Use of SAMPL for a study of DNA polymorphism,genetic diversity and possible gene tagging in bread wheat

Selective Amplification of Microsatellite Polymorphic Loci (SAMPL) technology was used in bread wheat for the first time for a study of genetic diversity, genotype identification and gene tagging. The diversity studies involved 55 wheat genotypes and two SAMPL primer pairs (SAMPL-6 and SAMPL-7, each with a M-CAG primer), which together gave 43 polymorphic bands out of a total of 87 SAMPL bands. The average polymorphic information content (PIC) of SAMPL primers was 0.221 and that of SAMPL markers was 0.264. The marker index of SAMPL markers was 9.61. The genetic similarity (GS) coefficients for 1,485 pairs of genotypes ranged from 0.35 to 0.96 with an average of 0.65. A dendrogram was prepared on the basis of a similarity matrix using the UPGMA algorithm, which corresponded well with the results of principal component analysis (PCA). From a total of 55 genotypes, 54 could be distinguished using the SAMPL banding patterns of both primers. For gene tagging, 568 bands from a total of 1,185 SAMPL bands detected polymorphism between each of the three pairs of parents differing for grain protein content (GPC), pre-harvest sprouting tolerance (PHST) and grain weight (GW). An association of six bands with GPC, of seven bands with PHST and four bands with GW was observed using bulked segregant analysis (BSA). Received: 5 April 2001 / Accepted: 17 May 2001     

Land surface phenology as an indicator of biodiversity patterns

With the rapid decline in biodiversity worldwide it is imperative to develop procedures for assessing changes in biodiversity across space. The synoptic view provided by imaging remote sensors constitutes a suitable approach for analyzing biodiversity from local to regional scales. A procedure based on the close relationship between floristic similarity and the similarity in land surface phenology was recently developed and successfully applied to assess diversity patterns using time series imagery acquired by the Moderate Resolution Imaging Spectro-radiometer (MODIS). However, as it depends on high temporal resolution remotely sensed data (e.g., MODIS), the procedure is constrained by the coarse spatial resolution characterizing these high temporal resolution data. Using an optimized technique for image fusion, we combined high temporal resolution data acquired by the MODIS sensor system with moderate spatial resolution data acquired by the Landsat TM/ETM+ sensor systems. Our results show that the MODIS/Landsat data fusion allows the characterization of land surface phenology at higher spatial resolutions, which better corresponded with information acquired within vegetation survey plots established in temperate montane forests located in Wolong Nature Reserve, Sichuan Province, China. As such, the procedure is useful for capturing changes in biodiversity induced by disturbances operating at large spatial scales and constitutes a suitable tool for monitoring and managing biodiversity.     

Soil‐based habitat partitioning in understorey palms in lower montane tropical forests

Aim Dispersal assembly and niche assembly are two competing theories proposed to explain the maintenance of species diversity in tropical forests. Dispersal theory emphasizes the role of chance colonization events and distance‐limited seed dispersal in explaining species abundance and distribution, whereas niche theory emphasizes differences among species in requirements for potentially limiting resources. Species distribution patterns in tropical forests often correlate with geology and topography, but tests of the relative importance of dispersal and niche partitioning have been hampered by an inadequate characterization of resource availability. The aim of this study was to explore how soil chemical and physical properties, climate, and geographic distance affect understorey palm communities in lower montane forests. Location Fortuna Forest Reserve, Chiriqui Province, and Palo Seco Forest Reserve, Bocas del Toro Province, in western Panama. Methods Understorey palms and soil nutrient concentrations were surveyed within 10 sites on different soil types across a 13‐km transect. Variation in palm community composition was examined in relation to spatial and environmental variables. Results The 25 understorey palm species recorded in the study were non‐randomly distributed among forests differing in soil nutrient availability. In support of dispersal theory, floristic similarity decreased predictably with increasing geographic distance. However, environmental and soil variables were also correlated with geographic distance. Floristic similarity was also highly associated with a subset of environmental variables. Variation in palm community similarity was most strongly correlated with inorganic nitrogen availability and cation concentration. A subset of soil variables had a stronger relationship with floristic similarity when geographic distance was controlled for than did geographic distance when differences in soils were controlled for. Main conclusions Both dispersal and niche processes affect palm species distribution patterns. Although spatially limited dispersal may influence species distribution patterns, soil‐based habitat associations, particularly with respect to soil nitrogen, cation availability and aluminium concentrations, remain important factors influencing palm community composition at the mesoscale level in this tropical montane forest.     

几种氧代丙酸化合物在诱捕白纹伊蚊中的应用

为了从氧代丙酸化合物中筛选出对白纹伊蚊Aedes albopictus具有良好引诱效果的化合物,采用陷阱诱捕法分别测定了丙酮酸(α-氧代丙酸)、3-甲氧基-2-甲基-3-氧代丙酸、3-(苄氧基)-3-氧代丙酸和3-氨基-3-氧代丙酸4种氧代丙酸化合物及丙酸对白纹伊蚊成虫的诱捕效果。结果表明,在供试的5种化合物中,α-氧代丙酸、3-甲氧基-2-甲基-3-氧代丙酸和3-(苄氧基)-3-氧代丙酸3种氧代丙酸化合物及丙酸的诱捕效果显著,同剂量的各化合物对白纹伊蚊的诱蚊效果依次是3-甲氧基-2-甲基-3-氧代丙酸>3-(苄氧基)-3-氧代丙酸>α-氧代丙酸=丙酸。相同质量α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶1至1∶2的配方比,具有协同增效作用,平均累计诱捕量均显著优于单组分α-氧代丙酸、3-(苄氧基)-3-氧代丙酸和对照纯水(P<0.05)。其中最优配方比是α-氧代丙酸∶3-(苄氧基)-3-氧代丙酸=1∶2,平均累计诱捕量比单组分α-氧代丙酸增加45.45%,比单组分3-(苄氧基)-3-氧代丙酸增加32.33%和比对照纯水增加73.11%(P<0.05)。现场...     

长江流域若干水体寡毛类区系组成及相似性分析

研究了长江流域十余个水体水栖寡毛类的区系组成及分布。共鉴定水栖寡毛类53种,隶3科27属,其中仙女虫科15属31种(占58.49%);颤蚓科11属20种(占37.74%);线蚓科1属2种(占3.77%).在河流、草型湖泊和藻型湖泊这三类水体中,以草型湖泊的物种数最多,达36种;其次为长江干流,34种;藻型湖泊仅24种。对寡毛类的种间关系及不同生境寡毛类种类组成的相似性进行了聚类分析,结果表明,寡毛类的种类分布具有明显的地域性,据此可将其划分为6类(A-F组).       

Phenotype and Micro-array characterization of duplication 11q22.1-q25 and review of the literature

Partial duplication of 11q is related to several malformations like growth retardation, intellectual disability, hypoplasia of corpus callosum, short nose, palate defects, cardiac, urinary tract abnormalities and neural tube defects. We have studied the clinical and molecular characteristics of a patient with severe intellectual disabilities, dysmorphic features, congenital inguinal hernia and congenital cerebral malformation which is referred to as cytogenetic exploration. We have used FISH and array CGH analysis for a better understanding of the double chromosomic aberration involving a 7p microdeletion along with a partial duplication of 11q due to adjacent segregation of a paternal reciprocal translocation t(7;11)(p22;q21) revealed after banding analysis. The patient's karyotype formula was: 46,XY,der(7)t(7;11)(p22;q21)pat. FISH study confirmed these rearrangement and array CGH technique showed precisely the loss of at least 140 Kb on chromosome7p22.3pter and 33.4 Mb on chromosome11q22.1q25. Dysmorphic features, severe intellectual disability and brain malformations could result from the 11q22.1q25 trisomy. Our study provides an additional case for better understanding and delineating the partial duplication 11q.     

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.     

Multi-class clustering and prediction in the analysis of microarray data

DNA microarray technology provides tools for studying the expression profiles of a large number of distinct genes simultaneously. This technology has been applied to sample clustering and sample prediction. Because of a large number of genes measured, many of the genes in the original data set are irrelevant to the analysis. Selection of discriminatory genes is critical to the accuracy of clustering and prediction. This paper considers statistical significance testing approach to selecting discriminatory gene sets for multi-class clustering and prediction of experimental samples. A toxicogenomic data set with nine treatments (a control and eight metals, As, Cd, Ni, Cr, Sb, Pb, Cu, and AsV with a total of 55 samples) is used to illustrate a general framework of the approach. Among four selected gene sets, a gene set omega(I) formed by the intersection of the F-test and the set of the union of one-versus-all t-tests performs the best in terms of clustering as well as prediction. Hierarchical and two modified partition (k-means) methods all show that the set omega(I) is able to group the 55 samples into seven clusters reasonably well, in which the As and AsV samples are considered as one cluster (the same group) as are the Cd and Cu samples. With respect to prediction, the overall accuracy for the gene set omega(I) using the nearest neighbors algorithm to predict 55 samples into one of the nine treatments is 85%.     

海南黎母山自然保护区两栖动物多样性及区系特征

2003年7月和2004年1月对海南省黎母山自然保护区两栖动物资源进行了调查,结果表明,该区内有两栖动物1目5科13属25种,全部为东洋界种类,其中华南区成分有15种,华中华南区有10种,分别占黎母山两栖动物总数的60%和40%,海南特有种有7种,具有典型的华南区系成分和热带山地林灌动物群特征。国家Ⅱ级保护动物有虎纹蛙1种;数量优势种有黑眶蟾蜍、小湍蛙、泽蛙、细刺蛙、海南溪树蛙和背条跳树蛙;保护区内两栖动物物种多样性指数为37109,均匀性指数为08321。     

The decay of similarity over geographical distance in parasite communities of marine fishes

Aim We evaluate, for the first time, the decay of similarity over distance in four species of marine fishes with different vagility: Trachurus murphyi (pelagic, highly vagile), Merluccius gayi (demersal, highly vagile), Sebastes capensis (demersal, low vagility) and Hippoglossina macrops (benthic, non‐vagile). Location We use our own data of the species composition of parasite communities in four host species: T. murphyi (Perciformes), M. gayi (Gadiformes), H. macrops (Pleuronectiformes) and S. capensis (Scorpaeniformes), from the coast of Chile and southern Argentina. Trachurus murphyi, M. gayi and H. macrops in the area studied live closely associated with the cold waters of the Humboldt Current System, while S. capensis in southern Chile is associated with the fjord areas south of c. 43° S, and in Argentina this species lives in close association with the cold water of the Malvinas Current, which mixes with the warm water of the Brazilian Current in the sampled area. Thus, for all four host species there are no known geographical (oceanographic) barriers that interrupt their continuous distributions. Methods Fish were collected and frozen (?18 °C) until examination in the laboratory. After thawing, each visceral organ was dissected separately, washed in running water, filtered using a mesh of 0.25 mm, and examined under a stereomicroscope (20×). For S. capensis, only ectoparasites were included in this study because data on endoparasites for some locations are not available. The approach of Poulin [Journal of Biogeography 30 (2003) 1609] was used. For each host species, we computed similarity in parasite composition using the Bray–Curtis distance on a presence/absence matrix. Similarity between each pair of localities was correlated (linear regression on raw and transformed data) with the distance (in nautical miles) among those sites. Results Among conspecific populations of host fish, there was no correlation between sample size and parasite species richness. The same pattern was evident when all host populations were pooled and treated as a single sample. Except for H. macrops, an important proportion of the geographical ranges of the host species was covered. The decay in similarity of parasite communities over distance was recorded in three of the four hosts analysed. For H. macrops, no relationship between distances and decay of similarity was evident. A linear regression on non‐transformed data provided a good fit, and the regression on log(n + 1) does not change significantly for both r² and probability, but slopes are smaller for log‐transformed than for non‐transformed data. Main conclusions Three of the four fish parasite systems studied fit well with the expected decay of similarity over distance. The slopes of the relationship between distance and similarity in the marine fishes studied are lower, but significant (three orders of magnitude) than those recorded in freshwater fishes by Poulin (2003) . In our case, Hippoglossina macrops (benthic, non‐vagile host) does not show any relationship, suggesting homogeneity over the geographical area studied for this species.