Visualization of Gluten and Starch Distributions in Dough by Fluorescence Fingerprint Imaging

A novel method combining imaging techniques and fluorescence fingerprint (FF) data measurement was developed to visualize the distributions of gluten and starch in dough without any preprocessing. Fluorescence images of thin sections of gluten, starch, and dough were acquired under 63 different combinations of excitation and emission wavelengths, resulting in a set of data consisting of the FF data for each pixel. Cosine similarity values between the FF of each pixel in the dough and those of gluten and starch were calculated. Each pixel was colored according to the cosine similarity value to obtain a pseudo-color image showing the distributions of gluten and starch. The dough sample was then fluorescently stained for gluten and starch. The stained image showed patterns similar to the pseudo-color FF image, validating the effectiveness of the FF imaging method. The method proved to be a powerful visualization tool, applicable in fields other than food technology.     

A decade of seasonal dynamics and co-occurrences within freshwater bacterioplankton communities from eutrophic Lake Mendota,WI, USA

With an unprecedented decade-long time series from a temperate eutrophic lake, we analyzed bacterial and environmental co-occurrence networks to gain insight into seasonal dynamics at the community level. We found that (1) bacterial co-occurrence networks were non-random, (2) season explained the network complexity and (3) co-occurrence network complexity was negatively correlated with the underlying community diversity across different seasons. Network complexity was not related to the variance of associated environmental factors. Temperature and productivity may drive changes in diversity across seasons in temperate aquatic systems, much as they control diversity across latitude. While the implications of bacterioplankton network structure on ecosystem function are still largely unknown, network analysis, in conjunction with traditional multivariate techniques, continues to increase our understanding of bacterioplankton temporal dynamics.     

基于SSR标记的陆地棉早熟相关种质遗传多样性分析

丰富的遗传变异对于提高作物的环境适应性和遗传改良进度至关重要。为了解我国早熟陆地棉种质资源遗传多样性,本研究利用136对SSR引物对186份陆地棉材料(96份早熟陆地棉材料和90份中、晚熟陆地棉材料)进行了遗传多样性分析,共检测到等位基因变异355个,平均2.61个。在早熟棉材料中,有134对多态性SSR引物扩增出341个条带,平均2.54个;中、晚熟材料中有133对多态性SSR引物,扩增出345个条带,平均2.59个。早熟棉材料的位点多态性信息含量(PIC)、有效等位基因数(Ne)、基因型多样性(H')分别为0.684、3.994和1.361;中、晚熟棉材料的PIC、Ne、H'分别为0.668、3.852和1.343。早熟棉材料和中、晚熟棉材料的Jaccard相似性系数分别在0.349~0.935和0.270~0.907之间,平均为0.635、0.666。遗传相似性系数总体平均值接近,但早熟棉变化范围较中、晚熟棉小。用类平均法(UPGMA)进行聚类可将186份材料分成2个类群。总体上来看,供试材料遗传相似性系数较高,说明我国陆地棉早熟相关种质遗传基础狭窄。本研究结果为早熟棉育种亲本选配,早熟棉种质创新提供依据。     

Protein‐fold recognition using an improved single‐source K diverse shortest paths algorithm

Protein structure prediction, when construed as a fold recognition problem, is one of the most important applications of similarity search in bioinformatics. A new protein‐fold recognition method is reported which combines a single‐source K diverse shortest path (SSKDSP) algorithm with Enrichment of Network Topological Similarity (ENTS) algorithm to search a graphic feature space generated using sequence similarity and structural similarity metrics. A modified, more efficient SSKDSP algorithm is developed to improve the performance of graph searching. The new implementation of the SSKDSP algorithm empirically requires 82% less memory and 61% less time than the current implementation, allowing for the analysis of larger, denser graphs. Furthermore, the statistical significance of fold ranking generated from SSKDSP is assessed using ENTS. The reported ENTS‐SSKDSP algorithm outperforms original ENTS that uses random walk with restart for the graph search as well as other state‐of‐the‐art protein structure prediction algorithms HHSearch and Sparks‐X, as evaluated by a benchmark of 600 query proteins. The reported methods may easily be extended to other similarity search problems in bioinformatics and chemoinformatics. The SSKDSP software is available at http://compsci.hunter.cuny.edu/~leixie/sskdsp.html . Proteins 2016; 84:467–472. © 2016 Wiley Periodicals, Inc.     

Structure‐based classification of FAD binding sites: A comparative study of structural alignment tools

A total of six different structural alignment tools (TM‐Align, TriangleMatch, CLICK, ProBis, SiteEngine and GA‐SI) were assessed for their ability to perform two particular tasks: (i) discriminating FAD (flavin adenine dinucleotide) from non‐FAD binding sites, and (ii) performing an all‐to‐all comparison on a set of 883 FAD binding sites for the purpose of classifying them. For the first task, the consistency of each alignment method was evaluated, showing that every method is able to distinguish FAD and non‐FAD binding sites with a high Matthews correlation coefficient. Additionally, GA‐SI was found to provide alignments different from those of the other approaches. The results obtained for the second task revealed more significant differences among alignment methods, as reflected in the poor correlation of their results and highlighted clearly by the independent evaluation of the structural superimpositions generated by each method. The classification itself was performed using the combined results of all methods, using the best result found for each comparison of binding sites. A number of different clustering methods (Single‐linkage, UPGMA, Complete‐linkage, SPICKER and k‐Means clustering) were also used. The groups of similar binding sites (proteins) or clusters generated by the best performing method were further analyzed in terms of local sequence identity, local structural similarity and conservation of analogous contacts with the FAD ligands. Each of the clusters was characterized by a unique set of structural features or patterns, demonstrating that the groups generated truly reflect the structural diversity of FAD binding sites. Proteins 2016; 84:1728–1747. © 2016 Wiley Periodicals, Inc.     

Constraint line methods and the applications in ecology北大核心CSCD

With increasing data availability in the big data era, many traditional statistical analyses based on the mean or median are insufficient or inappropriate to elucidate the complex patterns of variation. This is particularly the case when multiple factors are involved and the bivariate scatter occurs as scatter clouds. In such circumstances, constraint line (or envelope) method could be an alternative and effective tool to extract the data boundaries, thus improves our understanding of the complex relationships between limiting factor and response factor. Here, we synthesize the major findings and achievements in the field of applying the constraint line method in ecology. Specifically, we first describe the history and development of the constraint line method. We then discuss the techniques to establish the constraint lines with examples, and discuss the applications and implications of the constraint lines in species distribution, population performance, and optimization problem. We suggest simultaneously application of both constraint lines and regression techniques to the same datasets to achieve a comprehensive understanding of ecological process and underlying mechanisms. Such combined methods should be used with special attention to the role of spatial heterogeneity and scale dependency. We also discuss in detail the potential applicability of the constraint line method in studying the linkages between ecosystem services, and land system design.     

Similarities between invaders and native species: Moving past Darwin's naturalization conundrum

Darwin's naturalization conundrum states that successful invaders must be closely related to native species to possess the traits to tolerate that environment, but distantly related enough to possess traits allowing exploitation of underutilized niches, thereby minimizing competition. Although influential, this hypothesis is based on several simplistic assumptions. In particular, the relationship among phylogenetic relatedness, similarity, and competition is more complex than assumed and changes with spatial and phylogenetic scale. Competitive interactions are determined by limiting similarity and trait hierarchies associated with separate traits. Successful invaders thus need to be similar to native species in some respects, but different in others. This combination of similarities and differences is unlikely to be conserved. Further, many invasive species are represented in their novel range by genotypes with extreme trait values or plasticity relative to the species mean. Selection for these genotypes may alter the similarity between invasive and native species, thus obscuring the relationship between competition and phylogenetic relatedness. As environmental filtering and competition often act on different spatial scales, approaches assessing how individual traits relate to invasion at these scales (species pools vs local community) may improve our understanding of the relationship between similarity and invasion.     

Speciation and periodic restricted environments. The case of genus Ononis L. (subsections Natrix and Viscosae)

The morpho–environmental similarity between subsections Natrix and Viscosae has been pointed out as the reason for the genetic complexity of these groups of taxa. Based on this characterization a question emerges: could a very recent ongoing evolutionary process explain that morpho–environmental similarity? ISSR and cpSSR amplifications for 45 specimens belonging to taxa of Natrix and Viscosae subsections were developed, along their biogeographic distribution areas. Twenty-nine haplotypes were detected in the biogeographic area of both subsections, 79% were exclusive haplotypes, but the rest is shared between subsections Natrix and Viscosae species. Could that haplotype sharing be the result of potential hybridization between these taxa? Do current environmental conditions restrict the gene flow among taxa? The combination of ancestral genetic polymorphism, introgression, coalescence processes and periodic restricted environments (PRE) by glacial–interglacial environmental dynamics were discussed to explain the relevant percentage of exclusive haplotypes detected, as well as the persistence of shared haplotypes. These results are in accordance with the morpho–environmental proximity previously described for both subsections.     

Diversity and host associations of dipteran insects exploiting fungal fruiting bodies in Hokuriku,central Japan

To clarify the diversity and host associations of dipteran insects exploiting fungal fruiting bodies, we collected fruiting bodies at 18 localities in Hokuriku region, central Japan, from 2012 to 2015 and examined them for the emergence of insects. In total, 14,107 dipteran individuals belonging to 20 families emerged from fungi of 8 orders, 25 families, 49 genera and 129 species. Approximately 79% of dipteran individuals belonged to three families, Phoridae, Muscidae and Drosophilidae. The faunal similarity at the family level was relatively high between central (warm‐temperate) and northern (cool‐temperate) areas of Japan. However, the species composition of Drosophilidae was much different between central and northern Japan. The difference in the species composition was discussed in relation to the climatic conditions and fungal flora. None of the species from Drosophilidae, Phoridae, Muscidae, Mycetophilidae, Lonchaeidae and Chloropidae were specialists (they exploited more than one species of fungi), but they showed differences their fungi preference. Adults of some families, especially Drosophilidae, were frequently collected from fruiting bodies, but those of other families were seldom collected, probably reflecting differences in adult feeding ecology.