Development and characterization of microsatellites in Vanda varieties

The orchid genus Vanda includes more than 70 monopodial species and numerous hybrids. The aim of this study was to develop microsatellite markers for this horticultural valuable genus. Thirteen polymorphic microsatellite markers were isolated from the variety Vanda Miss Joaquim and were characterized in four Vanda species, 11 Vanda hybrids, and one Aranda intergenus hybrid. Populations from three species were also analysed. Number of alleles ranged from two to 19. For the V. sumatrana population, the expected heterozygosity ranged from 0 to 0.76 (mean 0.31) and the observed heterozygosity ranged from 0 to 1 (mean 0.36). All the varieties tested were distinct from one another (similarity index < 0.8). These microsatellites could be used for studying genetic diversity and population structure of wild populations within the orchid genus Vanda, as well as for distinguishing cultured Vanda varieties.     

Molecular diversity and relationships of North American Elymus trachycaulus and the Eurasian E. caninus species

The morphological similarity of Elymus trachycaulus to the Eurasian E. caninus has often been noted. This has lead to controversial and contradicting taxonomic treatments. Nevertheless, there has been no systematic investigation on molecular genetic similarity between E. trachycaulus and E. caninus. In this study, random amplified polymorphic DNA (RAPD) analysis was used to study the similarity between the two species. RAPD analysis of 38 samples representing E. caninus and E. trachycaulus complex yielded 111 interpretable RAPD bands. The Jaccard’s similarity values for E. caninus ranged from 0.38 between accessions H10345 and H10353 to 0.97 between accessions H8745 and H10096, with an average of 0.67. The Jaccard’s similarity values for E. trachycaulus complex ranged from 0.09 between E. trachycaulus ssp. subsecundus (PI 537321) and E. trachycaulus ssp. violaceus (PI 272612) to 0.78 between accessions PI 315368 and PI 372644, with an average of 0.43. The results from different analyses (NJ and PCA) were similar but not identical. The molecular genetic separation between E. caninus and E. trachycaulus was consistent. The PCA analysis clearly separated all E. caninus accessions from E. trachycaulus and its subspecies. The NJ analysis also showed separation between most accessions of E. caninus and E. trachycaulus. Further analysis excluding E. trachycaulus ssp. subsecundus and ssp. violaceus revealed that E. caninus species and E. trachycaulus species were clearly separated into two distinct groups. The RAPD data thus support the treatment of E. caninus and E. trachycaulus as distinct species. The analyses further indicate that E. violaceus is nested within E. trachycaulus, and more related to E. trachycaulus complex rather than to E. caninus.     

Ensifer alkalisoli YIC4027趋化受体基因的比较及相关蛋白序列分析

[目的] 田菁共生根瘤菌Ensifer alkalisoli YIC4027是从宿主植物田菁的根瘤中分离出来的一株新型高效的固氮菌。本研究对E.alkalisoli的趋化受体基因与其他研究透彻的物种进行比较以及相关蛋白分析。[方法] 利用NCBI的BLAST对E.alkalisoli趋化受体基因进行序列相似性搜索。以Pfam数据库为基础,用HMMR3对甲基化趋化受体蛋白（MCP）进行比较分析。[结果] E.alkalisoli有2个趋化基因簇,共有13个MCP,含有不同的信号传感结构。此外,这些MCPs的胞质结构域除了一个是由40个七肽重复序列组成,其余都是由36个七肽重复序列组成。[结论] 尽管E.alkalisoli的趋化受体与已被广泛研究的物种的趋化受体具有较高的相似性,但仍显示出其特性。通过基因的比对以及相关蛋白的分析,我们能够更好地理解E.alkalisoli是如何通过趋化系统来响应外界变化的。     

致病酵母菌基因组多态性及亲缘关系的研究

致病酵母是条件致病菌感染中最常见的菌群。其属间、种间及种内的分型具有重要的流行病学及临床意义。以随机扩增多态性(Randomly Amplified Polymorphism DNA markers,RAPD)的方法对48株临床上常见的酵母菌属间、种间及种内基因组型的多态性进行了研究,并以多种引物扩增带型的相似性系数的高低来评价酵母菌之间的亲缘关系。结果表明:RAPD带型可清楚的显示出假丝酵母(Candida)及相关酵母属间、种间及种内的差异,亲缘关系的研究表明假丝酵母属与隐球菌属(Cryptococcus)、丝孢酵母属(Trichosporon)的相似性系数为80％,除季也蒙假丝酵母(C. guilliermondii)外,假丝酵母属中不同种间的相似性系数为82％～87％,同种不同株间的相似性系数>90％。大多数属、种基因组分型的结果和形态学分类结果相符。     

Species-specific differences in the substrate-inhibitory specificity of cholinesterases from optical ganglia of squids of the Gonatidae family

A comparative study was carried out of the substrate and inhibitory specificity of cholinesterase preparations from squids, representatives of 3 genes and 5 species of the Gonatidae family:Berryteuthis (B. magister andB. anonichos),Gonatus (G. kamtschaticus andG. tinro), andGonatipsis (G. borealis), that have overlapping habitation areals in the Bering Sea. As substrates, there were used bromides of acetylthiocholine, propionylthiocholine, and butyrylthiocholine, as organophosphorus inhibitors, diisopropylfluorophosphate, a cation-containing inhibitor, and 4 hydrophobic compounds. The homogeneity of the cholinesterase activity in these preparations has been shown, the intergenus and interspecies differences in the enzyme properties are revealed, and also the peculiarity of properties of enzymes from Gonatidae squids is emphasized in comparison with cholinesterase from the Pacific squidTodarodes paciflcus and “standard” mammalian enzymes (from human erythrocytes and horse blood serum). The revealed interspecies differences are discussed in terms of evolutionary development of the Gonatidae family.     

Molecular cloning of a maltose transport gene from Bacillus stearothermophilus and its expression in Escherichia coli K-12

Genes responsible for maltose utilization from Bacillus stearothermophilus ATCC7953 were cloned in the plasmid vector pBR325 and functionally expressed in Escherichia coli. The 4.2 kb Bacillus DNA insert in clone pAM1750 suppressed the growth defects on maltose caused by mutations in E. coli maltose transport genes (malE, malK or complete malB deletion) but not mutations in genes affecting intracellular maltose metabolism (malA region). Transport studies in E. coli and B. stearothermophilus suggested that pAM1750 codes for a high affinity transport system, probably one of two maltose uptake systems found in B. stearothermophilus ATCC7953. Nucleotide sequence analysis of a 3.6 kb fragment of pAM 1750 revealed three open reading frames (ORFs). One of the ORFs, malA, encoded a putative hydrophobic protein with 12 potential transmembrane segments. MalA showed amino acid sequence similarity to proteins in the superfamily containing LacY lactose permease and also some similarity to MaIG protein, a member of a binding protein-dependent transport system in E. coli. The products of two other ORFs were not hydrophobic, did not show similarity to other known sequences and were found not to be essential for maltose utilization in transport-defective E. coli mutants. Hence MalA protein was the only protein necessary for maltose transport, but despite giving a detectable but low level of transport function in E. coli, the protein was very poorly expressed and could not be identified.     

O-antigen structure and gene clusters of Escherichia coli O51 and Salmonellaenterica O57; another instance of identical O-antigens in the two species

The O-polysaccharides were released by mild acid hydrolysis from the lipopolysaccharides of Escherichia coli O51 and Salmonella enterica O57 and found to possess the same structure, which was established by sugar analysis and 1D and 2D NMR spectroscopy: The O-antigen gene clusters of E. coli O51 and S. enterica O57 were sequenced and found to contain the same genes with a high-level similarity. All genes expected for the synthesis of the O-antigen were identified based on their similarity to genes from available databases.     

Close sequence identity between ribosomal DNA episomes of the non-pathogenicEntamoeba dispar and pathogenicEntamoeba histolytica

Entamoeba dispar andEntamoeba histolytica are now recognized as two distinct species-the former being nonpathogenic to humans. We had earlier studied the organization of ribosomal RNA genes inE. histolytica. Here we report the analysis of ribosomal RNA genes inE. dispar. The rRNA genes ofE. dispar, like their counterpart inE. histolytica are located on a circular rDNA molecule. From restriction map analysis, the size ofE. dispar rDNA circle was estimated to be 24·4 kb. The size was also confirmed by linearizing the circle withBsaHI, and by limited DNAseI digestion. The restriction map of theE. dispar rDNA circle showed close similarity to EhR1, the rDNA circle ofE. histolytica strain HM-1:IMSS which has two rDNA units per circle. The various families of short tandem repeats found in the upstream and downstream intergenic spacers (IGS) of EhR1 were also present inE. dispar. Partial sequencing of the cloned fragments ofE. dispar rDNA and comparison with EhR1 revealed only 2·6% to 3·8% sequence divergence in the IGS. The region Tr and the adjoiningPvuI repeats in the IGS of EhR1, which are missing in thoseE. histolytica strains that have one rDNA unit per circle, were present in theE. dispar rDNA circle. Such close similarity in the overall organization and sequence of the IGS of rDNAs of two different species is uncommon. In fact the spacer sequences were only slightly more divergent than the 18S rRNA gene sequence which differs by 1·6% in the two species. The most divergent sequence betweenE. histolytica andE. dispar was the internal transcribed spacer, ITS2. Therefore, it was concluded that probes derived from the ITS1 and ITS 2 sequences would be more reliable and reproducible than probes from the IGS regions used earlier for identifying these species.     

Comparative karyological studies on the species of Eubothrium Nybelin, 1922 (Cestoda: Pseudophyllidea)

Karyotypes of Eubothrium salvelini, E. crassum and Eubothrium sp. were studied using conventional Giemsa staining and comparative karyometric analysis. The karyotypes, reported here for the first time, consist of eight chromosome pairs. The two first pairs of homologues are metacentric and markedly larger than the remaining elements. The obvious similarity in karyotype structure does not exclude the possibility of discriminating E. salvelini and E. crassum using karyotypic characters. The best cytogenetic marker is the last pair of chromosomes, which is acrocentric in the karyotype of E. salvelini and metacentric in that ofE. crassum. Karyological observations provide strong evidence for assigning Eubothrium sp. from Clupea harengus membras to E. crassum. Comments are made on the karyotypes of these and related species with respect to their phylogenetic links.     

Molecular cloning and nucleotide sequence of the glycogen branching enzyme gene (glgB) from Bacillus stearothermophilus and expression in Escherichia coli and Bacillus subtilis.

Summary The structural gene for the Bacillus stearothermophilus glycogen branching enzyme (glgB) was cloned in Escherichia coli. Nucleotide sequence analysis revealed a 1917 nucleotide open reading frame (ORF) encoding a protein with an M_r of 74787 showing extensive similarity to other bacterial branching enzymes, but with a shorter N-terminal region. A second ORF of 951 nucleotides encoding a 36971 Da protein started upstream of the glgB gene. The N-terminus of the ORF2 gene product had similarity to the Alcaligenes eutrophus czcD gene, which is involved in cobalt-zinc-cadmium resistance. The B. stearothermophilus glgB gene was preceded by a sequence with extensive similarity to promoters recognized by Bacillus subtilis RNA polymerase containing sigma factor H (E - ^H). The glgB promoter was utilized in B. subtilis exclusively in the stationary phase, and only transcribed at low levels in B. subtilis spoOH, indicating that sigma factor H was essential for the expression of the glgB gene in B. subtilis. In an expression vector, the B. stearothermophilus glgB gene directed the synthesis of a thermostable branching enzyme in E. coli as well as in B. subtilis, with optimal branching activity at 53° C.     

Analysis of the Escherichia coli glycogen gene cluster suggests that catabolic enzymes are encoded among the biosynthetic genes

The nucleotide sequences of the Escherichia coli genome between the glycogen biosynthetic genes glgB and glgC, and 1170 bp of DNA which follows glgA have been determined. The region between glgB and glgC contains an open reading frame (ORF) of 1521 bp which we call glgX. This ORF is capable of coding for an M_r 56 684 protein. The deduced amino acid (aa) sequence for the putative product shows significant similarity to the E. coli glycogen branching enzyme, and to several different glucan hydrolases and transferases. The regions of sequence similarity include residues which have been reported to be involved in substrate binding and catalysis by taka-amylase. This suggests that the proposed product may catalyze hydrolysis or glycosyltransferase reactions. The cloned region which follows glgA contains an incomplete ORF (1149 bp), glgY, which appears to encode 383 aa of the N terminus of glycogen phosphorylase, based upon sequence similarity with the enzyme from rabbit muscle (47% identical aa residues) and with maltodextrin phosphorylase from E. coli (37% identical aa residues). Results suggest that neither ORF is required for glycogen biosynthesis. The localization of glycogen biosynthetic and degradative genes together in a cluster may facilitate the regulation of these systems in vivo.     

Structure and expression of the Chlorobium vibrioforme hemA gene

The green sulfur bacterium, Chlorobium vibrioforme, synthesizes the tetrapyrrole precursor, -aminolevulinic acid (ALA), from glutamate via the RNA-dependent five-carbon pathway. A 1.9-kb clone of genomic DNA from C. vibrioforme that is capable of transforming a glutamyl-tRNA reductase-deficient, ALA-dependent, hemA mutant of Escherichia coli to prototrophy was sequenced. The transforming C. vibrioforme DNA has significant sequence similarity to the E. coli, Salmonella typhimurium, and Bacillus subtilis hemA genes and contains a 1245 base open reading frame that encodes a 415 amino acid polypeptide with a calculated molecular weight of 46174. This polypeptide has over 28% amino acid identity with the polypeptides deduced from the nucleic acid sequences of the E. coli, S. typhimurium, and B. subtilis hemA genes. No sequence similarity was detected, at either the nucleic acid or the peptide level, with the Rhodobacter capsulatus or Bradyrhizobium japonicum hemA genes, which encode ALA synthase, or with the S. typhimurium hemL gene, which encodes glutamate-1-semialdehyde aminotransferase. These results establish that hemA encodes glutamyl-tRNA reductase in species that use the five-carbon ALA biosynthetic pathway. A second region of the cloned DNA, located downstream from the hemA gene, has significant sequence similarity to the E. coli and B. subtilis hemC genes. This region contains a potential open reading frame that encodes a polypeptide that has high sequence identity to the deduced E. coli and B. subtilis HemC peptides. hemC encodes the tetrapyrrole biosynthetic enzyme, porphobilinogen deaminase, in these species. Preliminary evidence was obtained for the existence of a 3.0-kb polycistronic meassge that includes the hemA sequence, in exponentially growing C. vibrioforme cells. Results of condon usage analysis for the C. vibrioforme hemA gene indicate that green sulfur bacteria are more closely related to purple nonsulfur bacteria than to enteric bacteria. Sequences corresponding to a polyadenylation signal and a poly(A) attachment site were found immediately downstream from the 3 end of the hemA open reading frame.     

The foraging ecology of sympatric marine fish in the genus Embiotoca (Embiotocidae): Importance of foraging behavior in prey size selection

Summary Two locally sympatric temperate marine reef fishes, Embiotoca jacksoni and E. lateralis (Embiotocidae), have high taxonomic similarity in diets. Subdivision of gammarid amphipods, their principal prey, was found. E. jacksoni took more tubicolous gammarid amphipods whereas E. lateralis consumed mostly free-living individuals. The species differed considerably with respect to between-individual variability in taxonomic compositions of their diets. Each E. jacksoni closely resembled other conspecifics in this regard while individual E. lateralis displayed very high between-fish variation. The principal interspecific difference in fish diets concerned the sizes of prey items taken. E. jacksoni ate small but very common items and the mean prey weight in their guts did not differ from random collections of available prey. E. lateralis concentrated on large, rarer sizes such that the average prey weight in their guts was much heavier than available or in the diet of E. jacksoni of the same length. Disparate foraging behaviors was a much better indicator of the relative differences in diets of these two fishes than was external fish morphology. E. jacksoni, which can winnow prey items from unwanted debris, was a relatively indiscriminant forager. E. lateralis did not winnow but actively searched for prey. This species was a much more discriminating forager, but displayed much variability in foraging behavior.     

Identification of Entamoeba polecki with Unique 18S rRNA Gene Sequences from Celebes Crested Macaques and Pigs in Tangkoko Nature Reserve,North Sulawesi,Indonesia

Unique species of macaques are distributed across Sulawesi Island, Indonesia, and the details of Entamoeba infections in these macaques are unknown. A total of 77 stool samples from Celebes crested macaques (Macaca nigra) and 14 stool samples from pigs were collected in Tangkoko Nature Reserve, North Sulawesi, and the prevalence of Entamoeba infection was examined by PCR. Entamoeba polecki was detected in 97% of the macaques and all of the pigs, but no other Entamoeba species were found. The nucleotide sequence of the 18S rRNA gene in E. polecki from M. nigra was unique and showed highest similarity with E. polecki subtype (ST) 4. This is the first case of identification of E. polecki ST4 from wild nonhuman primates. The sequence of the 18S rRNA gene in E. polecki from pigs was also unique and showed highest similarity with E. polecki ST1. These results suggest that the diversity of the 18S rRNA gene in E. polecki is associated with differences in host species and geographic localization, and that there has been no transmission of E. polecki between macaques and pigs in the study area.     

Transmission identification of Escherichia coli aerosol in chicken houses to their environments using ERIC-PCR

In order to study E. coli aerosol spreading from chicken houses to their surrounding air, air samples, including indoor and outdoor air (upwind 10 and 50 m as well as downwind 10, 50, 100, 200 and 400 m away) of 5 chicken houses were collected using six-stage Andersen microbial samplers and Reuter-Centrifugal samplers (RCS). E. coli concentrations (CFU/m3 air) collected from different sampling sites were calculated. E. coli strains from chicken feces samples were also isolated. Furthermore, the enterobacterial repetitive intergenic consensus (ERIC)-PCR method was applied to amplify the isolated E. coli strain DNA samples. Through the genetic similarity analyses of the E. coli obtained from different sampling sites, the spreading of bioaerosol from animal houses to the ambient air was characterized. The results showed that the isolated E. coli concentrations in indoor air (9―63 CFU/m3) in 5 chicken houses were higher than those in upwind and downwind air, but there were no significant differences between the indoor and downwind sites 10 m away from all the 5 houses (P>0.05). The phylogenetic tree indicated that a part of the E. coli (34.1%) isolated from indoor air had 100% similarity with those isolated from feces, and that most of E. coli isolated (54.5%) from downwind at 10, 50, 100 or even 200 m had 100% similarity with those isolated from indoor air or feces too. But those isolated from upwind air had a lower similarity (73%―92%) with corresponding strains isolated from indoor air or feces. Our results suggested that some strains isolated from downwind air and indoor air originated in the chicken feces, but most of isolates obtained from upwind air samples did not come from the chicken feces or indoor air. Effective hygienic measures should be taken in animal farms to prevent or minimize downwind spreading of microorganism aerosol.     

Functional relationship between Escherichia coli RNase E and the CafA protein

We analyzed the functional relationship between the Escherichia coli RNase E and the CafA protein, which show extensive sequence similarity. The temperature-sensitive growth of the RNase E mutant strain ams1 was partially suppressed by multicopy plasmids bearing the cafA gene. Introduction of a cafA::cat mutation enhanced the temperature sensitivity of the ams1 mutant. These results suggest that there is a functional homology between these two proteins. Received: 17 May 1996 / Accepted: 1 October 1996     

The structure and genetics of a montane population of the checkerspot butterfly,Chlosyne palla

Summary The population structure, genetics and ecology of the checkerspot butterfly, Chlosyne palla, in an area of Gunnison County, Colorado were investigated. The population structure was found to be quite different from that of most butterflies and from all of those aspects known for its thoroughly studied relative, Euphydryas editha. The population unit of Chlosyne palla may cover an area some five to eight times the size of the largest known Euphydryas population and twice the size of an Erebia epipsodea population in the same county of Colorado.Genetic variation at eleven loci of Chlosyne palla was examined by electrophoresis. Three samples of Chlosyne palla separated by 1.6, 4.7, and 12.0 km were not significantly different. Comparison with Euphydryas editha yields a genetic similarity of 0.186, about the same level as found by Ayala (1975) for different genera of Drosophila. Euphydryas editha from the same Colorado location were more similar to California E. editha than to C. palla, showing concordance with the phenetic classification. Decreased heterozygosity was observed for the Colorado E. editha and C. palla compared to California populations of E. editha and E. chalcedona.     

大果马蹄荷(Exbucklandia tonkinensis)群落的纬度地带性

大果马蹄荷主产南亚热带至中亚热带南缘,南至海南岛,北至罗霄山脉中段的井冈山、桃源洞地区,是常绿阔叶林的特征种。以纬度地带性(海南霸王岭、广东黑石顶、广东南岭、江西金盆山、江西井冈山、湖南桃源洞)为依托,选定6个具代表性的大果马蹄荷群落开展群落生态学研究,结果表明:(1)各样地物种多样性较高,尤以金盆山蕨类植物9科10属11种、种子植物42科78属128种和桃源洞蕨类植物9科11属12种、种子植物41科79属134种最为丰富。群落组成的优势科主要为金缕梅科、壳斗科、樟科、山茶科、杜鹃花科、山矾科等。(2)从区系特征和环境梯度看,大果马蹄荷群落以南亚热带为分布中心,向南或向北其物种多样性Simpson指数、Shannon-Wiener指数及相应的均匀度指数均呈下降趋势,其中霸王岭、黑石顶、南岭、金盆山、井冈山、桃源洞的Shannon-Wiener指数分别为3.453、4.021、4.130、3.790、3.415、3.712。(3)群落相似性聚类分析显示群落随纬度和随海拔高度形成两个梯度系列,一是以黑石顶、金盆山、井冈山、桃源洞的纬度地带性为一支,相似性系数0.51;二是以南岭和霸王岭聚成海拔梯度较高的另一支,但其相似性系数0.50,为0.33—0.48。(4)大果马蹄荷群落种类组成在区系性质上很相似,具有明显的南亚热带特征;同时,受海拔、地形、气温、降雨条件等因素的影响,种子植物属的热带成分随纬度增加而呈波动性下降趋势。(5)大果马蹄荷种群在各群落中的重要值水平和径级结构表现出一致性,在纬度地带性差异上无明显的相关性。霸王岭大果马蹄荷的径级结构为增长型,但重要值排名为32,说明向南分布该种群优势度明显下降;在南岭、黑石顶、金盆山、桃源洞该种群优势度较大,且为稳定型种群;在井冈山该群落受到人为干忧,大果马蹄荷的重要值排名第1,但为衰退型种群。