大数据时代杂合酶的设计及其新趋势

酶分子的高效性和稳定性是工业广泛应用的物质基础。利用分子生物学技术可以将不同酶分子通过串联、插入、翻译后融合等方式构建成符合工业需求的杂合酶,但应用中多结构域杂合酶在表达量与酶活等方面仍存在弊端,而基于特定蛋白质结构域的多功能设计成为新趋势。高通量测序技术的发展,使得生物学家正面临着爆炸式增长的大数据集。近年来"蛋白质功能区"概念的提出,拓宽了人们对蛋白质结构与功能组织层次的认知,功能区残基聚簇的协同演化可导致同一家族不同蛋白质功能的差异。基于海量大数据分析可以快速定位特定功能区以及协同进化的关键位点,再利用合成生物学技术就可实现多种功能残基在同一蛋白质中的精准嫁接,完成天然酶分子的再设计。这将是杂合酶技术发展的新阶段,也会成为生物大数据时代下蛋白质设计的新趋势。     

Extensive gaps and biases in our knowledge of a well‐known fauna: implications for integrating biological traits into macroecology

Aim Ecologists seeking to describe patterns at ever larger scales require compilations of data on the global abundance and distribution of species. Comparable compilations of biological data are needed to elucidate the mechanisms behind these patterns, but have received far less attention. We assess the availability of biological data across an entire assemblage: the well‐documented demersal marine fauna of the United Kingdom. We also test whether data availability for a species depends on its taxonomic group, maximum body size, the number of times it has been recorded in a global biogeographic database, or its commercial and conservation importance. Location Seas of the United Kingdom. Methods We defined a demersal marine fauna of 973 species from 15 phyla and 40 classes using five extensive surveys around the British Isles. We then quantified the availability of data on eight key biological traits (termed biological knowledge) for each species from online databases. Relationships between biological knowledge and our predictors were tested with generalized linear models. Results Full data on eight fundamental biological traits exist for only 9% (n= 88) of the UK demersal marine fauna, and 20% of species completely lack data. Clear trends in our knowledge exist: fish (median biological knowledge score = six traits) are much better known than invertebrates (one trait). Biological knowledge increases with biogeographic knowledge and (to a lesser extent) with body size, and is greater in species that are commercially exploited or of conservation concern. Main conclusions Our analysis reveals deep ignorance of the basic biology of a well‐studied fauna, highlighting the need for far greater efforts to compile biological trait data. Clear biases in our knowledge, relating to how well sampled or ‘important’ species are suggests that caution is required in extrapolating small subsets of biologically well‐known species to ecosystem‐level studies.     

Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data‐model integration

In an era of rapid global change, our ability to understand and predict Earth's natural systems is lagging behind our ability to monitor and measure changes in the biosphere. Bottlenecks to informing models with observations have reduced our capacity to fully exploit the growing volume and variety of available data. Here, we take a critical look at the information infrastructure that connects ecosystem modeling and measurement efforts, and propose a roadmap to community cyberinfrastructure development that can reduce the divisions between empirical research and modeling and accelerate the pace of discovery. A new era of data‐model integration requires investment in accessible, scalable, and transparent tools that integrate the expertise of the whole community, including both modelers and empiricists. This roadmap focuses on five key opportunities for community tools: the underlying foundations of community cyberinfrastructure; data ingest; calibration of models to data; model‐data benchmarking; and data assimilation and ecological forecasting. This community‐driven approach is a key to meeting the pressing needs of science and society in the 21st century.     

40多年来塔南策勒绿洲动态变化研究

 利用策勒绿洲1956、1990和1998年3个不同时期的遥感数据（航片、TM和SPOT）进行配准、解译与分类处理,比较分析绿洲40多年来的动态变化,并从自然和人为因素两个方面探讨绿洲变化的原因。结果表明,从1956年到1998年策勒绿洲西北部的景观格局发生了显著变化,绿洲面积增加了近20％;林地的分布明显改变;河道发生显著位移,据实地调查大约向北移动400 m。对1990年TM与1998年SPOT分类数据,用FRAGSTATS软件计算景观格局指数并比较分析,发现研究区的绿洲、绿洲 荒漠交错带、荒漠和沙丘4种景观类型发生了明显的变化。绿洲面积增加而斑块数减少了近一半;交错带面积减少而斑块数增加了35％;荒漠面积减少而斑块数增加了60％;沙丘面积基本没有变化但斑块数减少了20％。绿洲变化的总体趋势是人工绿洲的面积增大而绿洲 荒漠交错带的面积明显减少,同时整个绿洲的破碎度增加而连通性降低,绿洲的稳定性和自我调节的功能下降。     

Estimates of subtropical forest biomass based on airborne LiDAR and Landsat 8 OLI data

 快速、定量、精确地估算区域森林生物量一直是森林生态功能评价以及碳储量研究的重要问题。该研究基于机载激光雷达(LiDAR)点云与Landsat 8 OLI多光谱数据, 借助江苏省常熟市虞山地区55块调查样地数据, 首先提取并分析了87个特征变量(53个OLI特征变量, 34个LiDAR特征变量)与森林地上、地下生物量的Pearson’s相关系数以进行变量优选, 然后利用多元逐步回归法建立森林生物量估算模型(OLI生物量估算模型和LiDAR生物量估算模型), 并与基于两种数据建立的综合生物量估算模型的结果进行比较, 讨论预测结果及其精确性。结果表明: 3种模型(OLI模型、LiDAR模型和综合模型)在所有样地无区分分析时, 地上和地下生物量的估算精度均达到0.4以上, 基于不同森林类型(针叶林、阔叶林、混交林)分析时地上和地下生物量的估算精度均有明显提高, 达到0.67及以上。利用分森林类型模型估算生物量, 综合生物量估算模型精度(地上生物量: R²为0.88; 地下生物量: R²为0.92)优于OLI生物量估算模型(地上生物量: R²为0.73; 地下生物量: R²为0.81)和LiDAR生物量估算模型(地上生物量: R²为0.86; 地下生物量: R²为0.83)。     

缺失数据下蛋白质多结构叠加的迭代方法

蛋白质三维结构叠加面临的主要问题是,参与叠加的目标蛋白质的氨基酸残基存在某些缺失,但是多结构叠加方法却大多数需要完整的氨基酸序列,而目前通用的方法是直接删去缺失的氨基酸序列,导致叠加结果不准确。由于同源蛋白质间结构的相似性,因此,一个蛋白质结构中缺失的某个区域,可能存在于另一个同源蛋白质结构中。基于此,本文提出一种新的、简单、有效的缺失数据下的蛋白质结构叠加方法（ITEMDM）。该方法采用缺失数据的迭代思想计算蛋白质的结构叠加,采用优化的最小二乘算法结合矩阵SVD分解方法,求旋转矩阵和平移向量。用该方法成功叠加了细胞色素C家族的蛋白质和标准Fischer’s 数据库的蛋白质（67对蛋白质）,并且与其他方法进行了比较。数值实验表明,本算法有如下优点：①与THESEUS算法相比较,运行时间快,迭代次数少;②与PSSM算法相比较,结果准确,运算时间少。结果表明,该方法可以更好地叠加缺失数据的蛋白质三维结构。     

Taxonomic aggregation does not alleviate the lack of consistency in analysing diversity in long‐term phytoplankton monitoring data: a rejoinder to Pomati et al. (2015)

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