Salinivibrio sp.YH4胞外丝氨酸蛋白酶EYHS耐盐性及生物信息学分析

摘要：目的 探讨菌株Salinivibrio sp.YH4分泌的丝氨酸蛋白酶EYHS的耐盐性及结构特征。方法 明胶底物酶谱法分析EYHS的耐盐性。应用生物信息学手段对EYHS及6种耐盐的S8家族丝氨酸蛋白酶结构特征进行分析。结果 EYHS在4 mol/L的NaCl溶液中仍具有活性,属于耐盐蛋白酶。EYHS及6种S8家族丝氨酸蛋白酶分子表面的loop区等无规则卷曲所占比例较高,α-螺旋与β-片层则主要位于酶分子内部。EYHS分子表面酸性氨基酸含量较高,且具有弱疏水内核。多序列比对发现蛋白酶的催化三联体两侧存在高度保守的基序和保守的极性氨基酸及芳香族氨基酸,并存在多个保守的Gly与Ala。同源模建和表面电荷分布显示,α螺旋和β片层围成了蛋白酶的催化腔,EYHS活性中心包含由Asp32、His65与Ser215组成的催化三联体,且催化位点区域表面静电势为负。结论 上述结构特征可能有助于耐盐丝氨酸蛋白酶EYHS在高盐环境下维持其稳定性和适度柔性,并有助于其催化功能的发挥,为深入研究耐盐丝氨酸蛋白酶的高盐环境适应性提供了一定的理论依据。     

Building national eco-cultural protection areas and the Xiangxi practice in Hunan Province

Journal of Geographical Sciences - Since 2007, the Chinese government has initiated the building of national eco-cultural protection areas (NECPAs), thereby embarking on a significant...     

Spatiotemporal analysis of COVID-19 risk in Guangdong Province based on population migration

Journal of Geographical Sciences - Population migration, especially population inflow from epidemic areas, is a key source of the risk related to the coronavirus disease 2019 (COVID-19) epidemic....     

Simulating cross-sectional geometry of the main channel in response to changes in water and sediment in Lower Yellow River

Journal of Geographical Sciences - To understand the non-equilibrium morphological adjustment of a river in response to environmental changes, it is essential to (i) accurately identify how past...     

Tile‐based polygon overlay of vector data in a virtual globe

The demand for analysis of large‐scale data has increased with increased access to spatial vector data. Polygon overlay of vector data in a virtual globe requires proprietary data structures and proprietary analysis algorithms. A vector data structure is designed for rapid polygon overlay in a virtual globe by recording the metadata of the triangles (TriMeta) that constitute polygons. A polygon overlay algorithm is proposed based on this data structure. The overlay of two complex GIS polygons is transformed into the intersection computation of their 3D triangular presentations. The intersection computation of two sets of triangles is reduced considerably by utilizing TriMeta to filter out the disjoint triangle pairs and rapidly identify the contained triangle. The new method improves the overlay efficiency in a virtual globe because the amount of computation required to calculate the intersections of two large polygons and drape the intersections onto a terrain surface is reduced.     

Small‐area patch‐merging method accounting for both local constraints and the overall area balance

Small‐area patch merging is a common operation in land use data generalization. However, existing research on small‐area patch merging has mainly focused on local compatibility measures, which often lead to area imbalances among land use types from a global perspective. To address the shortcomings of previous studies by resolving local and global concerns simultaneously, this article proposes a merging method that considers both local constraints and the overall area balance. First, a local optimization model that considers three constraints—namely, the areas of neighboring patches, the lengths of shared arcs, and semantic similarity—is established. The areas of small patches are first pre‐allocated. Subsequently, in accordance with an area change threshold for individual land use types, land use types with area changes that exceed this threshold are identified. The patches corresponding to these land use types are subjected to iterative adjustments while considering the overall area balance. Based on their area splitting abilities, the split lines for small‐area patches are determined, and small‐area patches are merged. Finally, actual data from Guangdong Province are used for validation. The experimental results demonstrate that the proposed method is capable of preserving the local compatibility of patches while balancing the overall area associated with each land use type.     

Mapping 3D visibility in an urban street environment from mobile LiDAR point clouds

ABSTRACT

Visibility determination is a key requirement in a wide range of national and urban applications, such as national security, landscape management, and urban design. Mobile LiDAR point clouds can depict the urban built environment with a high level of details and accuracy. However, few three-dimensional visibility approaches have been developed for the street-level point-cloud data. Accordingly, an approach based on mobile LiDAR point clouds has been developed to map the three-dimensional visibility at the street level. The method consists of five steps: voxelization of point-cloud data, construction of lines-of-sight, construction of sectors of sight, construction of three-dimensional visible space, and calculation of volume index. The proposed approach is able to automatically measure the volume of visible space and openness at any viewpoint along a street. This approach has been applied to three study areas. The results indicated that the proposed approach enables accurate simulation of visible space as well as high-resolution (1 m × 1 m) mapping of the visible volume index. The proposed approach can make a contribution to the improvement of urban planning and design processes that aim at developing more sustainable built environments.     

渤海海域浮游病毒和浮游细菌的丰度变化与环境因子之间的耦联关系

Uncovering the role of environmental factors and finding critical factors which harbor significant fractions in governing microbial communities remain key questions in coastal marine systems. To detect the interactions between environmental factors and distributions of virio-and bacterioplankton in trophic coastal areas, we used flow cytometry to investigate the abundance of virio-and bacterioplankton covering 31 stations in the Bohai Sea of China. Our results suggested that the average abundance of total virus(TV) in winter(～2.29×10~8 particles/mL)was slightly lower than in summer(～3.83×10~8 particles/mL). The mean total bacterial abundance(TB) was much lower in winter(～2.54×107 particles/mL) than in summer(～5.43×10~7 particles/mL). Correlation analysis via redundancy analysis(RDA) and network analysis among virioplankton, bacterioplankton and environmental factors revealed that the abundances of viral and bacterial subpopulations depend on environmental factors. In winter, only temperature significantly influenced the abundances of virio-and bacterioplankton. In summer, in addition to temperature, both salinity and nutrient(SiO_2) had a remarkable impact on the distribution of virioand bacterioplankton. Our results showed a clear seasonal and trophic pattern throughout the whole water system, which revealed that temperature and eutrophication may play crucial roles in microbial distribution pattern.     

基于拉格朗日拟序结构的吕宋海峡表层水交换研究

黑潮通过吕宋海峡入侵南海呈现明显的瞬态特征。以往的研究通常将黑潮在吕宋海峡附近的流态分为几种不同类型。本文基于表层地转流计算得到的有限时间李雅普诺夫指数场（FTLE）,展示了拉格朗日视角下的吕宋海峡上层水交换特征。从FTLE场提取的拉格朗日拟序结构（LCSs）很好地识别了吕宋海峡附近的典型流态和旋涡活动。此外,这些LCSs还揭示了吕宋海峡周围复杂的输运路径和流体域,这些特征得到了卫星跟踪浮标轨迹的验证,且从流速场中是无法直接识别的。FTLE场显示,吕宋海峡附近表层水体的输运形态主要可分为四类。其中,黑潮直接向北流动的“跨越”形态和顺时针旋转的“流套”形态的发生频次明显高于直接进入南海的黑潮分支“渗入”形态和南海水流出至太平洋的“外流”形态。本文还进一步分析了黑潮在吕宋海峡处的涡旋脱落事件,突出强调了LCSs在评估涡旋输运方面的重要性。反气旋涡旋的脱落个例表明,这些涡旋主要源自黑潮“流套”,涡旋脱落之前可有效地俘获黑潮水。LCS所指示的输运通道信息有助于预测最终被反气旋涡所挟卷水体在上游的位置。而在气旋涡的形成过程中,LCS的分布特征表明,大部分气旋涡并未与黑潮水的输运路径相连通。因此,气旋涡对从太平洋到南海的上层水交换的贡献较小。