Open resource metagenomics: a model for sharing metagenomic libraries

Both sequence-based and activity-based exploitation of environmental DNA have provided unprecedented access to the genomic content of cultivated and uncultivated microorganisms. Although researchers deposit microbial strains in culture collections and DNA sequences in databases, activity-based metagenomic studies typically only publish sequences from the hits retrieved from specific screens. Physical metagenomic libraries, conceptually similar to entire sequence datasets, are usually not straightforward to obtain by interested parties subsequent to publication. In order to facilitate unrestricted distribution of metagenomic libraries, we propose the adoption of open resource metagenomics, in line with the trend towards open access publishing, and similar to culture- and mutant-strain collections that have been the backbone of traditional microbiology and microbial genetics. The concept of open resource metagenomics includes preparation of physical DNA libraries, preferably in versatile vectors that facilitate screening in a diversity of host organisms, and pooling of clones so that single aliquots containing complete libraries can be easily distributed upon request. Database deposition of associated metadata and sequence data for each library provides researchers with information to select the most appropriate libraries for further research projects. As a starting point, we have established the Canadian MetaMicroBiome Library (CM²BL [1]). The CM²BL is a publicly accessible collection of cosmid libraries containing environmental DNA from soils collected from across Canada, spanning multiple biomes. The libraries were constructed such that the cloned DNA can be easily transferred to Gateway® compliant vectors, facilitating functional screening in virtually any surrogate microbial host for which there are available plasmid vectors. The libraries, which we are placing in the public domain, will be distributed upon request without restriction to members of both the academic research community and industry. This article invites the scientific community to adopt this philosophy of open resource metagenomics to extend the utility of functional metagenomics beyond initial publication, circumventing the need to start from scratch with each new research project.     

超抗原SEA增强小鼠对HBV DNA 疫苗的免疫反应

观察超抗原SEA(D227A)的真核表达载体(pmSEA),对HBVDNA疫苗诱导Balbc小鼠(H2d)免疫应答的调节作用。肌内注射空载体pcDNA3、HBVDNA疫苗加pmSEA佐剂(pHBVS2S+pmSEA)或不加佐剂(pHBVS2S);ELISA法测定血清抗HBs;ELISPOT检测分泌IFNγ的脾淋巴细胞;4h51Cr释放法检测小鼠脾细胞CTL活性。HBVDNA佐剂组免疫小鼠抗HBsAg抗体滴度明显高于不加佐剂组,其IgG1IgG2a的比例不同于多肽免疫组,二者分别为0.282与10。HBVDNA佐剂组均能增强IgG1和IgG2a的产生,是不加佐剂组的1.36、1.73倍。佐剂组小鼠脾淋巴细胞IFNγ的分泌量是不加佐剂组2～3倍。CTL细胞杀伤活性(E:T=100)佐剂组与不加佐剂组分别为:69.77%±7.5%、42.81%±7.7%,差异显著(P<0.05)。HBVDNA疫苗具有较强的免疫原性,能够诱导机体产生特异性的抗体及CTL反应;pmSEA佐剂能够提高小鼠对DNA疫苗的免疫应答,有望成为DNA疫苗的免疫佐剂。     

Ⅰ型禽腺病毒AV208株在鸡肝癌细胞中增殖规律的研究

【目的】摸索鸡肝癌细胞系(LMH)培养条件,并采用LMH细胞系对Ⅰ型禽腺病毒AV208株(FAVⅠ-AV208)进行增殖规律的研究。【方法】细胞以不同血清浓度培养并以不同接种比例传代。观察最佳感染复数下的细胞病变和病毒增殖情况,并研究病毒接种物浓度与蚀斑形成数量之间的关系。【结果】LMH细胞系的最适培养条件为,以10%FBS的培养基以1:5比例传代培养。FAVⅠ-AV208毒株可以在LMH细胞中良好增殖并达到较高的滴度(107.5TCID50/0.1 mL)。在最佳感染复数(MOI)为0.01时,72 h细胞即出现明显的细胞病变(CPE),特征为细胞变大变圆,集聚成不规则的葡萄串状。病毒接种物浓度与蚀斑形成数量间呈线性相关。【结论】LMH细胞是FAVⅠ较合适的病毒培养系统,为研制禽腺病毒重组疫苗提供了有利工具。     

DHPLC检测胃癌微卫星不稳定性

为探讨一种快速、简便、可靠的胃癌微卫星不稳定性（MSI）检测方法,变性聚丙烯酰胺凝胶电泳-银染法检测28例胃癌12个微卫星位点(D1S548、D1S552、D5S346、TP53、IGFIIR(G)8、IGFIIR(CT)5、TGFßRII(GT)3、TGFßRII(A)10、hMSH3(A)8、hMSH6(G)8、BAX(G)8和Bat26）,DHPLC柱温50℃检测Bat26位点。凝胶电泳发现MSI-H 2例（7.14%）,MSI-L胃癌15例（53.6%）,Bat26+2例均为MSI-H,Bat26改变和MSI-H表型一致（P<0.01,Fisher’s确切概率法）。DHPLC亦证实2例Bat26+胃癌,结果和凝胶电泳完全一致。结果表明,DHPLC检测Bat26位点是研究胃癌MSI-H的较好方法,有一定的临床应用价值。Abstact: To establish a fast, simple and solid method of studying microsatellite instability (MSI) in gastric cancer, a panel of 12 microsatellite sites,D1S548, D1S552, D5S346, TP53, IGFIIR(G)8, IGFIIR(CT)5, TGFßRII(GT)3, TGFßRII(A)10, hMSH3(A)8, hMSH6(G)8, BAX(G)8 and Bat26, were detected by denatured polyacrymide gel electrophoresis-silver stain in 28 gastric cancers. Bat26 was also analyzed by denatured high performance liquid chromatograph (DHPLC) at 50℃ in the DNASep Cartridge. Two MSI-H (7.14%) and 15 MSI-L cancers (53.6%) were identified in 28 gastric cancers. Bat26 was positive only in 2 MSI-H cancers. The alterations of Bat26 and MSI-H status were coincident (P<0.01). The two Bat26+ cancers were also confirmed by DHPLC. Results obtained from DHPLC and gel electrophoresis were completely consistent. Thus, DHPLC analysis of Bat26 site may be a favorable method of detecting MSI-H status in gastric cancer, and be of clinical importance.     

Promoting human embryonic stem cell renewal or differentiation by modulating Wnt signal and culture conditions

We previously showed that Wnt3a could stimulate human embryonic stem （hES） cell proliferation and affect cell fate determination. In the absence of feeder cell--derived factors, hES cells cultured under a feeder-free condition survived and proliferated poorly. Adding recombinant Wnt3a in the absence of feeder cell derived-factors stimulated hES cell proliferation but also differentiation. In the present study, we further extended our analysis to other Wnt ligands such as Wntl and Wnt5a. While Wntl displayed a similar effect on hES cells as Wnt3a, Wnt5a had little effect in this system. Wnt3a and Wntl enhanced proliferation of undifferentiated hES cells when feeder-derived self-renewal factors and bFGF are also present. To explore the possibility to promote the proliferation of undifferentiated hES cells by activating the Wnt signaling, we overexpressed Wnt3a or Wntl gene in immortalized human adult fibroblast （HAFi） cells that are superior in supporting long-term growth of undifferentiated hES cells than primary mouse embryonic fibroblasts. HAFi cells with or without a Wnt tmnsgene can be propagated indefinitely. Over-expression of the Wnt3a gene significantly enhanced the ability of HAFi feeder cells to support the undifferentiated growth of 3 different hES cell lines we tested. Co-expression of three commonly-used drug selection genes in Wnt3a-overpressing HAFi cells further enabled us to select rare hES clones after stable transfection or transduction. These immortalized engineered feeder cells （W3R） that co-express growth-promoting genes such as Wnt3a and three drug selection genes should empower us to efficiently make genetic modified hES cell lines for basic and translational research.     

白背飞虱对水稻抗虫品种N22的适应性研究

在室内连续用感虫品种TN1和抗虫品种N22单管饲养白背飞虱(Sogatella furcifera)种群,研究它对抗虫水稻品种的适应性及其体内保护酶的变化,结果表明,白背飞虱在感虫品种TN1和抗虫品种N22品种上饲养1至2代,其卵历期、若虫期和全世代历期均无明显差异,从感虫品种TN1转移到抗虫品种N22上饲养1代,白背飞虱的若虫存活率、雌成虫寿命、体重、蜜露量、产卵量和内禀增长率等均低于在抗虫品种上连续饲养2代,而后者又低于在感虫品种上饲养的指标,白背飞虱在抗虫品种上连续饲养2代后,体内保护酶中超氧化物岐化酶(SOD)和过氧化氢酶(CAT)活性逐渐接近于感虫品种上连续饲养的结果,说明白背飞虱从感虫品种转到抗虫品种在开始时并不适应,经过连续繁殖多代后白背飞虱逐渐适应,最后导致抗虫品种的抗性丧失。     

Teleconnection between the early immigration of brown planthopper (Nilaparvata lugens St?l) and ENSO indices: implication for its medium- and long-term forecast

Teleconnection between the early immigration of brown planthopper (BPH) and El Nino/Southern Oscillation (ENSO) indices from January of two years previously to the current June was investigated to make long-term forecast. The teleconnection results were as follows: ENSO indices which were significantly correlated with the early immigration of BPH were primarily sea surface temperature anomalies (SSTA) in N3, N4 and N3.4 regions, accounting for 71.8% of the total. Significant ENSO indices from two years and one year before the immigration events had a proportion of about 84%, while those in the current year only accounted for 16.7%. There was significantly negative correlation between the early immigration of BPH and SSTA in each Nino region from two years before to the previous spring, whereas there was significantly positive correlation between these two factors during the period from the previous winter to the current spring. The significant correlation between the early immigration of BPH and SSTA in each Nino region in the last summer and autumn did not show any obvious tendencies. The relationship between the southern oscillation index (SOI) and the early immigration of BPH was opposite to that between the immigration and SSTA in each Nino region. The above mentioned significant ENSO indices were used as key factors to build forecasting models for the early immigration of BPH by step-wise multiple linear regression analysis. Finally, 12 integrated forecasting models were obtained, which could make predictions 3–27 months ahead and had a predictive accuracy of 88.9%.     

Enhancement of Astragalus polysaccharide on the immune responses in pigs inoculated with foot-and-mouth disease virus vaccine

The effects of Astragalus polysaccharides (APS) on the immune response in pigs immunized with foot-and-mouth disease virus (FMDV) vaccine were investigated. Fifteen pigs were randomly divided into five groups. Four groups were vaccinated with a FMDV inactivated vaccine. Pigs in three experimental groups were administered varying doses of APS (APS1, 5 mg/kg; APS2, 10 mg/kg; APS3, 20 mg/kg). The influence of APS on the number of CD3⁺CD4⁻CD8⁺ cytotoxic T cells, CD3⁺CD4⁺CD8⁺ T helper memory cells, and CD3⁻CD4⁻CD8⁺ natural killer cells among peripheral blood lymphocytes (PBL) in the three APS groups were significant compared to the vaccine group. In vitro stimulation of PBL by Con A and LPS in APS groups induced a stronger proliferative response at 2 and 6 weeks post-inoculation (PI). APS markedly increased the titer of FMDV-specific antibody in a dose-dependent manner, and up-regulated mRNA expression of IFN-γ and IL-6. APS could potentially be used as an immunomodulator for a FMDV vaccine and provide better protection against FMDV.     

Change in microbial communities in acetate- and glucose-fed microbial fuel cells in the presence of light

Power densities produced by microbial fuel cells (MFCs) in natural systems are changed by exposure to light through the enrichment of photosynthetic microorganisms. When MFCs with brush anodes were exposed to light (4000 lx), power densities increased by 8–10% for glucose-fed reactors, and 34% for acetate-fed reactors. Denaturing gradient gel electrophoresis (DGGE) profiles based on the 16S rRNA gene showed that exposure to high light levels changed the microbial communities on the anodes. Based on 16S rRNA gene clone libraries of light-exposed systems the anode communities using glucose were also significantly different than those fed acetate. Dominant bacteria that are known exoelectrogens were identified in the anode biofilm, including a purple nonsulfur (PNS) photosynthetic bacterium, Rhodopseudomonas palustris, and a dissimilatory iron-reducing bacterium, Geobacter sulfurreducens. Pure culture tests confirmed that PNS photosynthetic bacteria increased power production when exposed to high light intensities (4000 lx). These results demonstrate that power production and community composition are affected by light conditions as well as electron donors in single-chamber air-cathode MFCs.