中国7所高校校园大型真菌多样性研究进展

大型真菌是校园生态环境中重要的生物组分,优美的校园生态环境通常孕育着较高的生物多样性。对我国7所高校校园大型真菌资源多样性研究进行了综述,校订了已报道文献中校园大型真菌的物种名录,对校园大型真菌资源的研究、保育、利用与科普等方面提出了展望,以期为校园大型真菌的生态管理提供科学依据。     

Component plane presentation integrated self-organizing map for microarray data analysis

Wheat gliadin and other cereal prolamins have been said to be involved in the pathogenic damage of the small intestine in celiac disease via the apoptosis of epithelial cells. In the present work we investigated the mechanisms underlying the pro-apoptotic activity exerted by gliadin-derived peptides in Caco-2 intestinal cells, a cell line which retains many morphological and enzymatic features typical of normal human enterocytes. We found that digested peptides from wheat gliadins (i) induce apoptosis by the CD95/Fas apoptotic pathway, (ii) induce increased Fas and FasL mRNA levels, (iii) determine increased FasL release in the medium, and (iv) that gliadin digest-induced apoptosis can be blocked by Fas cascade blocking agents, i.e. targeted neutralizing antibodies. This favors the hypothesis that gliadin could activate an autocrine/paracrine Fas-mediated cell death pathway. Finally, we found that (v) a small peptide (1157 Da) from durum wheat, previously proposed for clinical practice, exerted a powerful protective activity against gliadin digest cytotoxicity.     

Emergence of invariant-feature detectors in the adaptive-subspace self-organizing map

 A new self-organizing map (SOM) architecture called the ASSOM (adaptive-subspace SOM) is shown to create sets of translation-invariant filters when randomly displaced or moving input patterns are used as training data. No analytical functional forms for these filters are thereby postulated. Different kinds of filters are formed by the ASSOM when pictures are rotated during learning, or when they are zoomed. The ASSOM can thus act as a learning feature-extraction stage for pattern recognizers, being able to adapt to many sensory environments and to many different transformation groups of patterns. Received: 14 September 1995 / Accepted in revised form: 8 May 1996     

Classifying habitat characteristics of wetlands using a self-organizing map

Wetlands are nutrient-rich and biodiverse ecosystems that provide habitats for various animals and plants and protect against flooding. Classification of wetlands provides information to conservation planners and resource managers for ecosystem service determination. Many ecological case studies illuminate the self-organizing map (SOM) as a robust and powerful data classification and visualization tool. In this study, we use the SOM to analyze the habitat characteristics of inland wetlands in South Korea. We surveyed the plants, benthic macroinvertebrates, and bird species inhabiting 530 nationwide wetlands for four years from 2016 to 2019. Nine environmental features, including the proportion of urban area, farmland, grassland, a forest within a 1 km buffer zone, distance from the river and nearest wetland, area, perimeter, and average slope of wetland polygons, were used to train the SOM and examine the habitat characteristics of the surveyed living components. A map size of 10 × 11 pixels was considered for SOM training, and the output data were classified into eight clusters. Based on the occurrence frequency of the surveyed species group, most species were distributed in all clusters, whereas some dominated in specific clusters. We believe that our study contributes significantly to the literature because it highlights the significance of the SOM approach to cluster wetlands with dependent habitats and provides ecological information to build sustainable wetland conservation policies.     

西藏东南高寒森林大型真菌多样性与植被及环境的关系

通过对西藏东南高寒森林地区3个样地的9个样方两年内较为系统的调查,研究了大型真菌多样性及其与植被类型和大型真菌发生的其他诸多因素之间的关系.基于不同样方物种种类的样方层序聚类分析表明大型真菌的物种发生受植被类型影响较大.多样性指数分析表明急尖长苞冷杉林内的物种丰富度指数和多样性指数大于青冈树和落叶松混交林,后者大于青冈林.应用典范对应分析研究不同植被类型大型真菌物种发生和环境因素的关系,结果表明大型真菌物种的发生受不同环境因子的驱动,其发生是植被类型和环境因素共同作用的结果.     

Identification of GPI anchor attachment signals by a Kohonen self-organizing map

MOTIVATION: Anchoring of proteins to the extracytosolic leaflet of membranes via C-terminal attachment of glycosylphosphatidylinositol (GPI) is ubiquitous and essential in eukaryotes. The signal for GPI-anchoring is confined to the C-terminus of the target protein. In order to identify anchoring signals in silico, we have trained neural networks on known GPI-anchored proteins, systematically optimizing input parameters. RESULTS: A Kohonen self-organizing map, GPI-SOM, was developed that predicts GPI-anchored proteins with high accuracy. In combination with SignalP, GPI-SOM was used in genome-wide surveys for GPI-anchored proteins in diverse eukaryotes. Apart from specialized parasites, a general trend towards higher percentages of GPI-anchored proteins in larger proteomes was observed. AVAILABILITY: GPI-SOM is accessible on-line at http://gpi.unibe.ch. The source code (written in C) is available on the same website. SUPPLEMENTARY INFORMATION: Positive training set, performance test sets and lists of predicted GPI-anchored proteins from different eukaryotes in fasta format.     

安徽琅琊山大型真菌区系多样性

对安徽省琅琊山自然保护区大型真菌区系多样性进行了分析.结果表明该地区共有大型真菌107种,分属于25科56属,其中优势科为多孔菌科Polyporaceae(20种,占18.69％)、口蘑科Tricholomataceae(14种,占13.08％)、丝膜菌科Cortinariaceae(11种,占10.28％)、红菇科Russulaceae(10种,占9.35％),以上4科仅占琅琊山大型真菌总科数的16％,而种数占全部种数的51.4％;优势属有鹅膏属Amanita(8种,占7.48％)、栓菌属Trametes(7种,占6.54％)、乳菇属Lactarius(5种,占4.67％)、小皮伞属Marasmius(5种,占4.67％)、红菇属Russula(5种,占4.67％),共包括30种,占全部种数的28.04％.从属的区系地理成分上可分为:世界性分布成分(66.07％)、泛热带分布成分(19.64％)、北温带分布成分(10.71％)、东亚分布成分(1.79％).琅琊山大型真菌主要是以世界广布成分为主,其次是泛热带成分和北温带成分,这种分布状况可能与该地区的气候、地理和植被等自然条件的特征有着密切的关系.从种的组成上可划分为世界性分布种(70.09％)、温带分布种(14.95％)、热带-亚热带分布种(14.02％)及中国-日本共有种(0.93％)等4个分布类型,表现出一定的热带向温带过渡的区系特征.     

Characterizing macroinvertebrate communities across China: Large-scale implementation of a self-organizing map

Understanding the geographical patterns and divisions of communities is a fundamental step in achieving the sustainable management of ecosystems, especially in deteriorating global and local environments. The idea of geographical division has been applied on all continents but Antarctica, but it has never been rigorously tested for stream ecosystems in China, leaving a gap in knowledge for many basic and applied research questions regarding, for example, diversity patterns, conservation issues or climate change effects. To fill this gap, we aimed to (1) evaluate the geographical divisions of the macroinvertebrate communities in Chinese streams using the self-organizing map (SOM) method and (2) to characterize the distribution patterns in relation to different environmental variables. Macroinvertebrates were collected from 57 relatively clean stream sites covering a south-north gradient along the boundary of the geographic ladder (or altitudinal divide) in China. SOM was used to analyze large-scale biogeographical divisions of the macroinvertebrate communities. The sampling sites were divided into six clusters, distinguishing the samples from northern, central, and southern China. This pattern was also reflected by biotic metrics (abundance, biomass, taxa and sum of Ephemeroptera, Plecoptera, and Trichoptera richness, and diversity). The gradient of environmental variables, particularly water quality variables, was similar between the clusters, with the exceptions of two clusters from southwestern China when considering altitude and one cluster from northern China when considering conductivity and TN. The different clusters from the SOM were associated with indicator species, with clean-water adapted species dominating in southwestern China and pollution tolerant species in northern China. However, there were no significant correlations between environmental variables and biotic metrics. The overall combination of environmental variables and organism data suggests that spatial variation was the main predictor determining the composition of the macroinvertebrate communities on a large-scale, and the trained SOM appeared to be efficient at classifying streams on a broad geographic scale.     

Potentially functional regions of nucleic acids recognized by a Kohonen's self-organizing map

Computer recognition of short frnctional sites on DNA, suchas promoter regions or intron—exon boundaries, has recentlyattracted much interest. In this paper we have focused our attentionon the automatic recognition of relevant features of human nucleicacid sequences by means of an unsupervised artificial neuralnetwork model. Sixty messenger RNA and 31 genomic DNA sequenceswere analysed. The results showed that in mRNA, the minimalsimilarity 60 base pattern was guanine-and cytosine-rich andlocated in most sequences in a range of 250 bases from eitherthe middle point of the signal peptide coding region or fromthe start of the coding region. On DNA sequences a region definedby a cluster of minimal similarity patterns was present in manyof the analysed genes. This zone may be related to alternativesplicing and DNA methylation.     

A revised fate map for amphioxus and the evolution of axial patterning in chordates

The chordates include vertebrates plus two groups of invertebrates(the cephalochordates and tunicates). Previous embryonic fatemaps of the cephalochordate amphioxus (Branchiostoma) were influencedby preconceptions that early development in amphioxus and ascidiantunicates should be fundamentally the same and that the earlyamphioxus embryo, like that of amphibians, should have ventralmesoderm. Although detailed cell lineage tracing in amphioxushas not been done because of limited availability of the embryosand because cleavage is radial and holoblastic with the blastomeresnearly equal in size and not tightly adherent until the mid-blastulastage, a compilation of data from gene expression and function,blastomere isolation and dye labeling allows a more realisticfate map to be drawn. The revised fate map is substantiallydifferent from that of ascidians. It shows (1) that the anteriorpole of the amphioxus embryo is offset dorsally from the animalpole only by about 20°, (2) that the ectoderm/mesendodermboundary (the future rim of the blastopore) is at the equatorof the blastula, which approximately coincides with the 3rdcleavage plane, and (3) that there is no ventral mesoderm duringthe gastrula stage. Involution or ingression of cells over theblastopore lip is negligible, and the blastopore, which is posterior,closes centripetally as if by a purse string. During the gastrulastage, the animal pole shifts ventrally, coming to lie about20° ventral to the anterior tip of the late gastrula/earlyneurula. Comparisons of the embryos of amphioxus and vertebratesindicate that in spite of large differences in the mechanicsof cleavage and gastrulation, anterior/posterior and dorsal/ventralpatterning occur by homologous genetic mechanisms. Therefore,the small, nonyolky embryo of amphioxus is probably a reasonableapproximation of the basal chordate embryo before the evolutionof determinate cleavage in the tunicates and the evolution largeamounts of yolk in basal vertebrates.     

INCA: synonymous codon usage analysis and clustering by means of self-organizing map

SUMMARY: INteractive Codon usage Analysis (INCA) provides an array of features useful in analysis of synonymous codon usage in whole genomes. In addition to computing codon frequencies and several usage indices, such as 'codon bias', effective Nc and CAI, the primary strength of INCA has numerous options for the interactive graphical display of calculated values, thus allowing visual detection of various trends in codon usage. Finally, INCA includes a specific unsupervised neural network algorithm, the self-organizing map, used for gene clustering according to the preferred utilization of codons. AVAILABILITY: INCA is available for the Win32 platform and is free of charge for academic use. For details, visit the web page http://www.bioinfo-hr.org/inca or contact the author directly. SUPPLEMENTARY INFORMATION: Software is accompanied with a user manual and a short tutorial.     

Identification of a new motif on nucleic acid sequence data using Kohonen's self-organizing map

Here we present a performance test of a Kohonen features mapapplied to the fast extraction of uncommon sequences from thecoding region of the human insulin receptor gene. We used anetwork with 30 neurons and with a variable input window. Theprogram was aimed at detecting unique or uncommon DNA regionspresent in crude sequence data and was able to automaticallydetect the signal peptide coding regions of a set of human insulinreceptor gene data. The testing of this program with HSIRPRcDNA release (EMBL data bank) indicated the presence of uniquefeatures in the signal peptide coding region. On the basis ofour results this program can automatically detect ‘singularity’from crude sequencing data and it does not require knowledgeof the features to be found. Received on August 27, 1990; accepted on March 14, 1991     

Patterning limnological characteristics of the Chilika lagoon (India) using a self-organizing map

In this study, a self-organizing map (SOM) was utilized to classify habitats in the Chilika lagoon located in India, the largest lagoon ecosystem in Asia (maximum length, 64.3 km; mean width, 20.1 km). The lagoon was marginally eutrophic (nitrate, 0.25 ± 0.22 mg L⁻¹; orthophosphate, 0.26 ± 0.22 mg L⁻¹; n = 1,980, respectively) for six years (1999–2004), and it used to be warm, shallow, turbid and predominantly brackish. The SOM model successfully identified the changing patterns of limnology in the lagoon using the monthly limnological dataset from 30 study sites (July 1999–December 2004). Comparative re-sectoring evaluation of current monitoring sites was accomplished based on the outcome of the modeling. The new site clustering that emerged from the model was similar to conventional ones, and several sites were reorganized. Water physicochemistry was affected by freshwater inflow during monsoon and the new lagoon mouth constructed in September 2000, which resulted in variations in site characteristics in terms of limnology. The results of this study may provide information on the limnological patterns in Chilika lagoon, and they leave room for further study into functional changes in the lagoon ecology with respect to changes in climatic factor, freshwater flow and lagoon morphology.     

Application of the self-organizing map as a prediction tool for an integrated constructed wetland agroecosystem treating agricultural runoff

A self-organizing map (SOM) model was applied as a prediction tool for the performance of an integrated constructed wetland (ICW) agroecosystem treating agricultural runoff to protect receiving watercourses. By utilizing the SOM model, the time-consuming to measure expensive biochemical oxygen demand outflow concentrations were predicted well by other inexpensive variables, which were quicker and easier to measure. Correct predictions for the outflow biochemical oxygen demand concentrations were between 89% and 100%. This novel approach allows for the real time control of the outflow water quality of the ICW and potentially also of other treatment system applications. Moreover, the missing values and outliers from the large but incomplete ICW data set were replaced accurately by most likely values determined by the SOM model. This was important because the proportions of unusable entries for chemical oxygen demand, suspended solids and biochemical oxygen demand were very high: 41%, 54%, and 61%, respectively.     

Application of Kohonen's self-organizing feature map algorithm to cortical maps of orientation and direction preference

Cortical maps of orientation preference in cats, ferrets and monkeys contain numerous half-rotation point singularities. Experimental data have shown that direction preference also has a smooth representation in these maps, with preferences being for the most part orthogonal to the axis of preferred orientation. As a result, the orientation singularities induce an extensive set of linear fractures in the direction map. These fractures run between and connect nearby point orientation singularities. Their existence appears to pose a puzzle for theories that postulate that cortical maps maximize continuity of representation, because the fractures could be avoided if the orientation map contained full-rotation singularities. Here we show that a dimension-reduction model of cortical map formation, which implements principles of continuity and completeness, produces an arrangement of linear direction fractures connecting point orientation singularities which is similar to that observed experimentally. We analyse the behaviour of this model and suggest reasons why the model maps contain half-rotation rather than full-rotation orientation singularities.     

Pattern detection of movement behaviors in genotype variation of Drosophila melanogaster by using self-organizing map

The two dimensional movement tracks of STAT92E⁰⁶³⁴⁶ mutant and two control strains (Oregon red (OR) and TM3) of Drosophila melonogaster were continuously observed with image processors. Subsequently Self-Organizing Map (SOM) was implemented to patterning of responding behaviors of the tested specimens. Movement behaviors were accordingly revealed in different strains and sex. SOM showed difference in degree of grouping in behaviors in different genotypes. Visualization through SOM further characterized the clusters of specimens with the variables regarding activities and spatial information. The study demonstrated that techniques in data mining in artificial neural networks could be a useful tool for analyzing complex behaviors induced by changes in genetic information.