Topological mirror images in protein structure computation: an underestimated problem.

When calculating three-dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solutions.     

Torsion angle approach to nucleic acid distance geometry: TANDY

Summary An efficient algorithm for generating DNA structures from a given set of distance constraints has been developed. The present implementation is suited for single-stranded DNA. The performance of the program has been tested with constraint sets representative of most stringent theoretical cases and also with usually available experimental ones. The results indicate that use of NOE-derived constraints alone generates an extremely large family of conformers and suggest that the quality of structure determination may be enhanced by incorporating additional constraints obtained by other means. The speed of the program makes it ideal for interactive use in conjunction with other complementary algorithms such as those for spectral simulation, energy minimization and molecular dynamics calculations.Dedicated to the memory of Professor V.F. Bystrov     

Simplified neuron model as a principal component analyzer

A simple linear neuron model with constrained Hebbian-type synaptic modification is analyzed and a new class of unconstrained learning rules is derived. It is shown that the model neuron tends to extract the principal component from a stationary input vector sequence.     

Genetic analysis of transpositions in the lac region of Escherichia coli

The lac region of Escherichia coli, carried on an F′ lacproB episome, was used as a target for the transposition of several transposable elements. Tn9 shows a preferential integration (by a factor of 50) into a region extending from the end of the Z gene through the Y gene. Throughout the remainder of the lacI, Z and Y genes one other short region, located in the middle of the I gene, is favored for integration. Within these favored regions many different integration points are evident. Inspection of the DNA sequence for the I and Y genes, and parts of the Z gene, shows a strong correlation between A + T richness and regions of preferential integration. Tn5 insertions follow a similar pattern, although with less preference; whereas Tn10 insertions (provided by T. J. Foster), also favor the Y gene and the end of Z, but are distributed among fewer integration points. Most of the Tn3 insertions into the episome are accompanied by a nearby or adjacent deletion.     

Does directed technological change get greener: Empirical evidence from Shanghai's industrial green development transformation

The degree of technological change biased to the environmental factor is crucial to industrial sustainable development. Using the stochastic frontier analysis method based on the translog production function and the panel data of 32 industrial sub-sectors in Shanghai over 1994–2011, this paper combines the evolution dynamic of the frontier technological structure with the evolution dynamic of technological change direction to estimate the output elasticities of production factors and the growth rate of green total factor productivity. Also, we investigate and compare the degrees of technological change biased to four production factors, i.e., capital, labor, energy, and carbon emissions. The results show that the industrial green total factor productivity in Shanghai presents an overall upward trend and mainly depends on the technical efficiency change. The improvements of labor productivity, R&D intensity, and energy efficiency can effectively enhance the green technical efficiency, while capital deepening has a mitigation effect on the green technical efficiency. The technological change of Shanghai's industrial production biases to energy use and capital saving, causing a high energy demand of industrial development. Under the dual impacts of economic development and energy-saving and emission-reduction policies, the degree of technological change biased to the environmental factor (carbon emissions) displays strong and weak alternations, indicating that the green bias of industrial technological change in Shanghai is not stable and that the green transformation of industrial development model needs to be further advanced.     

Hill coefficient-based stochastic switch-like signal directly governs damage-recovery dynamics in freshwater fish in response to pulse copper

Growing evidence demonstrates that fluctuating metal stressors can have profound impact on the ecophysiological responses in aquatic species. However, how environmental stochasticity affects the complex damage-recovery dynamics in organisms remains difficult to predict. The objective of this paper was to investigate the stochastic behavior in the damage-recovery dynamics in tilapia in response to pulse waterborne copper (Cu). We developed a mathematical framework that allows discrimination between damage and recovery processes in tilapia exposed to designed pulse Cu scenarios. We built deterministic nonlinear models for the damage-recovery dynamics that produce response surfaces describing killing/recovery rate–Cu-pulse interval interactions. Here we showed that the stochastic switching behavior arose from competition among killing, recovery rates, and Cu pulse frequency. This competition resulted in an ultrasensitivity appeared in whole body, gills, muscle, liver, and kidney with Hill coefficients of ≥7, 4, 7, 5, and 5, respectively, at Cu 3 mg L⁻¹, dilution rate 0.05 h⁻¹, and pulse interval 72 h, indicating that a stochastic switch-like response was generated. We argue that the role of gill-associated Hill coefficient as a direct signal of the stochastic switch-like response in the damage-recovery dynamics in response to pulse metal stressor can serve as a sensitive indicator for risk detection in fluctuating environments. Our approach constitutes a general method to identify the stochastic switch-like response for aquatic species exposed to fluctuating metal stressors, which may help to predict and, eventually, expand our understanding of the damage-recovery dynamics. Finally, we implicate that Hill coefficient-based switch-like signal and its damage with hazard response can be linked in an information theoretic framework to handle environmental stochasticity.     

Points on the curve: An analysis of methods for assessing the shape of vertebrate claws

The form of amniote claws has been extensively investigated, often with inferences about ecological association being drawn from studies of their geometry. Various methods have been used to quantify differences in the geometry of claws, but rarely have the underlying assumptions of such methods been addressed. Here, we use one set of bird claws and apply six methods (five that have been previously used, and a new one) that are tasked with comparing their shape. In doing so, we compare the (1) ability of these methods to represent the shape of the claw; (2) validity of the assumptions made about underlying claw geometry; (3) their ability to be applied unambiguously; and (4) their ability to differentiate between predetermined functional clusters. We find that of the six methods considered only the geometric morphometric approach reveals differences in the shapes of bird claws. Our comparison shows that geometry‐based methods can provide a general estimate of the degree of curvature of claw arcs, but are unable to differentiate between shapes. Of all of the geometry‐based approaches, we conclude that the adjusted version of the Zani (2000) method is the most useful because it can be applied without ambiguity, and provides a reliable estimate of claw curvature. The three landmarks that define that method (tip and base of the claw arc, plus the intersection between said claw arc and a line drawn perpendicular from the midpoint of tip and claw base) do not all bear biological significance, but relatively clearly circumscribe the length‐to‐height ratio of the claw, which relates to its curvature. Overall, our comparisons reveal that the shape of avian claws does not differ significantly between climbing and perching birds, and that the utilization of preordained functional clusters in comparative data analysis can hinder the discovery of meaningful differences in claw shape. J. Morphol. 278:150–169, 2017. © 2016 Wiley Periodicals,Inc.     

云南丽江古人类股骨的形态结构

1960年,在云南省丽江市发现了三根古人类股骨,通过地层观察,仅PA108可归为更新世晚期。前人对PA108做了初步报导,为了进一步了解丽江人股骨的演化分类地位和东亚早期现代人股骨形态变异,本文对PA108的内外结构进行了详尽的分析。研究发现,PA108具有明显的早期现代人特征,即明显的股骨粗线、骨干中部后侧骨密质最厚和中部横断面轮廓形状偏椭圆。PA108标本也有一定的特殊性,体现在骨干中近端和中部骨密质厚度分布上,这可能与其股骨嵴发育较弱有关,这一特征也导致了PA108与其他东亚早期现代人之间的形态差异,这些形态变异进一步扩大了目前已知的东亚地区早期现代人变异范围。同时,在采用骨密质厚度分布模式进行分类时,建议关注股骨骨干中部骨密质最厚部位。