极端嗜盐古菌中CRISPR结构的生物信息学分析

摘要：【目的】利用生物信息学方法了解目前拥有全基因组序列的极端嗜盐古菌中CRISPR结构的特征。【方法】通过比对,保守性分析,GC含量分析,RNA结构预测等方法对已有全基因组序列的嗜盐古菌基因组进行研究。【结果】在5株嗜盐古菌基因组中发现CRISPR结构,在leader序列内得到具有回文性质的保守motif。发现在大CRISPR结构内repeat序列具有很强的保守性。同时根据第四位碱基的不同,repeat序列可形成两类不同的RNA二级结构。【结论】leader序列中回文结构的发现对其可能为蛋白结合位点的假     

The Complete Mitochondrial Genome of Gossypium hirsutum and Evolutionary Analysis of Higher Plant Mitochondrial Genomes

Background

Mitochondria are the main manufacturers of cellular ATP in eukaryotes. The plant mitochondrial genome contains large number of foreign DNA and repeated sequences undergone frequently intramolecular recombination. Upland Cotton (Gossypium hirsutum L.) is one of the main natural fiber crops and also an important oil-producing plant in the world. Sequencing of the cotton mitochondrial (mt) genome could be helpful for the evolution research of plant mt genomes.

Methodology/Principal Findings

We utilized 454 technology for sequencing and combined with Fosmid library of the Gossypium hirsutum mt genome screening and positive clones sequencing and conducted a series of evolutionary analysis on Cycas taitungensis and 24 angiosperms mt genomes. After data assembling and contigs joining, the complete mitochondrial genome sequence of G. hirsutum was obtained. The completed G.hirsutum mt genome is 621,884 bp in length, and contained 68 genes, including 35 protein genes, four rRNA genes and 29 tRNA genes. Five gene clusters are found conserved in all plant mt genomes; one and four clusters are specifically conserved in monocots and dicots, respectively. Homologous sequences are distributed along the plant mt genomes and species closely related share the most homologous sequences. For species that have both mt and chloroplast genome sequences available, we checked the location of cp-like migration and found several fragments closely linked with mitochondrial genes.

Conclusion

The G. hirsutum mt genome possesses most of the common characters of higher plant mt genomes. The existence of syntenic gene clusters, as well as the conservation of some intergenic sequences and genic content among the plant mt genomes suggest that evolution of mt genomes is consistent with plant taxonomy but independent among different species.     

Marine Sediment Bacteria Harbor Antibiotic Resistance Genes Highly Similar to Those Found in Human Pathogens

The ocean is a natural habitat for antibiotic-producing bacteria, and marine aquaculture introduces antibiotics into the ocean to treat infections and improve aquaculture production. Studies have shown that the ocean is an important reservoir of antibiotic resistance genes. However, there is a lack of understanding and knowledge about the clinical importance of the ocean resistome. We investigated the relationship between the ocean bacterial resistome and pathogenic resistome. We applied high-throughput sequencing and metagenomic analyses to explore the resistance genes in bacterial plasmids from marine sediments. Numerous putative resistance determinants were detected among the resistance genes in the sediment bacteria. We also found that several contigs shared high identity with transposons or plasmids from human pathogens, indicating that the sediment bacteria recently contributed or acquired resistance genes from pathogens. Marine sediment bacteria could play an important role in the global exchange of antibiotic resistance.     

EST-based analysis of gene expression in the porcine brain

Since pig is an important livestock species worldwide, its gene expression has been investigated intensively, but rarely in brain. In order to study gene expression profiles in the pig central nervous system, we sequenced and analyzed 43,122 highquality 5’ end expressed sequence tags (ESTs) from porcine cerebellum, cortex cerebrum, and brain stem cDNA libraries, involving several different prenatal and postnatal developmental stages. The initial ESTs were assembled into 16,101 clusters and compared to protein and nucleic acid databases in GenBank. Of these sequences, 30.6% clusters matched protein databases and represented function known sequences; 75.1% had significant hits to nucleic acid databases and partial represented known function; 73.3% matched known porcine ESTs; and 21.5% had no matches to any known sequences in GenBank. We used the categories defined by the Gene Ontology to survey gene expression in the porcine brain.     

Design, synthesis and biological activity of novel C2-C3' N-Linked macrocyclic taxoids

A series of novel macrocyclic taxoids was designed and synthesized by connecting the C-2 and C-3' N positions of the taxoid framework with various tethers. Cytotoxicity of these macrocyclic taxoids was evaluated against a human breast cancer cell line LCC6-WT, and a couple of the taxoids exhibited 0.09-0.3 microM IC(50) values.     

Discovery, identification and comparative analysis of non-specific lipid transfer protein (nsLtp) family in Solanaceae

Plant non-specific lipid transfer proteins(nsLtps) have been reported to be involved in plant defense activity against bacterial and fungal pathogens.In this study,we identified 135 (122 putative and 13 previously identified) Solanaceae nsLtps,which are clustered into 8 different groups.By comparing with Boutrot's nsLtp classification,we classified these eight groups into five types (Ⅰ,Ⅱ,Ⅳ,Ⅸ and Ⅹ).We compared Solanaceae nsLtps with Arabidopsis and Gramineae nsLtps and found that (1) Types Ⅰ,Ⅱ and Ⅳ are shared by Solanaceae,Gramineae and Arabidopsis;(2) Types Ⅲ,Ⅴ,Ⅵ and Ⅷ are shared by Gramineae and Arabidopsis but not detected in Solanaceae so far;(3) Type Ⅶ is only found in Gramineae whereas type Ⅸ is present only in Arabidopsis and Solanaceae;(4) Type X is a new type that accounts for 52.59% Solanaceae nsLtps in our data,and has not been reported in any other plant so far.We further built and compared the three-dimensional structures of the eight groups,and found that the major functional diversification within the nsLtp family could be predated to the monocot/dicot divergence,and many gene duplications and sequence variations had happened in the nsLtp family after the monocot/dicot divergence,especially in Solanaceae.