Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids

Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned se- quences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitu- tion matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9.

Regions and Their Typical Paradigms for Soil and Water Conservation in China

China is experiencing conflicts between its large population and scarce arable land,and between a demand for high productivity and the severe soil erosion of arable land.Since 1949,China has committed to soil and water conservation(SWC),for which eight regions and 41 subregions have been developed to improve the environment and increase land productivity.To obtain information from the regional planning and strategies for SWC and to explore whether SWC practices simultaneously contribute to soil conservation,ecosystem functioning,and the livelihoods of local farmers,and to summarize the successful experiences of various SWC paradigms with distinct characteristics and mechanisms of soil erosion,this paper systematically presents seven SWC regions(excluding the Tibetan Plateau region)and 14 typical SWC paradigms,focusing on erosion mechanisms and the key challenges or issues in the seven regions as well as on the core problems,main objectives,key technologies,and the performance of the 14 typical paradigms.In summary,the 14 typical SWC paradigms successfully prevent and control local soil erosion,and have largely enhanced,or at least do not harm,the livelihoods of local farmers.However,there remain many challenges and issues on SWC and socioeconomic development that need to be addressed in the seven SWC regions.China,thus,still has a long way to go in successfully gaining the win-win objective of SWC and human aspects of development.

Driving forces and their interactions of soil erosion in soil and water conservation regionalization at the county scale with a high cultivation rate

Soil erosion control based on county scale Soil and Water Conservation Regionalization(SWCR)is an essential component of China's ecological civilization construction.In SWCR,the quantitative analysis of the spatial heterogeneity and driving factors of soil erosion among different regions is still lacking.It is of great significance for soil erosion control to deeply examine the factors contributing to soil erosion(natural,land use,and socioeconomic factors)and their interaction at the county and regional levels.This study focused on a highly cultivated area,Hechuan District of Chongqing in the Sichuan Basin.The district(with 30 townships)was divided into four soil and water conservation regions(Ⅰ-Ⅳ)using principal component and hierarchical cluster analysis.The driving factors of soil erosion were identified using the geographical detector model.The results showed thatⅰ)the high cultivation rate was a prominent factor of soil erosion,and the sloping farmland accounted for 78.4%of the soil erosion in the study area;ⅱ)land use factors demonstrated the highest explanatory power in soil erosion,and the average interaction of land use factors explained 60.1%of soil erosion in the study area;ⅲ)the interaction between natural factors,socioeconomic factors,and land use factors greatly contributes to regional soil erosion through nonlinear-enhancement of double-factor enhancement.This study highlights the importance of giving special attention to the effects of land use factors on soil erosion at the county scale,particularly in mountainous and hilly areas with extensive sloping farmland and a high cultivation rate.

The regional difference in engineering-control and tillage factors of Chinese Soil Loss Equation

Accurate assessment of soil erosion is an important prerequisite for controlling soil erosion.The engineering-control(E)and tillage(T)factors are the keys for Chinese Soil Loss Equation(CSLE)to accurately evaluate water erosion in China.Besides,the E and T factors can reflect the water and soil conservation effects of engineering-control and tillage practices.But in the current full coverage of soil erosion surveys in China(such as soil erosion dynamic monitoring),for the same practice,the E or T factors are assigned the same value across the country.We selected 469 E and T factors data based on runoff plots from 73 publications,and they came from six soil and water conservation regions.Correlation analysis,regression analysis,and nonparametric tests were used to determine the comparability of the data,and it was proved that the runoff plots dimensions are consistent with the local topography.The results of one-way ANOVA and nonparametric tests for E and T factors in different regions showed that the engineering-control practices have good soil and water conservation effects and weaken the regional differences of other environmental factors,so there were no significant differences in E factors between different regions.However,there were significant differences in T factors between different regions,and the geodetector was applied to explore the intrinsic driving force of the spatial distribution of T factors.The results of the geodetector showed that the dominant driving forces of the spatial distribution of different types of tillage practices were not completely the same.When using CSLE to calculate water erosion,the E factor of the same practice can be used uniformly throughout the country,and the T factor needs to be considered and selected according to regional differences.At the same time,when choosing tillage practices in each water and soil conservation region,practices with better sediment reduction benefits should also be selected according to the regional environmental conditions.

Ecosystem classification and inventory maps as surrogates for ground beetle assemblages in boreal forest

Aims We compare performance of ecosystem classification maps and provincial forest inventory data derived from air photography in reflecting ground beetle(Coleoptera:Carabidae)biodiversity patterns that are related to the forest canopy mosaic.Our biodiversity surrogacy model based on remotely sensed tree canopy cover is validated against field-collected ground data.Methods We used a systematic sampling grid of 198 sites,covering 84 km^(2) of boreal mixedwood forest in northwestern Alberta,Canada.For every site,we determined tree basal area,characterized the ground beetle assemblage and obtained corresponding provincial forest inventory and ecosystem classification information.We used variation partitioning,ordination and misclassification matrices to compare beetle biodiversity patterns explained by alternative databases and to determine model biases originating from air photo-interpretation.Important Findings Ecosystem classification data performed better than canopy cover derived from forest inventory maps in describing ground beetle biodiversity patterns.The biodiversity surrogacy models based on provincial forest inventory maps and field survey generally detected similar patterns but inaccuracies in air photo-interpretation of relative canopy cover led to differences between the two models.Compared to field survey data,air photo-interpretation tended to confuse two Picea species and two Populus species present and homogenize stand mixtures.This generated divergence in models of ecological association used to predict the relationship between ground beetle assemblages and tree canopy cover.Combination of relative canopy cover from provincial inventory with other georeferenced land variables to produce the ecosystem classification maps improved biodiversity predictive power.The association observed between uncommon surrogates and uncommon ground beetle species emphasizes the benefits of detecting these surrogates as a part of landscape management.In order to complement conservation efforts established in protected areas,accurate,high resolution,wide ranging and spatially explicit knowledge of landscapes under management is primordial in order to apply effective biodiversity conservation strategies at the stand level as required in the extensively harvested portion of the boreal forest.In development of these strategies,an in-depth understanding of vegetation is key.