牦牛NLRP基因家族全基因组鉴定及转录组分析

NLRP基因家族在哺乳动物基因组中分布广泛,在免疫应答和生殖相关过程中发挥重要作用。本研究根据已报道的人类NLRP基因,利用PFAM、CDD、UniProt等数据库,采用ClustalW、MEGA X、ExPASy、MEME、GSDS和STRING等软件对牦牛NLRP家族成员进行全基因组鉴定和分析,并且基于高通量测序数据分析NLRP基因在牦牛不同组织中的表达情况。研究共鉴定出8个不同的NLRP基因家族成员,包括NLRP2、NLRP3、NLRP5、NLRP6、NLRP8、NLRP9、NLRP12、NLRP14,其中NLRP9有2个可变剪切。牦牛NLRP蛋白均有多个磷酸化位点,GRAVY值均小于0,属于亲水性蛋白;不稳定系数均大于40,均为不稳定蛋白,无跨膜结构。系统进化树显示同一家族成员氨基酸序列相似性高,在 6个物种中都聚在一起,免疫相关基因与生殖发育相关基因在进化中已经分开。蛋白互作网络显示牦牛NLRP蛋白与其他物种已经研究的功能相似,不仅与参与免疫相关的蛋白互作,也与生殖标记蛋白互作。如NLRP3与多种参与炎症反应的蛋白PYCARD、MLKL、GSDMD互作,NLRP5也与生殖细胞标记蛋白GDF9、BMP15、ZAR1等互作。转录组分析结果显示,牦牛NLRP基因在6种组织中的表达较为微弱或者不表达,具有组织特异性。牦牛NLRP家族在结构及理化性质上与其他物种同源基因具有相同的特点,部分试验和预测证实其同样参与了免疫和生殖相关过程。本研究结论不仅对牦牛NLRP基因家族进行了系统分析,同时为进一步研究牦牛先天免疫和生殖相关过程提供理论依据。     

Pathway and ontology analysis: emerging approaches connecting transcriptome data and clinical endpoints

The increasing use of gene expression profiling offers great promise in clinical research into disease biology and its treatment. Along with the ability to measure changing expression levels in thousands of genes at once, comes the challenge of analyzing and interpreting the vast sets of data generated. Analysis tools are evolving rapidly to meet such challenges. The next step is to interpret observed changes in terms of the biological properties or relationships underlying them. One powerful approach is to make associations between the genes that are under investigation and well-known biochemical or signaling pathways, and further to assess the significance of such associations. Similarly, genes can be mapped to standardized biological categories via an ontology resource. We discuss these approaches and several web-based resources and tools designed to facilitate such analyses. This information can be used to facilitate understanding and to help design more focused experiments for validating the relevance and importance of these biological pathways and processes in human disease and therapeutics.     

Exploring the plant transcriptome through phylogenetic profiling

Publicly available protein sequences represent only a small fraction of the full catalog of genes encoded by the genomes of different plants, such as green algae, mosses, gymnosperms, and angiosperms. By contrast, an enormous amount of expressed sequence tags (ESTs) exists for a wide variety of plant species, representing a substantial part of all transcribed plant genes. Integrating protein and EST sequences in comparative and evolutionary analyses is not straightforward because of the heterogeneous nature of both types of sequence data. By combining information from publicly available EST and protein sequences for 32 different plant species, we identified more than 250,000 plant proteins organized in more than 12,000 gene families. Approximately 60% of the proteins are absent from current sequence databases but provide important new information about plant gene families. Analysis of the distribution of gene families over different plant species through phylogenetic profiling reveals interesting insights into plant gene evolution, and identifies species- and lineage-specific gene families, orphan genes, and conserved core genes across the green plant lineage. We counted a similar number of approximately 9,500 gene families in monocotyledonous and eudicotyledonous plants and found strong evidence for the existence of at least 33,700 genes in rice (Oryza sativa). Interestingly, the larger number of genes in rice compared to Arabidopsis (Arabidopsis thaliana) can partially be explained by a larger amount of species-specific single-copy genes and species-specific gene families. In addition, a majority of large gene families, typically containing more than 50 genes, are bigger in rice than Arabidopsis, whereas the opposite seems true for small gene families.     

Toward organism identification through analysis of bacterial colonies.

The clinical problem of bacterial identification has been approached by applying pattern-recognition techniques to multi-wavelength surface-scattering and reflectance data derived from real-time scans of isolated colonies. Preliminary results, obtained from blood-agar plates inoculated with a mixture of staphylococci, streptococci and escherichieae, indicate that these organisms can be differentiated with better than 90% certainty, provided the colonies are physically separated and their growth conditions closely controlled. Data collection and classification characteristics of the experimental system are briefly described; it is felt that the technique, possibly expanded to include boundary characteristics of the colonies, may offer a viable means of identifying clinically important bacteria.     

Concatenation cDNA sequencing for transcriptome analysis

We describe a high-throughput cDNA sequencing pipeline (http://www.hgsc.bcm.tmc.edu/projects/cdna) built in response to the emerging need for rapid sequencing of large cDNA collections. Using this strategy cDNA inserts are purified and joined through concatenation into large molecules. These 'pseudo-BACs' are subjected to random shotgun sequencing whereby the majority of cDNA inserts in the pool are sequenced. Using this concatenation cDNA sequencing platform, we have contributed more than 13000 full-length cDNA sequences from human and mouse to the Mammalian Gene Collection (MGC).