Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.

The 1,860,725-base-pair genome of Thermotoga maritima MSB8 contains 1,877 predicted coding regions, 1,014 (54%) of which have functional assignments and 863 (46%) of which are of unknown function. Genome analysis reveals numerous pathways involved in degradation of sugars and plant polysaccharides, and 108 genes that have orthologues only in the genomes of other thermophilic Eubacteria and Archaea. Of the Eubacteria sequenced to date, T. maritima has the highest percentage (24%) of genes that are most similar to archaeal genes. Eighty-one archaeal-like genes are clustered in 15 regions of the T. maritima genome that range in size from 4 to 20 kilobases. Conservation of gene order between T. maritima and Archaea in many of the clustered regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea.     

茅台酒曲中产淀粉酶细菌分离及性质

从茅台酒曲中分离出产α淀粉酶优良菌株,经鉴定为芽孢杆菌属。在这些菌株中,所产α-淀粉酶以中温型为主,最适宜温度在50~60℃之间,也分离到一株最适宜温度为80℃高温型酶的菌株。同时研究了发酵培养基中碳氮源比对一株芽孢杆菌酶活力的影响及酶活力与培养时间的关系,结果表明,当碳氮比为9∶4 5时酶活力较高,酶活力在生长周期稳定期后期到死亡期达到最高。     

Independent transfer of mitochondrial chromosomes and plasmids during unstable vegetative fusion in Neurospora

The sporadic distribution of similar introns in organelle, nuclear ribosomal RNA and bacteriophage genes suggests that at least some of these introns are mobile genetic elements. Some plasmids in fungal mitochondria contain intron-like sequences and, like introns, they have scattered distributions within and among species. The occurrence and evolutionary importance of such horizontal transfer of DNA, not only between fungi, but among a wide range of organisms have been matters of much discussion. Here, we report experimental evidence for transfer of Neurospora mitochondrial plasmids from one mitochondrial genotype to another at high frequency during unstable vegetative cell fusion. Exchange of mitochondrial and nuclear genomes can also occur. These observations suggest that vegetative fusion may have a more important role in the mitochondrial genetic structure of natural populations than is generally thought, and may provide an explanation for the distribution of certain plasmids and possibly other mobile genetic elements.     

细菌和酵母基因组中ORF结构特征的统计分析

将第一ATG规则用于细菌Hpyl，Hpyl99，E.coli，Aero，Tmar和Yeast基因组中，并用给出ORF(包含已知基因编码区)进行检验，其结果对以ATG起始的ORF序列正确率皆为89％以上，将五种细菌和酵母基因组中给出ORF分成第一种(已确定的编码序列)和第二种(还未确定为编码序列的)ORF，并计算L—Ter到第一ATG的平均距离，分析了五种细菌和酵母终止密码子在L-Ter位置和Ter位置上的使用频率，发现在Ter位置上终止密码子使用的偏置程度比在L-Ter位置上大．     

自来水中细菌宏基因组DNA的浓度与细菌菌落总数的相关性分析

分析自来水中细菌宏基因组DNA浓度与细菌菌落总数之间的相关性,探索新的自来水细菌菌落总数检测方法。采用国标法检测自来水中的细菌菌落总数约为(165±5)CFU/m L,高于国标限值(100 CFU/m L)。通过计算得出,检测600 m L本实验水样中的细菌菌落总数相当于检测1 000 m L(1 L)100 CFU/m L的自来水。首先将600 m L及低于和高于该体积不同体积梯度的自来水经滤膜过滤收集菌体;然后使用细菌基因组提取试剂盒提取滤膜上的细菌宏基因组DNA,电泳分析提取的宏基因组质量;最后检测各个体积自来水宏基因组DNA浓度,根据检测结果分析自来水中宏基因组DNA含量与细菌菌落总数之间的相关性。提取的自来水宏基因组DNA主条带清晰,可以进行基因组DNA含量测定分析;自来水中细菌宏基因组DNA浓度与细菌菌落总数之间呈正相关的线性关系。建立一种通过检测自来水中细菌宏基因组DNA浓度来反映细菌菌落总数的检测方法,检测灵敏度可达7 CFU/m L,且省时、重复性好。     

丙酮处理酵母菌吸附铅前后红外光谱分析比较

对丙酮处理酵母菌吸附铅前后的红外光谱进行了分析比较。生物材料的红外光谱图主要由蛋白质的吸收带、碳水化合物的吸收带组成。1652cm^-1、1534cm^-1、1239cm^-1处的吸收峰是蛋白质的三个特征吸收峰。1455cm^-1处的吸收峰为CH3和CH2的弯曲振动峰;1397cm^-1处中等强度的吸收归属于羧基的对称伸缩振动。1200-940cm^-1之间出现的强且复杂的谱带归属于醚和碳水化合物中的C-O伸缩振动。915cm^-1、890cm^-1处两个弱的吸收峰属于细胞壁中多糖的糖环键的振动。吸附pb^2 后,3375cm^-1处的吸收峰紫移至3388cm^-1,1398cm^-1处的峰红移到1384cm^-1,说明羟基和羧基在结合pb^2 起重要作用丙酮处理酵母菌的主要成份和结构吸附前后保持完整。     

Direct observation of hole transfer through DNA by hopping between adenine bases and by tunnelling.

The function of DNA during oxidative stress and its suitability as a potential building block for molecular devices depend on long-distance transfer of electrons and holes through the molecule, yet many conflicting measurements of the efficiency of this process have been reported. It is accepted that charges are transported over long distances through a multistep hopping reaction; this 'G-hopping' involves positive charges moving between guanines (Gs), the DNA bases with the lowest ionization potential. But the mechanism fails to explain the persistence of efficient charge transfer when the guanine sites are distant, where transfer rates do not, as expected, decrease rapidly with transfer distance. Here we show experimentally that the rate of charge transfer between two guanine bases decreases with increasing separation only if the guanines are separated by no more than three base pairs; if more bridging base pairs are present, the transfer rates exhibit only a weak distance dependence. We attribute this distinct change in the distance dependence of the rate of charge transfer through DNA to a shift from coherent superexchange charge transfer (tunnelling) at short distances to a process mediated by thermally induced hopping of charges between adenine bases (A-hopping) at long distances. Our results confirm theoretical predictions of this behaviour, emphasizing that seemingly contradictory observations of a strong as well as a weak influence of distance on DNA charge transfer are readily explained by a change in the transfer mechanism.     

Renaturation of DNA catalysed by yeast DNA repair and recombination protein RAD10.

The RAD10 gene of Saccharomyces cerevisiae is required for the incision step of excision repair of ultraviolet-damaged DNA, and it functions in mitotic recombination. RAD10 has homology to the human excision repair gene ERCC-1. Here we describe the purification of the protein encoded by RAD10 and show that it is a DNA-binding protein with a strong preference for single-stranded DNA. We also show that RAD10 promotes the renaturation of complementary DNA strands.     

Bacterial virulence proteins as tools to rewire kinase pathways in yeast and immune cells

Bacterial pathogens have evolved specific effector proteins that, by interfacing with host kinase signalling pathways, provide a mechanism to evade immune responses during infection. Although these effectors contribute to pathogen virulence, we realized that they might also serve as valuable synthetic biology reagents for engineering cellular behaviour. Here we exploit two effector proteins, the Shigella flexneri OspF protein and Yersinia pestis YopH protein, to rewire kinase-mediated responses systematically both in yeast and mammalian immune cells. Bacterial effector proteins can be directed to inhibit specific mitogen-activated protein kinase pathways selectively in yeast by artificially targeting them to pathway-specific complexes. Moreover, we show that unique properties of the effectors generate new pathway behaviours: OspF, which irreversibly inactivates mitogen-activated protein kinases, was used to construct a synthetic feedback circuit that shows novel frequency-dependent input filtering. Finally, we show that effectors can be used in T cells, either as feedback modulators to tune the T-cell response amplitude precisely, or as an inducible pause switch that can temporarily disable T-cell activation. These studies demonstrate how pathogens could provide a rich toolkit of parts to engineer cells for therapeutic or biotechnological applications.     

鲫鱼养殖池塘底泥菌群结构及常见可培养菌分析

为了研究江苏地区鲫鱼养殖池塘底泥细菌菌群结构与多样性,通过高通量测序技术对2017年8-10月间采集的江苏省不同区域养殖池塘底泥中所有细菌的16S rRNA V3-V4基因进行扩增测定,分析了底泥菌群结构特征;并通过平板计数法和选择培养基法检测池塘底泥中细菌总数和主要常见菌。结果表明,49个样品高通量测序共获得有效序列2152956条,可归为17735个分类操作单元(OTUs);物种注释结果显示,鲫鱼养殖池塘底泥中具有较高的菌群多样性,检测到的细菌归属于29个门类,所有池塘底泥都具有主要门类为变形菌门、绿弯菌门、厚壁菌门、拟杆菌门、水生古细菌门、酸杆菌门、放线菌门、硝化螺旋菌门、螺旋菌门、芽单胞菌门、蓝细菌门、浮霉菌门、疣微菌门等。在属的水平上主要以硫杆菌属,乳酸球菌属,硫氧化菌,甲烷菌,地杆菌属,假单胞菌属,厌氧粘杆菌属,甲烷绳菌属,芽孢杆菌属等为主;所有池塘底泥共有菌主要有乳酸球菌属,甲烷菌,盐单胞菌,芽孢杆菌,红杆菌属,链球菌属,肉杆菌属,微小杆菌属,土芽孢杆菌属等。通过细菌培养发现,池塘底泥中常见益生菌如乳酸菌、芽孢菌具有较高的比例。可见鲫鱼养殖池塘底泥菌群结构及组成具有多样性,不同养殖池塘中共有的细菌可作为益生菌开发的参考菌株。     

CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNA replication in budding yeast

In eukaryotic cells, cyclin-dependent kinases (CDKs) have an important involvement at various points in the cell cycle. At the onset of S phase, active CDK is essential for chromosomal DNA replication, although its precise role is unknown. In budding yeast (Saccharomyces cerevisiae), the replication protein Sld2 (ref. 2) is an essential CDK substrate, but its phospho-mimetic form (Sld2-11D) alone neither affects cell growth nor promotes DNA replication in the absence of CDK activity, suggesting that other essential CDK substrates promote DNA replication. Here we show that both an allele of CDC45 (JET1) and high-copy DPB11, in combination with Sld2-11D, separately confer CDK-independent DNA replication. Although Cdc45 is not an essential CDK substrate, CDK-dependent phosphorylation of Sld3, which associates with Cdc45 (ref. 5), is essential and generates a binding site for Dpb11. Both the JET1 mutation and high-copy DPB11 by-pass the requirement for Sld3 phosphorylation in DNA replication. Because phosphorylated Sld2 binds to the carboxy-terminal pair of BRCT domains in Dpb11 (ref. 4), we propose that Dpb11 connects phosphorylated Sld2 and Sld3 to facilitate interactions between replication proteins, such as Cdc45 and GINS. Our results demonstrate that CDKs regulate interactions between BRCT-domain-containing replication proteins and other phosphorylated proteins for the initiation of chromosomal DNA replication; similar regulation may take place in higher eukaryotes.     

基于NFS的UNIX与Netware间数据传送

文中介绍在UNIX多用户系统与Novell网络服务器建立网络互连情况下 ,应用网络文件系统NFS使UNIX系统主机与Novell网络服务器之间实现数据的互备份。     

Near-field radiative heat transfer between general materials and metamaterials

We investigated the near-field radiative heat transfer between general materials and metamaterials. We studied the effects of metamaterial parameters on the radiative heat exchange and used three kinds of natural or artificially-constructed materials such as Al, boron-doped Si and metamaterials as examples. We calculated and analyzed the near-field radiative heat transfer processes between two semi-infinite bodies. The numerical results indicate that the radiative heat exchange between the two different materials may be less or more than the radiative heat exchange between the corresponding identical materials. It was found out to depend on the radiative properties of the materials. The work would provide a valuable reference for the selection of practical materials.