally attractive male phenotype. Only responsiveness shows significant additive genetic variation. Variation in responsiveness appears to mask variation in discrimination and some preference functions and may be the most biologically relevant source of phenotypic and genetic variation in mate-choice behavior. To test the potential evolutionary importance of the phenotypic variation in mate choice that we report, we estimated the opportunity for and the intensity of sexual selection under models of mate choice that excluded and that incorporated individual female variation. We then compared these estimates with estimates based on measured mating success. Incorporating individual variation in mate choice generally did not predict the outcome of sexual selection any better than models that ignored such variation.