Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

Accurate and complete measurement of single nucleotide (SNP) and copy number (CNV) variants, both common and rare, will be required to understand the role of genetic variation in disease. We present Birdsuite, a four-stage analytical framework instantiated in software for deriving integrated and mutually consistent copy number and SNP genotypes. The method sequentially assigns copy number across regions of common copy number polymorphisms (CNPs), calls genotypes of SNPs, identifies rare CNVs via a hidden Markov model (HMM), and generates an integrated sequence and copy number genotype at every locus (for example, including genotypes such as A-null, AAB and BBB in addition to AA, AB and BB calls). Such genotypes more accurately depict the underlying sequence of each individual, reducing the rate of apparent mendelian inconsistencies. The Birdsuite software is applied here to data from the Affymetrix SNP 6.0 array. Additionally, we describe a method, implemented in PLINK, to utilize these combined SNP and CNV genotypes for association testing with a phenotype.     

Melatonin biosynthesis in the thymus of humans and rats

Melatonin is an indoleamine widely distributed in the evolution that shows a great functional versatility, playing an important role as a transmitter of photoperiodic information and exhibiting antioxidant, oncostatic, anti-aging and immunomodulatory properties. In vertebrates, this molecule is produced by the pineal gland and other extrapineal sites. The present study was carried out to investigate the presence of melatonin in thymus and the possibility of an endogenous melatonin synthesis in this organ, in which T cells are matured. In this work, we demonstrate in humans and rats that thymus contains melatonin, expresses the mRNAs encoding N-acetyltransferase and hydroxyindol-O-methyltransferase, the two key enzymes of the melatonin synthesis, and has this biosynthetic machinery activated. In addition, rat thymocytes cultured for 24 h exhibited high levels of melatonin. The results presented here suggest that human and rat thymuses are able to synthesize melatonin, which could have intracrine, autocrine and paracrine functions. Received 30 September 2006; received after revision 30 December 2006; accepted 15 February 2007     

基于DSP的CAN总线应用层协议开发与实现

针对某红外探测系统中信息交互的需要,结合TMS320F2812DSP中增强型CAN控制器模块的特点,设计了一种CAN应用层协议。该协议对扩展帧的报文标识符进行了详细定义,保证了重点探测目标的优先级,同时对信息的超时及不可靠节点制定了相应规则,满足了探测系统对信息更新的要求。最后简要介绍了协议的硬件和软件实现。     

瓜子壳生物炭的制备及其活化PMS降解有机染料的研究

近年来,生物炭材料作为无机非金属催化剂的应用得到了广泛关注.以瓜子壳为原料,于800℃和惰性气氛下,热解制备瓜子壳生物炭(MSAC).利用扫描电子显微镜(SEM)、孔隙度和比表面分析仪、拉曼光谱对MSAC的理化性质进行了表征.考察了MSAC对有机染料罗丹明B(RhB)、孔雀绿(MGO)、甲基橙(MO)、结晶紫(CV)的...     

卵泡刺激素促进卵巢颗粒细胞增殖分化的信号通路的研究进展

卵泡刺激素（FSH）是一种垂体前叶合成和分泌的糖蛋白激素,是卵巢发育的重要激素,可与卵巢颗粒细胞膜上的特异性受体结合从而促进细胞的增殖分化,激活细胞内芳香化酶生成雌激素和孕激素。FSH在卵巢颗粒细胞中主要依靠cAMP—PKA信号通路促进细胞增殖,同时也发生多种信号通路,ERK1／2、ERK5、p38MAPK、P13K／Akt、VEGF均参与FSH促进卵巢颗粒细胞的增殖分化;它们之间相互作用促进卵巢颗粒细胞的增殖。     

全氟辛酸对小鼠肝脏相关酶系的影响

目的:观察全氟辛酸对小鼠肝脏相关酶系的影响。方法:将小鼠随机分为4组,分别为空白组、1/16LD50、1/8LD50和1/4LD50组,染毒14 d后采用试剂盒法测定肝组织匀浆中琥珀酸脱氢酶(SDH)、血清中乳酸脱氢酶(LDH)和血清中单胺氧化酶(MAO)含量的变化。结果:染毒组肝组织中SDH活性显著低于空白组(P0.01),随染毒剂量增加呈递减趋势;染毒组血清中LDH和MAO活性显著高于空白组(P0.01)。随染毒剂量增加呈递增趋势。结论:全氟辛酸通过损伤肝细胞线粒体,破坏能量代谢,进而损伤肝组织,可致肝坏死。     

全氟辛酸在小鼠肝脂质过氧化损伤中的作用

确定全氟辛酸是否通过脂质过氧化造成小鼠肝脏的损伤.将小鼠随机分为4组,分别为空白组、1/16LD50、1/8LD50和1/4LD50组,染毒14 d后采用HE染色法观察肝脏病理变化,试剂盒法测定肝组织匀浆中超氧化物歧化酶(SOD);还原型谷胱甘肽(GSH);丙二醛(MDA)、血清中谷丙转氨酶(ALT)、谷草转氨酶(AST)、碱性磷酸酶(ALP)含量变化.HE染色观察到全氟辛酸染毒组肝组织损伤明显;试剂盒结果显示,与空白组相比,全氟辛酸组小鼠组织匀浆中SOD活性显著降低,MDA含量显著升高,GSH活性显著降低,均有统计学意义.全氟辛酸组小鼠血清中ALT和AST活性明显高于空白组(P<0.01),低剂量组小鼠血清ALP活性与空白组相比显著升高(P<0.05),高、中剂量组与空白组相比ALP活性有升高趋势,但是没有统计学意义.全氟辛酸通过脂质过氧化造成小鼠肝损伤.     

A Cenozoic record of the equatorial Pacific carbonate compensation depth

Atmospheric carbon dioxide concentrations and climate are regulated on geological timescales by the balance between carbon input from volcanic and metamorphic outgassing and its removal by weathering feedbacks; these feedbacks involve the erosion of silicate rocks and organic-carbon-bearing rocks. The integrated effect of these processes is reflected in the calcium carbonate compensation depth, which is the oceanic depth at which calcium carbonate is dissolved. Here we present a carbonate accumulation record that covers the past 53 million years from a depth transect in the equatorial Pacific Ocean. The carbonate compensation depth tracks long-term ocean cooling, deepening from 3.0-3.5?kilometres during the early Cenozoic (approximately 55?million years ago) to 4.6 kilometres at present, consistent with an overall Cenozoic increase in weathering. We find large superimposed fluctuations in carbonate compensation depth during the middle and late Eocene. Using Earth system models, we identify changes in weathering and the mode of organic-carbon delivery as two key processes to explain these large-scale Eocene fluctuations of the carbonate compensation depth.     

带回溯线搜索的新锥模型信赖域算法

结合线搜索方法计算量小的优点和信赖域算法很好的收敛性,将回溯线搜索应用到新锥模型自适应信赖域方法上构造了一类新的算法,并证明了该算法具有全局收敛性。初步的数值实验表明该算法是可行的。