链格孢菌酯酶同工酶分析及其分类学意义

分析了20株链格孢菌的酯酶同工酶聚丙烯酰胺凝胶电泳图谱,并将酶谱进行聚类分析。结果发现:20株链格孢菌在37%的相似系数处明显分为大孢子组和小孢子组;大孢子组在52%的相似系数处分为6组,每组代表1个种,小孢子组在较高的相似性水平上分组与形态分组结果基本一致。本试验结果还表明:酯酶同工酶电泳方法简单易行,能准确反映种间的微小差异,适用于链格孢属真菌的种级分类,可作为传统形态学分类的一个重要辅助手段。     

Bioinformatic analysis of outer membrane proteome of Neisseria meningitidis and Neisseria lactamica.

Two-dimensional electrophoresis (isoelectric focusing/SDS-PAGE) and Western-blotting techniques were used to analyze and compare common and/or specific outer-membrane proteins and antigens from Neisseria meningitidis and Neisseria lactamica. Bioinformatic image analyses of proteome and immunoproteome maps indicated the presence of numerous proteins and several antigens shared by N. meningitidis and N. lactamica, although the inter-strain variation in the maps was of similar magnitude to the inter-species variation, and digital comparison of the maps did not reveal proteins found to be identical by MALDI-TOF fingerprinting analysis. PorA and RmpM, two relevant outer-membrane antigens, manifested as various spots at several different positions. While some of these were common to all the strains analyzed, others were exclusive to N. meningitidis and their electrophoretic mobilities were different than expected. One such spot, with a molecular mass of 19 kDa, may be the C-terminal fragment of RmpM (RmpM-Cter). The results demonstrate that computer-driven analysis based exclusively on spot positions in the proteome or immunoproteome maps is not a reliable approach to predict the identity of proteins or antigens; rather, other identification techniques are necessary to obtain accurate comparisons.     

缘蝽科四种昆虫同工酶鉴别（半翅目：缘蝽科）

本研究运用聚丙烯酰胺垂直板电泳技术对缘蝽科4个种的酯酶同工酶进行了检测,酯酶酶谱可分为4个区,酯酶酶谱在属间表现明显差异,在属内具有某些共性,聚类分析显示4个种的分类地位,并说明性别差异大于个体差异但小于种间差异。     

Identification of oral Neisseria species of animals

Ninety-seven strains of presumptive Neisseria spp. obtained from the dental plaque of a wide variety of animals and 21 strains from culture collections were compared by physiological tests, enzyme electrophoresis and isoelectric focusing of proteins. Three physiological groups based on the fermentation of maltose and production of extracellular polysaccharide were established. The ability of strains within these groups to reduce nitrate and nitrite differed. The electrophoretic mobility of dehydrogenases and isoelectric focusing patterns of proteins were not, however, characteristic of species or physiological groups. It is difficult, therefore, to identify new isolates of Neisseria because the criteria for describing species overlap. A rapid spot test was devised to distinguish Branhamella catarrhalis from other Neisseria by the absence of glucose-6-phosphate dehydrogenase.     

樱亚科植物同工酶FUZZY聚类及最佳阈值的F检验

本研究采用聚丙烯酰胺凝胶电泳法,分析了樱亚科8个种共17个生物型枝皮、叶片的过氧化物同工酶（POD）,初步确定了各样品枝皮、叶片的POD同工酶酶谱特征．根据酶谱相似系数对样品进行了Fuzzy聚类分析．通过样品酶谱积值的F检验,选定了樱亚科植物分属的最佳阈值,为同工酶谱聚类效果研究提供新方法．     

Multicolonization of human nasopharynx due to Neisseria spp.

The colonization due to Neisseria spp. in the nasopharynx of forty healthy adults was studied by using a selective medium that allows the differentiation of Neisseria species and inhibits the rest of pharyngeal microbiota. The medium detected a variety of colonial morphology types and some metabolic characteristics of the isolates. We demonstrated the multicolonization by several Neisseria spp. in the same individual, and we isolated several strains of the same species, after analysis by pulsed-field gel electrophoresis (PFGE) patterns obtained from the different colonial types previously identified as the same species. The forty adults studied were colonized by 112 forms of Neisseria spp., and twelve colonization patterns were obtained: one species (45%), two (45%), three (7.5%) and four (2.5%). N. perflava-N. sicca, either alone or in combination with other species was the most frequent isolate (92.5%). The analysis of PFGE patterns obtained from different colonial types revealed the multicolonization by several strains of the same species in some individuals. This fact was found in N. perflava-N. sicca (50%) and N. mucosa (2.5%).     

沙坡头地区根瘤菌DNA同源性及16SrDNA全序列

数值分类和多位点酶电泳分析表明,分离自宁夏沙坡头 地区的12株根瘤菌构成一个独立的表观群。对这一菌群进行了DNA同源性和群内中心菌株1 6SrDNA全序列分析。12个菌株的G+C mol%在56.4～62.2范围内;群内DNA同源性为72.3% ～9.5%,大于70%,属种内水平;中心株N220的16SrDNA全序列与参比菌株的序列比较,从 模拟系统发育树看出,它与三株土壤杆菌、三株根瘤菌的16SrDNA序列同源性在94.8%～99 .2%的相似性水平上构成一个分支,看来沙坡头地区这群根瘤菌是一个独立的新种群。     

毛木耳种质资源的酯酶同工酶分析

采用垂直平板聚丙烯酰胺凝胶电泳技术对毛木耳56个菌株酯酶同工酶的酶谱多样性进行了研究。结果表明,56份材料有一定的遗传变异,共检测到迁移率不同的10条谱带,各菌株分别具有1~6条酶带,共有26种酶谱类型。菌株被分成了8大群:第一群包括黄耳zh等34个菌株;第二群包括白背木耳等8个菌株;第三、第四群分别为黑木耳和915两个单独的菌株;第五群包括99等4个菌株;第六群包括43等4个菌株;第七群包括50385和AP067两个菌株;第八群包括小上3和杂交34两个菌株。酯酶同工酶分析技术是鉴别种及品种以下菌株的有效手段。     

Heterogeneity ratio: a measure of beta-diversity and its use in community classification

Fifteen previously proposed similarity indices are examined for the effects of sample size and/or group size (the number of samples included in a cluster). The three indices ofCλ,NESS, andC′λ are free from effects, but the former two are unsuitable for arithmetic averaging unless all of the sample sizes are equal. Thus clustering usingC′λ is found to be superior to the combination of any other similarity index and the group-average strategy. Unfortunately none of these measures have the desirable property of measuring the difference in component species among samples independent of the alpha-diversity. A new index of similarity (HR) is developed based on the assumption that community from which samples are taken is described by a logseries distribution. This new index measures the beta-diversity among samples without the influence of sample size and group size, and has the advantage that the significance of fusing samples can statistically be tested. An example clustering withHR is shown and compared with those obtained by other clustering strategies.     

A study by high-resolution two-dimensional polyacrylamide gel electrophoresis of relationships between Neisseria gonorrhoeae and other bacteria

High-resolution two-dimensional polyacrylamide gel electrophoresis was used to analyse the soluble proteins from seven strains of Neisseria gonorrhoeae, six strains of Neisseria meningitidis and one or two strains of twelve other species. Approximately 200 individual polypeptides could be visualized as Coomassie Blue stained spots on an electrophoretogram of N. gonorrhoeae and similar numbers were found for the other bacteria. Each species of bacterium had a distinctly different pattern of spots which could be recognized. Quantitative comparisons of 48 selected spots derived from one strain of N. gonorrhoeae with those of five other strains of gonococcus, three strains of N. meningitidis and one of Branhamella catarrhalis, showed relationships in agreement with their current taxonomic classification but with a higher level of discrimination than that of previously used methods. It was also possible to distinguish the individual gonococcal strains. It is suggested that the method could be useful for bacterial classification and identification.     

A two-stage probabilistic approach to multiple-community similarity indices

SUMMARY: A traditional approach for assessing similarity among N (N > 2) communities is to use multiple pairwise comparisons. However, pairwise similarity indices do not completely characterize multiple-community similarity because the information shared by at least three communities is ignored. We propose a new and intuitive two-stage probabilistic approach, which leads to a general framework to simultaneously compare multiple communities based on abundance data. The approach is specifically used to extend the commonly used Morisita index and NESS (normalized expected species shared) index to the case of N communities. For comparing N communities, a profile of N- 1 indices is proposed to characterize similarity of species composition across communities. Based on sample abundance data, nearly unbiased estimators of the proposed indices and their variances are obtained. These generalized NESS and Morisita indices are applied to comparison of three size classes of plant data (seedling, saplings, and trees) within old-growth and secondary rain forest plots in Costa Rica.     

浙江沿岸水域软体动物群落结构分析

根据2019年全年4个航次浙江沿岸海域单船底拖网调查资料,分析了4个季节浙江沿岸海域软体动物的种类组成、优势种及资源密度分布,采用生态多样性指数、物种相似性指数(J_s)、群落季节更替指数(AI)和迁移指数(MI)、丰度/生物量比较曲线(ABC曲线)分析了群落物种多样性、动态变化及其稳定性。结果表明:浙江沿岸海域全年共捕获软体动物62种,隶属于3纲, 10目, 32科。腹足纲(螺类)出现种类30种,占软体动物总种类数的48.39%;头足纲(头足类)出现种类19种,占软体动物总种类数的32.63%;双壳纲(贝类)出现种类13种,占软体动物总种类数的20.98%。软体动物群落优势种为长蛸(Octopus variabilis)、剑尖枪乌贼(Loligo edulis)、棒锥螺(Turritella bacillum)、多钩钩腕乌贼(Abralia multihamatai)和双喙耳乌贼(Sepiola birostrata),优势种的季节变化差异较大。浙江沿岸海域软体动物年平均资源密度为204.94 kg/km²,其中夏季平均资源密度为全年最高,冬...     

Genome analysis and strain comparison of correia repeats and correia repeat-enclosed elements in pathogenic Neisseria

Whole genome sequences of Neisseria meningitidis strains Z2491 and MC58 and Neisseria gonorrhoeae FA1090 were analyzed for Correia repeats (CR) and CR-enclosed elements (CREE). A total of 533, 516, and 256 copies of CR and 270, 261, and 102 copies of CREE were found in these three genomes, respectively. The lengths of CREE range from 28 to 348 bp, and the lengths of multicopy CREE appear mainly in the ranges of 154 to 156 bp and 105 to 107 bp. The distribution of CREE lengths is similar between the two N. meningitidis genomes, with a greater number of 154- to 156-bp CREE (163 and 152 copies in N. meningitidis strain Z2491 and N. meningitidis strain MC58, respectively) than 105- to 107-bp CREE (72 and 77 copies). In the N. gonorrhoeae strain FA1090 genome there are relatively more 105- to 107-bp CREE (51 copies) than 154- to 156-bp CREE (36 copies). The genomic distribution of 107-bp CREE also shows similarity between the two N. meningitidis strains (15 copies share the same loci) and differences between N. meningitidis strains and N. gonorrhoeae FA1090 (only one copy is located in the same locus). Detailed sequence analysis showed that both the terminal inverted repeats and the core regions of CREE are composed of distinct basic sequence blocks. Direct TA dinucleotide repeats exist at the termini of all CREE. A survey of DNA sequence upstream of the sialyltransferase gene, lst, in several Neisseria isolates showed that 5 N. meningitidis strains contain a 107-bp CREE in this region but 25 N. gonorrhoeae strains show an exact absence of a 105-bp sequence block (i.e., the 107-bp CREE without a 5' TA dinucleotide) in the same region. Whole-genome sequence analysis confirmed that this 105-bp indel exists in many homologous 107-bp CREE loci. Thus, we postulate that all CREE are made of target TA with indels of various lengths. Analysis of 107-bp CREE revealed that they exist predominantly in intergenic regions and are often near virulence, metabolic, and transporter genes. The abundance of CREE in Neisseria genomes suggests that they may have played a role in genome organization, function, and evolution. Their differential distribution in different pathogenic Neisseria strains may contribute to the distinct behaviors of each Neisseria species.     

Similarity indices,sample size and diversity

Summary The effect of sample size and species diversity on a variety of similarity indices is explored. Real values of a similarity index must be evaluated relative to the expected maximum value of that index, which is the value obtained for samples randomly drawn from the same universe, with the diversity and sample sizes of the real samples. It is shown that these expected maxima differ from the theoretical maxima, the values obtained for two identical samples, and that the relationship between expected and theoretical maxima depends on sample size and on species diversity in all cases, without exception. In all cases but one (the Morisita index) the expected maxima depend strongly to fairly strongly on sample size and diversity. For some of the more useful indices empirical equations are given to calculate the expected maximum value of the indices to which the observed values can be related at any combination of sample sizes. It is recommended that the Morisita index be used whenever possible to avoid the complex dealings with effects of sample size and diversity; however, when previous logarithmic transformation of the data is required, which often may be the case, the Morisita-Horn or the Renkonen indices are recommended.     

Sequence diversity within the argF, fbp and recA genes of natural isolates of Neisseria meningitidis: interspecies recombination within the argF gene

Studies of natural populations of Neisseria meningitidis using multilocus enzyme electrophoresis have shown extensive genetic variation within this species, which, it has been proposed, implies a level of sequence diversity within meningococci that is greater than that normally considered as the criterion for species limits in bacteria. To obtain a direct measure of the sequence diversity among meningococci, we obtained the nucleotide sequences of most of the argF, recA and fbp genes of eight meningococci of widely differing electrophoretic type (from the reference collection of Caugant). Sequence variation between the meningococcal strains ranged from 0-0.6% for fbp, 0-1.3% for argF, and 0-3.3% for recA. These levels of diversity are no greater than those found within Escherichia coli 'housekeeping' genes and suggest that multilocus enzyme electrophoresis may overestimate the extent of nucleotide sequence diversity within meningococci. The average sequence divergence between the Neisseria meningitidis strains and N. gonorrhoeae strain FA19 was 1.0% for fbp and 1.6% for recA. The argF gene, although very uniform among the eight meningococcal isolates, had a striking mosaic structure when compared with the gonococcal argF gene: two regions of the gene differed by greater than 13% in nucleotide sequence between meningococci and gonococci, whereas the rest of the gene differed by less than 1.7%. One of the diverged regions was shown to have been introduced from the argF gene of a commensal Neisseria species that is closely related to Neisseria cinerea. The source of the other region was unclear.     

The Biochemical Identification of Vahlkampfiid Amoebae1

ABSTRACT. Isoenyme electrophoresis of three different enzymes was used to compare 16 strains of vahlkampfiid amoebae and a strain identified as a slime mold. The strain designated as an Echinostelium sp. was found to be an isolate of Naegleria fowleri on the basis of zymogram type and other characters, confirming Cursons & Brown's similar conclusion drawn in 1975. The N. fowleri strains examined expressed the typical zymograms of the species. The N. gruberi strains in this study presented two distinctive groups of patterns that were different from the two previously reported types for N. gruberi. Each of the remaining species studied formed single distinctive groups by which they could be identified.     

The production and characterization of monoclonal antibodies against the protein III of Neisseria gonorrhoeae

Monoclonal antibodies were produced against gonococcal protein III. Antibodies of two different specificities were obtained. One reacted with all Neisseria species tested (N. gonorrhoeae, N. meningitidis and five non-pathogenic species), whereas the other was specific for Neisseria gonorrhoeae and may provide the basis for improved diagnostic reagents.     

Detection of the lst gene in different serogroups and LOS immunotypes of Neisseria meningitidis

The sialylation of the lipooligosaccharide (LOS) of Neisseria meningitidis is mediated by the LOS sialyltransferase enzyme encoded by the lst gene. PCR using four sets of primers that targeted to different regions of the lst gene was used to survey the distribution of lst in different serogroups and LOS immunotypes of N. meningitidis as well as other Neisseria species. While the lst gene was found in N. meningitidis strains regardless of their capsular serogroup and LOS structures, the gene is also found in N. gonorrhoeae, N. lactamica, N. polysaccharea, and N. subflava biovar subflava. The presence of the lst gene in these organisms and the sialylation of their LOS antigens were discussed.     

Starch gel electrophoresis: an effective method for separation of pathogenic and nonpathogenic Naegleria strains

Isoenzyme electrophoresis of 7 different enzyme systems was used to compare 24 strains of Naegleria fowleri and 6 strains of N. gruberi. The 30 strains could be grouped into 4 distinct categories based upon zymogram patterns. No interstrain band variation in all enzyme systems was demonstrated in pathogenic strains of N. fowleri. Three nonpathogenic high temperature-tolerant strains of Naegleria had similar zymograms. Four of the 5 remaining nonpathogenic Naegleria strains had no interstrain band variation. Based upon zymograms, the 22 pathogenic strains constitute a homogenous species. Similarly the high temperature-tolerant nonpathogenic strains formed a cohesive group. The remaining nonpathogenic strains could be separated into 2 groups.     

Richness‐dependence of phylogenetic diversity indices

Phylogenetic diversity indices are widely used to characterize the structure and diversity of ecological communities. Most indices are based on a metric that is expected to vary with species richness, so they are standardized to remove this richness‐dependence. With this standardization, values of 0 are consistent with random phylogenetic structure, while phylogenetic clustering is associated with either negative or positive values (depending on the index). One common interpretation of phylogenetic clustering is that it indicates some combination of environmental and biological filtering that restricts the species that can be present in a community. Increasingly, studies are comparing phylogenetic indices along environmental gradients to infer differences in the factors structuring communities. This comparison implicitly assumes that index values are comparable among communities with different numbers of species. Using a set of simulations, I show here that this assumption is incorrect. Holding the strength of filtering constant, communities composed of more species show larger absolute index values. This problem is most pronounced when the environmental filter favors a moderate‐sized clade strongly over others and when using the net relatedness index (NRI) to measure clustering. This bias potentially casts doubt on studies studying phylogenetic index patterns along gradients where richness also varies. Fortunately, the arising generality that more stressful environments have lower species richness and stronger clustering is opposite to this bias and therefore robust. I also show that a simple rarefaction can remove the richness‐dependence of these indices, at the expense of increased error.