基于稀疏表示算法的蛋白质质谱数据特征选择

高维、小样本数据的特征选择方法在蛋白质质谱数据处理分析领域有着广泛应用。本文针对蛋白质质谱特征选择问题,结合稀疏表示这一新理论框架,提出了一种基于稀疏表示的特征选择算法(sparse representation based feature selection,SRFS)。该方法将稀疏表示分类的结果作为评定某一个特征子空间特征相对重要性的度量,然后通过对大量随机采样子空间计算结果的统计,得到特征空间中每个特征的排序,并进一步分析提炼出与肿瘤疾病相关的若干谱峰。通过在卵巢癌公共数据集OC-WCX2a和浙江省肿瘤医院乳腺癌数据集BC-WCX2a上的实验结果表明,SRFS算法可以有效应用于本文所使用的SELDI-TOF蛋白质质谱数据的分析。     

多聚亚基蛋白质在固-液界面团聚的测量与表征

以血红蛋白和乙肝表面抗原(HBsAg)为模型,联用双偏振光干涉分析仪(DPI)和原子力显微镜(AFM)研究在固-液界面上的吸附行为.结果发现:当溶液环境中血红蛋白的质量浓度为1.08 mg/mL时,测得在硅羟基表面吸附的平均厚度为3.54 nm,蛋白颗粒直径达60～ 150 nm,远高于血红蛋白的分子尺寸,说明血红蛋白在固-液界面上发生团聚.当HBsAg质量浓度为0.67 mg/mL时,测得在硅羟基表面及DEAE琼脂糖表面吸附的平均厚度分别为1.06和23.69 nm,表面吸附的蛋白颗粒直径分别为288～401和520 ～ 971 nm,是单分子HBsAg尺寸的13.1～44.1倍,表明在模型蛋白表面都形成了大的团聚体.     

Phylogenetic analysis of the species Theilovirus: emerging murine and human pathogens

The Cardiovirus genus of the family Picornaviridae includes two distinct species, Encephalomyocarditis virus and Theilovirus. We now report the complete nucleotide sequences of three Theiler's murine encephalomyelitis virus (TMEV) strains (TO Yale, TOB15, and Vie 415HTR) and of Vilyuisk human encephalomyelitis virus (VHEV). This information, together with the recently reported sequences of divergent theiloviruses (Theiler's-like rat virus [TRV] and Saffold viruses 1 and 2 [SAFV-1 and SAFV-2]), enables an updated phylogenetic analysis as well as a reexamination of several gene products important in the pathogenesis of this emerging group of viruses. In the light of the known neurotropism of TMEV and the new human SAFV-1 and SAFV-2, the resulting data suggest the existence of theiloviruses that cause human central nervous system infections. Our phylogenetic analyses point to the classification of presently known theiloviruses into five types: TMEV, VHEV, TRV, SAFV-1, and SAFV-2.     

Simultaneous nitrification, denitrification, and phosphorus removal from nutrient-rich industrial wastewater using granular sludge

The biological removal of nitrogen and phosphorus from nutrient-rich abattoir wastewater using granular sludge has been investigated. A lab-scale sequencing batch reactor, seeded with granular sludge developed using synthetic wastewater, was operated for 13 months under alternating anaerobic and aerobic conditions. It is demonstrated that the granules could be sustained and indeed further developed with the use of abattoir wastewater. The organic, nitrogen, and phosphorus loading rates applied were 2.7 gCOD L(-1) day(-1), 0.43 gN L(-1) day(-1), and 0.06 gP L(-1) day(-1), respectively. The removal efficiency of soluble COD, soluble nitrogen and soluble phosphorus were 85%, 93%, and 89%, respectively. However, the high suspended solids in the effluent limited the overall removal efficiency to 68%, 86%, and 74% for total COD, TN, and TP, respectively. This good nutrient removal was achieved through the process known as simultaneous nitrification, denitrification, and phosphorus removal, likely facilitated by the presence of large anoxic zones in the center of the granules. The removal of nitrogen was likely via nitrite optimizing the use of the limited COD available in the wastewater. Accumulibacter spp. were found to be responsible for most of the denitrification, further reducing the COD requirement for nitrogen and phosphorus removal. Mineral precipitation was evaluated and was not found to significantly contribute to the overall nutrient removal. It is also shown that the minimum HRT in a granular sludge system is not governed by the sludge settleability, as is the case with floccular sludge systems, but likely by the limitations associated with the transfer of substrates in granules.     

The denitrification capability of cluster 1 Defluviicoccus vanus-related glycogen-accumulating organisms

The denitrification capability of Cluster 1 Defluviicoccus vanus-related glycogen-accumulating organisms (DvGAOs) is investigated. A sequencing batch reactor (SBR) fed with acetate as the sole carbon source was operated under alternating anaerobic-aerobic conditions to enrich Cluster 1 DvGAOs. Fluorescence in situ hybridization (FISH) showed that more than 85% of the bacterial population present in the reactor bound to the probes previously designed for Cluster 1 DvGAOs. A series of batch tests were performed to evaluate the capability of the community to reduce nitrate and nitrite. The tests were carried out both before and after the adaptation of the culture to anoxic conditions, and with both the intracellularly stored carbon and acetate as the electron donors. It was found that Cluster 1 DvGAOs were able to reduce nitrate but most likely unable to reduce nitrite. When un-adapted Cluster 1 DvGAOs were exposed to nitrate for the first time, a lag phase of approximately 4 h occurred, which was likely required for the synthesis of the necessary enzymes.     

Heterologous expression, and biochemical and cellular characterization of CaPLA1 encoding a hot pepper phospholipase A1 homolog

Phospholipid signaling has been recently implicated in diverse cellular processes in higher plants. We identified a cDNA encoding the phospholipase A1 homolog (CaPLA1) from 5-day-old early roots of hot pepper. The deduced amino acid sequence showed that the lipase-specific catalytic triad is well conserved in CaPLA1. In vitro lipase assays and site-directed mutagenesis revealed that CaPLA1 possesses PLA1 activity, which catalyzes the hydrolysis of phospholipids at the sn -1 position. CaPLA1 was selectively expressed in young roots, at days 4–5 after germination, and rapidly declined thereafter, suggesting that the expression of CaPLA1 is subject to control by a development-specific mechanism in roots. Because transgenic work was extremely difficult in hot peppers, in this study we overexpressed CaPLA1 in Arabidopsis so as to provide cellular information on the function of this gene. CaPLA1 overexpressors had significantly longer roots, leaves and petioles, and grew more rapidly than the wild-type plants, leading to an early bolting phenotype with prolonged inflorescence. Microscopic analysis showed that the vegetative tissues of 35S:CaPLA1 plants contained an increased number of small-sized cells, which resulted in highly populated cell layers. In addition, mRNAs for cell cycle-controlled proteins and fatty acid catabolizing enzymes were coordinately upregulated in CaPLA1 -overexpressing plants. These results suggest that CaPLA1 is functionally relevant in heterologous Arabidopsis cells, and hence might participate in a subset of positive control mechanisms of cell and tissue growth in transgenic lines. We discuss possible biochemical and cellular functions of CaPLA1 in relation to the phospholipid signaling pathway in hot pepper and transgenic Arabidopsis plants.