An entropy-based approach for testing genetic epistasis underlying complex diseases

The genetic basis of complex diseases is expected to be highly heterogeneous, with complex interactions among multiple disease loci and environment factors. Due to the multi-dimensional property of interactions among large number of genetic loci, efficient statistical approach has not been well developed to handle the high-order epistatic complexity. In this article, we introduce a new approach for testing genetic epistasis in multiple loci using an entropy-based statistic for a case-only design. The entropy-based statistic asymptotically follows a χ² distribution. Computer simulations show that the entropy-based approach has better control of type I error and higher power compared to the standard χ² test. Motivated by a schizophrenia data set, we propose a method for measuring and testing the relative entropy of a clinical phenotype, through which one can test the contribution or interaction of multiple disease loci to a clinical phenotype. A sequential forward selection procedure is proposed to construct a genetic interaction network which is illustrated through a tree-based diagram. The network information clearly shows the relative importance of a set of genetic loci on a clinical phenotype. To show the utility of the new entropy-based approach, it is applied to analyze two real data sets, a schizophrenia data set and a published malaria data set. Our approach provides a fast and testable framework for genetic epistasis study in a case-only design.     

Social organization of black-and-white snub-nosed monkeys (Rhinopithecus bieti) at Deqin, China

Data on social organization of two bands of black-and-white snub-nosed monkeys (Rhinopithecus bieti) were collected when the monkeys were crossing an open spot at Nanren and Bamei (northwest of Yunnan, China) using a sampling rule where individuals within one social unit are spatially closer to each other than individuals between social units. The typical pattern of social organization in this sample was multiple adult females (AFs) and their offspring with one adult male (AM) in a one-male unit (OMU), similar to that of many other colobines. In such units, on average one male is associated with 4.0 AFs and 2.5 of their offspring. Moreover, there are multimale/multifemale units and monogamous units besides OMUs. All bisexual units traveled together with at least one all-male unit as a cohesive band. In two bands of monkeys, 87% of AMs in bisexual units were within OMUs, 7.8% within monogamous units and 5.2% within multimale, multifemale units. In the Bamei band, 6.7% of AMs were in the all-male unit. The size of OMUs in the Nanren band was larger than that of the Bamei band, with more AFs and juveniles, which may be related to better conservation in the Nanren band's habitat. For the Nanren band, the average number of AFs in OMUs varied across time, increasing from 4.3 in 1994 to 5.1 in 2001, and then decreasing to 3.8 in 2005. This article suggests three possible explanations for this variation, but more data are needed for these hypotheses to be tested.     

假单胞菌DLL-E4尿黑酸降解基因的克隆与功能的初步分析

通过接合转移将质粒pSC123上的转座子Tn5随机插入到DLL-E4基因组DNA中,从大约8,000个突变子中筛选到1株在LB培养基上积累红褐色物质的突变株M18,该突变株不能以L-苯丙氨酸(L-Phenylalanine, Phe)为唯一碳源生长。SEFA-PCR扩增转座子侧翼序列发现其与已报道的尿黑酸1,2-双加氧酶基因hmgA的同源性为92%。将hmgA定向克隆至表达载体pET-29a中,转化至Escherichia coli BL21,经IPTG诱导后可表达分子量约为48kD的蛋白;诱导后转化子粗酶液对尿黑酸有很好的降解效果。将hmgA连入自杀性载体pEX19Gm,通过同源重组整合至M18染色体中,使其恢复了DLL-E4利用Phe的能力,证实了HmgA是尿黑酸苯环裂解酶。     

黄芩甙对肝癌细胞BEL-7402形态学的影响

目的观察黄芩甙对肝癌细胞BEL-7402凋亡的影响,同时观察对肝癌细胞形态及超微结构、线粒体超微结构、线粒体膜电位和细胞内Ca^2＋的影响,探讨线粒体损伤在黄芩甙诱导肝癌细胞凋亡中的作用及可能的机制。方法应用细胞培养技术培养肝癌细胞BEL-7402,光镜、倒置显微镜、扫描电镜、透射电镜观察细胞形态及超微结构的变化尤其是线粒体的变化,应用流式细胞仪检测细胞凋亡百分率及线粒体膜电位、细胞内Ca^2＋的改变,免疫组化法检测细胞Bcl-2、Pax蛋白表达。结果黄芩甙诱导肝癌细胞BEL-7402凋亡呈剂量依赖关系,细胞形态、超微结构及线粒体超微结构出现明显改变,降低肝癌细胞线粒体膜电位,使细胞内Ca^2＋增加,细胞Pax表达增加,广泛分布于胞核和胞质中,Bcl-2表达减少。结论黄芩甙诱导肝癌细胞BEL-7402凋亡,线粒体损伤在黄芩甙诱导肝癌细胞凋亡中起重要作用,其机制可能为抑制肝癌细胞Bcl-2蛋白表达,促进Pax蛋白表达及细胞内Ca^2＋增加,激发线粒体膜通透性转运孔开放,线粒体跨膜电位降低,使肝癌细胞凋亡。     

Mitochondrial DNA analysis of human remains from the Yuansha site in Xinjiang,China

The Yuansha site is located in the center of the Taklimakan Desert of Xinjiang, in the southern Silk Road region. MtDNA was extracted from fifteen human remains excavated from the Yuansha site, dating back 2,000–2,500 years. Analysis of the phylogenetic tree and the multidimensional scaling (MDS) reveals that the Yuansha population has relatively close relationships with the modern populations of South Central Asia and Indus Valley, as well as with the ancient population of Chawuhu.     

Development of an enrichment culture growing at low temperature used for ensiling rice straw

To speed up the conversion of rice straw into feeds in a low-temperature region, a start culture used for ensiling rice straw at low temperature was selected by continuous enrichment cultivation. During the selection, the microbial source for enrichment was rice straw and soil from two places in Northeast China. Lab-scale rice straw fermentation at 10 degrees C verified, compared with the commercial inocculant, that the selected start culture lowered the pH of the fermented rice straw more rapidly and produced more lactic acid. The results from denatured gradient gel eletrophoresis showed that the selected start culture could colonize into the rice straw fermentation system. To analyze the composition of the culture, a 16S clone library was constructed. Sequencing results showed that the culture mainly consisted of two bacterial species. One (A) belonged to Lactobacillus and another (B) belonged to Leuconostoc. To make clear the roles of composition microbes in the fermented system, quantitative PCR was used. For species A, the DNA mass increased continuously until sixteen days of the fermentation, which occupied 65%. For species B, the DNA mass amounted to 5.5% at six days of the fermentation, which was the maximum relative value during the fermentation. To the authors' best knowledge, this is the first report on ensiling rice straw with a selected starter at low temperature and investigation of the fermented characteristics.     

Neurofibromin regulation of ERK signaling modulates GABA release and learning

We uncovered a role for ERK signaling in GABA release, long-term potentiation (LTP), and learning, and show that disruption of this mechanism accounts for the learning deficits in a mouse model for learning disabilities in neurofibromatosis type I (NF1). Our results demonstrate that neurofibromin modulates ERK/synapsin I-dependent GABA release, which in turn modulates hippocampal LTP and learning. An Nf1 heterozygous null mutation, which results in enhanced ERK and synapsin I phosphorylation, increased GABA release in the hippocampus, and this was reversed by pharmacological downregulation of ERK signaling. Importantly, the learning deficits associated with the Nf1 mutation were rescued by a subthreshold dose of a GABA(A) antagonist. Accordingly, Cre deletions of Nf1 showed that only those deletions involving inhibitory neurons caused hippocampal inhibition, LTP, and learning abnormalities. Importantly, our results also revealed lasting increases in GABA release triggered by learning, indicating that the mechanisms uncovered here are of general importance for learning.     

Effect of 2-mercaptoethanol and cysteine supplementation during in vitro maturation on the developmental competence of oocytes from hormone-stimulated lambs

The objective was to determine the effect of 2-mercaptoethanol and cysteine on in vitro developmental competence of oocytes from lambs (4-8-week old) stimulated with eCG and pFSH. Oocytes were matured in medium (TCM199) with no supplement (Control group) or with 100muM 2-mercaptoethanol and 600muM cysteine (GSH group). Oocytes from adult sheep were also included (Adult group). The addition of 2-mercaptoethanol and cysteine did not improve nuclear maturation or microtubule configuration 12, 15, 18, or 24h after placement in maturation medium. Sperm head decondensation and male pronucleus formation were evaluated at 6, 12, and 18h after commencement of IVF; sperm decondensation appeared earlier in the GSH group (6h after the start of IVF). There were differences (P<0.05) between the Control group and the GSH and Adult groups for: fertilization rate at both 12h (55.4, 77.0, and 80.6%, respectively) and 18h (67.9, 86.9, and 88.7%); parthenogenesis rate at both 12h (25.0, 10.8, and 5.6%) and 18h (28.3, 9.8, and 4.5%); and polyspermy rate at 18h (26.4, 4.9, and 5.7%). Blastocyst rate at 7d was higher in the GSH group than the Control group (23.9% vs. 14.9%, P<0.05), but both were lower (P<0.05) than the Adult group (38.3%). The addition of 2-mercaptoethanol and cysteine improved sperm decondensation and rates of fertilization and the blastocyst development to 7d, with no effect on blastocyst rate at 9d.     

Simultaneous quantitation of dexamethasone palmitate and dexamethasone in human plasma by liquid chromatography/tandem mass spectrometry

A rapid and sensitive liquid chromatography/tandem mass spectrometry (LC/MS/MS) method for simultaneous quantitation of dexamethasone palmitate and dexamethasone in human plasma was developed. After sample preparation by protein precipitation and liquid-liquid extraction, the analytes and internal standard (IS) were separated on a Venusil XBP-C8 column using gradient elution. Multiple reaction monitoring of dexamethasone palmitate, dexamethasone and IS used the precursor to product ion transitions at m/z 631.8-->373.1, m/z 393.2-->147.1 and m/z 264.2-->58.1, respectively. The method was linear over the ranges 1.5-1000ng/mL for dexamethasone palmitate and 2.5-250ng/mL for dexamethasone with intra- and inter-day precisions of <10% and accuracies of 100+/-7%. The assay was applied to a clinical pharmacokinetic study involving the injection of dexamethasone palmitate to healthy volunteers.