Disc-electrophoresis of albumin and globulin fractions from dormant achenes of Lasthenia

Albumin and globulin fractions were extracted from dormant seeds of all 20 taxa of Lasthenia. After disc-electrophoresis on basic 7% acrylamide gels, mean R_p values, coefficients of variation and 95% confidence intervals were computed for both types of protein bands. Dendrograms were produced using similarity coefficients, indicating interspecific affinities among the taxa which differ from the sectional taxonomy of the genus. Protein data concerning certain problematical relationships are compared with published taxonomical and chemical data.     

Algorithm of Regulatory Signal Recognition in DNA Sequences

An algorithm is proposed for extracting regulatory signals from DNA sequences. The algorithm complexity is nearly quadratic. The results of testing the algorithm on artificial and natural sequences are presented.     

Environmental filters shaping angiosperm tree assembly along climatic and geographic gradients

Question

Global‐scale forest censuses provide an opportunity to understand diversification processes in woody plant communities. Based on the climatic or geographic filtering hypotheses associated with tropical niche conservatism and dispersal limitation, we analysed phylogenetic community structures across a wide range of biomes and evaluated to what extent region‐specific processes have influenced large‐scale diversity patterns of tree species communities across latitude or continent.

Location

Global.

Methods

We generated a data set of species abundances for 21,379 angiosperm woody plants in 843 plots worldwide. We calculated net relatedness index (NRI) for each plot, based on a single global species pool and regional species pools, and phylogenetic β‐diversity (PBD) between plots. Then, we explored the correlations of NRI with climatic and geographic variables, and clarified phylogenetic dissimilarity along geographic and climatic differences. We also compared these patterns for South America, Africa, the Indo‐Pacific, Australia, the Nearctic, Western Palearctic and Eastern Palearctic.

Results

NRI based on a global‐scale species pool was negatively associated with precipitation and positively associated with Quaternary temperature change. PBD was positively associated with geographic distance and precipitation difference between plots across tropical and extratropical biomes. Moreover, phylogenetic dissimilarity was smaller in extratropical regions than in regions including the tropics, although temperate forests of the Eastern Palearctic showed a greater dissimilarity within extratropical regions.

Conclusions

Our findings support predictions of the climatic and geographic filtering hypotheses. Climatic filtering (climatic harshness and paleoclimatic change) relative to tropical niche conservatism played a role in sorting species from the global species pool and shaped the large‐scale diversity patterns, such as the latitudinal gradient observed across continents. Geographic filtering associated with dispersal limitation substantially contributed to regional divergence of tropical/extratropical biomes among continents. Old, long‐standing geographic barriers and recent climatic events differently influenced evolutionary diversification of angiosperm tree communities in tropical and extratropical biomes.     

Structural analysis of protein tyrosine phosphatase 1B reveals potentially druggable allosteric binding sites

Catalytic proteins such as human protein tyrosine phosphatase 1B (PTP1B), with conserved and highly polar active sites, warrant the discovery of druggable nonactive sites, such as allosteric sites, and potentially, therapeutic small molecules that can bind to these sites. Catalyzing the dephosphorylation of numerous substrates, PTP1B is physiologically important in intracellular signal transduction pathways in diverse cell types and tissues. Aberrant PTP1B is associated with obesity, diabetes, cancers, and neurodegenerative disorders. Utilizing clustering methods (based on root mean square deviation, principal component analysis, nonnegative matrix factorization, and independent component analysis), we have examined multiple PTP1B structures. Using the resulting representative structures in different conformational states, we determined consensus clustroids and used them to identify both known and novel binding sites, some of which are potentially allosteric. We report several lead compounds that could potentially bind to the novel PTP1B binding sites and can be further optimized. Considering the possibility for drug repurposing, we discovered homologous binding sites in other proteins, with ligands that could potentially bind to the novel PTP1B binding sites.     

太白山针叶林的Fuzzy分类研究

应用模糊聚类分析法和模糊图论分析对太白山针叶林进行了数量分类比较研究。将２６个样地分为两大类共７个群落类型。研究结果表明,两种方法在植物群落分类研究中,不但是可行的,而且所分类的实际结果是等价的,与实际观测情况也是吻合的。其中的图论法直接依据模糊相似系数得到树状图,简便易行,显示出更大的适用性。     

Effect of strain-specific hypersensitive resistance on spatial patterns of virus spread

Spatial patterns of spread were compared between strains of Bean yellow mosaic virus (BYMV) that differ in causing systemic necrotic (hypersensitive) or non‐necrotic symptoms in narrow‐leafed lupin (Lupinus angustifolius). Both types of BYMV were spread naturally by aphids from adjacent infected pasture into a large lupin block (‘natural spread site’), or from clover plants introduced as virus sources into two field experiments with lupin. Cumulative spatial data for plants with disease symptoms from a range of times in the growing period were assessed using Spatial Analysis by Distance IndicEs (SADIE). At the‘natural spread site’, with non‐necrotic BYMV, the extent of clustering of plants with symptoms increased gradually over time, while with necrotic BYMV there was less clustering and no increase over time. In both experiments, for the type of BYMV that was introduced into a plot, there was a gradual increase in clustering, but with this being greater with non‐necrotic BYMV. In the second experiment, there was also significant clustering of plants with symptoms of non‐necrotic BYMV in plots without introduced non‐necrotic foci but not for necrotic BYMV in plots without introduced necrotic foci. When clustering data for plants with newly recorded symptoms was tested for spatial association between successive assessment dates, association was positive for both BYMV types though stronger for the non‐necrotic type, declining as the temporal lag increased. Generally, association was strongest for assessments 2–3 wk apart, corresponding approximately to the period for BYMV to move systemically in plants and for obvious symptoms to appear in shoot tips. Contour maps for local association between dates showed that the strongest spatial associations were from coincidence of infection gaps rather than infection patches. The combination of information from clustering and association analysis showed that spread of non‐necrotic BYMV is less diffuse, with considerably more localised infection surrounding the infection sources. This work demonstrates how spatial virus spread can be diminished when hypersensitive (necrotic) resistance is deployed, and the limitations associated with employing hypersensitivity that is strain specific.     

Biogeography of European land mammals shows environmentally distinct and spatially coherent clusters

Aim  To produce a spatial clustering of Europe on the basis of species occurrence data for the land mammal fauna.
Location  Europe defined by the following boundaries: 11°W, 32°E, 71°N, 35°N.
Methods  Presence/absence records of mammal species collected by the Societas Europaea Mammalogica with a resolution of 50 × 50 km were used in the analysis. After pre-processing, the data provide information on 124 species in 2183 grid cells. The data were clustered using the k -means and probabilistic expectation maximization (EM) clustering algorithms. The resulting geographical pattern of clusters was compared against climate variables and against an environmental stratification of Europe based on climate, geomorphology and soil characteristics (EnS).
Results  The mammalian presence/absence data divide naturally into clusters, which are highly connected spatially and most strongly determined by the small mammals with the highest grid cell incidence. The clusters reflect major physiographic and environmental features and differ significantly in the values of basic climate variables. The geographical pattern is a fair match for the EnS stratification and is robust between non-overlapping subsets of the data, such as trophic groups.
Main conclusions  The pattern of clusters is regarded as reflecting the spatial expression of biologically distinct, metacommunity-like entities influenced by deterministic forces ultimately related to the physical environment. Small mammals give the most spatially coherent clusters of any subgroup, while large mammals show stronger relationships to climate variables. The spatial pattern is mainly due to small mammals with high grid cell incidence and is robust to noise from other subsets. The results support the use of spatially resolved environmental reconstructions based on fossil mammal data, especially when based on species with the highest incidence.     

Transient Acceleration of Epidermal Growth Factor Receptor Dynamics Produces Higher-Order Signaling Clusters

Cell signaling depends on spatiotemporally regulated molecular interactions. Although the movements of signaling proteins have been analyzed with various technologies, how spatial dynamics influence the molecular interactions that transduce signals is unclear. Here, we developed a single-molecule method to analyze the spatiotemporal coupling between motility, clustering, and signaling. The analysis was performed with the epidermal growth factor receptor (EGFR), which triggers signaling through its dimerization and phosphorylation after association with EGF. Our results show that the few EGFRs isolated in membrane subdomains were released by an EGF-dependent increase in their diffusion area, facilitating molecular associations and producing immobile clusters. Using a two-color single-molecule analysis, we found that the EGF-induced state transition alters the properties of the immobile clusters, allowing them to interact for extended periods with the cytoplasmic protein, GRB2. Our study reveals a novel correlation between this molecular interaction and its mesoscale dynamics, providing the initial signaling node.