Conditioning in 2 x 2 tables

Summary .  Two-by-two tables arise in a number of diverse settings in biomedical research, including analysis of data from a clinical trial with a binary outcome and gating methods in flow cytometry to separate antigen-specific immune responses from general immune responses. These applications offer interesting challenges concerning what we should really be conditioning on—the total number of events, the number of events in the control condition, etc. We give several biostatistics examples to illustrate the complexities of analyzing what appear to be simple data.     

2-amino-2-deoxy-D-erythrose in Agaricus bisporus

2-Amino-2-deoxy-D-erythrose was isolated from the cell wall of the fruit body of Agaricus bisporus. The structure of the amino sugar was determined by mass spectrography and 1H-NMR spectrography of its acetylated derivative and by paper chromatographic comparisons with authentic 2-amino-2-deoxy-D-erythrose. This amino sugar is a component of the glycoprotein fraction from the cell wall. Its content in the glycoprotein increased markedly, especially during the ripening stage of the fruit body.     

Ca2+位于H2O2上游参与H2S诱导的拟南芥气孔关闭过程

以拟南芥为材料,利用药理学实验,结合分光光度法和激光共聚焦显微技术,研究了Ca2+在硫化氢(H2S)诱导拟南芥气孔关闭过程中的作用及其与过氧化氢(H2O2)的关系。结果表明： H2S诱导气孔关闭, Ca2+螯合剂EGTA和质膜Ca2+通道阻断剂硝苯地平(Nif)能不同程度抑制H2S诱导的气孔关闭,而内质网钙泵阻断剂毒胡萝卜素(Thaps)对H2S的作用无显著影响。由此推测, Ca2+参与调节H2S诱导的拟南芥气孔关闭过程,且胞质中Ca2+来源于胞外Ca2+的内流。另外, H2S诱导拟南芥叶片NADPH氧化酶基因AtRBOHD和AtRBOHF以及细胞壁过氧化物酶基因AtPRX34表达增强,促进叶片和保卫细胞中H2O2积累, EGTA对此起抑制作用,而外源CaCl2处理上调AtRBOHD、AtRBOHF和AtPRX34的表达。表明Ca2+可能位于H2O2上游参与H2S诱导的拟南芥气孔关闭过程。     

Stereospecific 2'-amination and 2'-chlorination of adenosine by Actinomadura in the biosynthesis of 2'-amino-2'-deoxyadenosine and 2'-chloro-2'-deoxycoformycin

2'-Amino-2'-deoxyadenosine and 2'-chloro-2'-deoxycoformycin (2'-CldCF) are two nucleoside antibiotics produced by Actinomadura. The biosynthesis of these two nucleoside antibiotics has been studied by the addition of [U-14C]adenosine with or without unlabeled adenine to cultures of Actinomadura. By this experimental approach, it is possible to demonstrate that adenosine is the direct precursor for the biosynthesis of 2'-amino-2'-deoxyadenosine and 2'-CldCF. These conclusions are based on the observation that the percentage distribution of 14C in the aglyconic and pentofuranosyl moieties of 2'-amino-2'-deoxyadenosine and 2'-CldCF were similar to the distribution of 14C in the adenine and ribosyl moieties of the [U-14C]adenosine (i.e., 48:52) added to cultures of Actinomadura. Experimentally, the percentage distribution of 14C in the (i) adenine:2-amino-2-deoxy-beta-D-ribofuranose of 2'-amino-2'-deoxyadenosine is 51:49; (ii) 8-(R)-3,6,7,8-tetrahydroimidazo[4,5-d]-[1,3-diazepin-8-o1]:2 -chloro-2- beta-D-ribofuranose of 2'-CldCF is 45:55; and (iii) adenine:ribose of the adenosine isolated from the RNA of Actinomadura is 42:58. Further proof that adenosine is the direct precursor for the biosynthesis 2'-amino-2'-deoxyadenosine and 2'-CldCF was demonstrated by the addition of 75 mumol of unlabeled adenine together with [U-14C]adenosine to nucleoside-producing cultures of Actinomadura. The percentage distribution of 14C in the aglycon and the sugar moieties of 2'-amino-2'-deoxyadenosine and 2'-CldCF were 46:54 and 47:53, respectively; the percentage distribution of 14C in the adenine and ribose moieties of the adenosine isolated from the RNA of Actinomadura was 51:49. These data show that the hydroxyl on C-2' of the ribosyl moiety of adenosine undergoes a replacement by a 2'-amino or a 2'-chloro group to form 2'-amino-2'-deoxyadenosine or 2'-CldCF with retention of stereconfiguration at C-2'. Finally, Actinomadura can utilize inorganic chloride from the medium as demonstrated by the isolation of [36Cl]2'-CldCF following the addition of [36Cl]chloride to the culture medium. Mechanisms for the regioselective modification of the C-2' hydroxyl group and stereospecific insertion of the amino and chloro groups are discussed.     

植物体内重要的信号分子--H2O2

越来越多的证据表明,植物体内的H2O2作为信号分子发挥作用.在病原、诱发因子和激素应答中是调节细胞程序性死亡的关键因子.H2O2在环境胁迫防御反应中的信号作用也得到证实.已知H2O2直接调节无数基因的表达,其中有些基因与植物防御和超敏反应有关.H2O2还与其它信号系统特别是激素信号相互作用,是激素介导的信号传导通路上的上游或下游组分;更重要的是H2O2还影响和修饰其它第二信使如钙信号的作用,在H2O2信号和钙信号之间发生众多的交互作用且这两种信号分子都调节植物对多种胁迫的交互耐性.此外,现已广泛地认识到与H2O2相关的氧还状态调节是调整细胞活动的关键因子.本文主要概括和讨论了H2O2在不同生物过程中的信号作用.     

Luminescence in Li2BaP2O7

The photo‐, thermo‐ and optically stimulated luminescence in Li₂BaP₂O₇ activated with Eu²⁺/Cu⁺ are reported. Strong thermoluminescence, which is about two times greater than LiF‐TLD 100 was observed in the Eu²⁺‐activated sample. It also exhibited optically stimulated luminescence sensitivity of ~20% that of commercial Al₂O₃:C phosphor. Copyright © 2014 John Wiley & Sons, Ltd.     

Fundamental clusters in spatial 2x2 games

The notion of fundamental clusters is introduced, serving as a rule of thumb to characterize the statistical properties of the complex behaviour of cellular automata such as spatial 2 x 2 games. They represent the smallest cluster size determining the fate of the entire system. Checking simple growth criteria allows us to decide whether the cluster-individuals, e.g. some mutant family, are capable of surviving and invading a resident population. In biology, spatial 2 x 2 games have a broad spectrum of applications ranging from the evolution of cooperation and intraspecies competition to disease spread. This methodological study allows simple classifications and long-term predictions in various biological and social models to be made. For minimal neighbourhood types, we show that the intuitive candidate, a 3 x 3 cluster, turns out to be fundamental with certain weak limitations for the Moore neighbourhood but not for the Von Neumann neighbourhood. However, in the latter case, 2 x 2 clusters generally serve as reliable indicators to whether a strategy survives. Stochasticity is added to investigate the effects of varying fractions of one strategy present at initialization time and to discuss the rich dynamic properties in greater detail. Finally, we derive Liapunov exponents for the system and show that chaos reigns in a small region where the two strategies coexist in dynamical equilibrium.     

Casein kinase-2 phosphorylates serine-2 in the beta-subunit of initiation factor-2

We have previously presented evidence which suggests that casein kinase-2 phosphorylates a serine residue near the N-terminus of the beta-subunit of the initiation factor eIF-2 (Clark, S.J. et al. Biochim. Biophys. Acta 968, 211-219). We now report further data which confirm that it is serine-2 which is phosphorylated by casein kinase-2. This data includes (1) the electrophoretic mobilities of the phosphopeptides produced by different cleavage techniques, (2) the amino acid composition of the principal phosphopeptide generated by treatment with cyanogen bromide and (3) the resistance of this phosphopeptide to Edman degradation.     

Detoxification of SO2 in conifers differing in SO2-tolerance

Contents of organic sulfur, sulfate and the inorganic cations K⁺, Ca²⁺, Mg²⁺, Mn²⁺ and Na⁺ were compared in needles of three conifer species differing in tolerance to chronic SO₂ immissions. Sulfate and organic sulfur compounds were also measured in bark and wood. Field material was collected from Norway Spruce (Picea abies (L.) Karst.), Colorado Spruce (Picea pungens Engelm.) and Scots Pine (Pinus sylvestris L.) at sites where the SO₂ concentration in air was high, and at another site where it was low. In general, sulfate contents were higher but cation contents lower at the sites where SO₂ concentrations were high than where they were low. Up to 114mmol · (kg DW)^–1 sulfate was measured in fouryear-old needles of Norway Spruce from the Erzgebirge (annual mean of SO₂ in air 32 nl · 1^–1). Sulfate accumulation in this SO₂-sensitive conifer increased with SO₂ concentration in ambient air and with needle age, indicating that the main part of the sulfate resulted from the oxidative detoxification of SO₂. Loss of inorganic cations from ageing needles was reduced, or cation levels even increased, with increasing needle age, while sulfate accumulated. Apparently, cations served as counter-ions for sulfate, which is sequestered in the vacuoles. Individual trees differed in regard to the nature of cations which accumulated with sulfate. Calcium, potassium and magnesium were the dominating cations. Sodium levels were very low. Needles of the SO₂-tolerant conifers Colorado Spruce and Scots Pine growing next to Norway Spruce in the Erzgebirge did not accumulate, or accumulated less, sulfate with increasing needle age as compared to needles of Norway Spruce. However, somewhat more sulfate was found in the bark of the SO₂-tolerant species than in the bark of Norway Spruce. Scots Pine contained distinctly more sulfate in the wood than the other conifers. Since accumulation of organic sulfur compounds could not be observed with increasing needle age, or in bark and wood, reduction does not appear to play a major role in the detoxification of SO₂ by the investigated species. Physiological mechanisms permitting Colorado Spruce and Scots Pine to avoid the sulfate accumulation in the needles and the accompanying sequestration of cations that are observed in neighbouring Norway Spruce are discussed on the basis of the obtained data.Abbreviations S_org organic sulfur compounds Died June 10, 1991, aged 29, in a traffic accident. He initiated this work.This work was supported by the Sonderforschungsbereich 251 of the University of Würzburg and by the Projektgruppe Bayern zur Erforschung der Wirkung von Umweltschadstoffen (PBWU). The authors with to thank Prof. Dr. W Kaiser and Prof. Dr. W. Urbach (both Julius-von-Sachs-Institut, University of Würzburg, Germany) for HPLC-analysis and ICP-analysis.     

C_2H_2型锌指蛋白研究进展

遗传信息的实现过程离不开基因表达的调控 ,至今为止发现的转录调控因子中有很多含有锌指模体 (ｚｉｎｃ ｆｉｎｇｅｒｍｏｔｉｆ)结构。锌指蛋白是指含有通过结合Ｚｎ2 稳定的短的可以自我折叠形成“手指”结构的一类蛋白质。由于其自身的结构特点 ,可以选择性的结合特异的靶结构 ,使锌指蛋白在基因的表达调控、细胞分化、胚胎发育等生命过程中发挥重要作用。自从 1 983年在爪蟾卵母细胞中发现第一个具有基因转录调控作用的锌指蛋白ＴＦⅢＡ以来 ,在多种生物中发现的锌指基因已有约 50 0多个 ,其中人基因组中的锌指蛋白基因达 2 0 0多个。…     

C2H2型锌指蛋白的研究进展

锌指基因家族是人体中最大的基因家族,它参与细胞分化、胚胎发育,并与许多疾病的发生相关．根据半胱氨酸(c)和组氨酸(H)的数目和位置可将锌指蛋白分为c2H2、c2Hc2、c2c2 CHCC2C2、C2C2C2C2等亚类．c2H2型锌指是最普遍的类型,它们作为重要的转录调控因子参与许多的生理过程．c2H2型锌指蛋白包含的锌指数目从1个到30多个不等．依据锌指的数量以及在蛋白中的分布情况,大多数c2H2型锌指蛋白属于下列3类之一：1)含3个c：H：锌指的蛋白(tC2H2);2)含多个锌指的c2H2型锌指结构蛋白(mac2H2);3)锌指成对间隔排列的c2H2型锌指蛋白(spC2H2)、一些c2H2型锌指蛋白能识别并结合特异性RNA或DNA片段．另一些则只能与RNA结合．通常锌指蛋白含锌指数目越多。它选择结合的能力就越强．     

Starvation-Induced Multiresistance in Enterococcus faecalis JH2-2

Compared with growing bacteria, carbohydrate-starved cells of Enterococcus faecalis show development of a multiresistance state against heat, H₂O₂, acid, and ethanol, but not against UV irradiation. The kinetics of acquisition of resistance is different according to the stress. Three hours of starvation provide maximal resistance against ethanol, while the tolerance to heat, H₂O₂, and acid increases progressively with the duration of starvation. Chloramphenicol treatment does not abolish the ethanol tolerance. Protein synthesis inhibition during the transitional growth phase and the first hours of starvation partially inhibit the acquisition of heat and oxidative resistances. Antibiotic treatment after 3 h of starvation does not affect the increase of these resistances. We suggest that synthesis of specific proteins revealed by 2-D gel analysis in the first 3 h of starvation, followed by a second mechanism related to protein degradation or alteration, is necessary for acquisition of maximal resistance towards heat and oxidative stresses.     

PPP2R2A在乳腺癌细胞中结合GFPT2并导致其去磷酸化

PPP2R2A是PP2A磷酸酶的调控亚基之一,以往的研究报道显示,PPP2R2A可促进肿瘤细胞生存和生长。本研究通过串联亲和纯化联合HPLC-Chip-ESI/MS/MS筛选PPP2R2A的相互作用蛋白质,分析结果显示,L-谷氨酰胺-D-果糖-6-磷酸转氨酶1(Glutamine-fructose-6-phosphate transaminase 1,GFPT1)和L-谷氨酰胺-D-果糖-6-磷酸转氨酶2(Glutamine-fructose-6-phosphate transaminase 2,GFPT2)是PPP2R2A可能的结合蛋白。通过免疫荧光共定位、GST Pull-down和免疫共沉淀等方法,进一步确认了PPP2R2A和GFPT1及GFPT2的相互结合。通过shRNA下调PPP2R2A后,GFPT2的磷酸化水平显著增加,但GFPT1的磷酸化水平改变不明显。GFPT2是O-GlcNAC糖基化修饰通路中的一个限速酶,在乳腺癌细胞MDA-MB-231中下调PPP2R2A后,蛋白质O-GlcNAC糖基化修饰水平增加。这些结果表明,PPP2R2A可直接结合GFPT2,并导致其去磷酸化,进而影响细胞内O-GlcNAC糖基化修饰。     

Sulfenylation of ENOLASE2 facilitates H2O2-conferred freezing tolerance in Arabidopsis

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