Comparison of the 16S/23S ribosomal intergenic regions of "Candidatus Liberobacter asiaticum" and "Candidatus Liberobacter africanum," the two species associated with citrus huanglongbing (greening) disease

16S/23S intergenic spacer regions from the rRNA operons of two strains of "Candidatus Liberobacter asiaticum" and one strain of "Candidatus Liberobacter africanum" were cloned and sequenced. The intergenic spacers of the two "Candidatus L. asiaticum" strains studied are identical and contain the genes for isoleucine tRNA (tRNA(Ile)) and alanine tRNA (tRNA(Ala)) separated by 11 nucleotides. The intergenic spacer of the "Candidatus L. africanum" strain contains only one tRNA gene (tRNA(Ala)). The level of homology between the intergenic spacers of the two liberobacter species is 79.46%. Ribosomal operons with 16S/23S spacer regions other than those studied might be present in the two "Candidatus Liberobacter" species.     

"Candidatus phytoplasma australiense," a new phytoplasma taxon associated with Australian grapevine yellows

A phytoplasma was detected in naturally diseased 'Chardonnay' grapevines exhibiting symptoms of Australian grapevine yellows disease. The use of PCR designed to amplify phytoplasma DNA resulted in detection of phytoplasma DNA in all of the diseased plants examined; no phytoplasma DNA was detected in healthy seedling grapevines. The collective restriction fragment length polymorphism (RFLP) patterns of amplified 16S ribosomal DNA differed from the patterns described previously for other phytoplamas. On the basis of the RFLP patterns, Australian grapevine yellows phytoplasma was classified as a representative of a new subgroup, designated subgroup 16SrI-J, in phytoplasma 16S rRNA group 16SrI (aster yellows and related phytoplasmas). A phylogenetic analysis in which parsimony of 16S rRNA gene sequences from this and other group 16SrI phytoplasmas was used identified the Australian grapevine yellows phytoplasma as a member of a distinct subclade (subclade xii) in the phytoplasma clade of the class Mollicutes. A phylogenetic tree constructed on the basis of 16S rRNA gene sequences was consistent with the hypothesis that there was divergent evolution of Australian grapevine yellows phytoplasma and its closet known relative, European stolbur phytoplasma (subgroup 16SrI-G), from a common ancestor. The unique properties of the DNA from the Australian grapevine yellows phytoplasma clearly establish that it represents a new taxon, "Candidatus Phytoplasma australiense."     

Isolation and characterization of a monoclonal anti-quadruplex DNA antibody from autoimmune "viable motheaten" mice

A cell line that produces an autoantibody specific for DNA quadruplex structures has been isolated and cloned from a hybridoma library derived from 3-month-old nonimmunized autoimmune, immunodeficient "viable motheaten" mice. This antibody has been tested extensively in vitro and found to bind specifically to DNA quadruplex structures formed by two biologically relevant sequence motifs. Scatchard and nonlinear regression analyses using both one- and two-site models were used to derive association constants for the antibody-DNA binding reactions. In both cases, quadruplexes had higher association constants than triplex and duplex molecules. The anti-quadruplex antibody binds to the quadruplex formed by the promoter-region-derived oligonucleotide d(CGCG4GCG) (Ka = 3.3 x 10(6) M-1), and has enhanced affinity for telomere-derived quadruplexes formed by the oligonucleotides d(TG4) and d(T2G4T2G4T2G4T2G4) (Ka = 5.38 x 10(6) and 1.66 x 10(7) M-1, respectively). The antibody binds both types of quadruplexes but has preferential affinity for the parallel four-stranded structure. In vitro radioimmunofilter binding experiments demonstrated that purified anti-DNA quadruplex antibodies from anti-quadruplex antibody-producing tissue culture supernatants have at least 10-fold higher affinity for quadruplexes than for triplex and duplex DNA structures of similar base composition and length. The antibody binds intramolecular DNA triplexes formed by d(G4T3G4T3C4) and d(C4T3G4T3G4), and the duplex d(CGCGCGCGCG)2 with an affinities of 6. 76 x 10(5), 5.59 x 10(5), and 8.26 x 10(5) M-1, respectively. Competition experiments showed that melted quadruplexes are not effective competitors for antibody binding when compared to native structures, confirming that the quadruplex is bound structure-specifically. To our knowledge, this is the first immunological reagent known to specifically recognize quadruplex structures. Subsequent sequence analysis demonstrates homologies between the antibody complementarity determining regions and sequences from Myb family telomere binding proteins, which are hypothesized to control cell aging via telomeric DNA interactions. The presence of this antibody in the autoimmune repertoire suggests a possible linkage between autoimmunity, telomeric DNA binding proteins, and aging.     

Isolation of Deinococcus species from commercial oyster extract

Deinococci with radiation resistance greater than that of Deinococcus radiophilus (ATCC 27603) were isolated from three commercial oyster extracts stored at 4, 20, and 30 degreesC. During storage the number of other bacteria declined and deinococci became the predominant group in the microflora, particularly at 20 degreesC, although at 30 degreesC the number of deinococci as well rapidly declined. The results suggest that the natural habitat of deinococci is an aerobic environment containing a slightly elevated saline content, soluble protein, and low sugar levels.     

Individual DNA bands obtained by RAPD analysis of canine genomic DNA often contain multiple DNA sequences

We present a case of Langerhans' cell histiocytosis (LCH) of the liver and spleen in an adult. The imaging features are different from those in the few previously reported cases of individual organ involvement by LCH.     

Isolation of specific DNA probes from Cryptococcus neoformans

OBJECTIVE: To construct plasmid library and screen specific DNA probes for Cryptococcus neoformans. METHODS: Serotype A Cryptococcus neoformans was used as the study strain, plasmid pUC18 as vector, and Escherichia coli JM103 as host cell. The plasmid library of cryptococcus neoformans was constructed (pCN). Other pathogenes causing affection diseases which should be distinguished from cryptococcusis clinically, and other fungi similar to Cryptococcus neoformans with physiological and biochemical characteristics were used as a distinguishing system, specific colonies were screened by hibridization in double steps. RESULTS: The inserts of the library were 280 to 1800 base pairs and 580 base pairs in average length. Repeated sequence was 32.43% and single copy sequence was 67.57% in genome of cryptococcus neoformans respectively. Three specific colonies were isolated from the library. Colony pCNII A6 was serotype A specific, pCNII B5 species specific and pCNIII G1-specific for var. neoformans. CONCLUSION: A rapid diagnosis of Cryptococcus neoformans infection at early stage can be made by using species-specific probe, and serotype and variaty of neoformans and gattii be distinguished in epidemic study.     

Isolation and identification of glycosaminoglycans associated with purified nuclei from rat liver

The effects of nitrogen bases on the regulation of phospholipid metabolism in neuroblastoma cell cultures were investigated. An increase in the total cellular phospholipids was observed up to 24 h following plating. Addition of monomethyl- and dimethylethanolamine bases resulted in a stimulation of the synthesis of their corresponding phospholipids. The average rates of synthesis of phosphatidylmonomethyl- and phosphatidyldimethylethanolamine were 0.09 and 0.12 nmol/microgram DNA per h, respectively. The labeling patterns of the various phospholipid species from ortho[32P]phosphate have been determined. They suggest that the synthesis of the analogs proceeded entirely via a phosphate mediated pathway rather than through a base exchange mechanism. A number of distinct patterns for the incorporation of bases into acyl-, alkyl- and alkenyl-containing phosphoglyceride species were indicated. The polar head group composition appeared to be intimately related to the type of bond of the hydrocarbon residue.     

Isolation of Candida species from domestic sewage in Jordan

Saccharomyces cerevisiae and various species of Candida were isolated and identified from the Al-Baqa'a sewage treatment station. Potentially pathogenic yeasts were detected in sewage samples and Candida krusei was found in the treated effluent. There was a 90-100% reduction in the number of yeast found in treated sewage effluent compared with raw sewage. Seasonal variations of total yeast counts are also reported.     

Isolation and identification of Aeromonas species from human stools

One thousand and three diarrhoeal stool samples were processed in our laboratory during the period 1996/1997 for the presence of enteric pathogens especially Aeromonas spp., which has emerged as a new agent causing diarrhoea. Ampicillin sheep blood agar was found to be the best medium for the isolation of Aeromonas spp. from stool specimens. Enteric pathogens were found in 200 (20%) stools, of which Aeromonas spp. was the second commonest pathogen isolated amounting to 21% of isolates. This study clearly indicates that Aeromonas spp. must be looked for in every diarrhoeal stool samples, specially in children below 10 years of age. Isolation and identification is cost effective and easy, if the given protocol is observed.     

Isolation from genomic DNA of sequences binding specific regulatory proteins by the acceleration of protein electrophoretic mobility upon DNA binding

To examine a role for the medullary nucleus paragigantocellularis (PGi) in mediation of the symptomatology of opioid withdrawal, bilateral electrical stimulation of the PGi was performed in conscious, unrestrained, opioid naive (nondependent) rats. A characteristic series of behaviors was elicited during each 30-min session of PGi stimulation. The profile of these behaviors resembled qualitatively, but was not quantitatively identical with those seen during precipitated withdrawal from opioid dependence. This behavioral syndrome has been termed, opioid withdrawal-like behavior. The opioid withdrawal-like behaviors were voltage-, but not frequency-, dependent. Tolerance to repeated stimulation of the PGi did not develop following a series of 30-min runs of stimulation over 3.5 h. Intracerebroventricular (i.c.v.) injections of the nonselective opioid antagonist, naloxone, significantly decreased (by 40-50%) the intensity of stimulation-induced behavioral responses, as did injections of either the mu-selective (beta-funaltrexamine, beta-FNA) or the delta-selective (naltrindole, NTI) opioid antagonists. In contrast, similar i.c.v. injections of the kappa-selective antagonist, nor-binaltorphimine (nor-BNI), did not block behavioral responses to PGi stimulation. The results indicate that activation of the PGi by electrical stimulation can elicit behaviors similar to those observed during opioid withdrawal. Endogenous opioids, acting through mu- and delta-, but not kappa-opioid receptors, participate in mediating opioid withdrawal-like behaviors induced by PGi stimulation.     

Diversity of uncultured microorganisms associated with the seagrass Halophila stipulacea estimated by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes

Muscle phosphofructokinase deficiency (PFKD) is characterized by exercise intolerance due to the enzymatic block in muscle glycolysis. Glucose infusion increases exertional fatigue in these patients, probably by decreasing the availability of free fatty acids (FFA) and ketones, which play a crucial role in ATP production during exercise in PFKD. This suggests that a lower than normal hepatic glucose production would be appropriate during exercise in PFKD. To investigate glucoregulation in PFKD, we measured glucose turnover and hormonal and metabolic responses to 20 minutes of cycle exercise at near maximal effort in three patients with PFKD and in healthy matched controls studied at the same absolute (A, 15 to 30 Watts) and relative (R, 35 to 80 Watts, matched heart rates) work load as the patients. During exercise, mean glucose production was higher in all patients versus controls (30 +/- 4 versus A: 18 +/- 2 and R: 20 +/- 1 mumol.min-1.kg-1). Mean glucose utilization during exercise was similar in patients and controls working at the same relative work load and higher than in controls at the low work load. Exercise-induced increases in arterialized blood were higher in all patients for glucose, FFA, growth hormone, glucagon, and norepinephrine. Plasma alanine and lactate always decreased during exercise in patients and consistently increased in controls. In conclusion, an enhanced neuroendocrine response and a paradoxically exaggerated mobilization of glucose occurs during exercise in PFKD. The responses are probably initiated by neural feedback elicited by disturbances in local muscle metabolism. The responses promote delivery of oxidizable fat to muscle, but at the expense of accumulation and futile cycling of glucose.     

Cosmid library of the turkey herpesvirus genome constructed from nanogram quantities of viral DNA associated with an excess of cellular DNA

A protocol was designed for the rapid and efficient construction of cosmid libraries from cell-associated viral genomes available in very low quantities. Purification of viral DNA from cellular DNA was unnecessary. The vast excess of cellular DNA compensated for the limited amount of available viral DNA, enabling titration of the restriction endonuclease partial digest. A cosmid library of the turkey herpesvirus DNA genome was constructed from 1.5 micrograms of cellular DNA containing approximately 6 nanograms of viral DNA.     

Isolation of circular viral and complementary strand DNA from bacteriophage f1 duplex replicative-form DNA

A general method has been developed for the large scale isolation of intact, circular, single-stranded DNA molecules of each strand from supercoiled duplex DNA. The method involves the conversion of the supercoiled duplex DNA to singly nicked, relaxed duplex DNA; denaturation of the duplex DNA; separation of circular DNA molecules from linear DNA molecules; and separation of circular plus and minus strands. All separations involve zone sedimentation. No isopycnic gradient centrifugation is required. The last step in the purification, the separation of plus and minus strands, can be easily adapted for small scale analytical measurements of the amounts of plus and minus strand DNA.     

Isolation of adenoviruses and reoviruses from avian species other than domestic fowl

Adenoviruses and reoviruses were isolated from pigeons and mallard ducks. In addition, adenoviruses were isolated from budgerigars and a bantam and a reovirus was isolated from a turkey. Primary identification of these viruses was by electron-microscope examination. It was further possible to assign the 4 adenoviruses to recognized fowl serotypes, and the reoviruses shared a common antigen with fowl reoviruses. These viruses were isolated from a variety of clinical conditions.     

Plant tumor reversal associated with the loss of foreign DNA

Transformation of plant tissues into crown gall tumors has been associated with the transfer of a portion of a tumor-inducing plasmid (Ti-plasmid) into plant DNA. Various laboratories have regenerated normal-appearing plants from a number of crown gall tumors. This study investigates the fate of the foreign DNA in a series of tissues derived from various parts of a plant regenerated from the tumor BT-37 by Braum and his coworkers. It was found that all the foreign DNA sequences were lost from tissues that had lost all their tumorous traits; whereas the plasmid DNA sequences were still present in tissues that appeared normal but still exhibited tumorous traits when returned to tissue culture media. From these studies it would appear that the presence of the Ti-plasmid sequences in the plant DNA is required for the maintenance of the transformed state.