Evolutionary Dynamics of Variant Genomes of Human Papillomavirus Types 18, 45, and 97

Human papillomavirus type 18 (HPV18) and HPV45 account for approximately 20% of all cervix cancers. We show that HPV18, HPV45, and the recently discovered HPV97 comprise a clade sharing a most recent common ancestor within HPV α7 species. Variant lineages of these HPV types were classified by sequence analysis of the upstream regulatory region/E6 region among cervical samples from a population-based study in Costa Rica, and 27 representative genomes from each major variant lineage were sequenced. Nucleotide variation within HPV18 and HPV45 was 3.82% and 2.39%, respectively, and amino acid variation was 4.73% and 2.87%, respectively. Only 18 nucleotide variations, of which 10 were nonsynonymous, were identified among three HPV97 genomes. Full-genome comparisons revealed maximal diversity between HPV18 African and non-African variants (2.6% dissimilarity), whereas HPV18 Asian-American [E1 (AA)] and European (E2) variants were closely related (less than 0.5% dissimilarity); HPV45 genomes had a maximal difference of 1.6% nucleotides. Using a Bayesian Markov chain Monte Carlo (MCMC) method, the divergence times of HPV18, -45, and -97 from their most recent common ancestors indicated that HPV18 diverged approximately 7.7 million years (Myr) ago, whereas HPV45 and HPV97 split off around 5.7 Myr ago, in a period encompassing the divergence of the great ape species. Variants within the HPV18/45/97 lineages were estimated to have diverged from their common ancestors in the genus Homo within the last 1 Myr (<0.7 Myr). To investigate the molecular basis of HPV18, HPV45, and HPV97 evolution, regression models of codon substitution were used to identify lineages and amino acid sites under selective pressure. The E5 open reading frame (ORF) of HPV18 and the E4 ORFs of HPV18, HPV45, and HPV18/45/97 had nonsynonymous/synonymous substitution rate ratios (d_N/d_S) over 1 indicative of positive Darwinian selection. The L1 ORF of HPV18 genomes had an increased proportion of nonsynonymous substitutions (4.93%; average d_N/d_S ratio [M3] = 0.3356) compared to HPV45 (1.86%; M3 = 0.1268) and HPV16 (2.26%; M3 = 0.1330) L1 ORFs. In contrast, HPV18 and HPV16 genomes had similar amino acid substitution rates within the E1 ORF (2.89% and 3.24%, respectively), while HPV45 E1 was highly conserved (amino acid substitution rate was 0.77%). These data provide an evolutionary history of this medically important clade of HPVs and identify an unexpected divergence of the L1 gene of HPV18 that may have clinical implications for the long-term use of an L1-virus-like particle-based prophylactic vaccine.Papillomaviruses (PVs) are a large family of related viruses with circular double-stranded DNA genomes 8 kb in size. Some PV types cause epithelial hyperplasias ranging from benign exophytic warts to premalignant lesions that can progress to invasive cancer. Among the 61 currently designated alpha human PVs (HPVs), the majority have been isolated from the mucosal surface of the genital or oral region (8, 14). Of these, a select group have oncogenic potential and are associated with cervical cancer (11). Specifically, HPV type 16 (HPV16) and HPV18 have been identified in approximately two-thirds of cervical cancers, this tumor is the second most common cancer in women, and it is the principal cancer of women in developing countries (5, 24, 25, 30, 37).To date, studies of HPV18 variants have identified three lineages corresponding to the continental locations where the viral samples were obtained: European (E), Asian-American (AA), and African (Af) (29). The phylogeny of HPV18 variants is reflective of the migration patterns of Homo sapiens and suggests that HPV18 variant lineages might have diverged through genetic isolation at approximately the same time as Homo sapiens began establishing residence in different continental regions. Previous HPV18 intratypic phylogenetic analyses were limited to partial regions of the genome (3, 7, 29). Nevertheless, studies also suggest that HPV18 variants are associated with different levels of oncogenic potential and persistence and histological tumor types (1, 6, 35, 36, 46).HPV45 and HPV97 are the viral types most closely related to HPV18 and taken together form a clade and share a most recent common ancestor (MRCA). HPV97 is a recently described rare type (8, 17). HPV18 and HPV45 account for approximately 20% of all cervix cancers (25). Although HPV45 is a common type found in cervical cancer, its evolutionary history and sequence variability have not been extensively studied.In this report, 27 complete genomes representing the major variant lineages of HPV18, HPV45, and HPV97 were cloned and/or sequenced from clinical samples. Based on full genomes, the intratype/intertype evolutionary trees of HPV18, HPV45, and HPV97 were constructed. By examining the rate ratio of nonsynonymous (d_N) to synonymous (d_S) substitutions per site, diversifying selection acting on each of the eight protein-encoding regions of HPV18, HPV45, and HPV97 was evaluated. In addition, the times of divergence of HPV18/45/97 variants from their MRCA were investigated. These data provide an evolutionary history of this medically important clade of HPVs.     

人肠道病毒71型基因重组的研究进展

人肠道病毒71 型(Enterovirus 71,HEV-A71),是手足口病(Hand,footandmouthdisease,HFMD)的常见病因,属于人肠道病毒属中的肠道病毒A型,隶属于微小RNA病毒科.许多研究证明HEV-A71经常发生基因重组并且使得HEV-A71在全球内多次暴发,这对疫苗的研发和疾病的防控是一种新的挑战.本文对HEV-A71不同亚型内、不同型间和多重重组等不同基因重组类型及其毒力、抗原性变化进行了综述.     

Genetic and Evolutionary Correlates of Fine-Scale Recombination Rate Variation in Drosophila persimilis

Recombination is fundamental to meiosis in many species and generates variation on which natural selection can act, yet fine-scale linkage maps are cumbersome to construct. We generated a fine-scale map of recombination rates across two major chromosomes in Drosophila persimilis using 181 SNP markers spanning two of five major chromosome arms. Using this map, we report significant fine-scale heterogeneity of local recombination rates. However, we also observed “recombinational neighborhoods,” where adjacent intervals had similar recombination rates after excluding regions near the centromere and telomere. We further found significant positive associations of fine-scale recombination rate with repetitive element abundance and a 13-bp sequence motif known to associate with human recombination rates. We noted strong crossover interference extending 5–7 Mb from the initial crossover event. Further, we observed that fine-scale recombination rates in D. persimilis are strongly correlated with those obtained from a comparable study of its sister species, D. pseudoobscura. We documented a significant relationship between recombination rates and intron nucleotide sequence diversity within species, but no relationship between recombination rate and intron divergence between species. These results are consistent with selection models (hitchhiking and background selection) rather than mutagenic recombination models for explaining the relationship of recombination with nucleotide diversity within species. Finally, we found significant correlations between recombination rate and GC content, supporting both GC-biased gene conversion (BGC) models and selection-driven codon bias models. Overall, this genome-enabled map of fine-scale recombination rates allowed us to confirm findings of broader-scale studies and identify multiple novel features that merit further investigation.     

一起传染病暴发中肠道病毒血清型鉴定和ECHO30基因特征分析

2003年5～9月,山东省泰安市发生了由肠道病毒(Enterovirus,EV)感染所致的传染病暴发,临床症状以手足口病(HFMD)为主,同时有心肌炎和无菌性脑膜炎等中枢神经系统症状患者也占较大比例。131份病人(粪便、咽拭子、脑脊液)标本中共分离到EV62株,其中ECHO1939株,EV716株,ECHO304株,其它肠道病毒13株。4株ECHO30病毒中的2株分离自2个患者的粪便标本,但用WHO肠道组合血清中和试验未能定出型别。另外2株分离自同一患者的粪便和脑脊液标本。病原学分析表明,ECHO30是引起该患者无菌性脑膜炎的病原。抗E—CHO30标准株的血清中和这4株病毒的滴度低于标准株5～20倍。VP1区全基因序列测定和同源性比较分析表明,4株ECHO30分离株病毒核苷酸同源性在98．0％～98．5％,氨基酸同源性在98．9％～99．3％,提示这4株病毒来源于同一传播链,2003年5～9月ECHO30在该地区可能有局部流行。系统进化树分析表明,ECHO30病毒可以划分为6个基因型,其中基因型1～5为GenBank中已发表的ECHO30分离株,山东分离株与其它5个基因型成员核苷酸差异分别在9．4％～24．4％,在进化树上形成了较独立的分支,是一个新基因型,将其划分为第6基因型。     

Evolutionary Genetics of Human Enterovirus 71: Origin,Population Dynamics,Natural Selection,and Seasonal Periodicity of the VP1 Gene

Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.Enterovirus 71 (EV-71) is a member of the genus Enterovirus in the family Picornaviridae. Classified as human enterovirus species A (HEV-A) along with some group A coxsackieviruses (CV-A), EV-71 is a small, nonenveloped, positive-stranded RNA virus with a genome approximately 7,400 bases long and is genetically most related to CV-A16. EV-71 is divided into three major genogroups (denoted A, B, and C), and various subgenogroups within genogroups B and C.Since its first isolation in the United States in 1969 (71), EV-71 has been identified worldwide as a common cause of hand, foot, and mouth disease (HFMD) in young children and infants. Large EV-71-associated HFMD outbreaks have been reported in the United States, Europe, Australia, and Asia and constitute a significant and emerging threat to global public health (9, 50, 62, 63). Although EV-71 infection manifests most frequently as a mild, self-limited febrile illness characterized by papulovesicular lesions on the hands, feet, oropharyngeal mucosa, and buttocks, a small proportion of acute infections are associated with fatal neurological symptoms, including brain stem encephalitis, aseptic meningitis, and poliomyelitis-like paralysis (4, 28, 47). Such cases of neurological disease with a high case fatality rate were first reported in Bulgaria in 1975 (21) and Hungary in 1978 (52). However, large HFMD epidemics with high mortality rates resurfaced 2 decades later, in Malaysia in 1997 (2, 13, 16, 43) and Taiwan in 1998 (33, 42). Following these outbreaks, the Asia-Pacific region has experienced more frequent large-scale EV-71-associated HFMD epidemics—most with a high incidence of neurotropic infections and significant case fatality rates—and the virus has attracted global attention (3, 5, 14, 15, 18, 37, 46, 48, 55, 57, 74, 81, 82). Intriguingly, almost all outbreaks reported in the Asia-Pacific region during the last decade were caused by previously undefined EV-71 subgenogroups, raising questions about their origin, genetic complexity, and epidemiological behavior.The icosahedral particles of EV-71, which are structurally similar to those of other members of the Picornaviridae, consist of structural proteins (capsid proteins VP1 to VP4) assembled as pentameric subunits (66). The VP1 protein is highly exposed and usually targeted by host neutralizing antibodies, predisposing the VP1 gene to constant immune selective pressure. This selection may drive the adaptive evolution of the capsid region of many enteroviruses, possibly resulting in amino acid fixations in virus populations (19, 45, 79). Because the VP1 gene of enteroviruses is thought to play an important role in viral pathogenesis and virulence (10, 12, 30), understanding the tempo and mode of evolution of the capsid protein can provide new insights into the epidemiological dynamics of EV-71 that may be useful in predicting the genetic basis and periodicity of future EV-71 epidemics and in facilitating the development of an effective EV-71 vaccine candidate.In this study, we investigated the evolutionary dynamics and genetic history of EV-71. We estimate the dates of emergence of various subgenogroups identified in recent HFMD outbreaks. Using recently developed Bayesian methods of evolutionary analysis, we estimate the divergence time of EV-71 from its closely related ancestor CV-A16, thereby providing a date of origin for EV-71. We also reconstruct the global population dynamics of EV-71 over the past 40 years, revealing temporal trends in genetic diversity within and between major epidemics. Finally, despite finding little evidence of positive selection in the VP1 capsid protein, we observed a pattern of continuous strain and lineage replacement through time, with strong selective pressure detected at several potentially immunogenic sites. The impact of EV-71 evolution on the development of an EV-71 vaccine is also discussed.     

The Population and Evolutionary Dynamics of Homologous Gene Recombination in Bacteria

In bacteria, recombination is a rare event, not a part of the reproductive process. Nevertheless, recombination—broadly defined to include the acquisition of genes from external sources, i.e., horizontal gene transfer (HGT)—plays a central role as a source of variation for adaptive evolution in many species of bacteria. Much of niche expansion, resistance to antibiotics and other environmental stresses, virulence, and other characteristics that make bacteria interesting and problematic, is achieved through the expression of genes and genetic elements obtained from other populations of bacteria of the same and different species, as well as from eukaryotes and archaea. While recombination of homologous genes among members of the same species has played a central role in the development of the genetics and molecular biology of bacteria, the contribution of homologous gene recombination (HGR) to bacterial evolution is not at all clear. Also, not so clear are the selective pressures responsible for the evolution and maintenance of transformation, the only bacteria-encoded form of HGR. Using a semi-stochastic simulation of mutation, recombination, and selection within bacterial populations and competition between populations, we explore (1) the contribution of HGR to the rate of adaptive evolution in these populations and (2) the conditions under which HGR will provide a bacterial population a selective advantage over non-recombining or more slowly recombining populations. The results of our simulation indicate that, under broad conditions: (1) HGR occurring at rates in the range anticipated for bacteria like Streptococcus pneumoniae, Escherichia coli, Haemophilus influenzae, and Bacillus subtilis will accelerate the rate at which a population adapts to environmental conditions; (2) once established in a population, selection for this capacity to increase rates of adaptive evolution can maintain bacteria-encoded mechanisms of recombination and prevent invasion of non-recombining populations, even when recombination engenders a modest fitness cost; and (3) because of the density- and frequency-dependent nature of HGR in bacteria, this capacity to increase rates of adaptive evolution is not sufficient as a selective force to provide a recombining population a selective advantage when it is rare. Under realistic conditions, homologous gene recombination will increase the rate of adaptive evolution in bacterial populations and, once established, selection for higher rates of evolution will promote the maintenance of bacteria-encoded mechanisms for HGR. On the other hand, increasing rates of adaptive evolution by HGR is unlikely to be the sole or even a dominant selective pressure responsible for the original evolution of transformation.     

Complete Genome Sequence Analysis of Human Echovirus Type 30 Isolated in China

We report here the complete genome sequence of a human echovirus type 30 strain ECV30/GX10/05 isolated in Guangxi, China, in 2010. Phylogenetic analysis showed that ECV30/GX10/05 was closely related to a Korean strain isolated in 2008. The sequence information will help in an understanding of the molecular epidemiology and evolution of echovirus.     

Recombination in the Evolution of Enterovirus C Species Sub-Group that Contains Types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99

Genetic recombination is considered to be a very frequent phenomenon among enteroviruses (Family Picornaviridae, Genus Enterovirus). However, the recombination patterns may differ between enterovirus species and between types within species. Enterovirus C (EV-C) species contains 21 types. In the capsid coding P1 region, the types of EV-C species cluster further into three sub-groups (designated here as A–C). In this study, the recombination pattern of EV-C species sub-group B that contains types CVA-21, CVA-24, EV-C95, EV-C96 and EV-C99 was determined using partial 5′UTR and VP1 sequences of enterovirus strains isolated during poliovirus surveillance and previously published complete genome sequences. Several inter-typic recombination events were detected. Furthermore, the analyses suggested that inter-typic recombination events have occurred mainly within the distinct sub-groups of EV-C species. Only sporadic recombination events between EV-C species sub-group B and other EV-C sub-groups were detected. In addition, strict recombination barriers were inferred for CVA-21 genotype C and CVA-24 variant strains. These results suggest that the frequency of inter-typic recombinations, even within species, may depend on the phylogenetic position of the given viruses.     

Antigenic Variation in Group A Streptococci: Types 11 and 9

A strain of group A Streptococcus which was virulent but M-nontypable was isolated from patients in a hospital nursery during an epidemic. This strain, Boston 11, reacted in T-agglutination tests with antisera for types 9 and 11, an unusual combination. A comparison of this strain with Lancefield's M-11 strain (NCDC SS-721) and Alabama 11 (Provisional 61) revealed three serologically related but distinct strains. Antiserum produced with the Boston 11 strain exhibited similar reactivity with all three "11" strains as well as with M-9 (SS-501) as demonstrated in precipitin tests. Immunodiffusion studies indicated that the Boston 11 antigen was partially identical with the M-11 and M-9 strains and shared at least one antigen with the Alabama 11 strain. The Boston 11 antiserum could be made specific for precipitin tests, but bactericidal activity for the Alabama 11, M-11, and Boston 11 strains was essentially negative.     

Evolutionary History of the 11p15 Human Mucin Gene Family

The four human mucin genes MUC6, MUC2, MUC5AC, and MUC5B are located at chromosome 11p15.5. It has been demonstrated that the three mucins MUC2, MUC5AC, and MUC5B contain several Cys-subdomains of 108 amino acid residues. In contrast, little information is available concerning MUC6. These Cys-subdomains contain 10 cysteine residues that have a highly conserved position. We present here a coherent probable evolutionary history of this human gene family after comparison of the nucleotide sequences of these Cys-subdomains. The three MUC loci MUC2, MUC5AC, and MUC5B may have evolved from a common ancestral gene by two successive duplications. Moreover, we can postulate that MUC5AC and MUC5B have evolved in a concerted manner, while MUC2 has evolved separately. Received: 30 January 1997 / Accepted: 17 April 1997     

Epidemics and Frequent Recombination within Species in Outbreaks of Human Enterovirus B-Associated Hand,Foot and Mouth Disease in Shandong China in 2010 and 2011

The epidemiology and molecular characteristics of human enterovirus B (HEV-B) associated with hand, foot and mouth disease (HFMD) outbreaks in China are not well known. In the present study, we tested 201 HEV isolates from 233 clinical specimens from patients with severe HFMD during 2010–2011 in Linyi, Shandong, China. Of the 201 isolates, 189 were fully typed and 18 corresponded to HEV-B species (six serotypes CVA9, CVB1, CVB4, Echo 6, Echo 25 and Echo 30) using sensitive semi-nested polymerase chain reaction analysis of VP1 gene sequences. Phylogenetic analysis based on the VP1 region showed that eight E30SD belonged to a novel sub-genogroup D2; E25SD belonged to a novel sub-genogroup D6; E6SD belonged to sub-lineage C6 and five CVB1SD belonged to subgroup 4C; and B4SD belonged sub-lineage D2. The full viral genomes of the CVB1SD, E6SD, E25SD and E30SD isolates were sequenced. Analysis of phylogenetic and similarity plots indicated that E25SD recombined with E25-HN-2, E30FDJS03 and E4AUS250 at noncontiguous P2A–P3D regions, while E30SD, E30FDJ03, E25-HN-2 and E9 DM had shared sequences in discrete regions of P2 and P3. Both E6SD and B1SD shared sequences with E1-HN, B4/GX/10, B5-HN, and A9-Alberta in contiguous regions of most of P2 and P3. Genetic algorithm recombination detection analysis further confirmed the existence of multiple potential recombination points. In conclusion, analysis of the complete genomes of E25SD, E30SD, CVB1SD and E6SD isolated from HFMD patients revealed that they formed novel subgenogroup. Given the prevalence and recombination of these viruses in outbreaks of HFMD, persistent surveillance of HFMD-associated HEV-B pathogens is required to predict potential emerging viruses and related disease outbreaks.     

Paleontological Patterns, Macroecological Dynamics and the Evolutionary Process

Here we consider evolutionary patterns writ large in the fossil record. We argue that Darwin recognized but downgraded or de-emphasized several of these important patterns, and we consider what a renewed emphasis on these patterns can tell us about the evolutionary process. In particular, one of the key patterns we focus on is the role geographic isolation plays in fomenting evolutionary divergence; another one of the key patterns is stasis of species; the final pattern is turnovers, which exist at several hierarchical scales, including regional ecosystem replacement and pulses of speciation and extinction. We consider how each one of these patterns are related to the dynamic of changing ecological and environmental conditions over time and also investigate their significance in light of other concepts including punctuated equilibria and hierarchy theory. Ultimately, we tie each of these patterns into a framework involving macroecological dynamics and the important role environmental change plays in shaping evolution from the micro- to macroscale.     

PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination

Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes. PRDM9, a zinc finger protein with histone methyltransferase activity, initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks (DSB). The DSB repair mechanism suggests that hotspots should eventually self-destruct, yet genome-wide recombination levels remain constant, a conundrum known as the hotspot paradox. To test if PRDM9 drives this evolutionary erosion, we measured activity of the Prdm9 ^Cst allele in two Mus musculus subspecies, M.m. castaneus, in which Prdm9^Cst arose, and M.m. domesticus, into which Prdm9^Cst was introduced experimentally. Comparing these two strains, we find that haplotype differences at hotspots lead to qualitative and quantitative changes in PRDM9 binding and activity. Using Mus spretus as an outlier, we found most variants affecting PRDM9^Cst binding arose and were fixed in M.m. castaneus, suppressing hotspot activity. Furthermore, M.m. castaneus×M.m. domesticus F1 hybrids exhibit novel hotspots, with large haplotype biases in both PRDM9 binding and chromatin modification. These novel hotspots represent sites of historic evolutionary erosion that become activated in hybrids due to crosstalk between one parent''s Prdm9 allele and the opposite parent''s chromosome. Together these data support a model where haplotype-specific PRDM9 binding directs biased gene conversion at hotspots, ultimately leading to hotspot erosion.     

Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems

Homologous recombination is a housekeeping process involved in the maintenance of chromosome integrity and generation of genetic variability. Although detailed biochemical studies have described the mechanism of action of its components in model organisms, there is no recent extensive assessment of this knowledge, using comparative genomics and taking advantage of available experimental data on recombination. Using comparative genomics, we assessed the diversity of recombination processes among bacteria, and simulations suggest that we missed very few homologs. The work included the identification of orthologs and the analysis of their evolutionary history and genomic context. Some genes, for proteins such as RecA, the resolvases, and RecR, were found to be nearly ubiquitous, suggesting that the large majority of bacterial genomes are capable of homologous recombination. Yet many genomes show incomplete sets of presynaptic systems, with RecFOR being more frequent than RecBCD/AddAB. There is a significant pattern of co-occurrence between these systems and antirecombinant proteins such as the ones of mismatch repair and SbcB, but no significant association with nonhomologous end joining, which seems rare in bacteria. Surprisingly, a large number of genomes in which homologous recombination has been reported lack many of the enzymes involved in the presynaptic systems. The lack of obvious correlation between the presence of characterized presynaptic genes and experimental data on the frequency of recombination suggests the existence of still-unknown presynaptic mechanisms in bacteria. It also indicates that, at the moment, the assessment of the intrinsic stability or recombination isolation of bacteria in most cases cannot be inferred from the identification of known recombination proteins in the genomes.     

Cloning, genomic sequence, and chromosome mapping of Scyb11, the murine homologue of SCYB11 (alias betaR1/H174/SCYB9B/I-TAC/IP-9/CXCL11)

A T-cell attracting CXC chemokine phylogenetically related to MIG and SCYB10 was recently characterized and termed SCYB11 (alias betaR1/H174/SCYB9B/I-TAC/IP-9/CXCL11). Here, we cloned the cDNA of the murine homologue of this protein, Scyb11, from interferon-gamma/lipopolysaccharide-stimulated RAW264.7 mouse macrophage-like cells. The nucleotide sequence of Scyb11 shares 63% identity with its human counterpart. It encodes a 100 amino acid immature protein of 11,265 Da which contains a putative signal peptide of 21 amino acids. The molecular mass of the mature protein was calculated to be 9,113 Da. Sequence identity of the murine and human SCYB11 proteins is 68%. Phylogenetic tree analysis of mouse CXC chemokines places SCYB11 together with the murine homologues of MIG and SCYB10 (Crg-2/muIP-10) on an individual branch. A genomic sequence was obtained by genome walking and subcloning DNA fragments from a BAC clone containing Scyb11. Like human SCYB11, Scyb11 contains 4 exons with intron/exon boundaries at positions comparable to the human gene. Whereas introns 2 and 3 are of similar length in the murine and human genes, intron 1 of Scyb11 contains 1,260 bp more than intron 1 of the human gene. Intron 1 of Scyb11 is also characterized by a 201-bp stretch with repetitive sequences of high cryptic simplicity. Using a BAC clone containing Scyb11, this gene could be mapped to chromosome 5 at position 5E3. Since human SCYB11 is localized on 4q21.2, this result confirms the mouse/human homology of the two chromosome regions.     

Geographical,Temporal and Environmental Determinants of Bryophyte Species Richness in the Macaronesian Islands

Species richness on oceanic islands has been related to a series of ecological factors including island size and isolation (i.e. the Equilibrium Model of Island Biogeography, EMIB), habitat diversity, climate (i.e., temperature and precipitation) and more recently island ontogeny (i.e. the General Dynamic Model of oceanic island biogeography, GDM). Here we evaluate the relationship of these factors with the diversity of bryophytes in the Macaronesian region (Azores, Madeira, Canary Islands and Cape Verde). The predictive power of EMIB, habitat diversity, climate and the GDM on total bryophyte richness, as well as moss and liverwort richness (the two dominant bryophyte groups), was evaluated through ordinary least squares regressions. After choosing the best subset of variables using inference statistics, we used partial regression analyses to identify the independent and shared effects of each model. The variables included within each model were similar for mosses and liverworts, with orographic mist layer being one of the most important predictors of richness. Models combining climate with either the GDM or habitat diversity explained most of richness variation (up to 91%). There was a high portion of shared variance between all pairwise combinations of factors in mosses, while in liverworts around half of the variability in species richness was accounted for exclusively by climate. Our results suggest that the effects of climate and habitat are strong and prevalent in this region, while geographical factors have limited influence on Macaronesian bryophyte diversity. Although climate is of great importance for liverwort richness, in mosses its effect is similar to or, at least, indiscernible from the effect of habitat diversity and, strikingly, the effect of island ontogeny. These results indicate that for highly vagile taxa on oceanic islands, the dispersal process may be less important for successful colonization than the availability of suitable ecological conditions during the establishment phase.     

Recombination Dynamics of a Human Y-Chromosomal Palindrome: Rapid GC-Biased Gene Conversion,Multi-kilobase Conversion Tracts,and Rare Inversions

The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9–8.4×10⁻⁴ events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages.     

Evolutionary Dynamics of Human Toll-Like Receptors and Their Different Contributions to Host Defense

Infectious diseases have been paramount among the threats to health and survival throughout human evolutionary history. Natural selection is therefore expected to act strongly on host defense genes, particularly on innate immunity genes whose products mediate the direct interaction between the host and the microbial environment. In insects and mammals, the Toll-like receptors (TLRs) appear to play a major role in initiating innate immune responses against microbes. In humans, however, it has been speculated that the set of TLRs could be redundant for protective immunity. We investigated how natural selection has acted upon human TLRs, as an approach to assess their level of biological redundancy. We sequenced the ten human TLRs in a panel of 158 individuals from various populations worldwide and found that the intracellular TLRs—activated by nucleic acids and particularly specialized in viral recognition—have evolved under strong purifying selection, indicating their essential non-redundant role in host survival. Conversely, the selective constraints on the TLRs expressed on the cell surface—activated by compounds other than nucleic acids—have been much more relaxed, with higher rates of damaging nonsynonymous and stop mutations tolerated, suggesting their higher redundancy. Finally, we tested whether TLRs have experienced spatially-varying selection in human populations and found that the region encompassing TLR10-TLR1-TLR6 has been the target of recent positive selection among non-Africans. Our findings indicate that the different TLRs differ in their immunological redundancy, reflecting their distinct contributions to host defense. The insights gained in this study foster new hypotheses to be tested in clinical and epidemiological genetics of infectious disease.     

Importance of Illegitimate Recombination and Transposition in IS30-Associated Excision Events

In the present study we report on the excision of IS30 elements and IS30-derived composite transposons. Frequent loss of IS30 was observed during dissolution of dimeric IS30 structures, containing IR–IR junctions, leading to resealed donor molecules. In contrast, unambiguous transpositional excision resulting in resealed remainder products could not be identified in the case of a monomeric element. The bias in the excision of monomeric and dimeric IS30 structures indicates a difference in the molecular mechanism of transposition of IS30 monomers and dimers. Sequence data on the rarely detected plasmids missing full IS or Tn copies rather suggest that all products were derived from illegitimate recombination. The reaction occurred between short homologies and was independent of the transposase activity. Similar IS30 excision events accompanied by multiple plasmid or genome rearrangements were detected in Pseudomonas putida and Rhizobium meliloti, yielding stable replicons that retained the selective marker gene of the transposon. We provide evidence that both transposition and illegitimate recombination can contribute to the stabilization of replicons through the elimination of IS elements, which emphasizes the evolutionary significance of these events.     

Detection of Autoantibodies to Annexin A11 in Different Types of Human Cancer

Introduction  Annexin A11 was previously identified as an autoantigen in 4.1–10.1% of patients with various systemic autoimmune diseases. In this study, an enzyme-linked immunosorbent assay (ELISA) was developed to investigate the occurrence and features of anti-annexin A11 autoantibodies in sera from patients with different types of cancer. Methods  The recombinant protein of GST fused to the N-terminal domain (1–175 residues) of human annexin A11 was expressed and used as antigen in ELISA. A total of 246 serum specimens were analyzed, which includes sera from healthy women (77), patients with ovarian cancer (72), breast cancer (18), colon cancer (19), pancreatic cancer (20), prostate cancer (20), and diabetes (20). Results  The overall titer of anti-annexin A11 autoantibodies in ovarian cancer patients (or primary tumors only) was found much higher than that in healthy controls (P < 0.05). At the cut-off value designating positive reaction, anti-annexin A11 autoantibodies were detected in 12.5% (5/40) of primary ovarian cancer patients with a significant difference from 2.6% (2/77) of the healthy controls (P < 0.05), but only in 6.25% (2/32) of recurrent tumors. ROC curve demonstrated the potential diagnostic value of anti-annexin A11 autoantibodies in primary ovarian cancer patients with an AUC of 0.62 (0.52–0.73). Anti-annexin A11 autoantibodies were also detected in 5.26% (1/19) of colon cancer and 10% (2/20) of diabetes patients but without significant difference from the healthy controls. Conclusion  A convenient assay to detect anti-annexin A11 autoantibodies in patients was developed, and the experimental data are promising but need to be expanded to address their biological/clinical relevance.