Tracing the origin and evolution of plant TIR-encoding genes

Toll-interleukin-1 receptor (TIR)-encoding proteins represent one of the most important families of disease resistance genes in plants. Studies that have explored the functional details of these genes tended to focus on only a few limited groups; the origin and evolutionary history of these genes were therefore unclear. In this study, focusing on the four principal groups of TIR-encoding genes, we conducted an extensive genome-wide survey of 32 fully sequenced plant genomes and Expressed Sequence Tags (ESTs) from the gymnosperm Pinus taeda and explored the origins and evolution of these genes. Through the identification of the TIR-encoding genes, the analysis of chromosome positions, the identification and analysis of conserved motifs, and sequence alignment and phylogenetic reconstruction, our results showed that the genes of the TIR-X family (TXs) had an earlier origin and a wider distribution than the genes from the other three groups. TIR-encoding genes experienced large-scale gene duplications during evolution. A skeleton motif pattern of the TIR domain was present in all spermatophytes, and the genes with this skeleton pattern exhibited a conserved and independent evolutionary history in all spermatophytes, including monocots, that followed their gymnosperm origin. This study used comparative genomics to explore the origin and evolutionary history of the four main groups of TIR-encoding genes. Additionally, we unraveled the mechanism behind the uneven distribution of TIR-encoding genes in dicots and monocots.     

The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales

Simple sequence repeats (SSRs), or microsatellites, are special DNA/RNA sequences with repeated unit of 1–6 bp. The genomes of Herpesvirales have many repeating structures, which is an excellent system to study the evolution and roles of microsatellites and compound microsatellites in viruses. Therefore, 56 genomes of Herpesvirales were selected and the occurrence, composition and complexity of different repeats were investigated in the genomes. A total of 63,939 microsatellites and 5825 compound microsatellites were extracted from 56 genomes. It found that GC content has a significant strong correlation with both the counts of microsatellites (CM) and the counts of compound microsatellites (CCM). However, genome size has a moderate correlation only with CM and almost no correlation with CCM. The compound microsatellites occurring in genic regions are obviously more than that in intergenic regions. In general, the number of compound microsatellite decreases with the increase of complexity (C) (the count of individual microsatellites being part of a compound microsatellite) and the complexity hardly exceeds C = 4. The vast majority of compound microsatellites exist in intergenic regions, when C ≥ 10. The distributions of SSRs tend to be organism-specific rather than host-specific in herpesvirus genomes. The diversity of microsatellites and compound microsatellites may be helpful for a better understanding of the viral genetic diversity, genotyping, and evolutionary biology in herpesviruses genomes.     

Acrossocheilus multistriatus,a new species of barbine fish(Teleostei: Cyprinidae) from the Zhujiang River basin,South China

A new barbine cyprinid fish, Acrossocheilus multistriatus sp. nov., is described from the Zhujiang River(Pearl River) basin in South China. It is separated from all other barred congeners except A. monticola by its unique coloration pattern of 8–12 vs. 5–7 vertical dark bars on the dorsum and flank. Although 8 vertical black bars are also present in specimens of A. monticola, the new species is distinct from it by having a well-developed(vs. poor-developed) lower lip, with or without a median interruption(vs. with a median interruption which wider than 1/2 mouth width) on lower jaw, the lower jaw entirely covered(vs. uncoverd) by the lower lip, body depth 22.57%–25.22% SL(vs. 25.64%–32.26% SL). Additional characteristices as follows: last simple dorsal-fin ray soft without serration; dark stripes on membranes between dorsal-fin rays; dark stripes absent on membranes between anal fin rays; maxillary barbels longer than eye diameter, extending to posterior edge of eyes.     

大鲵铁蛋白重链FTH基因的克隆、鉴定及表达分析简

从大鲵皮肤cDNA文库中,筛选出大鲵铁蛋白重链AdFTH的cDNA序列,其全长为864 bp,开放阅读框为531 bp,编码176个氨基酸,5′和3′非翻译编码区(Untranslated region,UTR)分别为120 bp和214 bp,预测蛋白质的分子量为20.6 kD,理论等电点PI为5.41,预测蛋白无信号肽及跨膜结构,在5′-UTR的22—51 bp处有一个特殊的铁反应元件(Iron response element,IRE)。同源性和系统进化分析表明,铁蛋白重链在进化上有着较高的保守性。实时定量PCR结果表明,大鲵铁蛋白重链mRNA在各个组织中广泛表达,其中肝脏的表达量高于其他8种组织,表明肝脏是大鲵主要的参与铁储存代谢的器官。成功构建了大鲵铁蛋白重链的重组表达载体pET32a-AdFTH,利用大肠杆菌Escherichia coli BL21表达系统和Ni2+亲和层析方法,获得了纯度较高的重组大鲵铁蛋白,并证实重组大鲵铁蛋白(Recombinant AdFTH protein,rAdFTH)具有氧化和吸收铁离子的功能,为进一步制备AdFTH抗体了解其在大鲵体内的多种作用机制打下坚实的基础。     

8-甲氧基二氢血根碱化感潜能的评估

以莴苣幼苗为材料,检测了分离自细果角茴香的生物碱对莴苣幼苗根生长及根毛发育的影响。结果表明:50~200μmol·L-1浓度范围内,8-甲氧基二氢血根碱对莴苣幼苗根长显著抑制;10、20和30μmol·L-18-甲氧基二氢血根碱对莴苣幼苗根毛的长度和数量有显著的抑制作用,且抑制作用均表现了浓度依赖性。通过对莴苣根尖细胞有丝分裂研究发现,50μmol·L-1的8-甲氧基二氢血根碱能显著抑制根尖细胞的有丝分裂,而且莴苣幼苗净增值率与根尖细胞的有丝分裂之间呈正相关,证明8-甲氧基二氢血根碱主要通过抑制根尖细胞有丝分裂对莴苣根的生长产生影响。     

Integrative Functional Genomics of Hepatitis C Virus Infection Identifies Host Dependencies in Complete Viral Replication Cycle

Recent functional genomics studies including genome-wide small interfering RNA (siRNA) screens demonstrated that hepatitis C virus (HCV) exploits an extensive network of host factors for productive infection and propagation. How these co-opted host functions interact with various steps of HCV replication cycle and exert pro- or antiviral effects on HCV infection remains largely undefined. Here we present an unbiased and systematic strategy to functionally interrogate HCV host dependencies uncovered from our previous infectious HCV (HCVcc) siRNA screen. Applying functional genomics approaches and various in vitro HCV model systems, including HCV pseudoparticles (HCVpp), single-cycle infectious particles (HCVsc), subgenomic replicons, and HCV cell culture systems (HCVcc), we identified and characterized novel host factors or pathways required for each individual step of the HCV replication cycle. Particularly, we uncovered multiple HCV entry factors, including E-cadherin, choline kinase α, NADPH oxidase CYBA, Rho GTPase RAC1 and SMAD family member 6. We also demonstrated that guanine nucleotide binding protein GNB2L1, E2 ubiquitin-conjugating enzyme UBE2J1, and 39 other host factors are required for HCV RNA replication, while the deubiquitinating enzyme USP11 and multiple other cellular genes are specifically involved in HCV IRES-mediated translation. Families of antiviral factors that target HCV replication or translation were also identified. In addition, various virologic assays validated that 66 host factors are involved in HCV assembly or secretion. These genes included insulin-degrading enzyme (IDE), a proviral factor, and N-Myc down regulated Gene 1 (NDRG1), an antiviral factor. Bioinformatics meta-analyses of our results integrated with literature mining of previously published HCV host factors allows the construction of an extensive roadmap of cellular networks and pathways involved in the complete HCV replication cycle. This comprehensive study of HCV host dependencies yields novel insights into viral infection, pathogenesis and potential therapeutic targets.     

Plasmonic Photonic Bloch Oscillations in Composite Metal–Insulator–Metal Waveguide Structure

This study proposes the time-evolved plasmonic photonic Bloch oscillations (PBOs) in a composite metal–insulator–metal (CMIM) waveguide structure. This device contains two kinds of MIM waveguide with different thickness of the insulator gaps. The time-resolved plasmonic PBO motion in this CMIM waveguide can be observed by introducing a linearly graded dielectric material. The ray trajectory results from the Hamiltonian optics are consistent with the finite-difference time-domain simulation results.