基于转录组的肝豆状核变性调控网络的构建和分析

本研究旨在利用生物信息学方法构建经铜诱导的ATP7B基因敲除HepG2细胞系的转录调控网络。探讨关键转录因子在肝豆状核变性发生、发展中的潜在作用机制。收集公共基因表达数据库(gene expression omnibus, GEO)中包含野生型、ATP7B基因敲除型、铜诱导的野生型和铜诱导的ATP7B基因敲除型HepG2细胞系数据。筛选由铜诱导产生的差异表达基因(differentially expressed genes,DEGs)后进行基因本体论(gene ontology,GO)、京都基因和基因组百科全书(Kyoto encyclopedia of genes and genomes, KEGG)富集分析。基于蛋白相互作用网络,识别疾病关键基因和功能模块,并对关键功能模块中的基因进行富集分析。最后,构建转录调控网络,筛选核心转录因子。共筛选出1 034个差异表达基因,其中上调525个,下调509个。上、下调关键功能模块分别包括了3785个和3931个基因。关键功能模块中的基因主要定位于细胞-基质连接、染色体、剪接复合体、核糖体等区域,共同参与了mRNA加工、组蛋白修饰、RNA剪切...     

JURASSIC PALAEONTINIDAE FROM CHINA AND THE HIGHER SYSTEMATICS OF PALAEONTINOIDEA (INSECTA: HEMIPTERA: CICADOMORPHA)

Abstract:  Genera of Palaeontinidae (Insecta, Hemiptera: Cicadomorpha) are reviewed based on some newly-discovered material. An updated list of palaeontinid genera is provided. The genus Palaeontinopsis Martynov is assigned to Palaeontinidae incertae sedis . A new genus and species, Ningchengia aspera gen. et sp. nov., is described based on forewings and hindwings from the Middle Jurassic of Daohugou, China. Fletcheriana colorata Wang, Zhang and Fang and F . minuta Wang, Zhang and Fang are transferred to Suljuktocossus and Ningchengia respectively, resulting in Suljuktocossus coloratus comb. nov. and Ningchengia minuta comb. nov. Papilioncossus Wang, Ren and Shih, 2007 syn. nov. is considered to be a junior synonym of Eoiocossus Wang and Zhang, 2006 and Quadraticossus Wang and Ren 2007 syn. nov. is a junior synonym of Sinopalaeocossus   Hong, 1983 . The genus Fletcheriana is believed to represent a transition between Dunstaniidae and Palaeontinidae. This result is consistent with the previous view that Dunstaniidae is ancestral to Palaeontinidae. Furthermore, Suljuktocossus is a transitional genus between Fletcheriana and Cretaceous palaeontinids. The fusion of veins RP and M₁ in the palaeontinid hindwings implies a change of the mechanism of flight and an improvement in flight ability. The presence of a reduced costal area and the rigid basal leading edge of the palaeontinid forewings suggest gain of lift.     

Were Multiple Stressors a ‘Perfect Storm’ for Northern Gulf of Mexico Bottlenose Dolphins (Tursiops truncatus) in 2011?

An unusual number of near term and neonatal bottlenose dolphin (Tursiops truncatus) mortalities occurred in the northern Gulf of Mexico (nGOM) in 2011, during the first calving season after two well documented environmental perturbations; sustained cold weather in 2010 and the Deepwater Horizon oil spill (DWHOS). Preceding the stranding event, large volumes of cold freshwater entered the nGOM due to unusually large snowmelt on the adjacent watershed, providing a third potential stressor. We consider the possibility that this extreme cold and freshwater event contributed to the pattern of perinatal dolphin strandings along the nGOM coast. During the 4-month period starting January 2011, 186 bottlenose dolphins, including 46% perinatal calves (nearly double the percentage for the same time period from 2003-2010) washed ashore from Louisiana to western Florida. Comparison of the frequency distribution of strandings to flow rates and water temperature at a monitoring buoy outside Mobile Bay, Alabama (the 4(th) largest freshwater drainage in the U.S.) and along the nGOM coast showed that dolphin strandings peaked in Julian weeks 5, 8, and 12 (February and March), following water temperature minima by 2-3 weeks. If dolphin condition was already poor due to depleted food resources, bacterial infection, or other factors, it is plausible that the spring freshet contributed to the timing and location of the unique stranding event in early 2011. These data provide strong observational evidence to assess links between the timing of the DWHOS, other local environmental stressors, and mortality of a top local predator. Targeted analyses of tissues from stranded dolphins will be essential to define a cause of death, and our findings highlight the importance of considering environmental data along with biological samples to interpret stranding patterns during and after an unusual mortality event.     

Fifteen polymorphic simple sequence repeat markers from expressed sequence tags of Liriodendron tulipifera

We developed and evaluated simple sequence repeat (SSR) markers derived from expressed sequence tags (ESTs) of Liriodendron tulipifera. Characteristics of 15 EST‐SSR loci were investigated using 33 L. tulipifera individuals. The number of alleles per locus ranged from two to five. The expected and observed heterozygosities ranged from 0.216 to 0.751 and from 0.182 to 0.97, respectively. These loci were further tested for their cross‐species transferability to Liriodendron Chinense. Because of their high level of polymorphism and transferability, our 15 single‐locus EST‐SSR markers will be valuable tools for research on mating system, population genetics and systemic evolution of Liriodendron.     

Systematic review and meta-analysis of proton pump inhibitor therapy in peptic ulcer bleeding

Objectives To review randomised controlled trials of treatment with a proton pump inhibitor in patients with ulcer bleeding and determine the impact on mortality, rebleeding, and surgical intervention.Design Systematic review and meta-analysis.Data sources Cochrane Collaboration''s trials register, Medline, and Embase, handsearched abstracts, and pharmaceutical companies.Review methods Included randomised controlled trials compared proton pump inhibitor with placebo or H₂ receptor antagonist in endoscopically proved bleeding ulcer and reported at least one of mortality, rebleeding, or surgical intervention. Trials were graded for methodological quality. Two assessors independently reviewed each trial, and disagreements were resolved by consensus.Results We included 21 randomised controlled trials comprising 2915 patients. Proton pump inhibitor treatment had no significant effect on mortality (odds ratio 1.11, 95% confidence interval 0.79 to 1.57; number needed to treat (NNT) incalculable) but reduced rebleeding (0.46, 0.33 to 0.64; NNT 12) and surgery (0.59, 0.46 to 0.76; NNT 20). Results were similar when the meta-analysis was restricted to the 10 trials with the highest methodological quality: 0.96, 0.46 to 2.01, for mortality; 0.41, 0.25 to 0.68, NNT 10, for rebleeding; 0.62, 0.46 to 0.83, NNT 25, for surgery.Conclusions Treatment with a proton pump inhibitor reduces the risk of rebleeding and the requirement for surgery after ulcer bleeding but has no benefit on overall mortality.     

The glutathione-deficient, cadmium-sensitive mutant, cad2–1 , of Arabidopsis thaliana is deficient in γ-glutamylcysteine synthetase

This paper reports that the glutathione (GSH)-deficient mutant, cad2–1 , of Arabidopsis is deficient in the first enzyme in the pathway of GSH biosynthesis, γ-glutamylcysteine synthetase (GCS). The mutant accumulates a substrate of GCS, cysteine, and is deficient in the product, γ-glutamylcysteine. In vitro enzyme assays showed that the cad2–1 mutant has 40% of wild-type levels of GCS activity but is unchanged in the activity of the second enzyme in the pathway, GSH synthetase. The CAD2 locus maps to chromosome 4 and is tightly linked to a gene, GSHA , identified by a previously isolated cDNA. A genomic clone of GSHA complements both the phenotypic and biochemical deficiencies of the cad2–1 mutant. The nucleotide sequence of the gene has been determined and, in the mutant, this gene contains a 6 bp deletion within an exon. These data demonstrate that the CAD2 gene encodes GCS. The cad2–1 mutation is close to the conserved cysteine which is believed to bind the substrate glutamate and the specific inhibitor L-buthionine-[S,R] sulfoximine (BSO). Both root growth and GCS activity of the cad2–1 mutant was less sensitive than the wild-type to inhibition by BSO, indicating that the mutation may alter the affinity of the inhibitor binding site.