A new way to see RNA

Unlike proteins, the RNA backbone has numerous degrees of freedom (eight, if one counts the sugar pucker), making RNA modeling, structure building and prediction a multidimensional problem of exceptionally high complexity. And yet RNA tertiary structures are not infinite in their structural morphology; rather, they are built from a limited set of discrete units. In order to reduce the dimensionality of the RNA backbone in a physically reasonable way, a shorthand notation was created that reduced the RNA backbone torsion angles to two (η and θ, analogous to φ and ψ in proteins). When these torsion angles are calculated for nucleotides in a crystallographic database and plotted against one another, one obtains a plot analogous to a Ramachandran plot (the η/θ plot), with highly populated and unpopulated regions. Nucleotides that occupy proximal positions on the plot have identical structures and are found in the same units of tertiary structure. In this review, we describe the statistical validation of the η/θ formalism and the exploration of features within the η/θ plot. We also describe the application of the η/θ formalism in RNA motif discovery, structural comparison, RNA structure building and tertiary structure prediction. More than a tool, however, the η/θ formalism has provided new insights into RNA structure itself, revealing its fundamental components and the factors underlying RNA architectural form.     

A simple way to measure protein refolding rates in water.

Refolding of proteins is traditionally carried out either by diluting the denaturant-unfolded protein into buffer (GdmCl-jump) or by mixing the acid-denatured protein with strong buffer (pH-jump). The first method does not allow direct measurement of folding rates in water since the GdmCl cannot be infinitely diluted, and the second method suffers from the limitation that many proteins cannot be pH-denatured. Further, some proteins do not refold reversibly from low pH where they get trapped as aggregation prone intermediates. Here, we present an alternative approach for direct measurement of refolding rates in water, which does not rely on extrapolation. The protein is denatured in SDS, and is then mixed with alpha-cyclodextrin, which rapidly strips SDS molecules from the protein, leaving the naked unfolded protein to refold.     

A new method to measure foot contact

A new method to measure foot contact is described. It consists of a pressure sensitive transducer attached to one end of a flexible silicone rubber tube. A reliable indicator of foot contact is obtained with the tube glued to the outer perimeter of the sole of a shoe.     

A new assay to measure RNA N-glycosidase activity

We have developed a convenient procedure to measure the activity of Ricin A-chain and other enzymes with RNA N-glycosidase activity. The method is based on the use of a tritiated oligoribonucleotide as a substrate. The enzymatic activity is directly determined by measuring the release of adenine from the substrate. This method should prove useful in the study of the molecular mechanism of action of Ricin A and other RNA N-glycosidases.     

A new way for sterols to walk on water

The crystal structure of a homolog of oxysterol binding protein solved by Jim Hurley and coworkers (Im et al., 2005) shows that this large family acts as cholesterol transporters, taking not only the lipid but also large numbers of water molecules into an internal pocket.     

论保护区的管理体制

一个国家保护区管理体制是否合理和完善与该国保护区发展的速度和管理的有效程度有密切关系。世界各国保护区的管理体制很不相同,各有长处和不足。本文对保护区的主管部门和管理系统、管理现况、存在问题和发展趋势以及我国保护区管理体制的改革等作一些粗略的评论,期待引起有关方面的关注并进一步开展研究。     

Metabolomics shows the way to new discoveries

A report on the First Annual Meeting of the Metabolomics Society, Tsuruoka, Japan, 20-23 June 2005.     

Explaining the global pattern of protected area coverage: relative importance of vertebrate biodiversity, human activities and agricultural suitability

Aim Twelve per cent of the Earth’s terrestrial surface is covered by protected areas, but neither these areas nor the biodiversity they contain are evenly distributed spatially. To guide future establishment of protected areas, it is important to understand the factors that have shaped the spatial arrangement of the current protected area system. We used an information‐theoretic approach to assess the ability of vertebrate biodiversity measures, resource consumption and agricultural potential to explain the global coverage pattern of protected areas. Location Global. Methods For each of 762 World Wildlife Fund terrestrial ecoregions of the world, we measured protected area coverage, resource consumption, terrestrial vertebrate species richness, number of endemic species, number of threatened species, net primary production, elevation and topographic heterogeneity. We combined these variables into 39 a priori models to describe protected area coverage at the global scale, and for six biogeographical realms. Using the Akaike information criterion and Akaike weights, we identified the relative importance and influence of each variable in describing protected area coverage. Results Globally, the number of endemic species was the best variable describing protected area coverage, followed by the number of threatened species. Species richness and resource consumption were of moderate importance and agricultural potential had weak support for describing protected area coverage at a global scale. Yet, the relative importance of these factors varied among biogeographical realms. Measures of vertebrate biodiversity (species richness, endemism and threatened species) were among the most important variables in all realms, except the Indo‐Malayan, but had a wide range of relative importance and influence. Resource consumption was inversely related to protected area coverage across all but one realm (the Palearctic), most strongly in the Nearctic realm. Agricultural potential, despite having little support in describing protected area coverage globally, was strongly and positively related to protection in the Palearctic and Neotropical realms, as well as in the Indo‐Malayan realm. The Afrotropical, Indo‐Malayan and Australasian realms showed no clear, strong relationships between protected area coverage and the independent variables. Main conclusions Globally, the existing protected area network is more strongly related to biodiversity measures than to patterns of resource consumption or agricultural potential. However, the relative importance of these factors varies widely among the world’s biogeographical realms. Understanding the biases of the current protected area system may help to correct for them as future protected areas are added to the global network.     

A new method to measure cortical growth in the developing brain

Folding of the cerebral cortex is a critical phase of brain development in higher mammals but the biomechanics of folding remain incompletely understood. During folding, the growth of the cortical surface is heterogeneous and anisotropic. We developed and applied a new technique to measure spatial and directional variations in surface growth from longitudinal magnetic resonance imaging (MRI) studies of a single animal or human subject. MRI provides high resolution 3D image volumes of the brain at different stages of development. Surface representations of the cerebral cortex are obtained by segmentation of these volumes. Estimation of local surface growth between two times requires establishment of a point-to-point correspondence ("registration") between surfaces measured at those times. Here we present a novel approach for the registration of two surfaces in which an energy function is minimized by solving a partial differential equation on a spherical surface. The energy function includes a strain-energy term due to distortion and an "error energy" term due to mismatch between surface features. This algorithm, implemented with the finite element method, brings surface features into approximate alignment while minimizing deformation in regions without explicit matching criteria. The method was validated by application to three simulated test cases and applied to characterize growth of the ferret cortex during folding. Cortical surfaces were created from MRI data acquired in vivo at 14 days, 21 days, and 28 days of life. Deformation gradient and Lagrangian strain tensors describe the kinematics of growth over this interval. These quantitative results illuminate the spatial, temporal, and directional patterns of growth during cortical folding.     

A new apparatus to measure the rate of fall of seeds

1. Seed dispersal is widely recognized to be of crucial importance in the ecology of plant communities, yet characterization of dispersal capacity rarely goes beyond two categories: 'good' and 'poor' dispersers, defined on the basis of dispersule morphology.
2. We describe a new apparatus which determines the rate of fall of seeds in air by detecting their passage through two fans of laser light.
3. This apparatus is able to measure rate of fall in smaller seeds than previously published methods and reveals that there is no justification for the arbitrary division of species into two wind dispersal categories.     

A new method to measure autophagy flux in the nervous system

A current need in the neuroscience field is a simple method to monitor autophagic activity in vivo in neurons. Until very recently, most reports have been based on correlative and static determinations of the expression levels of autophagy markers in the brain, generating conflicting interpretations. Autophagy is a fundamental process mediating the degradation of diverse cellular components, including organelles and protein aggregates at basal levels, whereas alterations in the process (i.e., autophagy impairment) operate as a pathological mechanism driving neurodegeneration in most prevalent diseases. We have recently described a new simple method to deliver and express an autophagy flux reporter through the peripheral and central nervous system of mice by the intracerebroventricular delivery of adeno-associated viruses (AAV) into newborn mice. We obtained a wide expression of a monomeric tandem mCherry-GFP-LC3 construct in neurons through the nervous system and demonstrated efficient and accurate measurements of LC3 flux after pharmacological stimulation of the pathway or in disease settings of axonal damage. Here we discuss the possible applications of this new method to assess autophagy activity in neurons in vivo.