Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection.     

Polymorphisms in the selenoprotein S and 15-kDa selenoprotein genes are associated with altered susceptibility to colorectal cancer

Selenium (Se), a dietary trace metal essential for human health, is incorporated into ~25 selenoproteins including selenoprotein S (SelS) and the 15-kDa selenoprotein (Sep15) both of which have functions in the endoplasmic reticulum protein unfolding response. The aim of this study was to investigate whether genetic variants in such selenoprotein genes are associated with altered risk of colorectal cancer (CRC). A Korean population of 827 patients with CRC and 733 healthy controls was genotyped for 7 SNPs in selenoprotein genes and one SNP in the gene encoding manganese superoxide dismutase using Sequenom technology. Multivariate logistic regression analysis showed that after adjustment for lifestyle factors three SNP variants were associated with altered disease risk. There was a mean odds ratio of 2.25 [95% CI 1.13,4.48] in females homozygous TT for rs34713741 in SELS with the T variant being associated with higher risk of rectal cancer, and odds ratios of 2.47 and 2.51, respectively, for rs5845 and rs5859 in SEP15 with the minor A and T alleles being associated with increased risk of male rectal cancer. The data indicate that the minor alleles for rs5845, rs5859 and rs34713741 are associated with increased rectal cancer risk and that the effects of the three SNPs are dependent on gender. The results highlight potential links between Se, the function of two selenoproteins involved in the protein unfolding response and CRC risk. Further studies are required to investigate whether the effects of the variants on CRC risk are also modulated by dietary Se intake.     

Structure and characterization of amidase from Rhodococcus sp. N-771: Insight into the molecular mechanism of substrate recognition

In this study, we have structurally characterized the amidase of a nitrile-degrading bacterium, Rhodococcus sp. N-771 (RhAmidase). RhAmidase belongs to amidase signature (AS) family, a group of amidase families, and is responsible for the degradation of amides produced from nitriles by nitrile hydratase. Recombinant RhAmidase exists as a dimer of about 107 kDa. RhAmidase can hydrolyze acetamide, propionamide, acrylamide and benzamide with kcat/Km values of 1.14 ± 0.23 mM^− 1s^− 1, 4.54 ± 0.09 mM^− 1s^− 1, 0.087 ± 0.02 mM^− 1s^− 1 and 153.5 ± 7.1 mM^− 1s^− 1, respectively. The crystal structures of RhAmidase and its inactive mutant complex with benzamide (S195A/benzamide) were determined at resolutions of 2.17 Å and 2.32 Å, respectively. RhAmidase has three domains: an N-terminal α-helical domain, a small domain and a large domain. The N-terminal α-helical domain is not found in other AS family enzymes. This domain is involved in the formation of the dimer structure and, together with the small domain, forms a narrow substrate-binding tunnel. The large domain showed high structural similarities to those of other AS family enzymes. The Ser-cis Ser-Lys catalytic triad is located in the large domain. But the substrate-binding pocket of RhAmidase is relatively narrow, due to the presence of the helix α13 in the small domain. The hydrophobic residues from the small domain are involved in recognizing the substrate. The small domain likely participates in substrate recognition and is related to the difference of substrate specificities among the AS family amidases.     

单级自养脱氮系统中厌氧氨氧化菌的分子生物学鉴定

对具有厌氧氨氧化作用的细菌进行更深入的分析有助于了解该菌在生物脱氮过程的应用。对稳定运行、氨氮转化率及总氮去除率分别达到90%及80%左右的单级自养脱氮系统的底部取活性污泥,采用分子生物学方法提取活性污泥细菌总DNA,利用特异引物Pla46rc/Amx820对单级自养脱氮系统中的厌氧氨氧化菌16S rDNA基因进行PCR扩增。扩增产物经克隆、测序及BLAST分析,结果表明该单级自养脱氮系统中存在的厌氧氨氧化菌与Candidatus Kueneniastuttgartiensis和Candidatus Brocadia anammoxidans的16S rDNA序列同源性达99%,进化分析证明与Candidatus Kuenenia stuttgartiensis进化上较为接近。     

产紫杉醇内生真菌EFY-21的鉴定与生物学特性研究

利用PCR技术克隆了产紫杉醇内生真菌EFY-21的18S rDNA序列,通过同源性分析,初步确定该菌与拟盘多毛孢属(Pestalotiopsis)有较高的同源性,相似性为99%。为了进一步了解EFY-21的有关生物学特性,分别选用PDA、PSA、查氏、玉米粉琼胶、牛肉膏蛋白胨5种培养基,按照常规方法培养,用十字法测量菌落直径;同时选用查氏培养基为基本培养基,分别观察不同碳源葡萄糖、甘露醇、麦芽糖、果糖、可溶性淀粉,不同氮源KNO3、Ca(N03)2、(NH4)2SO4、NH4N03、(NH4)2HPO4、蛋白胨、尿素,不同培养温度10,15,20,25,28,30,37℃,不同pH值4,5,6,7,8,9对内生真菌菌丝的影响。试验结果表明:EFY-21在PDA培养基上生长最快,生长状况最好;供试的碳氮源中,对EFY-21菌丝生长影响的大小顺序为葡萄糖甘露醇果糖麦芽糖可溶性淀粉;蛋白胨KNO3Ca(N03)2NH4N03(NH4)2HPO4(NH4)2SO4尿素;最适培养温度为25～30℃;最适pH为5～7。     

越香竹——香竹属一新种

报导了从云南省金平县用种子(种子来源于越南莱州省的燕汤)繁殖的幼苗引入四川长宁县栽培的香竹属一新种越香竹(Chimonoca lamus peregrinus Yiet L.S.Ma)。新种与马关香竹(Ch.makuanensis Hsuehet Yi)相近似[1,3～5],但节间幼时微被灰粉,密被紫色小点,在分枝一侧中下部或基部扁平,并具纵脊和沟槽,无毛,刺状气生根较短,长约1～3mm,箨鞘短于节间长度,无不同颜色的纵条纹,箨舌三角形、"山"字形或稀近于截平形,高1～2mm,小枝具叶(4)6～8枚,叶鞘口繸毛2～4枚,长3～4mm,叶片下面淡绿色;也近似角香竹(Ch.bicorniculatusS.F.LietZ.P.Wang)[2,4,5],不同在于节间无毛,在分枝一侧中下部或基部扁平,并具纵脊与沟槽,节上气生根刺离生,箨鞘顶端两侧低于或远低于中部,箨舌高1～2mm,小枝具叶(4)6～8枚,叶片长8.5～13cm,宽6～10mm,次脉3(4)对,笋期在春季和秋季,易于区别。     

Cardioprotection in ischemia/reperfusion injury: Spotlight on sphingosine-1-phosphate and bradykinin signalling

Complex signal-transduction cascades are known to be involved in regulating cardiomyocyte function, death and survival during acute cardiac ischemia-reperfusion process, but detailed survival signalling pathways are not clear. This review presents and discusses the recent findings bearing upon the evidence on the cardioprotective effect of sphingosine-1-phosphate (S1P) and bradykinin in acute cardiac ischemia-reperfusion and underlying signalling mechanisms, particularly, through activation of P21 activated kinase.     

Determining the genetic diversity of lactobacilli from the oral cavity

Several methods for determining the diversity of Lactobacillus spp were evaluated with the purpose of developing a realistic approach for further studies. The patient population was comprised of young children with an oral disease called severe early childhood caries. The ultimate goal of these studies was to ascertain the role of lactobacilli in the caries process. To accomplish that goal, we evaluated several methods and approaches for determining diversity including AP-PCR, chromosomal DNA fingerprinting, denaturing gradient gel electrophoresis, and 16S rRNA gene sequencing. Central to these methods was the gathering and screening of isolates from cultivation medium. Using various estimates of diversity, we addressed the question as to how many isolates represent the overall diversity and how cultivation compares to non-cultivation techniques. Finally, we proposed a working approach for achieving the goals outlined framed by both practical constraints in terms of time, effort and efficacy while yielding a reliable outcome.     

拆分获得(S)-酮基布洛芬脂肪酶基因在枯草芽孢杆菌中的克隆与表达

【目的】筛选具有不对称拆分消旋酮基布洛芬氯乙酯能力的脂肪酶基因,构建其表达分泌型工程菌,并进一步提高该脂肪酶的立体选择性。【方法】以自筛选出的一株具有不对称拆分消旋酮基布洛芬氯乙酯能力的菌株NK13为材料,通过构建其基因组文库,筛选具有不对称拆分消旋酮基布洛芬氯乙酯能力的脂肪酶基因。通过构建该脂肪酶基因的分泌型诱导表达载体pHY300-plk-sacR-gene,将其转入枯草芽孢杆菌WB600,获得基因重组菌WB600(pHY300-plk-sacR-gene)。用SDS-PAGE检测其表达和转化情况,采用非变性聚丙烯酰胺凝胶电泳的方法纯化脂肪酶;并利用TLC和HPLC检测该酶的立体选择专一性。【结果】得到了具有专一性拆分获得(S)-酮基布洛芬能力、长度为633bp的脂肪酶基因(GenBank登录号为:EU381317)。该脂肪酶在枯草芽孢杆菌WB600中得到了分泌表达。TLC和HPLC检测结果显示,纯化的脂肪酶对底物转化40h时转化率为30%,生成(S)-酮基布洛芬的e.e.%值最高,达60.02%,与未加Tween-80的枯草芽孢杆菌转化子体系相同。而在含Tween-80的环境下,枯草芽孢杆菌表达重组菌对底物转化36h时转化率约为45%,生成(S)-酮基布洛芬的e.e.%值最高,达93.64%,是野生菌NK13的16倍。【结论】从NK13号菌株中筛选得到的新的脂肪酶具有很高的不对称拆分获得(S)-酮基布洛芬的能力,实现了NK13菌中633bp脂肪酶基因在枯草芽孢杆菌中的分泌表达,研究证明Tween-80能提高该脂肪酶的拆分专一性。     

新疆玛纳斯热气泉免培养土壤细菌多样性分析

【目的】了解新疆玛纳斯热气泉土壤免培养细菌群落组成及多样性。【方法】采用免培养法直接从土壤样品中提取总DNA,利用细菌通用引物对土壤总DNA进行16S rDNA扩增,构建细菌16SrDNA文库。使用HaeⅢ限制性内切酶对阳性克隆进行限制性片段长度多态性分析(restriction fragment length polymorphism,RFLP),挑选具有不同酶切图谱的克隆进行测序、比对并构建16SrDNA系统发育树。【结果】从土壤细菌16S rDNA文库中随机挑选了170个阳性克隆,共得到29个不同的分类单元(operational taxonomic unit,OTU)。系统发育分析归为6个门:酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)、拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)和浮霉菌门(Planctomycetes)。其中厚壁菌门(Firmicutes)为绝对优势类群,占整个细菌文库的71%。29个OTUs中有14条序列与GenBank中相关序列的相似性低于97%(序列长度约1.5kb),占序列总数的48%。【结论】热气泉土壤细菌种群多样性较低,但存在大量潜在细菌新种。