Deciphering the evolution and metabolism of an anammox bacterium from a community genome

Anaerobic ammonium oxidation (anammox) has become a main focus in oceanography and wastewater treatment. It is also the nitrogen cycle's major remaining biochemical enigma. Among its features, the occurrence of hydrazine as a free intermediate of catabolism, the biosynthesis of ladderane lipids and the role of cytoplasm differentiation are unique in biology. Here we use environmental genomics--the reconstruction of genomic data directly from the environment--to assemble the genome of the uncultured anammox bacterium Kuenenia stuttgartiensis from a complex bioreactor community. The genome data illuminate the evolutionary history of the Planctomycetes and allow us to expose the genetic blueprint of the organism's special properties. Most significantly, we identified candidate genes responsible for ladderane biosynthesis and biological hydrazine metabolism, and discovered unexpected metabolic versatility.     

Imbalance between pSmad3 and Notch induces CDK inhibitors in old muscle stem cells

Adult skeletal muscle robustly regenerates throughout an organism's life, but as the muscle ages, its ability to repair diminishes and eventually fails. Previous work suggests that the regenerative potential of muscle stem cells (satellite cells) is not triggered in the old muscle because of a decline in Notch activation, and that it can be rejuvenated by forced local activation of Notch. Here we report that, in addition to the loss of Notch activation, old muscle produces excessive transforming growth factor (TGF)-beta (but not myostatin), which induces unusually high levels of TGF-beta pSmad3 in resident satellite cells and interferes with their regenerative capacity. Importantly, endogenous Notch and pSmad3 antagonize each other in the control of satellite-cell proliferation, such that activation of Notch blocks the TGF-beta-dependent upregulation of the cyclin-dependent kinase (CDK) inhibitors p15, p16, p21 and p27, whereas inhibition of Notch induces them. Furthermore, in muscle stem cells, Notch activity determines the binding of pSmad3 to the promoters of these negative regulators of cell-cycle progression. Attenuation of TGF-beta/pSmad3 in old, injured muscle restores regeneration to satellite cells in vivo. Thus a balance between endogenous pSmad3 and active Notch controls the regenerative competence of muscle stem cells, and deregulation of this balance in the old muscle microniche interferes with regeneration.     

Calanoides natalis Brady, 1914 (Copepoda: Calanoida: Calanidae): identity and distribution in relation to coastal oceanography of the eastern Atlantic and western Indian Oceans

Until recently, Calanoides carinatus s.l. was assumed to be very widespread in the upwelling systems of the Atlantic, Indian and western Pacific Oceans. Molecular data, reported here, show that Calanoides from the eastern Atlantic and Arabian Sea are one species and distinct from C. carinatus s.s. The name Calanoides natalis Brady, 1914 is available for this species, which is fully re-described. The illustration by Brady of the male fifth leg and the currently reported genetic data lead us to conclude that C. natalis is distributed from the Bay of Biscay southwards along the eastern Atlantic, around the Cape of Good Hope, and northwards along the western boundary of the Indian Ocean as far as the Arabian Sea. A by-product of this study is the recognition that Calanoides macrocarinatus is a junior synonym of Calanoides brevicornis. Females of C. natalis are easy to distinguish morphologically from C. carinatus s.s. but are more similar to C. brevicornis, apart from size differences. From physical oceanographic evidence we conclude that the Indian Ocean is currently the upstream part of the distribution of C. natalis. Calanoides philippinensis is known to extend into the eastern Indian Ocean at tropical latitudes. It is not known if it is C. philippinensis that has been recorded along the western coast of Australia. An apparently undescribed species of Calanoides occurs on the eastern Australian coast.     

Quantitative analysis of mucosal oxygenation using ex vivo imaging of healthy and inflamed mammalian colon tissue

Colonic inflammation is associated with decreased tissue oxygenation, significantly affecting gut homeostasis. However, the crosstalk between O₂ consumption and supply in the inflamed tissue are not fully understood. Using a murine model of colitis, we analysed O₂ in freshly prepared samples of healthy and inflamed colon tissue. We developed protocols for efficient ex vivo staining of mouse distal colon mucosa with a cell-penetrating O₂ sensitive probe Pt-Glc and high-resolution imaging of O₂ concentration in live tissue by confocal phosphorescence lifetime-imaging microscopy (PLIM). Microscopy analysis revealed that Pt-Glc stained mostly the top 50–60 μm layer of the mucosa, with high phosphorescence intensity in epithelial cells. Measured O₂ values in normal mouse tissue ranged between 5 and 35 μM (4–28 Torr), tending to decrease in the deeper tissue areas. Four-day treatment with dextran sulphate sodium (DSS) triggered colon inflammation, as evidenced by an increase in local IL6 and mKC mRNA levels, but did not affect the gross architecture of colonic epithelium. We further observed an increase in oxygenation, partial activation of hypoxia inducible factor (HIF) 1 signalling, and negative trends in pyruvate dehydrogenase activity and O₂ consumption rate in the colitis mucosa, suggesting a decrease in mitochondrial respiration, which is known to be regulated via HIF-1 signalling and pyruvate oxidation rate. These results along with efficient staining with Pt-Glc of rat and human colonic mucosa reveal high potential of PLIM platform as a powerful tool for the high-resolution analysis of the intestinal tissue oxygenation in patients with inflammatory bowel disease and other pathologies, affecting tissue respiration.     

长江口滨海湿地有机碳循环过程及影响因素研究进展

滨海湿地是“蓝碳生态系统”的重要组成部分。综述了长江口滨海湿地土壤有机碳时空分布及含量、碳汇速率、有机碳横向输入输出通量及量化方法、有机碳循环定量分析模型以及有机碳储量和组分对不同影响因素所做出的动态响应规律,发现在土壤有机碳水平空间分布上,崇西湿地＞崇明东滩＞九段沙＞南汇潮滩;有机碳通量和浓度变化主要受到植物生物量和结构、水和土壤的理化性质、陆源输入和潮汐动力、间隙水交换以及人类活动和全球气候变化的影响。未来应加强长江口湿地土壤碳库和有机碳输运通量统一观测,准确量化各主要因素对有机碳的贡献,这对研究盐沼湿地的碳循环机理和碳汇评估具有重要意义。     

How the Investor's Risk Preferences Influence the Optimal Allocation in a Credibilistic Portfolio Problem

A classical portfolio theory deals with finding the optimal proportion in which an agent invests a wealth in a risk-free asset and a probabilistic risky asset. Formulating and solving the problem depend on how the risk is represented and how, combined with the utility function defines a notion of expected utility. In this paper the risk is a fuzzy variable and the notion of expected utility is defined in the setting of Liu's credibility theory. Thus, the portfolio choice problem is formulated as an optimization problem in which the objective function is a credibilistic expected utility. Different approximation calculation formulas for the optimal allocation of the credibilistic risky asset are proved. These formulas contain two types of parameters: Various credibilistic moments associated with fuzzy variables(expected value, variance, skewness and kurtosis) and the risk aversion, prudence and temperance indicators of the utility function.