Hybrid cytomegalovirus-U6 promoter-based plasmid vectors improve efficiency of RNA interference in zebrafish

Short hairpin RNA (shRNA) directed by RNA polymerase III (Pol III) or Pol II promoter was shown to be capable of silencing gene expression, which should permit analyses of gene functions or as a potential therapeutic tool. However, the inhibitory effect of shRNA remains problematic in fish. We demonstrated that silencing efficiency by shRNA produced from the hybrid construct composed of the CMV enhancer or entire CMV promoter placed immediately upstream of a U6 promoter. When tested the exogenous gene, silencing of an enhanced green fluorescent protein (EGFP) target gene was 89.18 +/- 5.06% for CMVE-U6 promoter group and 88.26 +/- 6.46% for CMV-U6 promoter group. To test the hybrid promoters driving shRNA efficiency against an endogenous gene, we used shRNA against no tail (NTL) gene. When vectorized in the zebrafish, the hybrid constructs strongly repressed NTL gene expression. The NTL phenotype occupied 52.09 +/- 3.06% and 51.56 +/- 3.68% for CMVE-U6 promoter and CMV-U6 promoter groups, respectively. The NTL gene expression reduced 82.17 +/- 2.96% for CMVE-U6 promoter group and 83.06 +/- 2.38% for CMV-U6 promoter group. We concluded that the CMV enhancer or entire CMV promoter locating upstream of the U6-promoter could significantly improve inhibitory effect induced by the shRNA for both exogenous and endogenous genes compared with the CMV promoter or U6 promoter alone. In contrast, the two hybrid promoter constructs had similar effects on driving shRNA.

Knock down of gfp and no tail expression in zebrafish embryo by in vivo-transcribed short hairpin RNA with T7 plasmid system

A short-hairpin RNA (shRNA) expression system, based on T7 RNA polymerase (T7RP) directed transcription machinery, has been developed and used to generate a knock down effect in zebrafish embryos by targeting green fluorescent protein (gfp) and no tail (ntl) mRNA. The vector pCMVT7R harboring T7RP driven by CMV promoter was introduced into zebrafish embryos and the germline transmitted transgenic individuals were screened out for subsequent RNAi application. The shRNA transcription vectors pT7shRNA were constructed and validated by in vivo transcription assay. When pT7shGFP vector was injected into the transgenic embryos stably expressing T7RP, gfp relative expression level showed a decrease of 68% by analysis of fluorescence real time RT-PCR. As a control, injection of chemical synthesized siRNA resulted in expression level of 40% lower than the control when the injection dose was as high as 2 mu g/mu l. More importantly, injection of pT7shNTL vector in zebrafish embryos expressing T7RP led to partial absence of endogenous ntl transcripts in 30% of the injected embryos when detected by whole mount in situ hybridization. Herein, the T7 transcription system could be used to drive the expression of shRNA in zebrafish embryos and result in gene knock down effect, suggesting a potential role for its application in RNAi studies in zebrafish embryos.

Broad host range plasmid-based gene transfer system in the cyanobacterium Gloeobacter violaceus which lacks thylakoids

Gloeobacter violaceus, a cyanobacterium lack of thylakoids, is refractory to genetic manipulations because its cells are enveloped by a thick gelatinous sheath and in colonial form. In this study, a large number of single cells were obtained by repeated pumping with a syringe with the gelatinous sheath removed. And an exogenous broad host range plasmid pKT210 was conjugatively transferred into G. violaceus. Analyses with dot-blot hybridization and restriction mapping showed that the exogenous plasmid pKT210 had been introduced into G. violaceus and stably maintained with no alteration in its structure. pKT210 extracted from G. violaceus exconjugants could be transformed into the mcr - mrr - E. coli strain DH10B but not the mcr(+) mrr(+) strain DH5alpha, which suggests that a methylase system may be present in G. violaceus.

Glutathione-Mediated Release of Functional Plasmid DNA from Positively Charged Quantum Dots

DNA was efficiently bound to water-soluble positively charged CdTe quantum dots (QDs) through complementary electrostatic interaction. These QDs-DNA complexes were disrupted and DNA was released by glutathione (GSH) at intracellular concentrations. Interestingly, there was almost no detectable DNA released by extracellular concentration of GSH. The formation of QDs-DNA complexes and GSH-mediated DNA release from the complexes were confirmed by dye displacement assay, electrophoretic mobility shift assay (EMSA), transmission electron microscopy (TEM) and X-ray photoelectron spectroscopy (XPS) experiments.

Fabrication of silver nanoparticles ring templated by plasmid DNA

Silver nanoparticles ring was successfully fabricated by electrostatic assembling 4-aminothiophenol (4-ATP) capped silver nanoparticles on predefined extended circular plasmid pBR322 DNA. The silver nanoparticles ring which was about 1.5 mu m in length, and about 2.2 nm in height can be obtained by adjusting the reaction time. The normal Raman scattering spectra reveal that the 4-ATP has contacted with the silver nanoparticles by forming a strong Ag-S bond. The AFM data show that the assembly of 4-ATP capped silver nanoparticles on DNA is ordered.

Construction and control of plasmid DNA network

The influences of different cations on plasmid DNA network structures on a mica substrate were investigated by atomic force microscopy (AFM). Interactions between the DNA strands and mica substrate, and between the DNA strands themselves were more strongly influenced by the complex cations (Fe(phen)(3)(2+), Ni(phen)(3)(2+), and Co(phen)(3)(3+)) than by the simple cations (Mg2+, Mn2+, Ni2+, Ca2+, Co3+). The mesh height of the plasmid DNA network was higher when the complex cations were added to DNA samples. The mesh size decreased with increasing DNA concentration and increased with decreasing DNA concentration in the same cation solution sample. Hence, plasmid DNA network height can be controlled by selecting different cations, and the mesh size can be controlled by adjusting plasmid DNA concentration.

烟草NtFtsZ2-1基因在叶绿体分裂中的作用机制研究及NtFtsZ1-2基因启动子的克隆

根癌农杆菌通过将一段含有“癌”基因的T-DNA导入植物基因组中，引起植物的肿瘤：冠瘿。根癌农杆菌的这种能力来源于Ti质粒（Tumor inducing plasmid）。遗传工程中，根癌农杆菌的这一特性被用来将连接入Ti质粒T-DNA区两个边界之间的外源基因转入植物基因组。随着植物分子生物学的发展，T-DNA转化的原理被进一步阐明，农杆菌介导的转基因技术也得到进一步优化，更适合遗传工程操作。特别是Ti质粒毒性区和T-DNA区的反式作用（即位于不同质粒的T-DNA和毒性区也能侵染植物）被发现以来，双元表达载体的构建使遗传工程操作大为简便。 常用的双元表达载体大小都在11kb以上，尽管远远小于几百kb的野生型Ti质粒，但在实际的体外操作中还是不够简便。常用的植物双元表达载体pBI121的基因序列被测定（Frisch et al.，1995），数据显示非T-DNA区一半以上的序列被发现和功能无关，这使双元载体的进一步缩小成为可能。本文即通过PCR方法克隆到pBI121非T-DNA区中载体复制、三亲杂交必需的片段，结合载体pART27中的T-DNA区（含有真核、原核表达活性的嵌合npt II基因）创造了小的合成型植物表达双元载体pSY1（小于7kb）。然后将pBI121上带有35S启动子和nos终止子的GUS基因克隆到pSY1的T-DNA区中，得到pSY2（约10kb）。进一步用pROK2上的35S启动子和nos终止子区替换pSY2上的GUS表达区，得到pSY3（约8kb）。通过三亲法将pSY2转入根癌农杆菌中，根癌农杆菌再通过叶盘法侵染烟草叶片，获得愈伤组织，愈伤组织进一步分化出小苗。GUS组织化学染色表明GUS基因在转基因的愈伤组织和小苗中均有表达，PCR检测也证明GUS基因被导入了植物基因组。pSY系列载体能成功的用于植物遗传转化。

能用于三亲杂交的植物双元表达小载体pSY系列的构建及转基因鉴定

根癌农杆菌通过将一段含有“癌”基因的T-DNA导入植物基因组中，引起植物的肿瘤：冠瘿。根癌农杆菌的这种能力来源于Ti质粒（Tumor inducing plasmid）。遗传工程中，根癌农杆菌的这一特性被用来将连接入Ti质粒T-DNA区两个边界之间的外源基因转入植物基因组。随着植物分子生物学的发展，T-DNA转化的原理被进一步阐明，农杆菌介导的转基因技术也得到进一步优化，更适合遗传工程操作。特别是Ti质粒毒性区和T-DNA区的反式作用（即位于不同质粒的T-DNA和毒性区也能侵染植物）被发现以来，双元表达载体的构建使遗传工程操作大为简便。 常用的双元表达载体大小都在11kb以上，尽管远远小于几百kb的野生型Ti质粒，但在实际的体外操作中还是不够简便。常用的植物双元表达载体pBI121的基因序列被测定（Frisch et al.，1995），数据显示非T-DNA区一半以上的序列被发现和功能无关，这使双元载体的进一步缩小成为可能。本文即通过PCR方法克隆到pBI121非T-DNA区中载体复制、三亲杂交必需的片段，结合载体pART27中的T-DNA区（含有真核、原核表达活性的嵌合npt II基因）创造了小的合成型植物表达双元载体pSY1（小于7kb）。然后将pBI121上带有35S启动子和nos终止子的GUS基因克隆到pSY1的T-DNA区中，得到pSY2（约10kb）。进一步用pROK2上的35S启动子和nos终止子区替换pSY2上的GUS表达区，得到pSY3（约8kb）。通过三亲法将pSY2转入根癌农杆菌中，根癌农杆菌再通过叶盘法侵染烟草叶片，获得愈伤组织，愈伤组织进一步分化出小苗。GUS组织化学染色表明GUS基因在转基因的愈伤组织和小苗中均有表达，PCR检测也证明GUS基因被导入了植物基因组。pSY系列载体能成功的用于植物遗传转化。

Frog skins keep redox homeostasis by antioxidant peptides with rapid radical scavenging ability

The question of how amphibians can protect themselves from reactive oxygen species when exposed to the sun in an oxygen-rich atmosphere is important and interesting, not only from an evolutionary viewpoint, but also as a primer for researchers interested in mammalian skin biology, in which such peptide systems for antioxidant defense are not well studied. The identification of an antioxidant peptide named antioxidin-RL from frog (Odorrana livida) skin in this report supports the idea that a peptide antioxidant system may be a widespread antioxidant strategy among amphibian skins. Its ability to eliminate most of the 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) radical tested within 2 s, which is much faster than the commercial antioxidant factor butylated hydroxytoluene, suggests that it has a potentially large impact on redox homeostasis in amphibian skins. Cys10 is proven to be responsible for its rapid radical scavenging function and tyrosines take part in the binding of antioxidin-RL to radicals according to our nuclear magnetic resonance assay. (C) 2010 Elsevier Inc. All rights reserved.

Genome-wide SNP and haplotype analyses reveal a rich history underlying dog domestication

Advances in genome technology have facilitated a new understanding of the historical and genetic processes crucial to rapid phenotypic evolution under domestication(1,2). To understand the process of dog diversification better, we conducted an extensive genome-wide survey of more than 48,000 single nucleotide polymorphisms in dogs and their wild progenitor, the grey wolf. Here we show that dog breeds share a higher proportion of multi-locus haplotypes unique to grey wolves from the Middle East, indicating that they are a dominant source of genetic diversity for dogs rather than wolves from east Asia, as suggested by mitochondrial DNA sequence data(3). Furthermore, we find a surprising correspondence between genetic and phenotypic/functional breed groupings but there are exceptions that suggest phenotypic diversification depended in part on the repeated crossing of individuals with novel phenotypes. Our results show that Middle Eastern wolves were a critical source of genome diversity, although interbreeding with local wolf populations clearly occurred elsewhere in the early history of specific lineages. More recently, the evolution of modern dog breeds seems to have been an iterative process that drew on a limited genetic toolkit to create remarkable phenotypic diversity.

D77, one benzoic acid derivative, functions as a novel anti-HIV-1 inhibitor targeting the interaction between integrase and cellular LEDGF/p75

Integration of viral-DNA into host chromosome mediated by the viral protein HIV-1 integrase (IN) is an essential step in the HIV-1 life cycle. In this process, Lens epithelium-derived growth factor (LEDGF/p75) is discovered to function as a cellular co-fa

Effects of exogenous double-stranded RNA on the basonuclin gene expression in mouse oocytes

In plants and less-advanced animal species, such as C.elegans, introduction of exogenous double-stranded RNA (dsRNA) into cells would trigger degradation of the mRNA with homologous sequence and interfere with the endogenous gene expression. It might represent an ancient anti-virus response which could prevent the mutation in the genome that was caused by virus infection or mobile DNA elements insertion. This phenomenon was named RNA interference, or RNAi. In this study, RNAi was used to investigate the function of basonuclin gene during oogenesis. Microinjection of dsRNA directed towards basonuclin into mouse germinal-vesicle-intact (GV) oocytes brought down the abundance of the cognate mRNA effectively in a time- and concentration-dependent manner. This reduction effect was sequence-specific and showed no negative effect on other non-homologous gene expression in oocytes, which indicated that dsRNA can recognize and cause the degradation of the transcriptional products of endogenous basonuclin gene in a sequence-specific manner. Immunofluorescence results showed that RNAi could reduce the concentration of basonuclin protein to some extent, but the effect was less efficient than the dsRNA targeting towards tPA and cMos which was also expressed in oocytes. This result might be due to the long half life of basonuclin protein in oocytes and the short reaction time which was posed by the limited life span of GV oocytes cultured in vitro. In summary, dsRNA could inhibit the expression of the cognate gene in oocytes at both mRNA and protein levels. The effect was similar to Knock-out technique which was based on homologous recombination. Furthermore, hairpin-style dsRNA targeting basonuclin gene could be produced by transcription from a recombinant plasmid and worked efficiently to deplete the cognate mRNA in oocytes. This finding offered a new way to study the function of basonuclin in the early stage of oogenesis by infection of primordial oocytes with the plasmid expressing hairpin-style basonuclin dsRNA.

The cytomegalovirus promoter-driven short hairpin RNA constructs mediate effective RNA interference in zebrafish in vivo

The ability to utilize the RNA interference (RNAi) machinery for silencing target-gene expression has created a lot of excitement in the research community. In the present study, we used a cytomegalovirus (CMV) promoter-driven DNA template approach to induce short hairpin RNA (shRNA) triggered RNAi to block exogenous Enhanced Green Fluorescent Protein (EGFP) and endogenous No Tail (NTL) gene expressions. We constructed three plasmids, pCMV-EGFP-CMV-shGFP-SV40, pCMV-EGFP-CMV-shNTL-SV40, and pCMV-EGFP-CMV-shScrambled-SV40, each containing a CMV promoter driving an EGFP reporter cDNA and DNA coding for one shRNA under the control of another CMV promoter. The three shRNA-generating plasmids and pCMV-EGFP control plasmid were introduced into zebrafish embryos by microinjection. Samples were collected at 48 h after injection. Results were evaluated by phenotype observation and real-time fluorescent quantitative reverse-transcription polymerase chain reaction (Q-PCR). The shGFP-generating plasmid significantly inhibited the EGFP expression viewed under fluorescent microscope and reduced by 70.05 +/- 1.26% of exogenous EGFP gene mRNA levels compared with controls by Q-PCR. The shRNA targeting endogenous NTL gene resulted in obvious NTL phenotype of 30 +/- 4% and decreased the level of their corresponding mRNAs up to 54.52 +/- 2.05% compared with nontargeting control shRNA. These data proved the feasibility of the CMV promoter-driven shRNA expression technique to be used to inhibit exogenous and endogenous gene expressions in zebrafish in vivo.

Identification and characterization of a MBP isoform specific to hypothalamus in orange-spotted grouper (Epinephelus coioides)

Myelin basic protein (MBP), as a major component of the myelin sheath, has been revealed to play an important role informing and maintaining myelin structure in vertebrate nervous system. In teleost, hypothalamus is an instinctive brain center and plays significant roles in many physiological functions, such as energy metabolism, growth, reproduction, and stress response. In comparison with other MBP identified in vertebrates, a smallest MBP is cloned and identified from the orange-spotted grouper hypothalamic cDNA plasmid library in this study. RT-PCR analysis and Western blot detection indicate that the EcMBP is specific to hypothalamus, and expresses mainly in the tuberal hypothalamus in adult grouper. Immunofluorescence localization suggests that EcMBP should be expressed by oligodendrocytes, and the expressing cells should be concentrated in hypothalamus and the area surrounding hypothalamus, such as NPOpc, VC, DP, NLTm, and NDLI The studies on EcMBP expression pattern and developmental behaviour in the brains of grouper embryos and larvae reveal that the EcMBP-expressing cells are only limited in a defined set of cells on the border of hypothalamus, and suggest that the EcMBP-expressing cells might be a subpopulation of oliaodendrocyte progenitor cells. This study not only identifies a smallest MBP isoform specific to hypothalamus that can be used as a molecular marker of oligodendrocytes in fish, but also provides new insights for MBP evolution and cellular distribution. (C) 2007 Elsevier B.V.. All rights reserved.