Genetic variation in Drechslera teres populations as indicated by RAPD markers

Random amplified polymorphic DNA (RAPD) was used to assess genetic variation among 48 isolates of Drechslera teres originating from different sites in Finland. RAPD profiles were generated with five arbitrary 10-mer primers and revealed polymorphisms suitable for screening differentiation in this fungal population. Using UPGMA clustering analysis, a similarity coefficient of approximately 63% was observed between all D. teres isolates studied. The variation was, however, distributed on a small scale as different genotypes were found from the same plant. The isolates could not be grouped according to geographic origin, aggressiveness, growth rate or morphological features, indicating that the primers used in this study were neutral markers for these characters. The primers were, however, able to differentiate between isolates of Helminthosporium species (D. teres, Drechslera graminea and Bipolaris sorokiniana).     

不同生境区稻田节肢动物群落相似性分析

根据不同生境区稻田节肢动物群落系统调查结果,应用组平均聚类分析法及主成分分析法,讨论节肢动物群落的相似（相异）性问题。结果表明：生境条件及管理措施的差异对群落的结构影响较为明显,不同生境区的稻田节肢动物群落,都能在一定距离取值时聚合成一类,而水稻品种对此影响较小。主成分分析结果由二维图表达已基本满足要求。结果说明大八镇生境区稻田节肢动物群落与岗列镇生境区稻田节肢动物群落差异较大,分别列于两个极端。海陵镇生境区稻田介于两者之间,而与岗列镇生境区稻田节肢动物群落重叠。与聚类分析结果有所差异。这可能与主成分分析法损失部分信息有关。     

Comparison of RAPD and RFLP genetic markers in determining genetic similarity among Brassica oleracea L. genotypes

Genetic similarity among 45 Brassica Oleracea genotypes was compared using two molecular markers, random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLPs). The genotypes included 37 broccolis (var. italica), five cauliflowers (var. botrytis) and three cabbages (var. capitata) which represented a wide range of commercially-available germplasm, and included open-pollinated cultivars, commercial hybrids, and inbred parents of hybrid cultivars. Fifty-six polymorphic RFLP bands and 181 polymorphic RAPD bands were generated using 15 random cDNA probes and 62 10-mer primers, respectively. The objectives were to compare RFLP and RAPD markers with regard to their (1) sampling variance, (2) rank correlations of genetic distance among sub-samples, and (3) inheritance. A bootstrap procedure was used to generate 200 random samples of size n (n=2,3,5,... 55) independently from the RAPD and RFLP data sets. The coefficient of variance (CV) was estimated for each sample. Pooled regressions of the coefficient of variance on bootstrap sample size indicated that the rate of decrease in CV with increasing sample size was the same for RFLPs and RAPDs. The rank correlation between the Nei-Li genetic similarity values for all pairs of genotypes (990) based on RFLP and RAPD data was 0.745. Differences were observed between the RFLP and RAPD dendrograms of the 45 genotypes. Overlap in the distributions of rank correlations between independent sub-samples from the RAPD data set, compared to correlations between RFLP and RAPD sub-samples, suggest that observed differences in estimation of genetic similarity between RAPDs and RFLPs is largely due to sampling error rather than due to DNA-based differences in how RAPDs and RFLPs reveal polymorphisms. A crossing algorithm was used to generate hypothetical banding patterns of hybrids based on the genotypes of the parents. The results of this study indicate that RAPDs provide a level of resolution equivalent to RFLPs for detemination of the genetic relationships among genotypes.     

Unexpected sequence similarity between nucleosidases and phosphoribosyltransferases of different specificity.

Amino acid sequences of enzymes that catalyze hydrolysis or phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides (nucleosidases and phosphoribosyltransferases) were explored using computer methods for database similarity search and multiple alignment. Two new families, each including bacterial and eukaryotic enzymes, were identified. Family I consists of Escherichia coli AMP hydrolase (Amn), uridine phosphorylase (Udp), purine phosphorylase (DeoD), uncharacterized proteins from E. coli and Bacteroides uniformis, and, unexpectedly, a group of plant stress-inducible proteins. It is hypothesized that these plant proteins have evolved from nucleosidases and may possess nucleosidase activity. The proteins in this new family contain 3 conserved motifs, one of which was found also in eukaryotic purine nucleosidases, where it corresponds to the nucleoside-binding site. Family II is comprised of bacterial and eukaryotic thymidine phosphorylases and anthranilate phosphoribosyltransferases, the relationship between which has not been suspected previously. Based on the known tertiary structure of E. coli thymidine phosphorylase, structural interpretation was given to the sequence conservation in this family. The highest conservation is observed in the N-terminal alpha-helical domain, whose exact function is not known. Parts of the conserved active site of thymidine phosphorylases and anthranilate phosphoribosyltransferases were delineated. A motif in the putative phosphate-binding site is conserved in family II and in other phosphoribosyltransferases. Our analysis suggests that certain enzymes of very similar specificity, e.g., uridine and thymidine phosphorylases, could have evolved independently. In contrast, enzymes catalyzing such different reactions as AMP hydrolysis and uridine phosphorolysis or thymidine phosphorolysis and phosphoribosyl anthranilate synthesis are likely to have evolved from common ancestors.     

Low species turnover of upland Amazonian birds in the absence of physical barriers

Aim

One of the oldest and most powerful ways for ecologists to explain distinct biological communities is to invoke underlying environmental differences. But in hyper-diverse systems, which often display high species richness and low species abundance, these sorts of community comparisons are especially challenging. The classic view for Amazonian birds posits that riverine barriers and habitat specialization determine local and regional community composition. We test the tacit, complementary assumption that similar bird communities should therefore permeate uniform habitat between major rivers, regardless of distance.

Location

Upland (terra firme) rainforests of central Amazonia.

Methods

We conducted intensive whole-community surveys of birds in three pairs of 100-ha plots, separated by 40–60 km. We then used dissimilarity indices, cluster analysis, and ordination to characterize differences among the six avian communities.

Results

In all, we detected 244 forest-dependent birds, with an average of 190 species (78%) per plot. Species turnover was negligible, no unique indicator species were found among plot pairs, and all documented species were already known from a complete inventory at one of the three sites.

Main Conclusions

Our study corroborates the classic biogeographical pattern and suggests that turnover contributes little to regional avian diversity within upland forests. Using a grain size of 100 ha, this implies that upland birds perceive the environment as uniform, at least over distances of ~60 km. Therefore, to maximize both local species richness and population persistence, our findings support the conservation of very large tracts of upland rainforest. Our analyses also revealed that the avifauna at Reserva Ducke, encroached by urban sprawl from the city of Manaus, shows the hallmarks of a disturbed community, with fewer vulnerable insectivores. This defaunation signals that even an enormous preserve (10 × 10 km) in lowland Amazonia is not insulated from anthropogenic degradation within the surrounding landscape.     

Selected factors limiting the microbial degradation of recalcitrant compounds

Summary The focus of this review is to examine some of the reasons biodegradation may not take place in the environment even though its occurrence in the laboratory has been demonstrated. Some approaches for dealing with chemical persistence will be discussed. In addition, the potential of bioremediation as an in situ clean-up technology will be considered.     

Pollen allergens: development and function

Pollen allergens interact with the human immune system and the resulting IgE antibodies provide specific probes for their identification and characterisation. In one case, grass allergenic proteins are expressed late in pollen development coincident with the laying down of reserves. Sequence similarity of allergens has indicated possible functions for some allergens. The major birch pollen allergen shows sequence similarity with pathogenesis-related proteins, which form a secondary response in plant host-pathogen interactions and show anti-microbial activity. Some allergens of unknown function are cysteine-rich proteins, while some others have cysteine-rich regions; for example, the major allergen from rye-grass pollen, Lol p 1, has a cysteine-rich N-terminal region, while at the C-terminal region four tryptophan residues together with tyrosine and phenylalanine residues resemble those of cellulose- or sugar-binding domains of other proteins. Several pollen allergens show sequence similarity to cell wall-associated enzymes, while others show hydrolytic enzyme activity often associated with cell walls.     

Enlarged Similarity of Nucleic Acid Sequences

The concept of nucleic acid sequence base alternations is presented.The number of base alterations for the sequences of differentlength is established. The definition of "enlarged similarity"of nucleic acids sequences on the basis of sequence base alterationsis introduced. Mutual information between sequences is usedas a quantitative measure of enlarged similarity for two comparedsequences. The method of mutual information calculation is developedconsidering the correlation of bases in compared sequences.The definitions of correlated similarity and evolution similaritybetween compared sequences are given. Results of the use ofenlarged similarity approach for DNA sequences analysis arediscussed.     

Spider biodiversity potential of an ungrazed and a grazed inland salt meadow in the National Park 'Neusiedler See-Seewinkel' (Austria): implications for management (Arachnida: Araneae)

To assess the biodiversity potential of an ungrazed and a grazed inland salt meadow in the Seewinkel (Eastern Austria), spider assemblages were recorded by pitfall trapping for 1 year. Both species assemblages consisted, to a large extent, of rare species of conservation interest. The species assemblage of the grazed site was dominated by Pardosa agrestis, but highly specific halotopobiontic species also occurred in higher numbers. Halotolerant species were also present in the ungrazed meadow, but their individual number was much lower. The species composition of this site reflects the more balanced microclimatical situation of the high sward. Comparison of the two assemblages with 207 other meadow spider assemblages of Central Europe shows a separated position, especially of the grazed site assemblage. High similarities with assemblages of meadows with a similar vegetation structure indicate a high importance of management. Considering the high proportion of rare species on both sites, the best management of the salt meadow and pan shores of the Seewinkel should combine areas of light grazing with ungrazed areas. However, the proportion of these parts and the intensity of grazing still remains to be determined by quantitative experiments.