An integrated approach to characterize genetic interaction networks in yeast metabolism

Although experimental and theoretical efforts have been applied to globally map genetic interactions, we still do not understand how gene-gene interactions arise from the operation of biomolecular networks. To bridge the gap between empirical and computational studies, we i, quantitatively measured genetic interactions between ～185,000 metabolic gene pairs in Saccharomyces cerevisiae, ii, superposed the data on a detailed systems biology model of metabolism and iii, introduced a machine-learning method to reconcile empirical interaction data with model predictions. We systematically investigated the relative impacts of functional modularity and metabolic flux coupling on the distribution of negative and positive genetic interactions. We also provide a mechanistic explanation for the link between the degree of genetic interaction, pleiotropy and gene dispensability. Last, we show the feasibility of automated metabolic model refinement by correcting misannotations in NAD biosynthesis and confirming them by in vivo experiments.     

Detection of polarization in the cosmic microwave background using DASI. Degree Angular Scale Interferometer

The past several years have seen the emergence of a standard cosmological model, in which small temperature differences in the cosmic microwave background (CMB) radiation on angular scales of the order of a degree are understood to arise from acoustic oscillations in the hot plasma of the early Universe, arising from primordial density fluctuations. Within the context of this model, recent measurements of the temperature fluctuations have led to profound conclusions about the origin, evolution and composition of the Universe. Using the measured temperature fluctuations, the theoretical framework predicts the level of polarization of the CMB with essentially no free parameters. Therefore, a measurement of the polarization is a critical test of the theory and thus of the validity of the cosmological parameters derived from the CMB measurements. Here we report the detection of polarization of the CMB with the Degree Angular Scale Interferometer (DASI). The polarization is deteced with high confidence, and its level and spatial distribution are in excellent agreement with the predictions of the standard theory.     

Endonuclease G is a novel determinant of cardiac hypertrophy and mitochondrial function

Left ventricular mass (LVM) is a highly heritable trait and an independent risk factor for all-cause mortality. So far, genome-wide association studies have not identified the genetic factors that underlie LVM variation, and the regulatory mechanisms for blood-pressure-independent cardiac hypertrophy remain poorly understood. Unbiased systems genetics approaches in the rat now provide a powerful complementary tool to genome-wide association studies, and we applied integrative genomics to dissect a highly replicated, blood-pressure-independent LVM locus on rat chromosome 3p. Here we identified endonuclease G (Endog), which previously was implicated in apoptosis but not hypertrophy, as the gene at the locus, and we found a loss-of-function mutation in Endog that is associated with increased LVM and impaired cardiac function. Inhibition of Endog in cultured cardiomyocytes resulted in an increase in cell size and hypertrophic biomarkers in the absence of pro-hypertrophic stimulation. Genome-wide network analysis unexpectedly implicated ENDOG in fundamental mitochondrial processes that are unrelated to apoptosis. We showed direct regulation of ENDOG by ERR-α and PGC1α (which are master regulators of mitochondrial and cardiac function), interaction of ENDOG with the mitochondrial genome and ENDOG-mediated regulation of mitochondrial mass. At baseline, the Endog-deleted mouse heart had depleted mitochondria, mitochondrial dysfunction and elevated levels of reactive oxygen species, which were associated with enlarged and steatotic cardiomyocytes. Our study has further established the link between mitochondrial dysfunction, reactive oxygen species and heart disease and has uncovered a role for Endog in maladaptive cardiac hypertrophy.     

Dynamics and roles of phragmoplast microfilaments in cell plate formation during cytokinesis of tobacco BY-2 cells

The phragmoplast is a special apparatus that functions in establishing a cell plate in dividing plant cells. It is known that microfilaments （MFs） are involved in constituting phragmoplast structure, but the dynamic distribution and role of phragmoplast MFs are far from being understood. In this study, the precise structure and dynamics of MFs during the initiation and the late lateral expansion of the phragmoplast were observed by using a tobacco BY-2 cell line stably expressing the microfilament reporter construct GFP-fABD2. Three-dimensional imaging showed that the phragmoplast MFs were initiated by two populations of MFs emerging between the reconstituting daughter nuclei at anaphase, which migrated to the mid-zone and gave rise to two layers of microfilament arrays. FM4-64 stained vesicles accumulated and fused with the cell plate between the two populations of MFs. The two layers of microfilament arrays of phragmoplast with ends overlapped always surrounded the centrifugally expanding cell plate. Partial disruption of MFs at metaphase by low concentration of latrunculin B resulted in the inhibition of the cell plate consolidation and the blockage of cell plate lateral expansion, whereas high concentration of latrunculin B restrained the progression of the cell cycle. Treating the cell after the initiation of phragmoplast led to the cease of the expansion of the cell plate. Our observations provide new insights into the precise structure and dynamics of phragmoplast MFs during cytokinesis and suggest that dynamic phragmoplast MFs are important in cell plate formation.     

铝抑制拟南芥根尖PIN2循环和囊泡运输

铝对植物毒害作用最明显的症状是迅速抑制根尖生长. 然而, 铝抑制根尖生长的机制并不清楚. 本文研究了铝对生长素和生长素运输载体(PIN2)囊泡运输的影响. 结果表明, 铝抑制拟南芥根尖生长素运输, 其中过渡区生长素抑制率最高, 达66%. 布雷菲尔德菌素(Brefeldin A, BFA, 一种囊泡运输抑制剂)明显诱导PIN2囊泡在细胞内形成点状结构, 铝处理降低点状结构的大小, 表明铝抑制PIN2囊泡在细胞内的运输. 实时定量PCR和蛋白印迹反应发现, 铝增加PIN2基因的转录表达, 促进PIN2蛋白在细胞膜水平方向累积. 细胞骨架解聚药物处理表明, 铝抑制PIN2囊泡的运输, 主要通过破坏肌球蛋白微丝来完成. 铝处理下, 拟南芥根尖伸长区细胞比过渡区具有较少的铝吸收和较低的囊泡运输频率. 上述结果表明, 通过调节生长素运输载体(PIN2)在质膜与胞内移动, 阻碍生长素的运输, 铝抑制了拟南芥根尖的生长.