Batch procedure for thermal elution of DNA from hydroxyapatite

Trophozoite and nuclear size, DNA base composition, and nucleotide sequence homology of several Entamoeba strains in axenic culture

We carried out a comparative study of nuclear and trophozoite diameters and of DNA thermal denaturation in eight Entamoeba strains cultured axenically (four of them E. histolytica, two initially designated as E. invadens, one E. moshkovskii, and one E. histolytica-like), as well as an analysis of the overall DNA sequence homology of the non-E. histolytica strains. The average nuclear (N) and trophozoite (T) diameters (in micron) were, respectively: global averages +/- SD for E. histolytica strains, 6.5 +/- 2.5 and 28.8 +/- 3.7; E. invadens IP101, 5.8 and 27.5, and PZ, 7.8 and 33.6; E. moshkovskii FIC, 4.1 and 12.9; E. histolytica-like Laredo strain, 5.0 and 20.6. The GC content of DNA, estimated by thermal elution in hydroxyapatite, was around 23% in HK9 and its clone HK9-1 and around 27% in the HM2 and HM3 E. histolytica strains; it was 37% in the Laredo strain, 26% in IP101, 35% in PZ, and 33% in FIC. The reassociation kinetics of PZ strain DNA showed that it consists of 40% repeated sequences and 60% unique sequences. By means of DNA association experiments in which one of each pair of DNAs tested had been labeled in vitro with 125I, we found the following overall sequence homology among the strains tested: PZ-FIC, 38%; IP101-Laredo, 38%; IP101-FIC, 47%; PZ-Laredo, 49%; Laredo-FIC, 69%; and IP101-PZ, 83%. We conclude that trophozoites of different E. histolytica strains have similar nuclear size and GC content, whereas these parameters and the nucleotide sequences are clearly different in every other Entamoeba species.(ABSTRACT TRUNCATED AT 250 WORDS)

Immunochemical approaches to gene probe assays

Antibodies specific for helical nucleic acids can be applied to assays for hybridized DNA and/or RNA. The assays can use either radioactive or nonradioactive detection systems. Antibodies specific for RNA-DNA hybrids are applicable to assays for measuring hybrid helices that are immobilized on plastic or nitrocellulose, whether the helices are preformed in solution or are formed on the solid-phase support. Alternatively, anti-RNA-DNA hybrid antibodies can be immobilized and used to capture hybrids formed in solution, resulting in an assay with a high signal-to-noise ratio. It has been applied to a test for the presence of ribosomal RNA of Campylobacter jejuni in biological samples.

Nucleic acid probes in clinical microbiology

The infectious disease applications of nucleic acid probe have been described. In addition, the basic procedures of nucleic acid probe technology have been discussed, as have the factors affecting implementation of probe technology in diagnostic laboratories. Despite the questions raised, nucleic acid probes will become part of the diagnostic laboratory in the near future. Commercial interests are developing and marketing new probes, reagents, and kits which will expedite the employment of this technology. High-volume reference laboratories will first use probes as part of a battery of tests which will include ELISA and monoclonal antibody methods. In all probability, probes will replace methods: that have proven to be ineffective, difficult, or costly such as culturing for some enteric pathogens and Legionella, that require long incubation periods, such as mycobacteria, or that have high costs and low yields, such as virology.

Clinical strains of Enterobacter agglomerans (synonyms: Erwinia herbicola, Erwinia milletiae) identified by DNA-DNA-hybridization

Using DNA-DNA-hybridization it could be shown that 52 of 86 clinical isolates of Enterobacter agglomerans were closely related to each other, to the type strain of the species and also to the type strains of Erwinia herbicola and Erwinia milletiae. Most of the strains investigated were of the biogroups 1 and G1 of Ewing & Fife. All strains of the genetically defined group belonged to these two biogroups; none of these isolates fermented dulcitol, and with few exceptions they were also cellobiose, lactose and sorbitol negative.

Phylogenetic relationships among Fusarium species measured by DNA reassociation

Deoxyribonucleic acid of 11 Fusarium species (F. acuminatum, F. arthrosporioides, F. avenaceum, F. culmorum, F. graminearum, F. heterosporum, F. moniliforme, F. oxysporum, F. sambucinum, F. semitectum, F. solani) have been compared with respect to their physical characteristics (Tm, % G + C), homology values and nucleotide sequence divergence. A phylogenetic tree based on physical characteristics, homology values and differences in percentage divergence of Fusarium species DNAs has been constructed.

DNA homologies between the rainbow trout, chum salmon and coho salmon

The thermal stabilities of hybrid duplexes between the DNAs from three salmonid fish species were monitored as measures of DNA homology. The chum salmon, Oncorhynchus keta, and coho salmon, Oncorhynchus kisutch, had more DNA homology with each other than either had with the rainbow trout, Salmo gairdnerii. Morphological, ecological and protein similarities between the coho salmon and the rainbow trout may be due to parallel or convergent evolution.

Immunological aspects of humidifier fever

An epidemiological investigation was made of eight employees working in a defined section of an office building who complained of febrile reactions accompanied by respiratory tract symptoms and fatigue. Culture of the water from the humidifier for their section yielded strains of Pseudomonas acidovorans and an unidentified Pseudomonas species. In vitro studies showed that these strains activated the alternative pathway of the complement system in Mg-EGTA supplemented serum, as evidenced by properdin depletion and conversion of C3-proactivator (Factor B) and C3. Whereas the employees with symptoms had significantly reduced properdin values during the symptomatic phase, a slight C3 conversion and antibodies to Pseudomonas spp., staff working in another part of the building with a different ventilation system did not. It was concluded that staff with humidifier fever symptoms had been exposed to Pseudomonas spp. through the faulty ventilation system, and their symptoms were most likely a result of complement activation.

[DNA-DNA hybridization in several species of Hansenula]

The genus Hansenula was considered a long time ago as a good pattern for phylogenetic research. In 1969, Wickerham proposed an evolutive scheme based upon morphological, physiological and ecological criteria. Recently, relatedness among yeasts were analysed by DNA-DNA hybridization in liquid medium. H. anomala var. anomala (G + C content: 37.1%) was compared with H. anomala var. schneggii (37.6%), H. subpelliculosa (33.8%) line 3, H. sydowiorum (40.1%) and H. muscicola (37.1%). These results showed little relatedness between H. anomala var. anomala/H. ciferrii and H. anomala var. anomala/H. subpelliculosa. On the other hand, H. anomala var. schneggii shared 89.5% of its nucleotide sequences with H. anomala var. anomala. These 2 strains were considered to represent the same species. H. holstii showed 67.1% complementarity with H. anomala var. anomala: this strain is considered to represent valid species, different from H. anomala var. anomala, but H. muscicola with 72.5% relatedness to H. anomala var. anomala could be considered as a 'limit species'. An unexpected finding was that H. beckii was closely related to H. anomala var. anomala (84.8%). These data suggested the inadequacy of current criteria used to establish the phylogenetic lines in genus Hansenula.

DNA homology studies in the taxonomy of dermatophytes

The taxonomy of the dermatophyte genera Trichophyton, Microsporum and Epidermophyton was investigated by determinations of DNA homology. DNA extracted from 10 isolates (seven species) of dermatophytes was reannealed by hydroxyapatite chromatography. DNA homology levels of 65-80% corresponded to species within a single genus. There was a general agreement with established classification, particularly in assigning species to separate genera. DNA from the Trichophyton state of Arthroderma benhamiae (NCPF 456) showed 71 and 76% homology with DNA from T. mentagrophytes (NCPF 224) and T. rubrum (NCPF 5034) respectively. T. terrestre showed low homology (25%) when compared with the other species of dermatophytes tested.

Isolation and characterization of a seventh serogroup of Legionella pneumophila

An environmental isolate (Chicago 8) and a clinical isolate (Dallas 5) of Legionella pneumophila were shown to have similar serological characteristics; however, these characteristics were distinct from those of L. pneumophila serogroups 1 through 6. Chicago 8, ATCC 33823, was designated as the reference strain for L. pneumophila serogroup 7. The use of Mongolian gerbils for the isolation of L. pneumophila from the environment is described. Even though guinea pigs are the animals of choice in such studies, the isolation of Chicago 8 illustrates that the use of gerbils may be a viable option when cost is a major consideration in study design.

Identification of Staphylococcus species with the API STAPH-IDENT system

The API STAPH-IDENT system was compared with conventional methods for the identification of 14 Staphylococcus species. Conventional methods included the Kloos and Schleifer simplified scheme and DNA-DNA hybridization. The API STAPH-IDENT strip utilizes a battery of 10 miniaturized biochemical tests, including alkaline phosphatase, urease, beta-glucosidase, beta-glucuronidase, and beta-galactosidase activity, aerobic acid formation from D-(+)-mannose, D-mannitol, D-(+)-trehalose, and salicin, and utilization of arginine. Reactions of cultures were determined after 5 h of incubation at 35 degrees C. Results indicated a high degree of congruence (greater than 90%) between the expedient API system and conventional methods for most species. The addition of a test for novobiocin susceptibility to the API system increased the accuracy of identification of S. saprophyticus, S. cohnii, and S. hominis, significantly. Several strains of S. hominis, S. haemolyticus, and S. warneri which were difficult to separate with the Kloos and Schleifer simplified scheme were accurately resolved by the API system.

Escherichia vulneris: a new species of Enterobacteriaceae associated with human wounds

The name Escherichia vulneris sp. nov. (formerly called Alma group 1 and Enteric group 1 by the Centers for Disease Control and API group 2 by Analytab Products, Inc.) is proposed for a group of isolates from the United States and Canada, 74% of which were from human wounds. E. vulneris is a gram-negative, oxidase-negative, fermentative, motile rod with the characteristics of the family Enterobacteriaceae. Biochemical reactions characteristic of 61 E. vulneris strains were positive tests for methyl red, malonate, and lysine decarboxylase; a delayed positive test for arginine dihydrolase; acid production from d-mannitol, l-arabinose, raffinose, l-rhamnose, d-xylose, trehalose, cellobiose, and melibiose; negative tests for Voges-Proskauer, indole, urea, H(2)S, citrate, ornithine decarboxylase, phenylalanine deaminase, and DNase; and no acid from dulcitol, adonitol, myo-inositol, and d-sorbitol. Two-thirds of the strains produced yellow pigment. Most strains gave negative or delayed positive reactions in tests for lactose, sucrose, and KCN. The E. vulneris strains tested were resistant to penicillin and clindamycin, were resistant or showed intermediate zones of inhibition to carbenicillin and erythromycin, and were susceptible to 14 other antibiotics. DNA relatedness of 15 E. vulneris strains to the type strain averaged 75% in reactions at 60 degrees C and 69% in reactions at 75 degrees C, indicating that they comprise a separate species. DNA relatedness to other species in the family Enterobacteriaceae was 6 to 39%, an indication that this new species belongs in the family. E. vulneris showed the highest relatedness to species of Escherichia (25 to 39%) and Enterobacter (24 to 35%). On the basis of biochemical similarity, the new species was placed in the genus Escherichia. The type strain of E. vulneris is ATCC 33821 (CDC 875-72).

Recognition of a second serogroup of Legionella longbeachae

A strain of Legionella longbeachae (Tucker 1) that was isolated from the postmortem lung tissue of a pneumonia patient was serologically distinct from four other strains of L. longbeachae. The recognition of a second serogroup of L. longbeachae represents the first reported instance of serogroup diversity within a species of Legionella other than L. pneumophila. The disease caused by the Tucker 1 strain does not seem to be readily distinguishable from that of pneumonia caused by other legionellae.

Tatumella ptyseos gen. nov., sp. nov., a member of the family Enterobacteriaceae found in clinical specimens

The name Tatumella ptyseos gen. nov., sp. nov., is proposed for a group of organisms (previously called group EF-9) isolated from clinical sources in the United States, Canada, and Puerto Rico. A total of 68% of these isolates were from sputum specimens. T. ptyseos strains are gram-negative, oxidase-negative, fermentative rods that grow on MacConkey agar. The distinctive biochemical characteristics of 44 T. ptyseos isolates were as follows: acid but no gas from D-glucose, sucrose, and, usually (71%), D-xylose (62% delayed); no acid from lactose, maltose, or D-mannitol; negative tests for indole, urea, methyl red, gelatin, L-lysine decarboxylase, and L-ornithine decarboxylase; L-arginine dihydrolase variable; phenylalanine deaminase positive; Voges-Proskauer positive by the Coblentz method but negative by the O'Meara method; nonmotile at 36 degrees C but 66% weakly motile (30% delayed) at 25 degrees C; Simmons citrate positive at 25 degrees C (89%) but Simmons citrate negative at 36 degrees C. Deoxyribonucleic acid-deoxyribonucleic acid relatedness studies on 26 T. ptyseos strains showed that they were 80 to 100% related at 60 degrees C, which indicated that they comprise a single species. The deoxyribonucleic acid relatedness to other species within the Enterobacteriaceae was 7 to 38%. This is evidence that this species belongs in this family, is distinct from all described species and is best placed in a new genus. The T. ptyseos isolates studied were susceptible to all of the antimicrobial agents tested by broth dilution; these antimicrobial agents were amikacin, ampicillin, cephalothin, chloramphenicol, gentamicin, kanamycin, tetracycline, and tobramycin. Three striking differences between T. ptyseos and other members of the Enterobacteriaceae were its large zone of inhibition around penicillin (mean diameter 24 mm), its tendency to die on some laboratory media (such as blood agar) within 7 days, and its small number (usually one) of flagella. Strain H36 (=ATCC 33301, =CDC D6168, =CDC 9591-78) is the type strain of this new species. T. ptyseos is the type species for the genus Tatumella.

Unusual groups of Morganella ("Proteus") morganii isolated from clinical specimens: lysine-positive and ornithine-negative biogroups

Morganella ("Proteus") morganii is the only species in the recently proposed genus Morganella, but we suspect there are yet undescribed species in the genus. Two candidates for new species were recently investigated. Nineteen strains isolated from clinical specimens resembled M. morganii but were lysine positive and nonmotile and fermented glycerol within 24 h. Typical M. morganii are lysine negative and motile and ferment glycerol slowly or not at all. The three-test variance from typical M. morganii suggested that this new group might be a new Morganella species; however, strains of the group were closely related to typical M. morganii by deoxyribonucleic acid (DNA)-DNA hybridization. A second group of 14 strains isolated from clinical specimens was ornithine negative but was otherwise very similar to M. morganii. This group was also closely related to M. morganii by DNA hybridization. Both sets of strains clearly belong in the species Morganella morganii as distinct biogroups; they are not separate species as originally suspected. Initially both biogroups posed a problem in identification until their true relationship to M. morganii was determined.

Conserved sequence related to the 3'-terminal region of retrovirus RNA'S In normal cellular DNAs

The nucleotide sequences related to the 3'-terminal protion of retrovirus genomic RNA have been detected in the DNA of animals, including humans. The DNA complementary to the 400 to 700 nucleotides from the 3'-terminal end of retrovirus RNA (cDNA3'), which contains the enriched conserved region, was hybridized with DNA from a variety of animal cells. Under the conditions of annealing in 0.72 M NaCl at 67 degrees C and hydroxyapatite chromatography at 55 degrees C, 20 to 50% of the radioactivity of the cDNA3' prepared from two retroviruses, a murine Rauscher virus (RLV) and a baboon virus (M7), annealed with normal cellular DNA of animals, including human tissue. The thermal denaturation profile revealed considerable mismatching between the duplex of the cDNA3' and human DNA, cDNA3' of retroviruses is most homologous to cellular DNA of the host species of origin and is less homologous to cellular DNA of species that are distant in the phylogeny of the host species. The conservation and evolution of nucleotide sequences related to the 3' end of retrovirus genomes in animal DNAs, including humans, suggest that the sequences may have important functions.

Detection, identification, and comparison of Capnocytophaga, Bacteroides ochraceus, and DF-1

Working independently, three laboratories had recognized considerable similarity among certain strains of dysgonic, fermentative, capnophilic, surface translocating, gram-negative bacilli referred to as Capnocytophaga, Bacteroides ochraceus, and Center for Disease Control biogroup DF-1. To determine the relationship among these groups, 21 strains were exchanged and independently characterized by the three laboratories. Additionally, a fourth laboratory examined the deoxyribonucleic acid homologies of the same strains. Using methods common to dental microbiology, eight of the strains had been isolated from the gingival sulcus and periodontal lesions and identified as Capnocytophaga. Three strains isolated from blood and transtracheal aspirate had been characterized by conventional anaerobic methods and recorded as B. ochraceus. Ten strains isolated from sputum, blood, throat, spinal fluid, and tracheal aspirate had been identified as DF-1 with the methods of E. O. King and a buffered single-substrate technique. All strains were similar in respect to colonial and microscopic morphology, surface translocation, biochemical features, gas-liquid chromatograms of metabolic end products, and deoxyribonucleic acid composition. We conclude that these biogroups should be termed Capnocytophaga species.

Specificity of DNA base release by bleomycin

DNA was treated with bleomycin in the presence of Fe2+ and 2-mercaptoethanol under conditions where only a few percent of the bases were released. Release of all four bases was a linear function of bleomycin concentration, but the amount of thymine released was twice that of cytosine, 7 times that of adenine, and twelve times that of guanine. Unidentified minor products of thymine, of cytosine and of a purine were also released. Bromouracil did not sensitize DNA to bleomycin-induced breakage, and was released at the same rate as thymine.

Strains of Achromobacter xylosoxidans from clinical material

Eleven strains of Achromobacter xylosoxidans have been received from among 1106 strains of Gram-negative, non-fermentative bacteria submitted to the National Collection of Type Cultures for computer-assisted identification since 1 January 1972. The strains showed resistance to a wide range of antimicrobial agents and five of the isolates possibly played a pathogenic role. The biochemical characteristics of these 11 strains were compared with those of three culture collection strains.

Stability of the individual globin genes during erythroid differentiation

The genes of sheep betaA, betaC, and gamma globin were all present in DNA from erythroid cells which synthesized only betaC globin. Similarly, selective excision of non-expressed genes was shown not to occur during human erythroid differentiation. In contrast, evolutionary deletion of the betaC gene accounts for the inability of many sheep to make this globin.

Conservation of transfer ribonucleic acid and 5S ribonucleic acid cistrons in Enterobacteriaceae

The genes for tranfer ribonucleic acid (tDNA) and 5S ribonucleic acid (5SDNA) were isolated from the total deoxyribonucleic acid (DNA) of Escherichia coli. The relatedness of tDNA and 5S from E. coli and other species of Enterobacteriaceae was determined by reassociation of the isolated genes labeled with 32PO4 to unlabeled, unfractionated DNA. Double-stranded DNA was separated from unreacted DNA by hydroxyapatite chromatography. Thermal elution profiles were done to determine the amount of unpaired bases present in related DNA sequences. Relative to total DNA, both 5S DNA and tDNA were highly conserved throughout the Enterobacteriaceae, including the genera Yersinia and Proteus.

Study of markers of human erythroid differentiation in hybrid cells

Somatic cell hybrids exhibiting co-expression of the globin genes of two species were generated by fusion of mouse erythroleukemia cells with Chinese hamster or human marrow erythroid cells. In contrast, extinction of the mouse globin genes occurred in hybrids formed between the erythroleukemia cells and human fibroblasts. Direct detection of the human globin genes in human X mouse fibroblast hybrids was achieved by annealing of DNA from these cells to human globin complementary DNA. This method was developed to permit the chromosomal assignment of the human globin genes.

Effects of X-irradiation on the hybridization of rat thymus nuclear RNA with repeated and unique DNA sequences

The kinetics of DNA hybridization with heterogeneous nuclear RNA (hnRNA) from normal and phytohaemagglutinin (PHA)-stimulated thymocytes has been studied in control rats and in animals 30 min after exposure to whole-body X-radiation with 400 rad. Irradiation results in a diminished ability of hnRNA to form hybrids with DNA at all C0t values ranging from 10(-3) to 10(4). Since this effect is most pronounced in the regions of low repetitive and unique DNA sequences, it is concluded that whole-body X-irradiation of animals may also suppress the transcription, particularly, in these regions.

Extinction of globin gene expression in human fibroblast x mouse erythroleukemia cell hybrids

We have chosen human fibroblast x mouse erythroleukemia hybrid cells as a model system to examine regulation of unique genes. The globin genes were studied as a marker of erythroid differentiation. Three separate hybrid cell lines were incubated in 2% dimethylsulfoxide, an agent which induces erythroid differentiation of the parental erythroleukemia cells. Neither human nor mouse globin mRNA sequences could be detected by a sensitive molecular hybridization assay which utilized globin complementary D N A. However, td n a from one of the cell lines was shown to contain both the mouse and humand globin genes. Thus, loss of the genes by chromosomal segregation did not account for their failure to be expressed. Cocultivation of the mouse erythroleukemia cells with excess human fibroblasts did not prevent erythroid differentiation of the erythroleukemia cells in the presence of dimethylsulfoxide. Similarly globin gene expression was preserved in tetraploid cells generated by fusion of two erythroleukemia lines. Thus, extinction of globin geneated by fusion of two erythroleukemia lines. Thus, extinction of blobin gene expression in the human fibroblast x erythroleukemia hybrids occurred at the level of mRNA production and appeared to be due to the presence of the fibroblast genome within the hybrial cell.

Hemoglobin synthesis in somatic cell hybrids: independent segregation of the human alpha- and beta-globin genes

Hybrid somatic cells containing a partial complement of human chromosomes were used to demonstrate that the human alpha- and beta-globin genes are located on different chromosomes. Two cell lines consisting of a cross of mouse with human fibroblasts contained the human alpha- and not the beta-globin gene, while a cross of human marrow cells with mouse erythroleukemia cells expressed the human beta- but not the alpha-globin gene.

Reassociation kinetics of DNA from x-irradiated ascites hepatoma cells of the rat

The kinetics of the reassociation fo DNA from ascites hepatoma cells has been studied. The curve exhibited three zones corresponding to 'fast', 'intermediate' and 'slow' speeds of DNA reassociation. The difference was observed in the DNA reassociation curves of the control and irradiated (1500 rad) cells which was particularly expressed in the 'slow' zone (10(2) less than C0t less than 10(4). The same dose, however, does not qualitatively effect the secondary DNA structure, which was estimated by the method of thermal elution from the hydroxyapatite column.