Morphology of temperate bacteriophage SfV and characterisation of the DNA packaging and capsid genes: the structural genes evolved from two different phage families

The entire genome of SfV, a temperate serotype-converting bacteriophage of Shigella flexneri, has recently been sequenced (Allison, G.E., Angeles, D., Tran-Dinh, N., Verma, N.K. 2002, J. Bacteriol. 184, 1974-1987). Based on the sequence analysis, we further characterised the SfV virion structure and morphogenesis. Electron microscopy indicated that SfV belongs to the Myoviridae morphology family. Analysis of the proteins encoded by orf1, orf2, and orf3 revealed that they were homologous to small and large terminase subunits, and portal proteins, respectively; the protein encoded by orf5 showed homology to capsid proteins. Western immunoblot of the phage with anti-SfV sera revealed two antigenic proteins, and the N-terminal amino acid sequence of the 32-kDa protein corresponded to amino acids 116 to 125 of the ORF5 protein, suggesting that the capsid may be processed. Functional analysis of orf4 showed that it encodes the phage capsid protease. The proteins encoded by orfs1, 2, 3, 4, and 5 are homologous to similar proteins in the Siphoviridae phage family of both gram-positive and gram-negative origin. The capsid and morphogenesis genes are upstream and adjacent to the genes encoding Myoviridae (Mu-like) tail proteins. The organisation of the structural genes of SfV is therefore unique as the head and tail genes originate from different morphology groups.     

Muscle-epidermis interactions affect exoskeleton patterning in Caenorhabditis elegans.

The C. elegans hypodermis is a single epithelial cell layer separated from the musculature by a thin basement membrane on its basal surface. The hypodermis secretes the extracellular material of the cuticle from its apical surface. The regulation of cuticle synthesis and apical secretion is not well understood. UNC-95 is a component of the muscle dense bodies and M-lines, which are integrin-based adhesion complexes required for force transduction to the cuticle. Using gene expression profiling and in vivo assays, we show that, in unc-95 mutant worms, there is an increase in expression levels of a group of hypodermal and pharyngeal genes related to cuticle structure and molting. Moreover, the cuticle structure of unc-95 mutant adult is impaired. Our findings suggest that aberrant force transduction from the structurally impaired muscle attachments across the basement membrane to the underlying hypodermis elicits intercellular signaling that plays a role in regulating cuticle synthesis and patterning.     

细菌对噬菌体感染的抵抗

噬菌体对其宿主菌具有特异性感染力,反之,宿主菌对噬菌体的感染具有抵抗现象.根据噬菌体侵入宿主的不同阶段,可以将宿主菌对噬菌体的天然抵抗机制分为4个主要的类别吸附抑制,流产感染,限制-修饰系统和穿入阻滞.此外,还有源于噬菌体的抗性作用以及通过人工插入突变获得的广谱噬菌体抗性菌株等.     

The genome of bacteriophage phiKMV,a T7-like virus infecting Pseudomonas aeruginosa

The complete DNA sequence of a new lytic T7-like bacteriophage phiKMV is presented. It is the first genome sequence of a member of the Podoviridae that infects Pseudomonas aeruginosa. The linear G + C-rich (62.3%) double-stranded DNA genome of 42,519 bp has direct terminal repeats of 414 bp and contains 48 open reading frames that are all transcribed from the same strand. Despite absence of homology at the DNA level, 11 of the 48 phiKMV-encoded putative proteins show sequence similarity to known T7-type phage proteins. Eighteen open reading frame products have been assigned, including an RNA polymerase, proteins involved in DNA replication, as well as structural, phage maturation, and lysis proteins. Surprisingly, the major capsid protein completely lacks sequence homology to any known protein. Also, the strong virulence toward many clinical P. aeruginosa isolates and a short replication time make phiKMV attractive for phage therapy or a potential source for antimicrobial proteins.     

Analysis of the Virus Population Present in Equine Faeces Indicates the Presence of Hundreds of Uncharacterized Virus Genomes

Virus DNA was isolated from horse faeces and cloned in a sequence-independent fashion. 268 clones were sequenced and 178140 nucleotides of sequence obtained. Statistical analysis suggests the library contains 17560 distinct clones derived from up to 233 different virus genomes. TBLASTX analysis showed that 32% of the clones had significant identity to GenBank entries. Of these 63% were viral; 20% bacterial; 7% archaeal; 6% eukarya; and 5% were related to mobile genetic elements. Fifty-two percent of the virus identities were with Siphoviridae; 26% unclassified phages; 17% Myoviridae; 4% Podoviridae; and one clone (2%) was a vertebrate Orthopoxvirus. Genes coding for predicted virus structural proteins, proteases, glycosidases and nucleic acid-binding proteins were common.     

Multiple Copies of the Upstream Regulatory Region of the Major Capsid Protein Gene of Bacteriophage MB78 Inhibit Phage Morphogenesis

The 2.311 kb EcoRI F fragment of bacteriophage MB78 has been cloned in multicopy vectors pUC19 and pCR90. Salmonella typhimurium strains carrying such plasmids cannot support development of phage MB78 while other Salmonella phages like P22 and 9NA grow normally. Most of the phage MB78 induced functions are normal in such transformed hosts but proper maturation of the phage particles does not take place. Deletion of 138 bp from the 3 end of the cloned fragment reverses the inhibitory effect. Analysis of nucleotide and the deduced amino acid sequence of a 1.2 kb HindIII-SalI fragment of the phage genome which overlaps the 138 bp confirms that this part contains the upstream regulatory region of the major structural protein gene. It seems that in presence of multiple copies of the upstream regulatory region (which includes a number of promoter like sequence) of the coat protein gene, the maturase gene is down regulated and this is effective only in cis, a situation quite similar to that of Q RNA phages.     

Cloning,Sequencing, Expression and Promoter Analysis of a Structural Protein of Bacteriophage MB78

Bacteriophage MB78, a virulent phage of Salmonella typhimurium isolated in our laboratory. It is different from the well-known temperate phage P22 and 9NA. A detailed physical map has been constructed. To understand more about the physiology and genetics of this interesting phage it has become necessary to fragment the phage genome, clone the fragments and analyze in depth. A number of promoters of bacteriophage MB78 have been cloned and characterized recently. As a part of this program, in this investigation, we report cloning, sequencing and expression and promoter analysis of the ClaI G fragment. We identified the expressed protein as phage structural. Phage structural proteins play a vital role in forming the core head of the phage particle.     

Identification of a Strong Promoter of Bacteriophage MB78 that Lacks Consensus Sequence Around Minus 35 Region and Interacts with Phage Specific Factor

A strong promoter of bacteriophage MB78 does not have minus 35 consensus sequence although it has a TGn motif immediately upstream of minus 10 sequence as well as the AT rich UP element. It is efficiently recognised by the sigma 70 RNA polymerase, however, a phage-specific factor competes with sigma 70 RNA polymerase for binding to this region, the binding of the factor being stronger than that of the polymerase. Contrary to the reports in the literature the polymerase appears not to bind to the UP element whereas the phage-specific factor does. The latter seems to be involved in the regulation of the promoter activity. This revised version was published online in July 2006 with corrections to the Cover Date.     

改质炉高温炉管运行损伤及剩余寿命分析

对高温运行70000h至90000h改质炉炉管进行试验研究及材料损伤分析,结果表明,炉管的材料性能已严重劣化（脆化）,炉管的内外壁已有微小裂纹萌生,测定了炉管材料在950℃、各种应力水平下的断裂时间,根据时间-温度参数L-M公式,推测炉管的剩余寿命为8510h。     

计算流体力学在组织工程中的应用进展

目的综述计算流体力学（computational fluid dynamics，CFD）在组织工程中的应用进展。方法广泛查阅 CFD 应用于组织工程的相关文献，主要对 CFD 用于生物反应器设计改良或优化、模拟体外组织再生过程中的流体动力学和细胞生长动力学等方面进行综述。结果CFD 的模拟预测能力可为生物反应器的设计优化和体外组织工程组织培养提供重要的指导作用，且结合实验研究能进一步提高模型预测结果的准确性。结论CFD 作为新兴和有效的研究工具，已在组织工程中展现出独特优势并取得显著进展，但更全面、准确地模拟组织再生全过程仍需进一步研究。