Databases and Web Tools for Cancer Genomics Study

Publicly-accessible resources have promoted the advance of scientific discovery. The era of genomics and big data has brought the need for collaboration and data sharing in order to make effective use of this new knowledge. Here, we describe the web resources for cancer genomics research and rate them on the basis of the diversity of cancer types, sample size, omics data comprehensiveness, and user experience. The resources reviewed include data repository and analysis tools; and we hope such introduction will promote the awareness and facilitate the usage of these resources in the cancer research community.     

proC及putP基因的敲除对钝齿棒杆菌产L-精氨酸生理代谢的影响

为了选育精氨酸高产菌株,基于谷氨酸棒杆菌的基因组尺度代谢网络模型的指导,以钝齿棒杆菌(Corynebacterium crenatum)MT-M4为出发菌株,通过基因敲除技术构建了pro C和put P敲除菌株。摇瓶发酵结果表明,pro C敲除菌株精氨酸产量达到9.94g/L,较出发菌株提高了15.90%,葡萄糖转化率提高了26.02%。由于其生长受到明显抑制,因此在发酵液中外源添加24mmol/L的脯氨酸,结果发现其精氨酸产量达到12.22g/L,且菌株恢复生长。put P敲除菌株精氨酸产量达到12.23g/L,较出发菌株提高了42.70%,葡萄糖转化率提高了49.31%。以上结果显示,put P的敲除比pro C的敲除更有利于精氨酸的合成,put P的敲除对菌株的生理代谢基本无影响且无需外添加脯氨酸。     

Glucose alleviates cadmium toxicity by increasing cadmium fixation in root cell wall and sequestration into vacuole in Arabidopsis

Glucose(Glu) is involved in not only plant physiological and developmental events but also plant responses to abiotic stresses. Here, we found that the exogenous Glu improved root and shoot growth, reduced shoot cadmium(Cd) concentration, and rescued Cdinduced chlorosis in Arabidopsis thaliana(Columbia ecotype,Col-0) under Cd stressed conditions. Glucose increased Cd retained in the roots, thus reducing its translocation from root to shoot signi fi cantly. The most Cd retained in the roots was found in the hemicellulose 1. Glucose combined with Cd(Glu t Cd) treatment did not affect the content of pectin and its binding capacity of Cd while it increased the content of hemicelluloses 1 and the amount of Cd retained in it signi fi cantly. Furthermore, Leadmium Green staining indicated that more Cd was compartmented into vacuoles in Glu t Cd treatment compared with Cd treatment alone, which was in accordance with the R e ssigni fi cant upregulation of the expression of tonoplastlocalized metal transporter genes, suggesting that compartmentation of Cd into vacuoles also contributes to the Glu-alleviated Cd toxicity. Taken together, we demonstrated that Glu-alleviated Cd toxicity is mediated through increasing Cd fi xation in the root cell wall and sequestration into the vacuoles.     

Analysis of expressed sequence tags (ESTs) from a normalized cDNA library and isolation of EST simple sequence repeats from the invasive cotton mealybug Phenacoccus solenopsis

The cotton mealybug, Phenacoccus solenopsis Tinsley, is a serious and invasive pest. At present, genetic resources for studying P. solenopsis are limited, and this negatively affects genetic research on the organism and, consequently, translational work to improve management of this pest. In the present study, expressed sequence tags (ESTs) were analyzed from a normalized complementary DNA library of P. solenopsis. In addition, EST‐derived microsatellite loci (also known as simple sequence repeats or SSRs) were isolated and characterized. A total of 1107 high‐quality ESTs were acquired from the library. Clustering and assembly analysis resulted in 785 unigenes, which were classified functionally into 23 categories according to the Gene Ontology database. Seven EST‐based SSR markers were developed in this study and are expected to be useful in characterizing how this invasive species was introduced, as well as providing insights into its genetic microevolution.     

Identification and characterization of Mini1, a gene regulating rice shoot development

The aerial parts of higher plants are generated from the shoot apical meristem(SAM). In this study, we isolated a small rice(Oryza sativa L.) mutant that showed premature termination of shoot development and was named mini rice 1(mini1). The mutant was first isolated from a japonica cultivar Zhonghua11(ZH11) subjected to ethyl methanesulfonate(EMS)treatment. With bulked segregant analysis(BSA) and map-based cloning method, Mini1 gene was finally fine-mapped to an interval of 48.6 kb on chromosome 9. Sequence analyses revealed a single base substitution from G to A was found in the region, which resulted in an amino acid change from Gly to Asp.The candidate gene Os09g0363900 was predicted to encode a putative adhesion of calyx edges protein ACE(putative HOTHEAD precursor) and genetic complementation experiment confirmed the identity of Mini1. Os09g0363900 contains glucose-methanol-choline(GMC) oxidoreductase and NAD(P)-binding Rossmann-like domain, and exhibits high similarity to Arabidopsis HOTHEAD(HTH). Expression analysis indicated Mini1 was highly expressed in young shoots but lowly in roots and the expression level of most genes involved in auxin biosynthesis and signal transduction were reduced in mutant.We conclude that Mini1 plays an important role in maintaining SAM activity and promoting shoot development in rice.     

姜黄素激活AMPK抑制高糖介导的氧化应激水平升高致血管内皮功能障碍

目的:探索姜黄素对高糖介导的血管氧化应激水平的升高和血管功能的保护作用未知及相关的机制。方法:以高糖DMEM培养基复制人脐静脉内皮细胞(HUVECs)的高糖损害模型。姜黄素干预24h后以DHE荧光探针分析姜黄素对高糖介导的活性氧产生的影响;分离健康C57BL/6J小鼠胸主动脉,以高糖DMEM培养基进行体外培养制作高糖介导的血管损害模型,分析姜黄素对高糖介导的血管功能的影响。利用western blotting方法检测血管内皮细胞中p-e NOS及p-AMPK的表达水平。结果:姜黄素可显著减少高糖介导的血管内皮细胞活性氧水平,该作用在给予AMPK抑制剂后显著降低;姜黄素可显著促进高糖环境血管内皮细胞e NOS的磷酸化并可显著改善高糖环境下小鼠胸主动脉的血管内皮依赖性舒张功能。Western blotting结果表明,姜黄素可显著增加p-AMPK的表达。结论:姜黄素显著减轻高糖血管内皮细胞的氧化应激水平,改善血管内皮依赖性舒张功能,而该作用可能与其通过激活AMPK/e NOS通路有关。     

棉花粉蚧热休克蛋白基因的鉴定

热休克蛋白(heat shock proteins,Hsps)是生物体或细胞受到热胁迫后新合成的一类遗传上高度保守的蛋白,在昆虫应对外界环境因子胁迫时起着重要作用。为了系统研究棉花粉蚧Phenacoccus solenopsis Hsp基因家族,对棉花粉蚧转录组基因注释信息进行分析、获得目标序列,并应用NCBI上Blast X等软件进行比对、共鉴定出24条热激蛋白(Hsp)基因,包括3个Hsp90、8个Hsp70、2个Hsp60和11个s Hsp(small heat shock protein,s Hsp)基因。对棉花粉蚧与模式昆虫家蚕Bombyx mori、黑腹果蝇Drosophila melanogaster、赤拟谷盗Tribolium castaneum系统进化关系分析显示,昆虫的小分子量热休克蛋白s Hsp具有很强的种属特异性,Hsp70家族的保守性比s Hsp强。棉花粉蚧热激蛋白基因的鉴定为深入研究该虫Hsp与生长发育、抗逆境的相互关系奠定了基础。     

Low Potassium Dialysate as a Protective Factor of Sudden Cardiac Death in Hemodialysis Patients with Hyperkalemia

AimHyperkalemia increases the risk of sudden cardiac death (SCD) in hemodialysis patients. Our objective was to determine the association between administering low potassium dialysate to hyperkalemic hemodialysis patients and SCD.MethodsWe conducted a retrospective cohort study with patients undergoing maintenance hemodialysis from May 1, 2006, through December 31, 2013. The dialysate composition was adjusted over time according to monthly laboratory results. A 1.0 mEq/L potassium dialysate was applied in patients with predialysis hyperkalemia (>5.5 mEq/L) and was included as a time-dependent confounding factor. The clinical characteristics of enrolled patients, the incidence and timing of SCD and risk factors for all-cause mortality and SCD were analyzed.ResultsThere were 312 patients on maintenance hemodialysis during the study period. One hundred and fifty-seven patients had been dialyzed against a 1.0 mEq/L potassium dialysate at least once. The rates of all-cause mortality and SCD were 48.17 and 20.74 per 1000 patient-years, respectively. A 1.12-fold increase in the risk of SCD in the 24-hour period starting with the hemodialysis procedure and a 1.36-fold increase in the 24 hours preceding a weekly cycle were found (p = 0.017). Multivariate Cox proportional hazards models showed that age, diabetes mellitus and predialysis hyperkalemia (>5.0 mEq/L) were significant predictors of all-cause mortality and SCD. Exposure to 1.0 mEq/L potassium dialysate, Kt/V, and serum albumin were independent protective factors against all-cause mortality. Only exposure to 1.0 mEq/L potassium dialysate significantly prevented SCD (hazard ratio = 0.33, 95% CI = 0.13–0.85).ConclusionsUsing low potassium dialysate in hyperkalemic hemodialysis patients may prevent SCD.