芦芽山华北落叶松林不同龄级立木的点格局分析

华北落叶松林是芦芽山自然保护区的重要林型。对其建群种华北落叶松不同龄级个体的分布格局及其相互关系进行了研究。植物种群在群落中的分布格局与空间尺度有着密切关系,这里采用能够分析各种尺度下格局的分析方法——点格局分析法,其是以种群个体空间分布的坐标点图为基础。结果表明,芦芽山华北落叶松不同龄级密度差异较大,高龄级密度较大;目前华北落叶松是稳定型种群,但从长远看．,仍需人工协助更新;华北落叶松5个龄级集群分布特征比较明显,且随着龄级的增加,集群特征有更明显的趋势;各个龄级个体之间在各种尺度下都有比较显著的正关联,3～5龄级个体关联更为显著;点格局分析法能够分析各种尺度下的种群格局和种间关系,所描述的结果更符合实际,尤其是对群落结构的描述。     

蛇足石杉COBRA基因家族的分子生物信息学及表达分析

为探明蛇足石杉COBRA基因家族成员分子生物信息学特征及组织表达规律,该文基于蛇足石杉的全长转录组数据,通过生物信息学技术对该家族成员(HsCOBRAs)的理化性质、结构域、保守基序、顺式作用元件、基因表达量等进行分析。结果表明:(1)在蛇足石杉全长转录组中共筛选出24个HsCOBRAs家族成员,其中酸性蛋白9个,稳定蛋白11个,疏水性蛋白5个,具有跨膜结构的蛋白7个,具有信号肽的蛋白3个。(2)亚细胞定位在细胞壁、叶绿体、细胞核、细胞膜上。(3)结构分析发现HsCOBRAs有7种结构域和6种保守基序,部分成员具有高度保守的CCVS结构。(4)HsCOBRAs具有CAAT-box、TATA-box等45种顺式作用元件。(5)HsCOBRA2在叶、孢子、茎、芽胞中的表达量均最高。该研究结果可为HsCOBRAs的进一步研究及生物学功能验证等提供理论依据。     

市售畜禽肉产CTX-M酶大肠杆菌的流行病学调查

【目的】调查市售畜禽肉类中大肠杆菌的耐药状况和bla_CTX-M基因的流行病学特征。【方法】采集广州市不同区域零售市场和超市畜禽肉类样品进行大肠杆菌的分离,通过基因phoA扩增和测序进行大肠杆菌鉴定,采用琼脂扩散法和微量肉汤稀释法测定药物敏感性,通过PCR扩增检测bla_CTX-M基因,对bla_CTX-M阳性大肠杆菌进行全基因组测序。【结果】从323份市售畜禽肉样品中分离获得大肠杆菌241株;药物敏感性结果表明大肠杆菌对氨苄西林(63.07%)、多西环素(47.72%)和复方新诺明(43.15%)耐药率较高;bla_CTX-M基因检出率为3.32%(n=8),其中4株携带bla_CTX-M-14,3株携带bla_CTX-M-65,1株携带bla_CTX-M-55;8株产CTX-M大肠杆菌可分为4种不同的ST型,且携带多种耐药基因和毒力基因。【结论】市售畜禽肉中大肠杆菌污染严重。产CTX-M酶大肠杆菌均为多重耐药菌株,且bla_CTX-M<...     

重庆大巴山国家级自然保护区森林植物多样性垂直格局

以重庆大巴山国家级自然保护区西南方向沿海拔梯度选择的20个样地为研究对象,通过等级聚类分析,结合物种重要值、物种丰富度、区系分化强度和α、β多样性指数等方面的分析,以揭示其森林植物多样性沿海拔梯度的分布特征。结果表明:(1)在20个样方中,共记录到维管植物97科226属335种;随着海拔上升,各样地植物科、属、种总数大体上呈先增加后降低的趋势。(2)植物群落在垂直梯度上差异显著;综合群落生长型和等级聚类分析结果,将群落沿海拔梯度划分为4个类型:海拔1 000m以下为常绿阔叶林和偏暖性针阔混交林,1 000~1 600m为常绿落叶阔叶混交林,1 600~2 100m为偏暖湿性针阔混交林,海拔2 100m以上为暗针叶林。(3)α多样性指数具有垂直变化规律;Simpson优势度和Pielou均匀度随海拔变化较小,乔木层Shannon-Wiener指数随海拔升高有明显降低的趋势,混交林类型的物种多样性和区系分化强度较高。(4)β多样性指数在低海拔区段起伏较大;随着海拔升高,乔木层Cody指数的变化格局总体上呈逐渐降低的趋势,相邻群落间物种异质性逐渐减小,物种的替代速率下降,最终达到相对稳定的状态。     

Functional divergence after gene duplication and sequence-structure relationship: a case study of G-protein alpha subunits

In this article, we use animal G-protein alpha subunit family as an example to illustrate a comprehensive analytical pipeline for detecting different types of functional divergence of protein families, which is phylogeny-dependent, combined with ancestral sequence inference and available protein structure information. In particular, we focus on (i) Type-I functional divergence, or site-specific rate shift, as typically exemplified by amino acid residue highly conserved in a subset of homologous genes but highly variable in a different subset of homologous genes, and (ii) Type-II functional divergence, or the shift of cluster-specific amino acid property, as exemplified by a radical shift of amino acid property between duplicate genes, which is otherwise evolutionally conserved. We utilized the software DIVERGE2 to carry out these analyses. In the case of G-protein alpha subunit gene family, we have predicted amino acid residues that are related to either Type-I or Type-II functional divergence. The inferred ancestral sequences for these sites are helpful to explore the trends of functional divergence. Finally, these predicted residues are mapped to the protein structures to test whether these residues may have 3D structure or solvent accessibility preference.     

Ultrafast catalytic processes in enzymes

The study of biocatalysis and biotransformation in the transition-state region has been challenging and difficult, but recent advances on two important photoenzymes in nature, DNA photolyase and protochlorophyllide oxidoreductase, have enabled the investigation of their catalytic processes in real time. By following the entire evolution of substrate transformation, the functional dynamics constituting a series of elementary reactions have been mapped out. The five fundamental reactions in the enzymes, namely electron transfer, bond breaking and making, proton and hydride transfer, all occur ultrafast within subnanosecond. The direct clocking of catalytic transition states probes central, unmasked chemical processes and provides mechanistic insights into the role of the dynamics in enzyme function, which not only facilitates the formation of the enzyme-substrate complex in the transition-state configurations, but also modulates the subsequent catalytic reactions for maximum biotransformation efficiency.     

Circulating and liver resident CD4+CD25+ regulatory T cells actively influence the antiviral immune response and disease progression in patients with hepatitis B

CD4+CD25+ regulatory T cells (Treg) have been shown to maintain immune tolerance against self and foreign Ags, but their role in persistent viral infection has not been well-defined. In this study, we investigated whether and where CD4+CD25+ Treg contribute to the development of chronic hepatitis B (CHB). One hundred twenty-one patients were enrolled, including 16 patients with acute hepatitis B, 76 with CHB, and 29 with chronic severe hepatitis B. We demonstrated that in chronic severe hepatitis B patients, the frequencies of CD4+CD25+ Treg in both PBMC and liver-infiltrating lymphocytes were significantly increased and there was a dramatic increase of FoxP3(+)-cell and inflammatory cell infiltration in the liver compared with healthy controls. In CHB patients, circulating CD4+CD25+ Treg frequency significantly correlates with serum viral load. In acute hepatitis B patients, circulating CD4+CD25+ Treg frequency was initially low and with time, the profile reversed to exhibit an increased number of circulating Treg in the convalescent phase and restored to normal levels upon resolution. In PBMC taken from infected patients, depletion of CD4+CD25+ Treg led to an increase of IFN-gamma production by HBV-Ag-stimulated PBMC. In addition, CD4+CD25+ Treg were capable of suppressing proliferation of autologous PBMC mediated by HBV Ags, which probably reflects the generation of HBV-Ag-specific Treg in circulation and in the liver of HBV-infected patients. Together, our findings suggest that CD4+CD25+ Treg play an active role not only in modulating effectors of immune response to HBV infection, but also in influencing the disease prognosis in patients with hepatitis B.     

大鼠CXCR4基因RNAi慢病毒载体的构建及其在骨髓间质干细胞中的表达

为深入研究CXCR4在骨髓间质干细胞(MSCs)体内迁移中的作用, 构建CXCR4基因RNA干扰(RNAi)慢病毒载体并实现其在大鼠MSCs (rMSCs)中表达。根据大鼠CXCR4 mRNA序列, 设计并合成包含各靶序列的互补DNA链,插入pSUPER载体的H1 RNA启动子后面, 产生pRiCXCR4, 将其中的CXCR4 shRNA表达结构酶切插入慢病毒载体质粒pNL-EGFP, 产生pNL-RiCXCR4-EGFP。在脂质体介导下与包装质粒pHELPER和包膜质粒pVSVG共转染293T细胞, 包装生产慢病毒,测定慢病毒功能滴度。慢病毒转导rMSCs后, 用Real-time RT-PCR、Western blotting和流式细胞术检测RNAi组(CXCR4a、CXCR4b和CXCR4c)、空载体组(Mock)和对照组(Control)中CXCR4表达情况。结果显示, 酶切和测序证实pRiCXCR4质粒构建正确, 产生能同时表达增强型绿色荧光蛋白(EGFP)和CXCR4 shRNA的慢病毒载体质粒pNL-RiCXCR4-EGFP, 未浓缩和浓缩慢病毒悬液的功能滴度分别为6.4×104TU/mL和6.9×106TU/mL。慢病毒转导rMSCs 48 h后, 与空载体组和空白组相比, 3个RNAi组均不同程度抑制CXCR4表达, CXCR4b-MSC组在mRNA水平抑制了95.6%, 抑制作用最明显。大鼠CXCR4基因RNAi慢病毒载体构建成功, 为深入研究CXCR4在rMSCs向损伤组织定向迁移的作用奠定了基础。     

Y-Chromosome Evidence for Common Ancestry of Three Chinese Populations with a High Risk of Esophageal Cancer

High rates of esophageal cancer (EC) are found in people of the Henan Taihang Mountain, Fujian Minnan, and Chaoshan regions of China. Historical records describe great waves of populations migrating from north-central China (the Henan and Shanxi Hans) through coastal Fujian Province to the Chaoshan plain. Although these regions are geographically distant, we hypothesized that EC high-risk populations in these three areas could share a common ancestry. Accordingly, we used 16 East Asian-specific Y-chromosome biallelic markers (single nucleotide polymorphisms; Y-SNPs) and six Y-chromosome short tandem repeat (Y-STR) loci to infer the origin of the EC high-risk Chaoshan population (CSP) and the genetic relationship between the CSP and the EC high-risk Henan Taihang Mountain population (HTMP) and Fujian population (FJP). The predominant haplogroups in these three populations are O3*, O3e*, and O3e1, with no significant difference between the populations in the frequency of these genotypes. Frequency distribution and principal component analysis revealed that the CSP is closely related to the HTMP and FJP, even though the former is geographically nearer to other populations (Guangfu and Hakka clans). The FJP is between the CSP and HTMP in the principal component plot. The CSP, FJP and HTMP are more closely related to Chinese Hans than to minorities, except Manchu Chinese, and are descendants of Sino-Tibetans, not Baiyues. Correlation analysis, hierarchical clustering analysis, and phylogenetic analysis (neighbor-joining tree) all support close genetic relatedness among the CSP, FJP and HTMP. The network for haplogroup O3 (including O3*, O3e* and O3e1) showed that the HTMP have highest STR haplotype diversity, suggesting that the HTMP may be a progenitor population for the CSP and FJP. These findings support the potentially important role of shared ancestry in understanding more about the genetic susceptibility in EC etiology in high-risk populations and have implications for determining the molecular basis of this disease.