联合TCGA和GEO数据库筛选乳腺癌易感基因

本研究是利用公共基因芯片数据库筛选乳腺癌的预后基因,预测和探索这些基因在乳腺癌进展中的可能机制和临床价值.首先,我们筛选了公共基因芯片数据库(gene expression omnibus,GEO)GSE22820和癌症基因组图谱(the cancer genome atlas,TCGA)乳腺癌数据库的重叠差异表达基因,联合R语言分析乳腺癌组织与癌旁正常组织差异表达的基因;其次,基于STRING数据库及Cytoscape软件构建蛋白质相互作用网络图,分析并识别了中枢基因和前3个模块;之后进行了更多的功能分析,包括基因本体(gene ontology,GO)和京都基因与基因组百科全书(kyoto encyclopedia of genes and genomes,KEGG)通路分析以及基因集富集分析(gene set enrichment analysis,GSEA),以研究这些基因的作用以及潜在的潜在机制;最后进行了Kaplan-Meier分析和Cox比例风险分析,以阐明这些基因的诊断和预后效果.相关数据分析表明15个基因的表达水平与生存预后相关,高表达基因患者的总生存时间短于低表达患者(P＜0.05);Cox比例风险分析表明UBE2T、ER-CC6L和RAD51这3个基因是预后生存的独立因素(P＜0.05);GSEA分析表明在UBE2T、ERCC6L和RAD51基因中细胞周期、基础转录因子和卵母细胞减数分裂明显富集.最终,我们得出结论,这3种基因标志物的高表达是乳腺癌预后不良因素,可作为预测乳腺癌患者转移和预后的有效生物标志物.     

NEDD9 overexpression: Prognostic and guidance value in acute myeloid leukaemia

It has been demonstrated that neural precursor cell expressed developmentally downregulated protein (NEDD) plays crucial roles in tumorigenesis and may serve as potential biomarkers in cancer diagnosis and prognosis. However, few studies systematically investigated the expression of NEDD family members in acute myeloid leukaemia (AML). We systemically determined the expression of NEDD family members in AML and determined their clinical significance. We identified that NEDD9 expression was the only member among NEDD family which was significantly increased in AML. NEDD9 overexpression was more frequently classified as FAB-M4/M5 (p = 0.008 and 0.013, respectively), hardly as FAB-M2/M3. Moreover, NEDD9 overexpression was significantly associated with complex karyotype and TP53 mutation. The significant association between NEDD9 overexpression and survival was also observed in whole-cohort AML and non-M3 AML patients. Notably, AML patients with NEDD9 overexpression may benefit from hematopoietic stem cell transplantation (HSCT), whereas those cases without NEDD9 overexpression did not. Finally, a total of 822 mRNAs and 31 microRNAs were found to be differentially expressed between two groups. Among the microRNAs, miR-381 was also identified as a microRNA that could direct target NEDD9. Taken together, our findings demonstrated that NEDD9 overexpression is associated with genetic abnormalities as well as prognosis and might act as a potential biomarker guiding the choice between HSCT and chemotherapy in patients with AML after achieving complete remission.     

Superior japonica rice variety YJ144 with improved rice blast resistance,yield, and quality achieved using molecular design and multiple breeding strategies

Molecular Breeding - The stem color of young mung bean is a very useful tool in germplasm identification. Flowering time and plant height (PH) are known to be strongly correlated with crop adaption...     

Plant derived coumestrol phytochemical targets human skin carcinoma cells by inducing mitochondrial-mediated apoptosis,cell cycle arrest,inhibition of cell migration and invasion and modulation of m-TOR/PI3K/AKT signalling pathway

The current study was undertaken to investigate anticancer activity of coumestrol phytoestrogen against human skin cancer. MTT assay was performed for cell viability assessment and clonogenic assay for cell colony formation assessment. Apoptosis was analysed by Annexin V/FITC staining, AO/EB staining and western blotting assays. Effects on the m-TOR/PI3K/AKT signalling pathway were investigated by western blotting. Results indicated that coumestrol induced significant toxicity in human skin cancer cells in contrast to mouse skin cancer cells. The proliferation rate in normal skin cells remained almost intact. Annexin V-FITC and AO/EB staining assays indicated coumestrol induced cytotoxicity in skin cancer cells is mediated through apoptosis stimulation. The apoptosis in skin cancer cells was mediated through caspase-activation. Cell migration and invasion was inhibited by coumestrol in human skin cancer cells via inhibition of MMP-2 and MMP-9 expressions. Moreover, m-TOR/PI3K/AKT signalling pathway in SKEM-5 cells was blocked by coumestrol.     

Morphogenesis and Molecular Phylogeny of a New Freshwater Ciliate,Notohymena apoaustralis n. sp. (Ciliophora,Oxytrichidae)

The live morphology, infraciliature, and morphogenesis of a new oxytrichid ciliate, Notohymena apoaustralis n. sp. collected from a freshwater pond in Qingdao (Tsingtao), China, were studied in vivo and after protargol impregnation. Notohymena apoaustralis n. sp. is characterized as follows: undulating membranes in Notohymena‐pattern; cortical granules yellow‐green, grouped around the marginal cirri and dorsal bristles, and in short irregular rows elsewhere in the cell; single contractile vacuole positioned at anterior 1/3 of the body length; two macronuclear nodules and one micronucleus; about 39 adoral membranelles; 18 frontoventral transverse cirri in typical Oxytricha‐pattern; one right and one left marginal row, almost confluent posteriorly; dorsal ciliature in typical Oxytricha‐pattern; 8–10 caudal cirri arranged in three rows, one each at the posterior end of dorsal kineties 1, 2, and 4, indistinguishable from marginal cirri in life. The morphogenetic process in N. apoaustralis n. sp. is consistent with that of the type species, Notohymena rubescens Blatterer and Foissner, 1988. Phylogenetic analyses based on small subunit rDNA sequence data suggest a sister relationship between N. apoaustralis n. sp. and Paraurostyla weissei, which cluster in a clade with Rubrioxytricha ferruginea.     

OPTIMIZATION OF AFFINITY DIGESTION FOR THE ISOLATION OF CELLULOSOMES FROM Clostridium thermocellum

The affinity digestion process for cellulase purification consisting of binding to amorphous cellulose, and amorphous cellulose hydrolysis in the presence of dialysis (Morag et al., 1991), was optimized to obtain high activity recoveries and consistent protein recoveries in the isolation of Clostridium thermocellum cellulase. Experiments were conducted using crude supernatant prepared from C. thermocellum grown on either Avicel or cellobiose. While no difference was observed between Avicel-grown or cellobiose-grown cellulase in the adsorption step, differences were observed during the hydrolysis step. The optimal amorphous cellulose loading was found to be 3 mg amorphous cellulose per milligram supernatant protein. At this loading, 90–100% of activity in the crude supernatant was adsorbed. Twenty-four-hour incubation with the amorphous cellulose during the adsorption stage was found to result in maximal and stable adsorption of activity to the substrate. By fitting the adsorption data to the Langmuir model, an adsorption constant of 410 L/g and a binding capacity of 0.249 g cellulase/g cellulose were obtained. The optimal length of time for hydrolysis was found to be 3 hr for cellulase purified from Avicel cultures and 4 hr for cellulase purified from cellobiose cultures. These loadings and incubation times allowed for more than 85% activity recovery.     

Flow‐injection chemiluminescence determination of diazepam by oxidation with N‐bromosuccinimide

A rapid and sensitive flow‐injection chemiluminescence (FI–CL) method is described for the determination of diazepam based on its reaction with N‐bromosuccinimide (NBS) in alkaline medium in the presence of dichlorofluorescein (DCF) as an effective energy‐transfer agent. Under optimum conditions, the proposed method allowed the measurement of diazepam over the range of 2.0 × 10^?6 to 2.0 × 10^?4 mol/L with a detection limit of 5.0 × 10^?7 mol/L. The relative standard deviation for 11 parallel measurements of 2.0 × 10^?5 mol/L diazepam was 2.1%. The method was applied satisfactorily for the determination of diazepam in pharmaceutical preparations, and the results agree well with those obtained by spectrophotometry. The use of the proposed system for the determination of diazepam in urine and plasma samples was also tested. The possible mechanism of the chemiluminescence reaction is discussed briefly. Copyright © 2012 John Wiley & Sons, Ltd.     

Efficient and fine mapping of RMES1 conferring resistance to sorghum aphid Melanaphis sacchari

Melanaphis sacchari causes serious damage to sorghum (Sorghum bicolor (L.) Moench) growth, development and productivity in many countries. A dominant gene (RMES1) conferring resistance to M. sacchari has been found in the grain sorghum variety Henong 16 (HN16), but fine mapping of the RMES1 locus remains to be reported. In this study, genetic populations segregating for RMES1 were prepared with HN16 and BTx623 as parental lines. The latter had been used for sorghum genome sequencing but was found to be susceptible to M. sacchari in this work. A total of 11 molecular markers were mapped to the short arm of chromosome 6 harboring RMES1. The closest markers flanking the RMES1 locus were Sb6m2650 and Sb6rj2776, which delimited a chromosomal region of about 126 kb containing five predicted genes. The utility of the newly identified DNA markers for tagging RMES1 in molecular breeding of M. sacchari resistance, and further efforts in cloning RMES1, are discussed.