草菇菌丝体与原基差异表达基因分析

采用Solexa测序技术,对草菇菌丝体和原基进行了数字基因表达谱(DGE)测序,在菌丝体和原基文库中分别得到5701781个和5659262个高质量测序标签(cleantags),对应的标签种数(distinct clean tags)分别为85626和95363。将所有高质量测序标签与参考基因库进行比对,在菌丝体和原基文库中,占标签种数的43.32%和52.57%的标签可以唯一定位(map)到参考序列上,占标签种数的21.65%和21.47%的标签可以被定位到基因组序列上。最终,被菌丝体和原基标签唯一定位的基因数(unambiguous tag-mapped genes)分别为14794和15534。差异基因分析显示,两个文库中共有显著性差异表达的基因4163个,其中在原基中上调、下调的基因数分别为2486和1677,只在原基中表达的基因321个。经过Blastnr比对,在原基中特异表达的基因,涉及蛋白质(氨基酸)合成与代谢、糖代谢、脂类代谢和抗逆反应等多个代谢途径。GO功能富集分析结果表明,葡萄糖、己糖和乙醇等代谢途径大部分基因下调表达。Pathway功能富集分析结果表明,合成核糖体蛋白的基因均下调表达,表明原基形成时细胞代谢减弱,蛋白质合成量减小。     

Lignocellulolytic Enzymes Produced by Volvariella volvacea, the Edible Straw Mushroom

Volvariella volvacea, commonly known as the straw or paddy mushroom, had the following growth characteristics: minimum temperature, 25°C; optimal temperature, 37°C; maximal temperature, 40°C; pH optimum 6.0. Optimal pH for cellulase production was 5.5. The optimal initial pH for cellulase production and mycelial growth was found to be 6.0. The pH and temperature optima for cellulolytic activity were 5.0 and 50°C, respectively. Maximal cellulolytic activity was obtained within 5 days in shake-flask culture. The cellulases were found to be partly cell free and partly cell bound during growth on microcrystalline cellulose. The endoglucanase activity was primarily extracellular, and β-glucosidase activity was found exclusively extracellularly. Weak cellulase activity was detected when cells were grown on cellobiose and lactose. V. volvacea could not digest the lignin portion of newspaper in shake-flask cultivation. Phenol oxidase, an important enzyme in lignin biodegradation, also was lacking in the cell-free filtrate. However, the organism oxidized phenolic compounds when it was cultured on agar plates containing commercial lignin.     

Community phylogenetic analysis of moderately thermophilic cyanobacterial mats from China, the Philippines and Thailand

Most community molecular studies of thermophilic cyanobacterial mats to date have focused on Synechococcus occurring at temperatures of ~50–65°C. These reveal that molecular diversity exceeds that indicated by morphology, and that phylogeographic lineages exist. The moderately thermophilic and generally filamentous cyanobacterial mat communities occurring at lower temperatures have not previously been investigated at the community molecular level. Here we report community diversity in mats of 42–53°C recovered from previously unstudied geothermal locations. Separation of 16S rRNA gene-defined genotypes from community DNA was achieved by DGGE. Genotypic diversity was greater than morphotype diversity in all mats sampled, although genotypes generally corresponded to observed morphotypes. Thirty-six sequences were recovered from DGGE bands. Phylogenetic analyses revealed these to form novel thermophilic lineages distinct from their mesophilic counterparts, within Calothrix, Cyanothece, Fischerella, Phormidium, Pleurocapsa, Oscillatoria and Synechococcus. Where filamentous cyanobacterial sequences belonging to the same genus were recovered from the same site, these were generally closely affiliated. Location-specific sequences were observed for some genotypes recovered from geochemically similar yet spatially separated sites, thus providing evidence for phylogeographic lineages that evolve in isolation. Other genotypes were more closely affiliated to geographically remote counterparts from similar habitats suggesting that adaptation to certain niches is also important.     

Influence of Steinernema feltiae and Diflubenzuron on Yield and Economics of the Cultivated Mushroom Agaricus bisporus in Dutch Mushroom Culture

The insect pathogenic nematode Steinernema feltiae (Nematoda: Steinernematidae) was shown to offer an alternative to the use of diflubenzuron for the control of the mushroom fly Lycoriella auripila (Diptera: Sciaridae). The influence of diflubenzuron and S. feltiae treatments on the yield and numbers of the mushroom, Agaricus bisporus , was studied. Applications of diflubenzuron after casing significantly reduced total mushroom yields by 10-13%. The greatest yield reductions were observed in the first flush. In the second flush, high yields were found despite significantly lower numbers of mushrooms. These high yields, however, could not compensate for the yield loss of the first flush. Some of the treatments with S. feltiae significantly increased yields, but these were not associated with a particular time of application. As nematodes did not reduce mushroom yields they were able to compete with diflubenzuron. Although the purchase costs of nematodes were high, their use was more economical than that of diflubenzuron when the yield losses of 10% due to casing treatments were taken into account.     

Occurrence, characterisation and detection of potential virulence determinants of emerging aquatic bacterial pathogens from the Philippines and Thailand

Strains of Aeromonas spp., 'non-cholera vibrios' (NCVs) and Plesiomonas shigelloides isolated from aquatic environments, fish and human diarrhoeal cases in the Philippines and Thailand were characterised for potential virulence markers. Thus, the production of cytotoxin, cell-associated and cell-free haemolysin and their capacity to adhere to human intestinal (Henle 407) cells in vitro was investigated. In addition, the occurrence of tlh and tdh haemolysin genes and urease activity among V. parahaemolyticus strains was investigated. The results showed that strains recovered from clinical sources (human and fish) produced these virulence factors, whereas these are absent in environmental strains.     

Bacterial Populations Colonizing and Degrading Rice Straw in Anoxic Paddy Soil

Rice straw is a major substrate for the production of methane, a greenhouse gas, in flooded rice fields. The bacterial community degrading rice straw under anoxic conditions was investigated with molecular methods. Rice straw was incubated in paddy soil anaerobically for 71 days. Denaturing gradient gel electrophoresis (DGGE) of the amplified bacterial 16S rRNA genes showed that the composition of the bacterial community changed during the first 15 days but then was stable until the end of incubation. Fifteen DGGE bands with different signal intensities were excised, cloned, and sequenced. In addition, DNA was extracted from straw incubated for 1 and 29 days and the bacterial 16S rRNA genes were amplified and cloned. From these clone libraries 16 clones with different electrophoretic mobilities on a DGGE gel were sequenced. From a total of 31 clones, 20 belonged to different phylogenetic clusters of the clostridia, i.e., clostridial clusters I (14 clones), III (1 clone), IV (1 clone), and XIVa (4 clones). One clone fell also within the clostridia but could not be affiliated to one of the clostridial clusters. Ten clones grouped closely with the genera Bacillus (3 clones), Nitrosospira (1 clone), Fluoribacter (1 clones), and Acidobacterium (2 clones) and with clone sequences previously obtained from rice field soil (3 clones). The relative abundances of various phylogenetic groups in the rice straw-colonizing community were determined by fluorescence in situ hybridization (FISH). Bacteria were detached from the incubated rice straw with an efficiency of about 80 to 90%, as determined by dot blot hybridization of 16S rRNA in extract and residue. The number of active (i.e., a sufficient number of ribosomes) Bacteria detected with a general eubacterial probe (Eub338) after 8 days of incubation was 61% of the total cell counts. This percentage decreased to 17% after 29 days of incubation. Most (55%) of the active cells on day 8 belonged to the genus Clostridium, mainly to clostridial clusters I (24%), III (6%), and XIVa (24%). An additional 5% belonged to the Cytophaga-Flavobacterium cluster of the Cytophaga-Flavobacterium-Bacteroides phylum, 4% belonged to the α, β, and γ Proteobacteria, and 1.3% belonged to the Bacillus subbranch of the gram-positive bacteria with a low G+C content. The results show that the bacterial community colonizing and decomposing rice straw developed during the first 15 days of incubation and was dominated by members of different clostridial clusters, especially clusters I, III, and XIVa.     

Agrobacterium tumefaciens-Mediated Transformation of the Vegetative Dikaryotic Mycelium of the Cultivated Mushroom Flammulina velutipes

Agrobacterium tumefaciens was used to transform the vegetative dikaryotic mycelium of Flammulina velutipes using a hygromycin B resistance gene as selectable marker. The gene coding for urogen III methyltransferase (cob) was introduced into F. velutipes dikaryotic cells. The resulting transformant cells generated a bright red fluorescence, indicating that cob is promising as a reporter gene in F. velutipes.     

Some Properties of an Extracellular Proteolytic Enzyme of Verticillium fungicola, a Pathogen of the Cultivated Mushroom Agaricus bisporus

In a casein nutrient solution, Verticillium fungiocla, the causal agent of the dry bubble disease of the cultivated mushroom Agaricus bisporus, produces a proteolytic enzyme. The effects of the pH and of inhibitors on the protease activity and the heat stability of the enzyme are described. The protease is of interest in connection with the attacking mechanism of Verticillium fungicola.     

丁型肝炎病毒抗原的表达纯化和抗原性分析

丁型肝炎病毒(Hepatitis D virus,HDV)是一种缺陷负链RNA病毒,其表面被乙肝病毒抗原(HBsAg)所包裹,内为丁型肝炎抗原(HDAg)及其基因组RNA.HDV基因组中有多个开放读码框架(ORF),其中只有抗基因组RNA链上的一个ORF编码的蛋白与HDAg相关[1,2].     

丁型肝炎病毒抗原的表达纯化和抗原性分析

丁型肝炎病毒(Hepatitis D virus, HDV)是一种缺陷负链RNA病毒,其表面被乙肝病毒抗原(HBsAg)所包裹,内为丁型肝炎抗原(HDAg)及其基因组RNA。HDV基因组中有多个开放读码框架(ORF),其中只有抗基因组RNA链上的一个ORF编码的蛋白与HDAg相关[1,2]。HDV的抗原、抗体的测定是HDV感染诊断的主要标志,为了改进和提高HDV ELISA诊断试剂的质量,制备高纯度和高效价的HDAg尤为重要。为此,我们构建了HDAg基因表达株,以pQE表达系统为载体,利用该载体本身具备的6个组氨酸序列结构(6×histag)来纯化蛋白,直接提取高度纯化的HDAg,并应…     

Composition Shifts of Arbuscular Mycorrhizal Fungi between Natural Wetland and Cultivated Paddy Field

The community assembly change of arbuscular mycorrhizal fungi (AMF) during the reclamation of wetlands to paddy fields is mostly unknown. In this study, we applied the high-throughput sequencing technique to investigate the composition of the AMF community in natural wetland (common wild rice and Leersia hexandra Swartz) and paddy field (Asian cultivated rice), as well as the soil elements effective on the community of AMF. Soil properties including soil organic carbon, available nitrogen (AN), available phosphorus (AP), available potassium, and pH were also measured. Operational taxonomic units (OTUs) of nine genera in four orders (Glomerales, Diversisporales, Archaeosporales, and Paraglomerales) of AMF were detected. All detected AMF genera were found in the wild rice wetland, while about half of the detected AMF genera were absent in paddy field; however, the absolute amount of total AMF in the paddy field and wetland was not different. Among all measured soil properties, AMF community was affected significantly by soil AN and AP. Results indicate that agricultural managements affect AMF community significantly, but do not have negative effects on the absolute amount of all the AMF genera. Soil AP may be the main factor resulting in the decreased AMF genus in paddy field. In addition, AMF may have contributed to the survival and evolution of plants.     

Forces and Straw Cutting Performance of Double Disc Furrow Opener in No-Till Paddy Soil

Conservation tillage is an energy efficient and low cost tillage system to improve soil environment compared with conventional tillage systems. However, the rice residue management becomes an “impossible to achieve” task due to high soil moisture content at harvest time and the thickness of rice straw. Disc type furrow openers are used for both seed drilling as well as straw cutting during no tillage sowing. A study was conducted to evaluate the draft requirement and straw cutting performances of different sized furrow openers in no-till paddy soil conditions. Double disc furrow opener was tested on an in-field traction bench for three working depths, i.e. 30, 60 and 90 mm, and three forwarding speeds, i.e. 0.1, 0.2 and 0.3 m/s. The draft and vertical forces on the disc were recorded with load cells. These sensors were connected to a data acquisition system developed with hardware and software. The results revealed that the size of the furrow opener, operating depth and the forwarding speed had significant effects (P<0.05) on the horizontal and vertical forces, and the straw cutting performance. Mean values of the draft were 648.9, 737.2 and 784.6 N for the opener with diameters of 330, 450 and 600 mm respectively, and the vertical forces for similar openers were 904.7, 1553.9 and 1620.4 N, respectively. Furthermore, the mean straw cutting efficiencies for the double disc opener with diameters of 330, 450 and 600 mm were 39.36, 78.47 and 65.46%, respectively. The opener with 450 mm diameter provided higher straw cutting efficiency as compared to 600 mm diameter disc, while lowest straw cutting efficiency was observed with 330 mm diameter disc. The 450 mm diameter opener provided the highest straw cutting efficiency (88.6%) at 90 mm working depth and expressed optimum performance compared with other furrow openers.     

环境因子对草菇生长发育影响的灰色综合评判

本文运用灰色系统理论,进行了环境因子对草菇生长发育的影响的灰色关联评判．结果表明：以A_2B_2C_2D_1E_1,A_4B_1C_2D_2E_1两个处理组合为最佳处理组合,草菇栽培适宜条件为废棉,pH值8.0～8.5,CO_2浓度＜0.2%等．     

Production and Distribution of Endoglucanase, Cellobiohydrolase, and β-Glucosidase Components of the Cellulolytic System of Volvariella volvacea, the Edible Straw Mushroom

The edible straw mushroom, Volvariella volvacea, produces a multicomponent enzyme system consisting of endo-1,4-β-glucanase, cellobiohydrolase, and β-glucosidase for the conversion of cellulose to glucose. The highest levels of endoglucanase and cellobiohydrolase were recorded in cultures containing microcrystalline cellulose (Avicel) or filter paper, while lower but detectable levels of activity were also produced on carboxymethyl cellulose, cotton wool, xylitol, or salicin. Biochemical analyses of different culture fractions in cultures exhibiting peak enzyme production revealed that most of the endoglucase was present either in the culture filtrate (45.8% of the total) or associated with the insoluble pellet fraction remaining after centrifugation of homogenized mycelia (32.6%). Cellobiohydrolase exhibited a similar distribution pattern, with 58.9% of the total enzyme present in culture filtrates and 31.0% associated with the pellet fraction. Conversely, most β-glucosidase activity (63.9% of the total) was present in extracts of fungal mycelia whereas only 9.4% was detected in culture filtrates. The endoglucanase and β-glucosidase distribution patterns were confirmed by confocal laser scanning microscopy combined with immunolabelling. Endoglucanase was shown to be largely cell wall associated or located extracellularly, with the highest concentrations being present in a region 1 to 2 μm wide immediately adjacent to the outer surface of (and possibly including) the hyphal wall and extending 60 to 70 μm from the hyphal tip. Immunofluorescence patterns indicated little if any intracellular endoglucanase. Most β-glucosidase was located intracellularly in the apical area extending 60 to 70 μm below the hyphal tip, although enzyme was also evident in the extracellular region extending approximately 15 μm all around the hyphal tip and trailing back along the length of the hypha. The regions of the hypha located some distance from the apical region appeared to be devoid of intracellular β-glucosidase, and the enzyme appears to be associated almost exclusively with, or located on the outside surface of, the hyphal wall.