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71.
Multi-class protein fold recognition using support vector machines and neural networks 总被引:25,自引:0,他引:25
MOTIVATION: Protein fold recognition is an important approach to structure discovery without relying on sequence similarity. We study this approach with new multi-class classification methods and examined many issues important for a practical recognition system. RESULTS: Most current discriminative methods for protein fold prediction use the one-against-others method, which has the well-known 'False Positives' problem. We investigated two new methods: the unique one-against-others and the all-against-all methods. Both improve prediction accuracy by 14-110% on a dataset containing 27 SCOP folds. We used the Support Vector Machine (SVM) and the Neural Network (NN) learning methods as base classifiers. SVMs converges fast and leads to high accuracy. When scores of multiple parameter datasets are combined, majority voting reduces noise and increases recognition accuracy. We examined many issues involved with large number of classes, including dependencies of prediction accuracy on the number of folds and on the number of representatives in a fold. Overall, recognition systems achieve 56% fold prediction accuracy on a protein test dataset, where most of the proteins have below 25% sequence identity with the proteins used in training. 相似文献
72.
Three new species of Nepalomyia henanensis species group are described from China, N. damingshanus sp. nov., N. dongae sp. nov., and N. shennongjiaensis sp. nov. A key to known species of this species group is presented. 相似文献
73.
褐飞虱饲养于不同水稻品种、不同生育期以及不同种群密度条件下,5龄若虫翅芽长度与成虫翅型具有稳定的相关性:翅芽长于1.10mm羽化后为长翅型雌虫,介于0.96~1.09mm之间为长翅型雄虫或短翅型雌虫,小于0.95mm为短翅型雄虫。根据5龄若虫翅芽长度结合外生殖器特征,编制了成虫翅型检索表。由此,可在5龄若虫期预测成虫的翅型和种群盛衰的趋势。 相似文献
74.
Top-down modulations from dorsal stream in lexical recognition: an effective connectivity FMRI study
Both the ventral and dorsal visual streams in the human brain are known to be involved in reading. However, the interaction of these two pathways and their responses to different cognitive demands remains unclear. In this study, activation of neural pathways during Chinese character reading was acquired by using a functional magnetic resonance imaging (fMRI) technique. Visual-spatial analysis (mediated by the dorsal pathway) was disassociated from lexical recognition (mediated by the ventral pathway) via a spatial-based lexical decision task and effective connectivity analysis. Connectivity results revealed that, during spatial processing, the left superior parietal lobule (SPL) positively modulated the left fusiform gyrus (FG), while during lexical processing, the left SPL received positive modulatory input from the left inferior frontal gyrus (IFG) and sent negative modulatory output to the left FG. These findings suggest that the dorsal stream is highly involved in lexical recognition and acts as a top-down modulator for lexical processing. 相似文献
75.
Xiaohuan Cheng Junfa Ding Fang Zheng Xin Zhou Chenling Xiong 《Molecular biology reports》2009,36(8):2053-2057
Familial hypercholesterolemia (FH) (OMIM 143890) is an autosomal dominantly inherited disease mainly caused by mutations of
the gene encoding the low density lipoprotein receptor (LDLR) and Apolipoprotein (Apo) B. First the common mutation R3500Q
in ApoB gene was determined using PCR/RFLP method. Then the LDLR gene was screened for mutations using Touch-down PCR, SSCP
and sequencing techniques. Furthermore, the secondary structure of the LDLR protein was predicted with ANTHEPROT5.0. The R3500Q
mutation was absent in these two families. A heterozygous p.W483X mutation of LDLR gene was identified in family A which caused
a premature stop codon, while a homozygous mutation p.A627T was found in family B. The predicted secondary structures of the
mutant LDLR were altered. We identified two known mutations (p.W483X, p.A627T) of the LDLR gene in two Chinese FH families
respectively. 相似文献
76.
湖北地区宫颈癌组织中人乳头瘤病毒16型E7基因的分离、克隆和序列分析 总被引:5,自引:1,他引:5
采用加端聚合酶链反应技术,从湖北地区一宫颈癌患者癌组织DNA中分离出人乳头瘤病毒16型(HPV16)E7基因,并在pUC18载体中克隆。经限制性核酸内切酶分析和DNA序列分析,确认了含HPV16E7重组克隆质粒,命名pHPV16E7─HB。DNA序列分析表明,HPV16E7─HB基因全长294bp(与报道的标准株基因长度相同),但其核苷酸顺序中有两处发生了C→T突变,即第43位密码子CAA变为TAA,第76位CGT变为TGT;前者使谷氨酰胺密码子变为终止密码,即无义奕变(nonsensemutation)。这种突变发生在294个碱基的DNA扩增产物之中,不像是PCR本身的错配,而很可能是湖北株与标准株之间的结构差异。 相似文献
77.
78.
Phosphoproteome profiling of human skin fibroblast cells in response to low- and high-dose irradiation 总被引:4,自引:0,他引:4
Yang F Stenoien DL Strittmatter EF Wang J Ding L Lipton MS Monroe ME Nicora CD Gristenko MA Tang K Fang R Adkins JN Camp DG Chen DJ Smith RD 《Journal of proteome research》2006,5(5):1252-1260
A hallmark of the response to high-dose radiation is the up-regulation and phosphorylation of proteins involved in cell cycle checkpoint control, DNA damage signaling, DNA repair, and apoptosis. Exposure of cells to low doses of radiation has well documented biological effects, but the underlying regulatory mechanisms are still poorly understood. The objective of this study is to provide an initial profile of the normal human skin fibroblast (HSF) phosphoproteome and explore potential differences between low- and high-dose irradiation responses at the protein phosphorylation level. Several techniques including Trizol extraction of proteins, methylation of tryptic peptides, enrichment of phosphopeptides with immobilized metal affinity chromatography (IMAC), nanoflow reversed-phase HPLC (nano-LC)/electrospray ionization, and tandem mass spectrometry were combined for analysis of the HSF cell phosphoproteome. Among 494 unique phosphopeptides, 232 were singly phosphorylated, while 262 peptides had multiple phosphorylation sites indicating the overall effectiveness of the IMAC technique to enrich both singly and multiply phosphorylated peptides. We observed approximately 1.9-fold and approximately 3.6-fold increases in the number of identified phosphopeptides in low-dose and high-dose samples respectively, suggesting both radiation levels stimulate cell signaling pathways. A 6-fold increase in the phosphorylation of cyclin dependent kinase (cdk) motifs was observed after low- dose irradiation, while high-dose irradiation stimulated phosphorylation of 3-phosphoinositide-dependent protein kinase-1 (PDK1) and AKT/RSK motifs 8.5- and 5.5-fold, respectively. High- dose radiation resulted in the increased phosphorylation of proteins involved in cell signaling pathways as well as apoptosis while low-dose and control phosphoproteins were broadly distributed among biological processes. 相似文献
79.
80.
DNA methylation changes in photoperiod-thermo-sensitive male sterile rice PA64S under two different conditions 总被引:1,自引:0,他引:1
Epigenetic modification can occur at a high frequency in crop plants and might generate phenotypic variation without changes in DNA sequences. DNA methylation is an important epigenetic modification that may contribute to environmentally-induced phenotypic variations by regulating gene expression. Rice Photoperiod-Thermo-Sensitive Genic Male Sterile (PTGMS) lines can transform from sterility to fertility under lower temperatures and short-day (SD) conditions during anther development. So far, little is known about the DNA methylation variation of PTGMS throughout the genome in rice. In this study, we investigated DNA cytosine methylation alterations in the young panicles of PTGMS line PA64S under two different conditions using methylation sensitive amplified polymorphism (MSAP) method. Compared with the DNA methylation level of PA64S under lower temperatures and SD conditions (fertility), higher methylation was observed in PA64S (sterility). The sequences of 25 differentially amplified fragments were successfully obtained and annotated. Three methylated fragments, which are homologous to D2, NAD7 and psaA, were confirmed by bisulfite sequencing and their expression levels were also evaluated by qPCR. Real time quantitative PCR analysis revealed that five of the six selected methylated genes were downregulated in PA64S (sterility). These results suggested that DNA methylation may be involved in the sterility–fertility transition of PA64S under two different environmental conditions. 相似文献