Visualizing spatially correlated dynamics that directs RNA conformational transitions

RNAs fold into three-dimensional (3D) structures that subsequently undergo large, functionally important, conformational transitions in response to a variety of cellular signals. RNA structures are believed to encode spatially tuned flexibility that can direct transitions along specific conformational pathways. However, this hypothesis has proved difficult to examine directly because atomic movements in complex biomolecules cannot be visualized in 3D by using current experimental methods. Here we report the successful implementation of a strategy using NMR that has allowed us to visualize, with complete 3D rotational sensitivity, the dynamics between two RNA helices that are linked by a functionally important trinucleotide bulge over timescales extending up to milliseconds. The key to our approach is to anchor NMR frames of reference onto each helix and thereby directly measure their dynamics, one relative to the other, using 'relativistic' sets of residual dipolar couplings (RDCs). Using this approach, we uncovered super-large amplitude helix motions that trace out a surprisingly structured and spatially correlated 3D dynamic trajectory. The two helices twist around their individual axes by approximately 53 degrees and 110 degrees in a highly correlated manner (R = 0.97) while simultaneously (R = 0.81-0.92) bending by about 94 degrees. Remarkably, the 3D dynamic trajectory is dotted at various positions by seven distinct ligand-bound conformations of the RNA. Thus even partly unstructured RNAs can undergo structured dynamics that directs ligand-induced transitions along specific predefined conformational pathways.     

A general integrative model for scaling plant growth, carbon flux, and functional trait spectra

Linking functional traits to plant growth is critical for scaling attributes of organisms to the dynamics of ecosystems and for understanding how selection shapes integrated botanical phenotypes. However, a general mechanistic theory showing how traits specifically influence carbon and biomass flux within and across plants is needed. Building on foundational work on relative growth rate, recent work on functional trait spectra, and metabolic scaling theory, here we derive a generalized trait-based model of plant growth. In agreement with a wide variety of empirical data, our model uniquely predicts how key functional traits interact to regulate variation in relative growth rate, the allometric growth normalizations for both angiosperms and gymnosperms, and the quantitative form of several functional trait spectra relationships. The model also provides a general quantitative framework to incorporate additional leaf-level trait scaling relationships and hence to unite functional trait spectra with theories of relative growth rate, and metabolic scaling. We apply the model to calculate carbon use efficiency. This often ignored trait, which may influence variation in relative growth rate, appears to vary directionally across geographic gradients. Together, our results show how both quantitative plant traits and the geometry of vascular transport networks can be merged into a common scaling theory. Our model provides a framework for predicting not only how traits covary within an integrated allometric phenotype but also how trait variation mechanistically influences plant growth and carbon flux within and across diverse ecosystems.     

Positive darwinian selection at the imprinted MEDEA locus in plants

In mammals and seed plants, a subset of genes is regulated by genomic imprinting where an allele's activity depends on its parental origin. The parental conflict theory suggests that genomic imprinting evolved after the emergence of an embryo-nourishing tissue (placenta and endosperm), resulting in an intragenomic parental conflict over the allocation of nutrients from mother to offspring. It was predicted that imprinted genes, which arose through antagonistic co-evolution driven by a parental conflict, should be subject to positive darwinian selection. Here we show that the imprinted plant gene MEDEA (MEA), which is essential for seed development, originated during a whole-genome duplication 35 to 85 million years ago. After duplication, MEA underwent positive darwinian selection consistent with neo-functionalization and the parental conflict theory. MEA continues to evolve rapidly in the out-crossing species Arabidopsis lyrata but not in the self-fertilizing species Arabidopsis thaliana, where parental conflicts are reduced. The paralogue of MEA, SWINGER (SWN; also called EZA1), is not imprinted and evolved under strong purifying selection because it probably retained the ancestral function of the common precursor gene. The evolution of MEA suggests a late origin of genomic imprinting within the Brassicaceae, whereas imprinting is thought to have originated early within the mammalian lineage.     

Efficient export of carbon to the deep ocean through dissolved organic matter

Oceanic dissolved organic carbon (DOC) constitutes one of the largest pools of reduced carbon in the biosphere. Estimated DOC export from the surface ocean represents 20% of total organic carbon flux to the deep ocean, which constitutes a primary control on atmospheric carbon dioxide levels. DOC is the carbon component of dissolved organic matter (DOM) and an accurate quantification of DOM pools, fluxes and their controls is therefore critical to understanding oceanic carbon cycling. DOC export is directly coupled with dissolved organic nitrogen and phosphorus export. However, the C:N:P stoichiometry (by atoms) of DOM dynamics is poorly understood. Here we study the stoichiometry of the DOM pool and of DOM decomposition in continental shelf, continental slope and central ocean gyre environments. We find that DOM is remineralized and produced with a C:N:P stoichiometry of 199:20:1 that is substantially lower than for bulk pools (typically >775:54:1), but greater than for particulate organic matter (106:16:1--the Redfield ratio). Thus for a given mass of new N and P introduced into surface water, more DOC can be exported than would occur at the Redfield ratio. This may contribute to the excess respiration estimated to occur in the interior ocean. Our results place an explicit constraint on global carbon export and elemental balance via advective pathways.     

Seasonal oscillations in water exchange between aquifers and the coastal ocean

Ground water of both terrestrial and marine origin flows into coastal surface waters as submarine groundwater discharge, and constitutes an important source of nutrients, contaminants and trace elements to the coastal ocean. Large saline discharges have been observed by direct measurements and inferred from geochemical tracers, but sufficient seawater inflow has not been observed to balance this outflow. Geochemical tracers also suggest a time lag between changes in submarine groundwater discharge rates and the seasonal oscillations of inland recharge that drive groundwater flow towards the coast. Here we use measurements of hydraulic gradients and offshore fluxes taken at Waquoit Bay, Massachusetts, together with a modelling study of a generalized coastal groundwater system to show that a shift in the freshwater-saltwater interface-controlled by seasonal changes in water table elevation-can explain large saline discharges that lag inland recharge cycles. We find that sea water is drawn into aquifers as the freshwater-saltwater interface moves landward during winter, and discharges back into coastal waters as the interface moves seaward in summer. Our results demonstrate the connection between the seasonal hydrologic cycle inland and the saline groundwater system in coastal aquifers, and suggest a potentially important seasonality in the chemical loading of coastal waters.     

Molecular Weight Distributions of Cotton Cellulose Treated with a Polycarboxylic Acid at Different pH

In last paper, the average molecular weight of a control cotton fabric and cotton fabrics treated with the polycarboxylic acid at different pH were measured. The result doesn‘t support the hypothesis that the pH of the finishing bath can affect the depolymerization of the finished cotton fabric. In order to understand more about it, the molecular weight distributions of the control and finished cotton fabrics were measured and the reason was fund. From the ratio and the molecular weight of the low molecular part one can see that the pH of the finishing bath can affect the depelymerization of the f‘mished cotton fabrics. The phenomenon that the average molecular weights of the cotton fabric crosslinked with BTCA at different pH are almost same is attributed to that the crosslinks are not broken completely when treated with 0.5 M NaOH solution at 50℃ for 144 h.     

生命起源前手性对映体富集与放大的数学规律与实验

生命起源前的原始海洋(池)中，由于没有手性源，手性化合物在合成过程中可能受到其他不对称因素(如手性对称性破缺)等影响，它们几乎都是以极小%ee值的非外消旋体(non-racemic enantiomers)存在。从数学理论出发，结合化学反应原理，推导出这些非外消旋体在通过某种反应后，其较小的%ee值(%ee₁)可以富集到较大的%ee值(%ee₂),尤其在很低%ee值的情况下，理论上其放大倍数(%ee₂/%ee₁)可以是指数级别的增加，而这是生命起源前得到高含量对映体(如L-氨基酸)所需要的。进一步使用约1%ee值的L-色氨酸甲酯(L-TME),通过与双功能基团物质(如乙二醛)发生反应，在0℃～室温条件下，将其放大富集到3.4%(%ee₂)。系列实验表明：最大放大倍数(%ee₂/%ee₁)可达1.9(从6.1%的%ee₁提高到11.7%的%ee₂);单次最大增量(Δ%ee=%ee_2<...