Modification of Schaefer's Procedure for Serotyping of Organisms of the Mycobacterium avium-M. intracellulare-M. scrofulaceum complex

Modifications to the tube-agglutination procedure which Schaefer developed for serotyping of organisms of the Mycobacterium avium-M. intracellulare-M. scrofulaceum complex are proposed.     

The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria.

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationships among selected species of mycobacteria and related organisms. The phylogeny inferred reflects the traditional classification, with major branches of the phylogenetic tree in general correspondence to the four Runyon groups and with numerical classification analyses. All the mycobacterial species compared, with the exception of M. chitae, are closely related (average similarity values greater than 95%). The slow growers form a coherent line of descent, distinct from the rapid growers, within which the overt pathogens are clustered. The distant relationship between M. chitae and the remaining mycobacteria suggests that this organism is incorrectly classified with the mycobacteria. M. paratuberculosis 18 was indistinguishable from M. avium-M. intracellulare-M. scrofulaceum serovar 1 by this analysis.     

Biochemical characteristics and fatty acid compositions of some armadillo-derived mycobacteria and their relation to Mycobacterium gordonae

The long-chain components of 75 strains of mycobacteria, cultivated from Mycobacterium leprae-infected or non-infected armadillos, and of eight clinical and 15 environmental isolates of M. gordonae, were compared. Four major groups could be distinguished based on the presence of 10-methyloctadecanoic (tuberculostearic) and 2-methyl 3-hydroxyeicosanoic acids and secondary alcohols (2-octadecanol and 2-eicosanol). Some heterogeneity was found in strains assigned to M. gordonae: the characteristic absence of tuberculostearic acid and secondary alcohols and the presence of the branched C14 and the hydroxylated C20 acids were seen in only 34 of the 49 strains studied. Three strains were identified as M. malmoense, one as M. kansasii, ten as belonging to the M. avium-M. intracellulare-M. scrofulaceum complex and eight as belonging to new groups of armadillo-derived mycobacteria (ADM 1, ADM 2 and ADM 3) by conventional bacteriological tests and fatty acid compositions, though M. malmoense was heterogeneous in its fatty acids composition. Four strains, identified as M. avium by conventional tests, differed from this species by their fatty acid compositions. Thirteen strains showed some similarity to M. simiae and ten strains differed from all other known mycobacteria.     

Construction of improved vectors for gene cloning inMicromonospora melanosporea

Two vectors forMicromonospora melanosporea have been constructed with theStreptomyces plasmid pIJ702 along with thesgm gene (sisomicin-gentamicin resistance gene fromM. zionensis) as the second antibiotic resistance marker. These plasmids, containingsgm gene as the second selectable marker, may be an attractive alternative to pIJ702, which is incapable of conferring melanin production inM. melanosporea and consequently is not useful for insertional inactivation in this bacterium. The constructions remove restriction site forM. melanosporea restriction endonuclease and provide additional unique sites for the insertional inactivation of selectable markers, which enhance the use of these plasmids as general cloning vectors in bothM. melanosporea andS. lividans. On the other side, inS. lividans, plasmid pMK33-1 facilitates isolation and studies of promoters based on detection of extremely convenient phenotype of melanin production. This has been proved by shotgun cloning of chromosomal DNA fragments ofM. melanosporea and chromogenic identification ofS. lividans transformants which were capable of producing a melanin.     

The Use of Polyvalent Sera for the Serotyping of Mycobacteria within the Mycobacterium avium– M. intracellulare-M. scrofulaceum Complex

A modification to Schaefer's agglutination method for serotyping mycobacteria within the Mycobacterium avium-M. intracellulare-M. scrofulaceum complex is described. The antigens are screened against polyvalent sera and subsequently a reduced range of absorbed antisera. This expedites the serotyping procedure and conserves expensive antiserum stocks.     

Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.     

Recherches Cytotaxonomiques et Cytogéographiques surMinuartia sect.Sabulina en Turquie (Caryophyllaceae)

25 populations from Turkey and one of Syria belonging to theSabulina section of the genusMinuartia have been karyologically examined. New chromosome numbers have been recorded forM. mesogitana andM. hybrida subsp.turcica, and a new variety was found in theM. hybrida complex. The origin of the taxa with n = 23 and n = 35 is discussed.

     

DNA sequence homology analysis of<Emphasis Type="Italic">ars</Emphasis> genes in arsenic-resistant bacteria

Homology ofars (arsenic-resistance system) genes was examined among the indigenous bacteria isolated from the soils and sediments of two abandened Au mines, which are highly contaminated with arsenic. The DNA and amino acid sequence homology of thears determinants were investigated using anars genotype. The isolated showed As(III)-oxidation ability containedarsAB genes encoding the efflux pump as well asarsR andarsD regulator genes. ThearsR andarsD leader gene are required for an arsenic resistance system when the high-homology genes (arsR; pl258 52.09% andarsD;Shewanell sp. 42.33%) are controlled by thears inducer-independent regulatory amino acid sequence. These leader gene were observed under weak acidic conditions in the Myoung-bong (pH; 5.0 to 6.0) and Duck-um (pH; 4.0 to 7.0) mines In addition, the strains with the ability of As (V)-reduction involved thearsC gene homologues, as in the strain CW-16 (Pseudomonas putida). The arsenic-resistance genes in the isolated indigenous bacteria showed varying degrees of amino acid similarity to the homologous genes found in the database (GenBank) such asP. putida KT2440: 39–53% forarsR, 22–42% forarsD, 16–84% forarsA, 26–45% forarsB, 17–44% forarsAB, 37–41% forarsC, and 14–47% forarsH. These findings suggested that the function of the variousars gene in indigenous bacteria existing in weakly oxidative conditions may be the key factor for redox mechanisms and biogeochemical systems in arsenic contaminated soils.     

Synthetic oligonucleotide probes for detection of mercury-resistance genes in environmental freshwater microbial communities in response to pollutants

Mercury-resistance genes were detected byin situ hybridization using new synthetic oligonucleotide probes specific formerA andmerB genes according to the published sequences of the corresponding enzymes. These DNA probes were used for the detection of specific mercury-resistant microorganisms isolated from the Rhine River which had been polluted 3 years previously in 1986. Mercuric reductase and organomercurial lyase genes persist in the bacterial genome even after the disappearance of the pollutant but are absent in axenic amoebae. A total of 49 bacterial isolates showed DNA homologies with the³²P-labelled DNA probes and 15 free-living amoebae were selected due to their harboured symbiotic mercury-resistant bacteria.     

Fluorescent Acid-Fast Microscopy for Measuring Phagocytosis of Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum by Tetrahymena pyriformis and Their Intracellular Growth

Fluorescent acid-fast microscopy (FAM) was used to enumerate intracellular Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum in the ciliated phagocytic protozoan Tetrahymena pyriformis. There was a linear relationship between FAM and colony counts of M. avium cells both from cultures and within protozoa. The Ziehl-Neelsen acid-fast stain could not be used to enumerate intracellular mycobacteria because uninfected protozoa contained acid-fast, bacterium-like particles. Starved, 7-day-old cultures of T. pyriformis transferred into fresh medium readily phagocytized M. avium, M. intracellulare, and M. scrofulaceum. Phagocytosis was rapid and reached a maximum in 30 min. M. avium, M. intracellulare, and M. scrofulaceum grew within T. pyriformis, increasing by factors of 4- to 40-fold after 5 days at 30°C. Intracellular M. avium numbers remained constant over a 25-day period of growth (by transfer) of T. pyriformis. Intracellular M. avium cells also survived protozoan encystment and germination. The growth and viability of T. pyriformis were not affected by mycobacterial infection. The results suggest that free-living phagocytic protozoa may be natural hosts and reservoirs for M. avium, M. intracellulare, and M. scrofulaceum.     

Efficient transformation ofMicromonospora melanosporea protoplasts byStreptomyces plasmid

An efficient and relatively simple procedure forMicromonospora melanosporea protoplast preparation and transformation is described. Transformation ofM. melanosporea protoplast by theStreptomyces plasmid pIJ702 was optimized by altering parameters affecting the formation, regeneration, and transformation of protoplasts. Improvement of regeneration medium resulted in relatively quick growth of transformants (only 7 days). As a result of these experiments we describe a new transformation method that has routinely yielded 10⁶ transformants/µg plasmid DNA.     

Mitochondrial DNA evolution in theobscura species subgroup ofDrosophila

Summary Mitochondrial DNA (mtDNA) restriction site maps for nine species of theDrosophila obscura subgroup and forDrosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the mtDNA genome. Based on nucleotide divergences, two phylogenetic trees were constructed assuming either constant or variable rates of evolution. Both methods led to the same relationships. Five differentiated clusters were found for theobscura subgroup species, one Nearctic, represented byDrosophila pseudoobscura, and four Palearctic, two grouping the related triads of speciesDrosophila subobscura, Drosophila madeirensis, Drosophila guanche, andDrosophila ambigua, Drosophila obscura, Drosophila subsilvestris, and two more represented by one species each,Drosophila bifasciata, andDrosophila tristis. The different Palearctic clusters are as distant between themselves as with the Nearctic one. For the related speciesD. subobscura, D. madeirensis, andD. guanche, the pairD. subobscura-D. madeirensis is the closest one. The relationships found by nucleotide divergence were confirmed by differences in mitochondrial genome size, with related species sharing similar genome lengths and differing from the distant ones. The total mtDNA size range for theobscura subgroup species was from 15.5 kb forD. pseudoobscura to 17.1 forD. tristis.     

Transformation of distinct mycobacterial species by shuttle vectors derived from theMycobacterium fortuitum pAL5000 plasmid

Mycobacterium tuberculosis H37Ra,M. smegmatisATCC 607,M. smegmatis MC²155,M. aurum A +,M. aurum A11, and one representative strain ofM. flavescens were transformed by electroporation with plasmid pMY10 and cosmid pDC100. Plasmid pMY 10 contained the origin of replication of pAL5000, the origin of replication of pBR322, a kanamycin resistance gene, and the origin of transfer of the Inc plasmid RK2; the cosmid pDC100 contained the pHC79 SS cosmid, the origin of replication of pAL5000, and a kanamycin resistance gene. The efficiency of transformation varied with the recipient cells used and was in decreasing order: 7×10⁵ forM. smegmatis MC²155, 6×10³ forM. tuberculosis H37Ra, 10³ forM. aurum, 50 forM. smegmatis ATCC 607, and 5 forM. flavescens. A rapid protocol for plasmid extraction from mycobacteria was developed.The satisfactory transformation of the nonvirulentM. tuberculosis strain H37Ra was of interest for future studies on cloning of virulence genes, while the satisfactory transformation ofM. aurum was of interest for future studies on the genetics of drug resistance because these bacteria are sensitive to drugs specifically used in the treatment of tuberculosis and leprosy. However, neither vector was stably maintained inM. smegmatis, indicating that further investigations are still necessary to resolve this difficulty.     

Magnetic capture hybridisation for improved PCR detection ofNectria galligena from lignified apple extracts

In order to reduce the effects of inhibitors present in DNA extracts from lignified apple tissues, a magnetic capture-hybridisation PCR (MCH-PCR) technique was developed forNectria galligena using the ITS 1 region of the rRNA gene repeats as target. The trapping reagent used to coat the magnetic beads was an 81 bp single-stranded DNA oligonucleotide biotin-labelled on the 5é-terminal and designed to be complementary to part of the rRNA gene ITS 1 region ofN. galligena. For specificity, the probe was located from 14 bp downstream from the 3é-terminal nucleotide of theN. galligena forward primer Ch1 to the last ITS 1 nucleotide immediately upstream of the 5.8S rRNA gene. Following hybridisation in a total DNA extract of woody tissue, magnetic recovery of the bead-oligomer-template conjugate separated target template from other DNA species and inhibitory compounds. Magnetic capture-hybridisation was followed by PCR amplification with the previously designed species-specific primers, Ch1 and Ch2. Application of the MCH-PCR technique resulted in increased levels of sensitivity and reliability when compared to PCR without MCH when used on total DNA extracts from lignified tissues.     

Imparired DNA synthesis and envelope defect in a mutant of Salmonella typhimurium

Summary S. typhimurium mutants with temperature-sensitive synthesis of DNA have been isolated. One of these mutants,dna-26, has been studied in detail. DNA synthesis is stopped indna-26 without any residual replication after shift to 42° though increase in cell mass is not inhibited. Mutantdna-26 shows increased sensitivity to deoxycholate, to nalidixic acid and rifampicin. This suggests a cell envelope defect. Inhibition of DNA synthesis at 42° can be phenotypically cured indna-26 by 0.25 M NaCl and KCl and 0.44 M sucrose but not by 0.44 M glycerol. This DNA synthesis induced by hypertonic medium proceeds at a slower rate than increase in cell mass but is predominantly due to normal sequential chromosome replication. The position of mutationdna-26 has been approximately mapped in thepurD region of the chromosome.     

Two distinct subtypes of theHLA-DRw12 haplotypes in the Japanese population detected by nucleotide sequence analysis and oligonucleotide genotyping

We determined the DNA sequence of the enzymatically amplified second exon of theDRB1 gene of theDRw12 haplotypes derived from three Japanese donors and found two distinct subtypes of theDRw12 haplotype. The two subtypes, designatedDRw12a andDrw12b, had single-base substitutions that predicted one amino acid change at residue number 67. The sequence of theDrw12a andDRw12b subtypes differed from those of the otherDR haplotypes, but in the first hypervariable region of theDRB1 gene the sequences were identical to those of theDRw8(Dw8.1) andDRw8(Dw8.3) haplotypes. TheDRw12a andDRw12b subtypes were detected in a wide range of Japanse donors by genotyping with sequence-specific oligonucleotide probes synthesized according to the DNA sequence of the two subtypes. Results of this study demonstrated that theDRw12 haplotypes in the Japanese population are genetically diverse, as many otherDR haplotypes are. The nucleotide sequence data reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned the accession numbers M27509, M27510, M27511.     

Linkage of genes for laminin B1 and B2 subunits on chromosome 1 in mouse

Summary We have used cDNA clones for the B1 and B2 subunits of laminin to find restriction fragment length DNA polymorphisms for the genes encoding these polypeptides in the mouse. Three alleles were found forLamB2 and two forLamB1 among the inbred mouse strains. The segregation of these polymorphisms among recombinant inbred strains showed that these genes are tightly linked in the central region of mouse Chromosome 1 betweenSas-1 andLy-m22, 7.4±3.2 cM distal to thePep-3 locus. There is no evidence in the mouse for pseudogenes for these proteins. This work was supported by U. S. Public Health Service Grant GM28464 to R.W.E. Editor's Statement Investigation into the biosynthesis of laminin indicates that several different polypeptides are assembled to form the intact molecule. This paper represents an extension of previous work which takes a genetic approach to further define the relationships among the polypeptides involved. Gordon H. Sato     

伤寒沙门菌基因组DNA芯片的制备与基因表达谱分析应用

伤寒沙门菌是一种具有鞭毛的革兰阴性人类肠道致病菌,也是一种重要的原核生物研究用模式菌．基因组芯片能够系统、全面且高效地观察生物的基因表达及进行基因组结构比较．利用伤寒沙门菌现有的全基因组序列,以Ty2菌株的基因组为基准,选取CT18菌株和z66阳性菌株的特异性蛋白编码基因,设计特异性引物,经PCR有效扩增出4 201个基因,产物纯化后点样于多聚赖氨酸玻片制备伤寒沙门菌基因组DNA芯片,并验证了芯片样点位次与效果．通过对基因表达谱分析的各种条件进行优化,建立相应的表达谱分析方法,并用于比较伤寒沙门菌野生株在高渗、低渗条件下的基因表达差异,结果与以前的报道基本一致．结果表明,成功建立了伤寒沙门菌基因组DNA芯片及表达谱分析方法,可为有关伤寒沙门菌基因表达调控及致病性机理、进化和基因多样性等方面的深入研究提供有效的技术支持．     

The novel light-harvesting pigment-protein complex ofMantoniella squamata (Chlorophyta): Phylogenetic implications

Summary A light-harvesting pigment-protein complex has been isolated fromMantoniella squamata (Micromonadophyceae, Chlorophyta) by nondenaturing polyacrylamide-gel electrophoresis. The complex runs as two bands of molecular weights 54,000 and 55,000. There are two constituent polypeptides of molecular weights 20,500 and 22,000. Antibodies were raised to the 20,500-dalton polypeptides from this complex and to the 24,500-dalton polypeptide from the analogous complex ofPedinomonas minor (Micromonadophyceae). The antibodies to theM. squamata polypeptide are specific for both polypeptides of theM. squamata light-harvesting complex, as well as for a 27,000-dalton polypeptide of undetermined function. The antibodies to theP. minor polypeptide are specific for polypeptide components of the light-harvesting complex of that alga. The antibodies specific for theM. squamata light-harvesting complex polypeptides do not cross react with any polypeptides ofP. minor thylakoid membranes, as demonstrated by crossed immunoelectrophoresis. Similarly, no polypeptides ofM. squamata thylakoids cross react with the antibodies specific forP. minor light-harvesting complex polypeptides. These results indicate that the light-harvesting complex ofM. squamata is structurally very different from that ofP. minor. In a survey of several land plants and green algae, including representatives of all classes of green algae, a light-harvesting complex homologous to that ofM. squamata was found only inMicromonas pusilla. All other organisms tested possessed a lightharvesting complex homologous to that ofP. minor. The evolutionary and taxonomic implications of the novelM. squamata light-harvesting complex are discussed.     

DNA typing forHLA-DPB1*02 and−DPB1*04 in multiple sclerosis and juvenile rheumatoid arthritis

DP gene typing using in vitro DNA amplification combined with sequence-specific oligonucleotide probes (SSOP) has recently been reported. The amplification step may be specific for theHLA-DPB locus, or it may be specific for one or a group ofHLA-DPB alleles, thus increasing the discriminatory power of the system. We report the combined use of group-specific DNA in vitro amplification followed by SSOP in typing forDPB1*02 andDPB1*04 variants. The method was used to type for these variants in 96 randomly selected, healthy Danes, in 37 patients with pauciarticular juvenile rheumatoid arthritis (PJRA); and in 38 patients with multiple sclerosis (MS). Increased frequencies of the cellularly defined HLA-DPw2 in PJRA and of HLA-DPw4 in MS have previously been reported. In the patient groups, the frequencies of theDPB1*02 andDPB1*04 variants did not differ significantly from those expected based on the cellularly defined HLA-DP types of the patients and the frequencies of theDPB1*02 andDPB1*04 variants among healthy Danes.