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At least 109 records · Page 6Linked to original sources
PubMed1969

Cold-sensitive mutations in Salmonella typhimurium which affect ribosome synthesis.

A number of mutations (45) expressed as cold-sensitive conditional lethal pheno-types were screened by transduction for their linkage to the streptomycin-resistance locus; 7 showed such linkage. Of these, two were studied in greater detail. The sedimentation profiles of ribosomes from cultures grown at low temperature differed from wild type and from one another. Both mutants lost ribonucleic acid control at low temperature. It is suggested that a high proportion of mutants expressing a cold-sensitive phenotype harbor mutations in genes affecting ribosome synthesis or regulation.

Bacterial Proteins↗
PubMed1995

Two-dimensional gel electrophoresis of ribosomal proteins as a novel approach to bacterial taxonomy: application to the genus Arthrobacter.

Ribosomal proteins from 22 strains of 15 different species belong to the genus Arthrobacter were analyzed by an improved two-dimensional gel electrophoresis. Electrophoretograms of ribosomal proteins from 15 type strains had species-specific patterns. Similarity coefficients (SAB values) of ribosomal proteins with mol. wt. of greater than about 20,000, among strains of the same species (DNA relatedness values of more than 61%) were greater than 0.85, but the SAB values among strains of different species were less than 0.60. The N-terminal amino acid sequences of the AL2 proteins, which migrated into similar positions in this method, from 5 type strains were shown to be highly homologous. Our results indicated that ribosomal proteins have been conserved within species during evolution and that the members of the genus Arthrobacter are phylogenetically homogeneous. Thus, ribosomal protein profiles by this method are a potential tool for strain identification.

Amino Acid Sequence↗
PubMed1999

The phenotype of mutations of G2655 in the sarcin/ricin domain of 23 S ribosomal RNA.

The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA forms a part of the site for the association of the elongation factors with the ribosome and hence is critical for the binding of aminoacyl-tRNA and for translocation. The domain is also the site of action of the eponymous toxins which catalyze covalent modification of single nucleotides that inactivate the ribosome. The conformation of the conserved guanosine at position 2655 is an especially prominent feature of the structure of the SRD: the nucleotide is bulged out of a helix and forms a base-triple with A2665 and U2656. G2655 in 23 S rRNA is protected from chemical modification when the elongation factors, EF-Tu and EF-G, are bound to ribosomes and the analog of G2655 in oligoribonucleotides is critical for recognition by the toxin sarcin and by EF-G. The contribution of G2655 to the function of the ribosome has been evaluated by constructing mutations in the nucleotide and determining the phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a deletion of, or transversions in, G2655 is lethal to E. coli cells, whereas a defect in the growth of cells with a G2655A transition is observed only in competition with wild-type cells. The sedimentation profiles of ribosomes with mutations in G2655 are altered; most markedly by deletion or transversion of the nucleotide, less severely by transition to adenosine. Mutations of G2655 confer resistance to sarcin on ribosomes. Ribosomes with G2655Delta, G2655C, or G2655U mutations in 23 S rRNA are not active in protein synthesis, whereas those with the G2655A transition mutation suffer decreased activity.

Base Sequence↗
PubMed1977

Polyamines and protein synthesis: studies in various polyamine-requiring mutants of Escherichia coli.

Different Escherichia coli mutants auxotrophic for polyamines were studied in order to investigate the relationships among polypeptide synthesis in cell-free systems, ribosomal distribution profiles and endogenous polyamine pools. The in vitro protein synthetic activity and the polyribosomal content were reduced in extracts from putrescine-starved cells of the double mutans MA 255 and MA 261, but not in the arginine-conditional auxotroph DK 6. Putrescine addition to the cultures of all these strains previously starved for polyamines, provoked a shift towards monomers in the equilibrium involving ribosomal particles. Concomitant changes in the intracellular levels of polyamines were observed: putrescine and spermidine increased markedly, and cadaverine disappeared.

Bacterial Proteins↗
PubMed1981

Light and immunoelectronmicroscopic study of Hodgkin's disease: evidence of immunoglobulin synthesis by tumor cells.

The direct immunoperoxidase technique with peroxidase-conjugated F(ab')2 fragments was used at the light and electron microscopic levels to identify intracytoplasmic immunoglobulin (CIg) components in malignant cells of Hodgkin's disease. In each of the 27 cases studied, Hodgkin and Reed-Sternberg cells contained either IgG or IgM, with both light chains often present simultaneously. The number of IgG-positive malignant cells was inversely related to changes in the lymphoid compartment, as defined by the Rye grading system. The evolution from lymphocytic predominance to lymphocytic depletion was paralleled by a decrease of IgM-positive cells and by a substantial increase (to exclusiveness) of IgG-containing cells. These immunoelectronmicroscopic studies disclosed definite morphologic evidence of CIg synthesis by Hodgkin, Reed-Sternberg and lacunar cells. The immunoglobulin components were also synthesized by lymphoid B cells at different levels of modulation. Immunoglobulin synthesis by malignant cells was localized in perinuclear zone, on free cytoplasmic ribosomes and profiles of rough endoplasmic reticulum. The results of this joint light and electron microscopic study support the view that Hodgkin, Reed-Sternberg and lacunar cells belong to the B-cell compartment within Hodgkin's disease.

B-Lymphocytes↗
PubMed2000

The phenotype of mutations of the base-pair C2658.G2663 that closes the tetraloop in the sarcin/ricin domain of Escherichia coli 23 S ribosomal RNA.

The sarcin/ricin domain (SRD) in Escherichia coli 23 S rRNA is a part of the site for the association of elongation factors with ribosomes and for that reason is critical for the binding of aminoacyl-tRNA and for translocation during the reiterative elongation reactions of protein synthesis. The SRD has a GAGA tetraloop that is shut off by a Watson-Crick C2658 x G2663 pair. The contribution of this pair to the function of the ribosome has been evaluated by constructing mutations in the nucleotides and determining their phenotype. Constitutive expression of a plasmid-encoded rrnB operon with a G2663C transversion mutation that disrupts the Watson-Crick pair was lethal. Double transversion mutations, C2658G x G2663C and C2658A x G2663U, that reverse the polarity of the pyrimidine and the purine but restore the potential to form a canonical pair, were also lethal. Induction of transcription of 23 S rRNA with the same mutations, but encoded in a plasmid with a lambdaP(L) promoter and expressed at a lower level, retarded growth. The sedimentation profiles of ribosomes with transversion mutations in C2658 and/or G2663 are altered; the ratio of 50 S subunits to 30 S particles is changed and polysomes are reduced. Ribosomes with a G2663C, a C2658G x G2663C, or a C2658A x G2663U mutation in 23 S rRNA were not active in protein synthesis, indeed, they appeared to inhibit the activity of ribosomes with wild-type 23 S rRNA. Transversion mutations in the analogs of C2658 and G2663 decreased binding of EF-G to SRD oligoribonucleotides; the same mutations in 23 S rRNA decreased binding of the factor to intact ribosomes. The most severe phenotype, in growth, in protein synthesis, and in the binding of EF-G, was associated with a C2658G x G2663C mutation; it is surprising that this was more severe than an analogous C2658A x G2663U mutation. A double transition mutation, C2658U x G2663A, which is not known to have occurred in nature, had no effect on the growth of cells or on the function of ribosomes. The lethal phenotype of transversion mutations in C2658 and G2663 appears to derive from a loss of the capacity of ribosomes to bind EF-G and by indirection the EF-Tu ternary complex.

Bacterial Proteins↗
PubMed1978

Morphometric and fine structural study of experimental autoallergic sialadenitis of rat submandibular glands.

To further our understanding of the immunopathologic mechanisms involved in experimental autoallergic sialadenitis of rat submandibular gland (EAS), histometric and fine structural studies were undertaken. Rats were immunized with allogeneic submandibular glands (SMG) emulsified in complete Freund's adjuvant. Control rats were not treated (C) or adjuvant treated (At). The rats were sacrificed 7, 14, 21 and 28 days after immunization and their SMG were processed for light and electron microscopy. Groups "C" and "at" showed normal acini and ducts. The SMG at 14 days showed significant loss of acini and granular ducts, severe lymphocytic infiltration and the appearance of undifferentiated ducts. The cells of the latter showed abundant free ribosomes, few profiles of rer, no secretory granules and in some cells autophagic vacuoles. Pseudopods of many lymphocytes were found in juxtaposition to degenerating parenchymal cells, mast cells and eosinophils. The extralobular ducts were significantly increased at 7, 14, and 21 days. The immunized glands showed evidence of regeneration at 21 and 28 days. Terminal tubule cells, proacinar cells and acinar cells, at various stages of maturation, were found in the regenerating glands.

Animals↗
PubMed1974

Influence of ascorbic acid on ribosomal patterns and collagen biosynthesis in healing wounds of scorbutic guinea pigs.

Scorbutic guinea pigs were wounded and the influence of administering ascorbic acid 6 days later was studied with respect to cellular morphology, ribosomal distribution and protein synthesis. Electron-microscopic studies revealed that the dilated endoplasmic reticulum observed in the fibroblasts of scorbutic wound tissue had reverted to a normal configuration 24h after intraperitoneal injection of 100mg of ascorbate. Quantitative determination of the distribution of free and membrane-bound ribosomes indicated a significant increase in membrane-bound ribosomes in wound tissue from ascorbate-supplemented (recovery) animals. Sucrose-density-gradient centrifugation indicated a significant increase in the proportion of large membrane-bound polyribosomes in the range 300-350S and a concomitant decrease in 80S monoribosomes in the ribosome sedimentation profile of recovery tissue. Determination of the synthesis of non-diffusible [(3)H]hydroxyproline in scorbutic and recovery wounds showed a 3-4-fold stimulation in peptidyl-proline hydroxylation in recovery tissues. Studies carried out in which scorbutic and recovery tissues were incubated with [(14)C]leucine indicated that general protein synthesis, as measured by (14)C incorporated into non-diffusible material/mug of DNA, was unaltered by ascorbate supplementation. Similar studies of [(3)H]proline incorporation suggested that in recovery tissues there was a small but significant increase in [(3)H]proline incorporated/mug of DNA, which probably represents an increase in protocollagen synthesis. This observation correlates well with the increase seen in recovery tissues of large polyribosomes on which collagen precursor polypeptides are known to be synthesized. Preliminary characterization of the repair collagen synthesized by recovery animals showed it to be a typical Type I collagen having the chain composition (alpha(1))(2)alpha(2). The extent of glycosylation of the hydroxylysine of the newly synthesized collagen was greater than that reported for either normal guinea-pig dermal collagen or dermal scar collagen.

Animals↗
PubMed2003

Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus).

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

Bacteria↗
PubMed1996

Establishment and characterization of a novel human promonocytic cell line from peripheral blood of a patient with psoriasis.

Human monocyte/macrophage lineages have unique phagocytic and immune-regulatory functions. We established a promonocytic cell line from the peripheral blood of a patient with psoriasis vulgaris. The newly established cells, termed YAP cells, grew in a suspension culture. In Wright-Giemsa-stained preparations, YAP cells were round or polygonal in shape. Transmission electron microscopy showed that the cells had clear nuclei with well-defined nucleoli. There were frequent mitochondria, a relatively abundant endoplasmic reticulum profile, free ribosomes and an occasional Golgi apparatus. Cytochemical studies showed a positive reaction for alpha-naphthyl butyrate esterase, which was completely inhibited by sodium fluoride, a diffuse positive reaction for periodic acid-Schiff, and a negative result for alkaline phosphatase and peroxidase. A large population of YAP cells reacted with the CD4, CD11b, CD25 and CD33 surface markers, but not with CD2, CD3, CD8 or CD19. We also found that YAP cells produced considerable amounts of TNF alpha, which was detected in the culture supernatant when the cells were treated with 1 ng/ml 12-O-tetradecanoylphorbol-13-acetate (TPA). Chromosome analyses showed that YAP cells contained a variety of marker chromosomes. It should be stressed that YAP cells were derived from a patient with a non-neoplastic disorder, whereas most monocytic cell lines previously reported are of malignant origin. This newly established cell line might be valuable for studying the pathogenesis of psoriasis, especially the role of monocytes/macrophages in the aetiology of the disease.

Adult↗
PubMed2005

Life-threatening chronic enteritis due to colonization of the small bowel with Stenotrophomonas maltophilia.

Chronic diarrheal illness and malabsorption are challenging diagnostic and clinical problems. The identification of the causative pathogens that are involved in gastrointestinal infections is often difficult. It took 85 years after the first description of a case of intestinal lipodystrophy by Georg Whipple in 1907 until the causative bacterium was characterized by using molecular genetics techniques. We here report the complicated clinical course of a young patient with chronic diarrhea accompanied by severe, life-threatening malabsorption with extensive weight loss. Histology and glucose hydrogen breath test were suggestive of a bacterial overgrowth syndrome in the small bowel, but standard culture-based techniques and serology failed to identify the causative bacteria. Thus, bacterial ribosomal DNA (16S ribosomal DNA) was extracted from duodenal biopsy samples and analyzed by community fingerprinting and species-specific polymerase chain reaction. Stenotrophomonas maltophilia was identified as the cause of chronic infectious enteritis. Only specific long-term antibiotic treatment with co-trimoxazole had a durable clinical effect and led to normalization of 16S ribosomal DNA profiles. This case shows the role of rare and uncommon bacteria in refractory and chronic human gastrointestinal infections. Genomic techniques, including 16S-based single-strand conformation polymorphism analysis, will play an increasing role in the diagnosis of chronic infections with facultatively pathogenic bacteria or in the clinical analysis of complex bacterial communities such as the intestinal bacterial microflora. Future enhancements in detection techniques will show that chronic bacterial infections are more frequent as a cause of gastrointestinal malfunction than commonly thought.

Adult↗
PubMed2002

Characterization of a novel gene up-regulated during anoxia exposure in the marine snail, Littorina littorea.

Gene expression was investigated during anoxia exposure in the marine snail, Littorina littorea. Differential screening of a cDNA library made from hepatopancreas of anoxic L. littorea yielded a 525 bp clone coding for the novel gene kvn. The deduced amino acid sequence of the KVN protein contained 99 amino acid residues with a predicted molecular weight of 12 kDa and showed an N-terminal secretory signal. Analysis of hepatopancreas samples over a time course of anoxia exposure showed a maximum increase in transcript levels of 5.8-fold after 48 h relative to normoxic animals, with a subsequent decrease in transcript levels during normoxic recovery. Nuclear run-off assays confirmed the observed transcriptional up-regulation of kvn during anoxia. Organ culture experiments were performed to determine a possible pathway of up-regulation of kvn, with data indicating a putative role for cGMP in signal transduction. Profiles of ribosome distribution in polysomes versus monosomes revealed a reduction in the polysome peak during anoxia and a shift in the position of kvn transcripts to association with the lower density polysome/higher density monosome region. The data suggest that the kvn transcript is both transcribed and translated during anoxia, indicating a possible significant role for the KVN protein in the survival of anoxia by L. littorea.

Amino Acid Sequence↗
PubMed2005

Viral metagenomics.

Viruses, most of which infect microorganisms, are the most abundant biological entities on the planet. Identifying and measuring the community dynamics of viruses in the environment is complicated because less than one percent of microbial hosts have been cultivated. Also, there is no single gene that is common to all viral genomes, so total uncultured viral diversity cannot be monitored using approaches analogous to ribosomal DNA profiling. Metagenomic analyses of uncultured viral communities circumvent these limitations and can provide insights into the composition and structure of environmental viral communities.

Bacteriophages↗
PubMed2003

Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.

We have analyzed the translational status of each mRNA in rapidly growing Saccharomyces cerevisiae. mRNAs were separated by velocity sedimentation on a sucrose gradient, and 14 fractions across the gradient were analyzed by quantitative microarray analysis, providing a profile of ribosome association with mRNAs for thousands of genes. For most genes, the majority of mRNA molecules were associated with ribosomes and presumably engaged in translation. This systematic approach enabled us to recognize genes with unusual behavior. For 43 genes, most mRNA molecules were not associated with ribosomes, suggesting that they may be translationally controlled. For 53 genes, including GCN4, CPA1, and ICY2, three genes for which translational control is known to play a key role in regulation, most mRNA molecules were associated with a single ribosome. The number of ribosomes associated with mRNAs increased with increasing length of the putative protein-coding sequence, consistent with longer transit times for ribosomes translating longer coding sequences. The density at which ribosomes were distributed on each mRNA (i.e., the number of ribosomes per unit ORF length) was well below the maximum packing density for nearly all mRNAs, consistent with initiation as the rate-limiting step in translation. Global analysis revealed an unexpected correlation: Ribosome density decreases with increasing ORF length. Models to account for this surprising observation are discussed.

Genome, Fungal↗
PubMed2005

Chitosan inactivates spoilage yeasts but enhances survival of Escherichia coli O157:H7 in apple juice.

AIMS: To develop new measures for controlling both spoilage and pathogenic micro-organisms in unpasteurized apple juice using chitosan. METHODS AND RESULTS: Micro-organisms were isolated and identified from apple juice treated or untreated with chitosan using enrichment, selective media, microscopy, substrate assimilation patterns and ribosomal DNA profiling. Chitosan (0.05-0.1%) delayed spoilage by yeasts at 25 degrees C for up to 12 days but the effect was species specific: Kloeckera apiculata and Metschnikowia pulcherrima were inactivated but Saccharomyces cerevisiae and Pichia spp. multiplied slowly. In challenge experiments at 25 degrees C, total yeast counts were 3-5 log CFU ml(-1) lower in chitosan-treated juices than in the controls for 4 days but the survival of Escherichia coli O157:H7 was extended from 1 to 2 days; at 4 degrees C, chitosan reduced the yeast counts by 2-3 log CFU ml(-1) for up to 10 days but survival of the pathogen was prolonged from 3 to 5 days. The survival of Salmonella enterica serovar Typhimurium was unaffected by chitosan at either temperature. CONCLUSIONS: The addition of chitosan to apple juice delayed spoilage by yeasts but enhanced the survival of E. coli O157:H7. SIGNIFICANCE AND IMPACT OF THE STUDY: The results suggest that the use of chitosan in the treatment of fruit juices may potentially lead to an increased risk of food poisoning from E. coli O157:H7.

Beverages↗
PubMed1995

Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber.

A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.

Amber↗