Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

Genome‐scale metabolic models (GEMs) are widely used to calculate metabolic phenotypes. They rely on defining a set of constraints, the most common of which is that the production of metabolites and/or growth are limited by the carbon source uptake rate. However, enzyme abundances and kinetics, which act as limitations on metabolic fluxes, are not taken into account. Here, we present GECKO, a method that enhances a GEM to account for enzymes as part of reactions, thereby ensuring that each metabolic flux does not exceed its maximum capacity, equal to the product of the enzyme's abundance and turnover number. We applied GECKO to a Saccharomyces cerevisiae GEM and demonstrated that the new model could correctly describe phenotypes that the previous model could not, particularly under high enzymatic pressure conditions, such as yeast growing on different carbon sources in excess, coping with stress, or overexpressing a specific pathway. GECKO also allows to directly integrate quantitative proteomics data; by doing so, we significantly reduced flux variability of the model, in over 60% of metabolic reactions. Additionally, the model gives insight into the distribution of enzyme usage between and within metabolic pathways. The developed method and model are expected to increase the use of model‐based design in metabolic engineering.     

中国丙型肝炎病毒基因型研究新进展

为了进一步了解中国丙型肝炎病毒基因型感染状态 ,我们建立了 5′ ＮＣＲＡＢＣ程序酶切分型法 :首先采用ＲＴＰＣＲ技术 5′ ＮＣＲ扩增ＨＣＶＲＮＡ阳性样品中的ｃＤＮＡ ,然后按照ＡＢＣ程序进行分型 ,Ａ应用ＢＨＨ(ＢｓｒＢⅠ ,ＨａｅⅡ ,ＨｉｎｆⅠ )复合内切酶消化 5′ ＮＣＲｃＤＮＡ ,Ｂ应用ＢｓｔＵⅠ消化 ,Ｃ应用ＨａｅⅢ消化 ,电泳检测片段大小。应用该方法对临床采集的ＨＣＶＲＮＡ阳性血清进行分型 ,在国内首次发...     

成熟促进因子对克隆重构胚核重编程的调控

成熟促进因子(maturation promoting factor,MPF)由催化亚单位P34cdc2和调节亚单位cyclin组成,对细胞周期的调控起着重要作用。目前,在核移植研究中发现：供体核在MPF的作用下发生核膜破裂(nuclear envelop breakdown．NEBD)和早熟染色体凝集(premature chromosome condensation,PCC),促进了核、质蛋白质因子的交换,有利于核重编程的进行。PCC还会对供体核的倍性及形态产生影响。     

Invasive cane toads are unique in shape but overlap in ecological niche compared to Australian native frogs

Invasive species are an important issue worldwide but predicting invasiveness, and the underlying mechanisms that cause it, is difficult. There are several primary hypotheses to explain invasion success. Two main hypothesis based on niche spaces stand out as alternative, although not exclusive. The empty niche hypothesis states that invaders occupy a vacant niche space in the recipient community, and the niche competition hypothesis states that invaders overlap with native species in niche space. Studies on trait similarity/dissimilarity between the invader and native species can provide information on their niche overlap. Here, we use the highly invasive and well‐studied cane toad (Rhinella marina) to test these two hypotheses in Australia, and assess its degree of overlap with native species in several niche dimensions. We compare extensive morphological and environmental data of this successful invader to 235 species (97%) of native Australian frogs. Our study is the first to document the significant morphological differences between the invasive cane toad and a continent‐wide frog radiation: despite significant environmental overlap, cane toads were distinct in body size and shape from most Australian frog species, suggesting that in addition to their previously documented phenotypic plasticity and wide environmental and trophic niche breadth, their unique shape also may have contributed to their success as an invasive species in Australia. Thus, the invasive success of cane toads in Australia may be explained through them successfully colonizing an empty niche among Australian anurans. Our results support that the cane toad's distinct morphology may have played a unique role in the invasiveness of this species in Australia, which coupled with a broad environmental niche breadth, would have boosted their ability to expand their distribution across Australia. We also propose RLLR (Relative limb length ratio) as a potentially useful measure of identifying morphological niche uniqueness and a potential measure of invasiveness potential in anuran amphibians.     

Noggin and bFGF cooperate to maintain the pluripotency of human embryonic stem cells in the absence of feeder layers

Human embryonic stem (hES) cells are typically maintained on mouse embryonic fibroblast (MEF) feeders or with MEF-conditioned medium. However, these xenosupport systems greatly limit the therapeutic applications of hES cells because of the risk of cross-transfer of animal pathogens. Here we showed that the bone morphogenetic protein antagonist noggin is critical in preventing differentiation of hES cells in culture. Furthermore, we found that the combination of noggin and basic fibroblast growth factor (bFGF) was sufficient to maintain the prolonged growth of hES cells while retaining all hES cell features. Since both noggin and bFGF are expressed in MEF, our findings suggest that they may be important factors secreted by MEF for maintaining undifferentiated pluripotent hES cells. Our data provide new insight into the mechanism how hES cell self-renewal is regulated. The newly developed feeder-free culture system will provide a more reliable alternative for future therapeutic applications of hES cells.     

Different seasonal feeding activity of diverse herbivores in two temperate forests

The aim of the present study was to understand the effects of abiotic conditions on seasonal feeding activity of diverse herbivores on the same oak tree species in two different forests. We tracked changes in herbivore feeding activities on an oak tree species (Quercus serrata) in two localities: a low elevation small hillock forest patch (Muan, MN) and a middle elevation mountain forest patch (Mt. Jirisan, JR). A total of five sites were selected in each of two forest localities. Data for leaf expansion, leaf chemical qualities, leaf damage ratio, and numbers of lepidopteran caterpillars were collected during spring (May) and summer (July to August), 2012. Leaf expansion rate was higher at the low hillock forest than the mid‐mountain forest from spring to summer. Nitrogen and carbon content decreased seasonally at both localities. Lepidopteran larval diversity was high in the mid‐mountain forest, and two‐way ANOVA showed that species richness of lepidopteran larvae was significantly affected by the interaction between season and locality. Leaf damage by all herbivores was higher in the low hillock forest than the mid‐mountain forest in spring, but was higher in the mid‐mountain forest in summer. Relative proportion of general herbivores increased from spring to summer in the mid‐mountain forest, but not in the low hillock forest. Canonical Correspondence Analysis (CCA) ordination showed that altitude‐ and season‐related variables were significant species and environment interaction factors. Our data indicate that locality and temperature disproportionally affected the feeding activities of diverse herbivores in two different temperate forests.     

漆酶及其应用

结合当今该领域的最新研究进展,综述了漆酶来源、结构、作用机制、介体系统及其在水相和非水相中的应用,以期为漆酶催化性能的进一步研究提供一定的借鉴和参考.     

Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay

Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N*) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N* implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N*. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N*. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.