Application of self-organizing neural networks to classification of plant communities in Pangquangou Nature Reserve, North China

Vegetation classification is an important topic in plant ecology and many quantitative techniques for classification have been developed in the field. The arti-ficial neural network is a comparatively new tool for data analysis. The self-organizing feature map (SOFM) is powerful tool for clustering analysis. SOFM has been applied to many research fields and it was applied to the classification of plant communities in the Pangquangou Nature Reserve in the present work. Pangquangou Nature Reserve, located at 37°20'-38°20' N, 110°18'-111°18' E, is a part of the Luliang Mountain range. Eighty-nine samples (quadrats) of 10 m x 10 m for for-est, 4 m × 4 m for shrubland and 1m x 1m for grass-land along an elevation gradient, were set up and species data was recorded in each sample. After discussion of the mathematical algorism, clustering technique and the pro-cedure of SOFM, the classification was carried out by using NNTool box in MATLAB (6.5). As a result, the 89 samples were clustered into 13 groups representing 13 types of plant communities. The characteristics of each community were described. The result of SOFM clas-sification was identical to the result of fuzzy c-mean clus-tering and consistent with the distribution patterns of vegetation in the study area and shows significant eco-logical meanings. This suggests that SOFM may clearly describe the ecological relationships between plant com-munities and it is a very effective quantitative technique in plant ecology research.     

cDNA捕捉法——从大的基因组区域直接分离编码序列

cDNA捕捉法或cDNA直选法是一种以表达为基础的基因分离技术,直接利用目的区域的基因组DNA捕捉cDNA,快速从大的基因组区域分离表达序列。该法已成功地应用于定位克隆和详尽的转录图谱的构建。     

庞泉沟自然保护区华北落叶松林的自组织特征映射网络分类与排序

自组织特征映射网络（SOM）是新近引入植物生态学的分析方法,对复杂问题和非线性问题具有较强的分析和求解功能。本研究应用SOM分类和排序研究了庞泉沟自然保护区华北落叶松林。研究结果表明,SOM将120个样方分为7个植物群落类型,分类结果具有明确的生态意义;样方和物种在SOM训练图上呈现一定规律的分布;7个群落类型各有其分布范围和界限,揭示了群落间的生态关系。在此基础上,通过引入一种在SOM训练图上可视化环境因子梯度的方法,能够较好地完成样方、物种和环境因子相互关系的分析,揭示了海拔是影响该区华北落叶松林生长和分布的最主要因子。生态分析表明SOM分类和排序是一种有效的梯度分析方法,适用于表征生态特征和探索群落和环境相互关系的研究。     

蝗虫染色体C带带型示意图的计算机绘制

该程序用C语言和FoxPro混合编写,把C语言的绘图优势和FoxPro强大的制表优势完美地结合起来, 通过输入实验测量的有关数据,可显示和打印出蝗虫C带带型的示意图,并可显示和打印出数据的统计表,以便于同模式图进行对照分析,并可将有关数据进行贮存。该程序稍作改动后可推广到其他动植物的C带以及其他带型示意图的绘制中。 Abstract:Using this program,we can draw all chromosomes of a species in line.Moreover,it can express centromere C-band,terminal C-band and internal C-band of each chromosome.This program not only can be used for locusts,after a little change,it can be used for all animals and plants.     

An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R-banding

Presented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R-banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH-mapping and R-banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH-mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA-DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat.     

Genetic and physical characterization of grain texture-related loci in diploid wheat

Endosperm texture, i.e. the hardness or softness of the grain, is an important quality criterion in cereals because it determines many grain end-use properties. Grain softness is the dominant trait and is mainly controlled by the Ha locus on the short arm of chromosome 5D in hexaploid bread wheat. Genes for puroindoline a (Pina-D1), puroindoline b (Pinb-D1), and grain softness related protein (Gsp-D1) have been shown to be linked to the Ha locus in different mapping populations and have been associated with the expression of grain softness. The study of the linkage relationships among these genes has been limited by the low level of polymorphism in the D genome of hexaploid Triticum aestivum. In the present study, a highly polymorphic Triticum monococcum mapping population was used to analyze linkage relationships among these three genes. Gsp-A ^m 1 and Pina-A ^m 1 were found to be completely linked and lie 0.14 cM distal to Pinb-A ^m 1 in the distal region of the short arm of chromosome 5A^m. The tight genetic linkage among these three genes was paralleled by their physical proximity within a single 105-kb clone isolated from a T. monococcum bacterial artificial chromosome (BAC) library. A restriction map of this BAC clone showed that Pina-A ^m 1 is located between Pinb-A ^m 1 and Gsp-A ^m 1. Partial sequences of the T. monococcum genes showed a high degree of similarity with their T. aestivum counterparts (≥ 94%). Marker-assisted selection strategies based on the tight linkage among Ha-related genes are discussed. Received: 27 June 1999 / Accepted: 18 August 1999     

Too hot to handle: Unprecedented seagrass death driven by marine heatwave in a World Heritage Area

The increased occurrence of extreme climate events, such as marine heatwaves (MHWs), has resulted in substantial ecological impacts worldwide. To date, metrics of thermal stress within marine systems have focussed on coral communities, and less is known about measuring stress relevant to other primary producers, such as seagrasses. An extreme MHW occurred across the Western Australian coastline in the austral summer of 2010–2011, exposing marine communities to summer seawater temperatures 2–5°C warmer than average. Using a combination of satellite imagery and in situ assessments, we provide detailed maps of seagrass coverage across the entire Shark Bay World Heritage Area (ca. 13,000 km²) before (2002 and 2010) and after the MHW (2014 and 2016). Our temporal analysis of these maps documents the single largest loss in dense seagrass extent globally (1,310 km²) following an acute disturbance. Total change in seagrass extent was spatially heterogeneous, with the most extensive declines occurring in the Western Gulf, Wooramel Bank and Faure Sill. Spatial variation in seagrass loss was best explained by a model that included an interaction between two heat stress metrics, the most substantial loss occurring when degree heating weeks (DHWm) was ≥10 and the number of days exposed to extreme sea surface temperature during the MHW (DaysOver) was ≥94. Ground truthing at 622 points indicated that change in seagrass cover was predominantly due to loss of Amphibolis antarctica rather than Posidonia australis, the other prominent seagrass at Shark Bay. As seawater temperatures continue to rise and the incidence of MHWs increase globally, this work will provide a basis for identifying areas of meadow degradation, or stability and recovery, and potential areas of resilience.     

美洲黑杨无性系AFLP指纹分析

１９９２年由Ｚａｂｅａｕ和Ｖｏｓ发明的扩增酶切片段长度多态性ＡＦＬＰ标记技术（Ｅｕｒｏｐｅａｎｐａｔｅｎｔ,０５３５８５８Ａ１,１９９３０３３１）,是目前国际上构建ＤＮＡ指纹图谱的最新方法,ＡＦＬＰ能检测到大量的基因位点,因而灵敏度高。选用不同的...     

利用脉冲电场凝胶电泳测定小鼠CK-4、Hox3.1和Hox3.3基因间的距离

利用脉冲电场凝胶电泳(PFGE,Pulse Field Gel Electrophoresis)和Southern印迹杂交,测定了小鼠第15染色体上Ⅱ型细胞角蛋白CK-4基因与含同源区序列的Hox 3.3基因之间的最大距离为130kb。Hox 3.3和Hox 3.1基因之间的距离不超过50kb。同时还确定了这三个基因所在的1100kb DNA片段上MluⅠ、NotⅠ、SacⅡ、SolⅠ和SfiⅠ五种限制酶的物理图。     

BioNano genome mapping of individual chromosomes supports physical mapping and sequence assembly in complex plant genomes

The assembly of a reference genome sequence of bread wheat is challenging due to its specific features such as the genome size of 17 Gbp, polyploid nature and prevalence of repetitive sequences. BAC‐by‐BAC sequencing based on chromosomal physical maps, adopted by the International Wheat Genome Sequencing Consortium as the key strategy, reduces problems caused by the genome complexity and polyploidy, but the repeat content still hampers the sequence assembly. Availability of a high‐resolution genomic map to guide sequence scaffolding and validate physical map and sequence assemblies would be highly beneficial to obtaining an accurate and complete genome sequence. Here, we chose the short arm of chromosome 7D (7DS) as a model to demonstrate for the first time that it is possible to couple chromosome flow sorting with genome mapping in nanochannel arrays and create a de novo genome map of a wheat chromosome. We constructed a high‐resolution chromosome map composed of 371 contigs with an N50 of 1.3 Mb. Long DNA molecules achieved by our approach facilitated chromosome‐scale analysis of repetitive sequences and revealed a ~800‐kb array of tandem repeats intractable to current DNA sequencing technologies. Anchoring 7DS sequence assemblies obtained by clone‐by‐clone sequencing to the 7DS genome map provided a valuable tool to improve the BAC‐contig physical map and validate sequence assembly on a chromosome‐arm scale. Our results indicate that creating genome maps for the whole wheat genome in a chromosome‐by‐chromosome manner is feasible and that they will be an affordable tool to support the production of improved pseudomolecules.