多肽配体技术在植物功能基因组学中的应用前景

人工智能配体或适配体(Aptamer)技术是近年来兴起的一项特异性极强的基因干扰技术。通过人工合成特异的智能配体结合靶基因的蛋白产物, 达到特异干扰靶基因的生物学功能, 这是人工智能配体技术的基本设想。文章综述了多肽配体(Peptide aptamer)技术在基因功能验证中的主要进展, 着重阐明它在植物基因功能验证和作物抗病毒育种中的应用前景, 并提出克服该技术主要风险对策。     

整合电路理论的生态廊道及其重要性识别

景观连接度被认为是影响诸多生态过程的一个重要因素.基于最小累积阻力模型的最小成本路径识别方法可以有效识别异质性景观中的功能连接,已被广泛应用到景观的功能连接评价与生态廊道模拟的研究中.基于电路理论的连接度模型用电阻代替了图论中的边、用电阻距离代替成本距离,来衡量异质性景观的功能连接.本文以SIMMAP 2.0软件生成的模拟景观为对象,借助于Linkage Mapper工具和Circuitscape软件,探讨如何将最小累积阻力模型与基于电路理论的连接度模型相结合来识别生态廊道及其景观要素的相对重要性.结果表明: 两种模型在应用中各有优势,互为补充.最小成本路径方法可以有效识别栖息地之间的最小成本廊道,基于电路理论的连接度模型通过电流密度的计算可以有效识别对景观连接性有重要影响的景观要素和“夹点”地区,并且“夹点”的位置不受廊道宽度的影响,在廊道重要性识别研究中具有明显优势.该方法可为区域生态保护规划和生态廊道设计提供科学依据.     

Transferability of microsatellite markers from Eucalyptus spp. to Eugenia dysenterica (Myrtaceae family)

Cagaita (Eugenia dysenterica) is a widespread plant found in the Brazilian cerrado. Its fruit is used for popular consumption and for industrial purposes. A battery of 346 primer pairs developed for Eucalyptus spp. was tested on cagaita. Only 10 primer pairs were found to be transferable between the two species. Using a polyacrilamide gel, an average of 10.4 alleles per locus was detected, in a sample of 116 individuals from 10 natural populations of cagaita. Seven polymorphic loci allowed estimation of genetic parameters, including expected average heterozigosity H_E = 0.442, diversity among populations, R_ST = 0.268 and gene flow Nm = 0.680.     

Mitogenomic phylogeny of the Percichthyidae and Centrarchiformes (Percomorphaceae): comparison with recent nuclear gene-based studies and simultaneous analysis

Delineation of the fish family Percichthyidae (Percomorphaceae) has a long and convoluted history, with recent morphological-based studies restricting species members to South American and Australian freshwater and catadromous temperate perches. Four recent nuclear gene-based phylogenetic studies, however, found that the Percichthyidae was not monophyletic and was nested within a newly discovered inter-familial clade of Percomorphaceae, the Centrarchiformes, which comprises the Centrarchidae and 12 other families. Here, we reexamined the systematics of the Percichthyidae and Centrarchiformes based on new mitogenomic information. Our mitogenomic results are globally congruent with the recent nuclear gene-based studies although the overall amount of phylogenetic signal of the mitogenome is lower. They do not support the monophyly of the Percichthyidae, because the catadromous genus Percalates is not exclusively related to the freshwater percichthyids. The Percichthyidae (minus Percalates) and Percalates belong to a larger clade, equivalent to the Centrarchiformes, but their respective sister groups are unresolved. Because all recent analyses recover a monophyletic Centrarchiformes but with substantially different intra-relationships, we performed a simultaneous analysis for a character set combining the mitogenome and 19 nuclear genes previously published, for 22 centrarchiform taxa. This analysis furthermore indicates that the Centrarchiformes are divided into three lineages and the superfamily Cirrhitoidea is monophyletic as well as the temperate and freshwater centrarchiform perch-like fishes. It also clarifies some of the relationships within the freshwater Percichthyidae.     

Molecular basis of bacterial resistance to chloramphenicol and florfenicol

Chloramphenicol (Cm) and its fluorinated derivative florfenicol (Ff) represent highly potent inhibitors of bacterial protein biosynthesis. As a consequence of the use of Cm in human and veterinary medicine, bacterial pathogens of various species and genera have developed and/or acquired Cm resistance. Ff is solely used in veterinary medicine and has been introduced into clinical use in the mid-1990s. Of the Cm resistance genes known to date, only a small number also mediates resistance to Ff. In this review, we present an overview of the different mechanisms responsible for resistance to Cm and Ff with particular focus on the two different types of chloramphenicol acetyltransferases (CATs), specific exporters and multidrug transporters. Phylogenetic trees of the different CAT proteins and exporter proteins were constructed on the basis of a multisequence alignment. Moreover, information is provided on the mobile genetic elements carrying Cm or Cm/Ff resistance genes to provide a basis for the understanding of the distribution and the spread of Cm resistance--even in the absence of a selective pressure imposed by the use of Cm or Ff.     

甲状腺乳头状癌组织微小RNA-93-5p、微小RNA-98-5p表达与临床病理特征和增殖、侵袭基因表达的关系研究

摘要 目的：研究甲状腺乳头状癌（PTC）组织微小核糖核酸-93-5p（miR-93-5p）、微小RNA-98-5p（miR-98-5p）表达与临床病理特征和增殖、侵袭基因表达的关系。方法：选取2020年10月到2023年10月在广东省中医院行手术切除的PTC患者153例作为研究对象,收集术中切除的癌组织以及癌旁组织。检测并比较癌组织与癌旁组织miR-93-5p、miR-98-5p及增殖基因、侵袭基因mRNA表达水平,分析miR-93-5p及miR-98-5p表达与PTC患者临床病理特征的关系。利用Pearson法分析miR-93-5p、miR-98-5p表达水平与增殖基因、侵袭基因mRNA表达的相关性。结果：癌组织的miR-93-5p表达水平较癌旁组织更高,miR-98-5p表达水平较癌旁组织更低（P<0.05）。miR-93-5p高表达PTC患者TNM分期Ⅲ~Ⅳ期、有淋巴结转移及低分化的比例较miR-93-5p低表达PTC患者更高（P<0.05）。miR-98-5p低表达PTC患者TNM分期Ⅲ~Ⅳ期、有淋巴结转移及低分化的比例较miR-98-5p高表达PTC患者更高（P<0.05）。癌组织的增殖基因程序性细胞死亡因子4（PDCD4）及蛋白磷酸酶4调节亚基 （PP4R1）水平较癌旁组织更低（P<0.05）,侵袭基因金属蛋白酶解离素9（ADAM9）及Bcl-6共抑制因子样蛋白（BCORL1）水平较癌旁组织更高（P<0.05）。Pearson法分析结果显示,miR-93-5p表达与增殖基因PDCD4及PP4R1表达水平呈负相关,与侵袭基因ADAM9及BCORL1表达水平呈正相关。miR-98-5p表达水平与增殖基因PDCD4及PP4R1水平呈正相关,与侵袭基因ADAM9及BCORL1表达水平呈负相关。结论：PTC患者癌组织miR-93-5p表达升高,miR-98-5p表达降低,与TNM分期、淋巴结转移及分化程度等临床病理特征有关,还可促进PTC癌细胞增殖、侵袭。     

Differential patterns of spatial divergence in microsatellite and allozyme alleles: further evidence for locus‐specific selection in the acorn barnacle,Semibalanus balanoides?

We compared patterns of genetic structure at potentially selected (two allozyme loci) and neutral molecular markers (six microsatellite loci) in the acorn barnacle, Semibalanus balanoides from the Gulf of St. Lawrence. Our results confirmed the presence of a geographical shift in alleles MPI and GPI near the Miramichi River. In contrast, no significant patterns of population differentiation among samples located north and south of the river mouth were detected for four of six microsatellite loci. However, analysis of molecular variance (amova) at individual loci revealed that a significant proportion of the total variance in allele frequencies was partitioned among samples located north and south of the river for both the allozyme and the other two microsatellite loci. The two most common alleles at these microsatellites showed frequencies that were highly correlated (r = 0.65-0.74, P < 0.05) with those of the MPI*2 allele, perhaps because of either physical linkage or epistasis. The two allozyme loci were significantly correlated in barnacles located north of the Miramichi River (r = 0.86, P < 0.05). Overall, our results supported the hypothesis that the broad scale pattern of allozyme allelic shifts is maintained by selection. They also indicated that microsatellites may not always behave in a neutral way and must be used cautiously, especially when evidence for genetic structuring relies on only a few assayed loci.     

Assessing differential gene expression with small sample sizes in oligonucleotide arrays using a mean-variance model

The identification of the genes that are differentially expressed in two-sample microarray experiments remains a difficult problem when the number of arrays is very small. We discuss the implications of using ordinary t-statistics and examine other commonly used variants. For oligonucleotide arrays with multiple probes per gene, we introduce a simple model relating the mean and variance of expression, possibly with gene-specific random effects. Parameter estimates from the model have natural shrinkage properties that guard against inappropriately small variance estimates, and the model is used to obtain a differential expression statistic. A limiting value to the positive false discovery rate (pFDR) for ordinary t-tests provides motivation for our use of the data structure to improve variance estimates. Our approach performs well compared to other proposed approaches in terms of the false discovery rate.