The pattern of nucleotide difference at individual codons among mouse, rat, and human

The patterns of nucleotide difference were compared at 3,473,111 codons from 9,390 aligned orthologous genes of mouse (Mus musculus), rat (Rattus norvegicus), and human (Homo sapiens). The results showed evidence of a higher frequency of both synonymous and nonsynonymous differences from human in the rat than in the mouse. However, contrary to a previous report, there was no evidence of a greater frequency of codons with multiple nonsynonymous substitutions between the two rodent species than expected under random substitution.     

Genome scans of variation and adaptive change: extended analysis of a candidate locus close to the phantom gene region in Drosophila melanogaster

Nucleotide variation in populations originating from the recent range expansion of a species should reflect their adaptation to new habitats as well as their demographic history. A survey of nucleotide variation at 109 noncoding X-chromosome fragments in a European population of Drosophila melanogaster allowed identifying some candidates to have been recently affected by positive selection. Adaptive changes leave a spatial differential footprint that can be used to discriminate among candidates by extending their study to neighboring regions. Here, we surveyed variation at an approximately 190-kb region spanning a locus exhibiting a significantly skewed frequency spectrum. A stretch of approximately 12 kb with reduced variation was detected within a continuously sequenced region that included the focal fragment. Moreover, the regions flanking this stretch exhibited an excess of high-frequency derived variants. Application of maximum likelihood ratio and goodness-of-fit tests suggested that the pattern of variation detected at the studied region (at cytological bands 17C-17D) might have been shaped by a recent selective change, most probably at or around the phantom gene that encodes CYP306A1, a cytochrome P450 enzyme in the ecdysteroidogenic pathway.     

猪源支气管败血波氏杆菌百日咳杆菌黏附素基因的原核表达及其抗体检测ELISA方法

[目的]以猪源支气管败血波氏杆菌(Bordetella bronchiseptica,Bb)百日咳杆菌黏附素(PRN)基因的原核表达产物为抗原建立检测PRN抗体的间接ELISA方法。[方法和结果]利用谷胱甘肽-S-转移酶(GST)表达系统对PRN基因在大肠杆菌中进行融合表达。SDS-PAGE和Westernblot检测证实该基因获得高效表达,产物易于纯化且具有良好的免疫学活性。通过凝血酶酶切GST-PRN并回收,获得不含GST载体蛋白的PRN蛋白片段。以PRN蛋白片段为抗原建立检测天然PRN抗体的间接ELISA方法。该方法对猪巴氏杆菌病等7种常见细菌性疾病阳性血清的检测结果均为阴性,其敏感性比乳胶凝集试验提高4～128倍,能检测到人工感染14d后的仔猪血清抗体IgG,对临床送检的1,229份猪血清的检测阳性率为32.7%。ELISA方法对阳性猪场的监测结果预示了保育期仔猪的合群导致猪群大量感染支气管败血波氏杆菌。[结论]该方法具有特异性强、敏感性高、重复性好的特点,可用于猪群PRN抗体水平监测和猪波氏菌病流行病学调查。     

重组百日咳杆菌黏附素蛋白免疫小鼠可完全抵抗支气管败血波氏杆菌的致死性感染

【目的】通过建立的小鼠呼吸道感染模型评价重组百日咳杆菌黏附素蛋白(GST-PRN)对小鼠的免疫保护效力。【方法和结果】在主动免疫保护试验中,GST-PRN免疫组小鼠能产生较高的PRN抗体水平,在使用3×LD50的支气管败血波氏杆菌HH0809株进行呼吸道气雾攻毒后,其保护率为100%(20/20),但载体蛋白GST和PBS对照组小鼠的存活率仅为15%(3/20)和20%(4/20)。在被动免疫保护试验中,腹腔免疫GST-PRN兔抗血清能100%(10/10)保护小鼠抵抗10×LD50的HH0809株的腹腔攻击,但GST兔抗血清和PBS免疫组小鼠的存活率均为0(0/10和0/9)。【结论】研究结表明重组PRN蛋白具有良好的免疫学活性,可作为亚单位疫苗或疫苗添加成分。     

Haplotype structure and evidence for positive selection at the human IL13 locus

Interleukin-13 (IL13) is believed to play an important role in the pathogenesis of atopy and allergic asthma. To better understand genetic variation at the IL13 locus, we resequenced a 5.1-kb genomic region spanning the entire locus and identified 26 single-nucleotide polymorphisms (SNPs) in 74 individuals from three major populations-Chinese, Caucasian, and African. Our survey suggests exceptionally high and significant geographic structure at the IL13 locus between African and outside Africa populations. This unusual pattern suggests that positive selection that acts in some local populations may have played a role on the IL13 locus. In support of this suggestion, we found a significant excess of high frequency-derived SNPs in the Chinese population and Caucasian population, respectively, as expected after a recent episode of positive selection. Further, the unusual haplotype structure indicates that different scenarios of the action of positive selection on the IL13 locus in different populations may exist. In the Caucasian population, the skewed haplotype distribution dominated by one common haplotype supports the hypothesis of simple directional selection. Whereas, in the Chinese population, the two-round hitchhiking hypothesis may explain the skewed haplotype structure with three dominant ones. These findings may provide insight into the likely relative roles of selection and population history in establishing present-day variation at the IL13 locus, and, motivate further studies of this locus as an important candidate in common diseases association studies.     

百日咳杆菌粘附素对猪源支气管败血波氏杆菌的保护性抗原的筛选

摘要：【目的】本研究通过百日咳杆菌黏附素(PRN)基因的分段克隆表达及其在BALB/c小鼠的主动和被动免疫保护试验筛选PRN中的保护性抗原肽。【方法和结果】利用大肠杆菌进行PRN的完整蛋白、N端和C端多肽及其RI和RII区域多肽（双拷贝）的表达,命名为GST-PRN、GST-PN、GST-PC、GST-2PRI和GST-2PRII。Western blot检测证实5种表达产物均具有良好的反应原性。在主动免疫保护试验中,5种表达产物均能诱导小鼠产生较高的PRN抗体水平;当使用3 LD50的支气管败血波氏杆菌     

Evolutionary rate variation in anthocyanin pathway genes

Over a broad taxonomic range that spans monocots and dicots, upstream enzymes of the anthocyanin pigment pathway have evolved less rapidly than downstream enzymes. In this article we show that this pattern is also evident within the genus Ipomoea. Specifically, the most upstream enzyme, chalcone synthase (CHS-D), evolves more slowly than the two most downstream enzymes, ancyocyanidin synthase (ANS) and UDP glucose flavonoid 3-oxy-glucosyltransferase (UFGT). This pattern appears not to be due to variation in mutation rates, because the CHS-D gene exhibits higher synonymous substitution rates than the genes for the other two enzymes. Codon-based tests for positive selection suggest that it has been negligible or absent in all three genes. In addition, the mean number of indel-creating events is four times as high in the downstream genes as in CHS-D. Unlike the downstream genes, CHS-D also exhibits evidence of codon bias. Together, the evidence suggests that the difference in nonsynonymous substitution rates between upstream and downstream genes is due to relaxed constraint on the downstream genes rather than a greater frequency of positively selected substitutions.     

csd alleles in the red dwarf honey bee (Apis florea,Hymenoptera: Apidae) show exceptionally high nucleotide diversity

Abstract The single locus complementary sex determination (sl‐csd) gene is the primary gene determining the gender of honey bees (Apis spp.). While the csd gene has been well studied in the Western honey bee (Apis mellifera), and comparable data exist in both the Eastern honey bee (Apis cerana) and the giant honey bee (Apis dorsata), no studies have been conducted in the red dwarf honey bee, Apis florea. In this study we cloned the genomic region 3 of the A. florea csd gene from 60 workers, and identified 12 csd alleles. Analysis showed that similar to A. mellifera, region 3 of the csd gene contains a RS domain at the N terminal, a proline‐rich domain at the C terminal, and a hypervariable region in the middle. However, the A. florea csd gene possessed a much higher level of nucleotide diversity, compared to A. mellifera, A. cerana and Apis dorsata. We also show that similar to the other three Apis species, in A. florea, nonsynonymous mutations in the csd gene are selectively favored in young alleles.     

An Mhc class I allele associated to the expression of T-dependent immune response in the house sparrow

The major histocompatibility complex (Mhc) encodes for highly variable molecules, responsible for foreign antigen recognition and subsequent activation of immune responses in hosts. Mhc polymorphism should hence be related to pathogen resistance and immune activity, with individuals that carry either a higher diversity of Mhc alleles or one specific Mhc allele exhibiting a stronger immune response to a given antigen. Links between Mhc alleles and immune activity have never been explored in natural populations of vertebrates. To fill this gap, we challenged house sparrows (Passer domesticus) with two T-dependent antigens (phytohemagglutinin and sheep red blood cells) and examined both primary and secondary immune responses in relation to their Mhc class I genotypes. The total number of Mhc alleles had no influence on either primary or secondary response to the two antigens. One particular Mhc allele, however, was associated with an increased response to both antigens. Our results point toward a contribution of the Mhc, or of other genes in linkage disequilibrium with the Mhc, in the regulation of immune responses in a wild animal species.     

Variation in the pattern of synonymous and nonsynonymous difference between two fungal genomes

The proportion of synonymous nucleotide differences per synonymous site (p(S)) and the proportion of nonsynonymous differences per nonsynonymous site (p(N)) were computed at 1,993,217 individual codons in 4,133 protein-coding genes between the two yeast species Saccharomyces cerevisiae and Saccharomyces paradoxus. When the modified Nei-Gojobori method was used, significantly more codons with p(N) > p(S) were observed than expected, based on random pairing of observed p(S) and p(N) values. However, this finding was most likely explained by the presence of a strong negative correlation between the number of synonymous differences and the number of nonsynonymous differences at codons with at least one difference. As a result of this correlation, codons with p(N) > p(S) were characterized not only by unusually high p(N) but also by unusually low p(S). On the other hand, the number of codons with p(N)>p(S) (where p(S) is the mean p(S) for all codons) was very similar to the random expectation, and the observed number of 30-codon windows with p(N) > p(S) was significantly lower than the random expectation. These results imply that the occurrence of a certain number of codons or codon windows with p(N) > p(S) is expected given the nature of nucleotide substitution and need not imply the action of positive Darwinian selection.     

补体系统基因单核苷酸多态性及其与疾病的关系

天然免疫系统在病原微生物入侵的初始阶段发挥着重要的防御作用,其中补体系统可快速识别、杀伤和清除病原微生物,对疾病的发生、发展和转归起着重要的作用。文章综述了补体系统各成份单核苷酸多态性与疾病的关联研究进展,在DNA水平上揭示了补体系统遗传多态性对疾病发生、发展和转归的影响,对疾病的预防和个体化治疗具有重要的意义。     

hRFT2基因单核苷酸多态性的生物信息学分析

旨在筛选可能与人类疾病有关的hRFT2基因单核苷酸多态性(single nucleotide polymorphisms,nsSNPs)和突变位点,从SNP数据库中检索并筛选出395个有效的hRFT2基因SNPs,其中包括30个同义SNPs(synonymous SNPs,sSNPs)和31个非同义SNPs(non-synonymous single nucleotide polymorphisms,nsSNPs)。分别采用SIFT、SNPs3D和PolyPhen-2方法分析nsSNPs引起的氨基酸替换是否可能影响hRFT2的功能。结果表明,5个nsSNPs(rs11477762、rs146302587、rs146492942、rs76947760和rs145431028)可能严重影响hRFT2蛋白的功能,其中rs76947760和rs145431028的影响已得到临床证明,另外3个nsSNPs(rs148387972、rs140391358和rs3746802)也可能对hRFT2有较大的影响。     

An exceptionally high nucleotide and haplotype diversity and a signature of positive selection for the eIF4E resistance gene in barley are revealed by allele mining and phylogenetic analyses of natural populations

In barley, the eukaryotic translation initiation factor 4E (eIF4E) gene situated on chromosome 3H is recognized as an important source of resistance to the bymoviruses Barley yellow mosaic virus and Barley mild mosaic virus. In modern barley cultivars, two recessive eIF4E alleles, rym4 and rym5, confer different isolate-specific resistances. In this study, the sequence of eIF4E was analysed in 1090 barley landraces and noncurrent cultivars originating from 84 countries. An exceptionally high nucleotide diversity was evident in the coding sequence of eIF4E but not in either the adjacent MCT-1 gene or the sequence-related eIF(iso)4E gene situated on chromosome 1H. Surprisingly, all nucleotide polymorphisms detected in the coding sequence of eIF4E resulted in amino acid changes. A total of 47 eIF4E haplotypes were identified, and phylogenetic analysis using maximum likelihood provided evidence of strong positive selection acting on this barley gene. The majority of eIF4E haplotypes were found to be specific to distinct geographic regions. Furthermore, the eI4FE haplotype diversity (uh) was found to be considerably higher in East Asia, whereas SNP genotyping identified a comparatively low degree of genome-wide genetic diversity in 16 of 17 tested accessions (each carrying a different eIF4E haplotype) from this same region. In addition, selection statistic calculations using coalescent simulations showed evidence of non-neutral variation for eIF4E in several geographic regions, including East Asia, the region with a long history of the bymovirus-induced yellow mosaic disease. Together these findings suggest that eIF4E may play a role in barley adaptation to local habitats.