Engineering evolution to study speciation in yeasts

The Saccharomyces 'sensu stricto' yeasts are a group of species that will mate with one another, but interspecific pairings produce sterile hybrids. A retrospective analysis of their genomes revealed that translocations between the chromosomes of these species do not correlate with the group's sequence-based phylogeny (that is, translocations do not drive the process of speciation). However, that analysis was unable to infer what contribution such rearrangements make to reproductive isolation between these organisms. Here, we report experiments that take an interventionist, rather than a retrospective approach to studying speciation, by reconfiguring the Saccharomyces cerevisiae genome so that it is collinear with that of Saccharomyces mikatae. We demonstrate that this imposed genomic collinearity allows the generation of interspecific hybrids that produce a large proportion of spores that are viable, but extensively aneuploid. We obtained similar results in crosses between wild-type S. cerevisiae and the naturally collinear species Saccharomyces paradoxus, but not with non-collinear crosses. This controlled comparison of the effect of chromosomal translocation on species barriers suggests a mechanism for the generation of redundancy in the S. cerevisiae genome.     

Multiple intron gain and loss events occurred during the evolution of Cenp-A gene

Centromere protein A(CENP-A) is a histone H3 like protein,and it plays a very important role in chromosomal segregation during mitosis and meiosis.The analyses on the exon-intron organization of the Cenp-A gene in representative genomes revealed that multiple intron gain and loss events have occurred during the evolution of Cenp-A gene in opisthokonta(common ancestor of fungi and animals).Moreover,our results revealed that at least two positions were conserved in the intron gain and loss events during the evolution of the Cenp-A gene.     

Habitat-induced reciprocal transformation in the root phenotype of Oriental ginseng is associated with alteration in DNA methylation

Oriental ginseng is an important medicinal plant that grows in 2 major forms or ecotypes, wild and domesticated. Each form differs conspicuously in root phenotype, but can be converted from one type to another by habitat. Here we show that the habitat-induced transformation of ginseng root phenotype was accompanied by alteration in cytosine methylation at a large number of 5′-CCGG-3′ sites detected by the methylation-sensitive polymorphism (MSAP) marker. The collective CG and CHG methylation levels of all 4 landraces of the domesticated form were significantly lower than those of the wild form. Interestingly, artificially transplanted ginseng plants recreated in both directions the methylation levels (at least in CHG) of their natural counterparts. The methylation differences between the 2 ginseng ecotypes were validated at 2 isolated MSAP loci bearing homology to a 5S rRNA gene or a copia retrotransposon. Our results implicate a link between epigenetic variation and habitat-induced phenotypic flexibility in Oriental ginseng.     

Lack of association between intrachromosomal gene conversion and reciprocal exchange

The association of reciprocal exchange with intrachromosomal gene conversion has been examined using an inverted repeat at the HIS3 locus of Saccharomyces cerevisiae. Intrachromosomal gene conversions between the duplicated inverted sequences are frequent. In contrast to gene conversion events between homologous chromosomes, intrachromosomal gene conversion is not associated with reciprocal exchange in flanking sequences. This observation has important consequences for the role of gene conversion in the maintenance of multigene families.     

拟南芥基因倍增及基因流失分析

基因倍增指基因组中含有基因的DNA片段复制出一个或更多拷贝的过程,是进化出新物种的主要原因。采用新的数据和方法研究拟南芥基因组的基因倍增过程,通过分析串联基因倍增和大规模基因倍增的存在比例和同义置换率分布,并估计大规模倍增后基因流失的比例,揭示了拟南芥基因组一次非常明显的全基因组倍增,采用科学的方法估计这次倍增发生在约8000万年前。比较该结果与之前的研究,提出了一种解释拟南芥基因倍增过程更合理的模型。     

拟南芥基因倍增及基因流失分析

基因倍增指基因组中含有基因的DNA片段复制出一个或更多拷贝的过程，是进化出新物种的主要原因。采用新的数据和方法研究拟南芥基因组的基因倍增过程，通过分析串联基因倍增和大规模基因倍增的存在比例和同义置换率分布，并估计大规模倍增后基因流失的比例，揭示了拟南芥基因组一次非常明显的全基因组倍增，采用科学的方法估计这次倍增发生在约8000万年前。比较该结果与之前的研究，提出了一种解释拟南芥基因倍增过程更合理的模型。     

小麦中与低脱氧雪腐镰刀菌烯醇含量关联的抗性基因类似物

脱氧雪腐镰刀菌烯醇(Deoxynivalenol,DON)是小麦遭受赤霉病危害后由赤霉病菌———禾谷镰刀菌产生的一种真菌毒素,这种毒素对人类和家畜的健康产生危害,严重地影响小麦的利用价值.种植低DON含量的品种是减少这种毒素危害的有效措施,而分子标记辅助育种技术能加速低DON品种的选育进程.在采用AFLP、SSR分子标记的基础上,进一步利用抗性基因类似物(RGA)对‘宁7840’(低DON含量的品种)和‘Clark’(高DON含量的品种)建立的133个重组自交系进行了DON含量的遗传特性分析.研究结果发现两个DON含量的数量特性位点(QTL),它们中含有4个与低DON含量密切相关RGAs,其中三个RGAs(RGA14-1,RGA16-1,RGA18-1)座落在染色体1A的长臂上,另一个(RGA14-2)座落在染色体5B的长臂上.座落在1AL和5BL上的QTL分别解释16.81%和7.84%的DON含量变异.DNA序列分析表明这些RGAs均与现已发现的抗性基因同源/类似,它们可能在小麦的低DON含量和赤霉病抗性上扮演着重要的角色.     

基于递归预测方差倒数的元模型组合构建

元模型常用于替代计算代价高昂的工程模拟。常用的做法是基于一组数据来构建一系列的元模型,然后再在众多的元模型中选择出拟合精度最高的一个作为复杂的、高精度的模型的一个近似。但是,由于元模型的选择依赖于所获得的样本集,即不同的样本集可能选择到的是不同的元模型,这就增大了使用一个并不合适的模型的概率,而组合建模技术正是弥补这一不足的有效途径。此外,在复杂产品(或复杂系统)的设计当中,由于其具有单件小批量的特征,要获得大量的样本有时成本是高昂的甚至是难以实现的。因此,在不牺牲设计精度的前提下,通过组合建模的方法来减少采样的数量将是一个较为合理的选择。Zerpa等提出了基于预测方差倒数来确定组合权系数的组合建模方法。在其启发下,通过引入递归的思想,提出了递归预测方差倒数的组合建模方法。该方法以组合模型预测平方和达到理想的精度为停机准则,提出的递归思想比通过单次确定权系数来建模能达到更为理想的预测精度。算法通过5个测试函数和1个实际中的例子进行验证,并采用了均方根误差进行评判。结果表明,基于递归预测方差倒数的组合模型比单个的元模型在预测精度上有较大的改善,并且胜过基于现有的组合技术所得到的组合模型。     

秋水仙素诱导秋花独蒜兰多倍化的研究

以秋花独蒜兰(Pleione maculata Lindl.)拟原球茎为材料,研究不同浓度及时间条件下,对秋水仙素诱导秋花独蒜兰多倍化的诱变效果.实验结果表明:秋水仙素浓度为0.2%、处理时间为60 h时,诱导结果最佳,变异率为25.64%;细胞学鉴定表明,该方法诱导培育的植株具有多倍体表型特征,其体细胞染色体数多为2n=76～80条,而对照2n=38～40条.     

Cloning of a novel gene associated with human nasopharyngeal carcinoma

One EST N27741 with high expression in normal adult nasopharynx tissues but low expression in adult poorly differentiated squamous nasopharyngeal carcinoma has been selected out by the high-density cDNA array expression profiling technique. The differential expression has been confirmed by RT-PCR. One novel gene of 1096 bp has been cloned based on this EST. Bioinformatics analysis found that the new gene sequence contains a whole reading frame encoding 256 amino acids. There is a stop codon TAA in front of the 5′ end start codon, and a tailing signal AATAAA and poly A tail at the 3′ end. There is no homologous known gene found after searching by blasting this sequence to non-redundancy nucleotide database. Therefore it is considered a novel gene related to nasopharyngeal carcinoma.     

A stop-codon mutation in the BRI gene associated with familial British dementia

Familial British dementia (FBD), previously designated familial cerebral amyloid angiopathy-British type, is an autosomal dominant disorder of undetermined origin characterized by progressive dementia, spasticity, and cerebellar ataxia, with onset at around the fifth decade of life. Cerebral amyloid angiopathy, non-neuritic and perivascular plaques and neurofibrillary tangles are the predominant pathological lesions. Here we report the identification of a unique 4K protein subunit named ABri from isolated amyloid fibrils. This highly insoluble peptide is a fragment of a putative type-II single-spanning transmembrane precursor that is encoded by a novel gene, BRI, located on chromosome 13. A single base substitution at the stop codon of this gene generates a longer open reading frame, resulting in a larger, 277-residue precursor. Release of the 34 carboxy-terminal amino acids from the mutated precursor generates the ABri amyloid subunit. The mutation creates a cutting site for the restriction enzyme XbaI, which is useful for detecting asymptomatic carriers. Antibodies against the amyloid or homologous synthetic peptides recognize both parenchymal and vascular lesions in FBD patients. A point mutation at the stop codon of BRI therefore results in the generation of the ABri peptide, which is deposited as amyloid fibrils causing neuronal disfunction and dementia.     

Cx32 gene mutation associated with X-linked recessive Charcot-Marie-Tooth disease

The form of Charcot-Marie-Tooth (CMT) neuropathy that maps to Xql3 is X-linked dominant, or X-linked intermediate. Heterozygous females are more mildly affected than hemizygous males. It has been known that this type of CMT is caused by mutations of connexin32 (Cx32) gene. A typical X-linked recessive Charcot-Marie-Tooth Chinese family was analyzed with single strand conformation polymorphism method. A Cx32 gene point mutation, ArglSGln, in exon 2 was identified in all affected family members, suggesting that this mutation is responsible for the CMT incidence of this family.     

Comparative analysis and evolutionary significance of the HMG1 gene in crucian carp,blunt snout bream,and their polyploid progeny

The full-length mRNA of the high mobility group protein 1 coding gene (HMG1) was obtained by RACE-PCR from red crucian carp (Carassius auratus red var.),blunt snout bream (Megalobrama amblycephala),and their triploid and tetraploid progeny.The sequence contained an open reading frame of 579 nucleotides coding for 193 amino acids.The nucleotide identity of HMG1 was higher between the tetraploid hybrid and the maternal red crucian carp (99%) than between the tetraploid hybrid and the paternal blunt snout bream (97%).The nucleotide identity between the triploid hybrids and each parent (95%) was lower than that between the parents (98%).The protein identity between the tetraploid hybrid and each parent (100%) was higher than that between the triploid hybrid and each parent (97%).Our results suggest that interspecific hybridization generates a shock to the HMG1 gene in triploid hybrids,causing divergence of nucleotides.The HMG1 protein of the tetraploid hybrids was consistent with that of its parents,which reduced the barrier of cross incompatibility between alleles,providing the basis for the bisexual fertile tetraploid hybrids forming a new polyploid species in nature.The secondary and tertiary structures of the HMG1 protein contain eight helices,three switches,two DNA-binding domains in the N-terminus,and a long acidic tail in the C-terminus.Together,these data suggest that the HMG1 protein plays a role of protein-DNA interactions,facilitating various DNA-dependent activities in the nucleus.We also investigated the phylogeny of fish,amphibian,reptilian,bird,and mammalian HMG1 proteins.Our results suggest that HMG1 is an ancestral protein that has been highly conserved.These data provide clues as to how interspecific hybridization may form polyploid hybrids.     

籼粳杂种多倍体结实情况的初步研究

用10个籼粳交组合的二倍体和四倍体为试材，研究了加倍对每穗总粒数、每穗实数数和结实经的影响。结果表明：加倍对结实率等性能的影响因组合不同而不同，四倍体籼粳杂种的结实率显高于二倍体，加倍正反交的结实情况也有影响，要提高籼粳多倍体的结实经，应注重同时增加总数数的实数数。     

中风患者口腔念珠菌负荷的研究

目的:研究不同时期中风患者口腔念珠菌的负荷变化。方法:采用舌印记法和漱口水法收集43位中风患者在急性期、出院期及出院后半年的口腔微生物样本进行培养分析。结果:急性期中风患者口腔念珠菌负荷明显增高。急性期中风患者口腔念珠菌负荷明显高于出院及出院后半年中风患者口腔念珠菌负荷(P0.05)。伴随刷牙困难及佩带活动义齿的中风患者的口腔念珠菌负荷较高(P0.05)。结论:中风患者口腔念珠菌负荷与不同时期中风患者的身体功能的水平有密切的联系。     

Transposon-induced deletions in unc-22 of C. elegans associated with almost normal gene activity

The unc-22 gene of Caenorhabolitis elegans encodes a protein which is a component of the myosin-containing A-band of the worm's striated body-wall muscle. Among 51 revertants of a transposon-induced mutant, we have identified four which retain a barely detectable mutant phenotype. Molecular analysis shows that three of these have in-frame deletions of 1.0, 1.3 and 2.0 kilobases, whereas the fourth partial revertant and two other apparently complete revertants have small insertions. All these rearrangements involve coding sequence and, in the case of the deletions, result in polypeptides that are shorter than the wild-type protein. The region of the gene containing these rearrangements contains 10 copies of a motif recognized in other regions of the gene (our unpublished data). We suggest that one explanation for the minimally mutant phenotype associated with the deletions is that the size and the repeated nature of the unc-22 protein structure make it relatively tolerant of substitutions or deletions involving one or a small number of repeated motifs. These results could explain why in some human genetic diseases, such as Duchenne's muscular dystrophy, deletions can be associated with only mild forms of the disease.