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PubMed2004

Characterization of three new enterococcal species, Enterococcus sp. nov. CDC PNS-E1, Enterococcus sp. nov. CDC PNS-E2, and Enterococcus sp. nov. CDC PNS-E3, isolated from human clinical specimens.

As a reference laboratory, the Streptococcus Laboratory at the Centers for Disease Control and Prevention (CDC) is frequently asked to confirm the identity of unusual or difficult-to-identify catalase-negative, gram-positive cocci. In order to accomplish the precise identification of these microorganisms, we have systematically applied analysis of whole-cell protein profiles (WCPP) and DNA-DNA reassociation experiments, in conjunction with conventional physiological tests. Using this approach, we recently focused on the characterization of three strains resembling the physiological groups I (strain SS-1730), II (strain SS-1729), and IV (strain SS-1728) of enterococcal species. Two strains were isolated from human blood, and one was isolated from human brain tissue. The results of physiological testing were not consistent enough to allow confident inclusion of the strains in any of the known enterococcal species. Resistance to vancomycin was detected in one of the strains (SS-1729). Analysis of WCPP showed unique profiles for each strain, which were not similar to the profiles of any previously described Enterococcus species. 16S ribosomal DNA (rDNA) sequencing results revealed three new taxa within the genus ENTEROCOCCUS: The results of DNA-DNA relatedness experiments were consistent with the results of WCPP analysis and 16S rDNA sequencing, since the percentages of homology with all 25 known species of Enterococcus were lower than 70%. Overall, the results indicate that these three strains constitute three new species of Enterococcus identified from human clinical sources, including one that harbors the vanA gene. The isolates were provisionally designated Enterococcus sp. nov. CDC Proposed New Species of Enterococcus 1 (CDC PNS-E1), type strain SS-1728(T) (= ATCC BAA-780(T) = CCUG 47860(T)); Enterococcus sp. nov. CDC PNS-E2, type strain SS-1729(T) (= ATCC BAA-781(T) = CCUG 47861(T)); and Enterococcus sp. nov. CDC PNS-E3, type strain SS-1730(T) (= ATCC BAA-782(T) = CCUG 47862(T)).

Centers for Disease Control and Prevention, U.S.↗
PubMed2000

Successful strategy for the selection of new strawberry-associated rhizobacteria antagonistic to Verticillium wilt.

In order to isolate and characterize new strawberry-associated bacteria antagonistic to the soil-borne pathogenic fungus Verticillium dahliae Kleb., rhizobacterial populations from two different strawberry species, Greenish Strawberry (Fragaria viridis) and Garden Strawberry (F. x ananassa) obtained after plating onto King's B and glycerol-arginine agar, were screened for in vitro antagonism toward V. dahliae. The proportion of isolates with antifungal activity determined in in vitro assay against V. dahliae was higher for the Garden Strawberry than for the Greenish Strawberry. From 300 isolates, 20 isolates with strong antifungal activity were selected characterized by physiological profiling and molecular fingerprinting methods. Diversity among the isolates was characterized with molecular fingerprints using amplified ribosomal DNA restriction analysis (ARDRA) and the more discriminating BOX-PCR fingerprint method. The physiological profiles were well correlated with molecular fingerprinting pattern analysis. Significant reduction of Verticillium wilt by bacterial dipping bath treatment was shown in the greenhouse and in fields naturally infested by V. dahliae. The relative increase of yield ranged from 117% (Streptomyces albidoflavus S1) to 344% (Pseudomonas fluorescens P10) in greenhouse trials, and 113% (Streptomyces albidoflavus S1) to 247% (Pseudomonas fluorescens P6) in field trials. Evaluation resulted in the selection of three effective biocontrol agents (Pseudomonas fluorescens P6, P10, and Streptomyces diastatochromogenes S9) antagonistic to the Verticillium wilt pathogen.

Antibiosis↗
PubMed2025

Integrated 16 S rRNA and transcriptome analysis reveal molecular and microbial mechanisms of cold-tolerant germination in hulless barley.

BACKGROUND: Elucidating the mechanisms underlying cold-tolerant germination is crucial for enhancing crop resilience to low temperatures. Hulless barley (Hordeum vulgare var. coeleste L.), with remarkable natural cold adaptation, serves as an ideal model to study cold stress tolerance mechanisms in gramineous crops. In this study, cold-tolerant variety 37 and cold-sensitive variety 44 were screened and used to investigate the molecular mechanisms of cold-tolerant germination, via seed germination assays, combined with phytohormone determination, transcriptome sequencing and 16 S rRNA amplicon sequencing. RESULTS: Low temperature significantly inhibited hulless barley seed germination: the germination rate of cold-sensitive variety 44 decreased by 69%, while that of cold-tolerant variety 37 only decreased by 2%. Transcriptome analysis identified 2,647 and 2,392 differentially expressed genes (DEGs) in variety 37 and 44, respectively. Weighted gene co-expression network analysis (WGCNA) revealed a green module significantly positively correlated with gibberellic acid (GA) content, containing 10 core genes such as late embryogenesis abundant protein (LEA) and Homeobox genes. 16 S rRNA sequencing showed that the cold-tolerant variety 37 had enriched abundances of dominant endophytes including Sphingomonas and Pelomonas, with correlation coefficients of 0.70 and 0.87 with GA content, respectively. Additionally, exogenous GA treatment significantly increased germination rates under cold stress by 176.67% in cold-sensitive variety 44. CONCLUSIONS: This study confirms that the enhanced cold tolerance of hulless barley during seed germination originates from the synergistic interaction between beneficial endophytes (Sphingomonas, Pelomonas), GA, and core genes (e.g., LEA, Homeobox). Exogenous GA application can significantly restore the germination ability of cold-sensitive varieties. These findings provide a critical theoretical basis for improving cold tolerance in hulless barley germplasm.

Hordeum↗
PubMed1980

Effect of cyproterone acetate on mouse adenohypophysis. I. The adrenocorticotrophs.

The adenohypophyses of adult male C57BL/6J mice pituitaries injected with cyproterone acetate for four weeks were examined with the electron microscope. The adrenocorticotrophs of the adenohypophysis showed an absence of the 200-nm granules that were lined along the plasma membrane, a decrease in profiles of rough endoplasmic reticulum, sparse distribution of ribosomes, and flatten Golgi membranes. It is believed the antiandrogen cyproterone acetate inhibited ACTH synthesis and release and that this was responsible for adrenocortical atrophy.

Adrenocorticotropic Hormone↗
PubMed1994

Small granule-containing (SGC) cells in the hamster adrenal medulla.

In addition to adrenalin (A)- and noradrenaline (NA)-containing cells in the hamster adrenal medulla, a third type of small granule-containing (SGC) cells was identified. These cells were characterized by their small size (about 15 microns in diameter) and location adjacent to A-cells. Numerous pleomorphic dense-cored cytoplasmic granules (306 +/- 44.5 nm x 204.5 +/- 58.3 nm, mean +/- standard error) were present in their cytoplasm. The ultrastructure of these granules were similar to that of NA-containing granules but smaller in size. The granular inclusions of the granules were moderate to high in electrol density. The cytoplasm of the SGC cells contained short profiles of rough endoplasmic reticulum and some free ribosomes.

Adrenal Medulla↗
PubMed1977

[Effect of triterpene glycosides on RNA biosynthesis in a yeast cell culture of Saccharomyces carlsbergensis].

The effect of triterpen glycosides of cauloside C from Caulophyllum robustum, theasaponine from Thea sinensis ahd stichoposide A from Stichopus japonicus on multiplication and biosynthesis of RNA in the cells of a 7-hour culture of Saccharomyces carlsbergensis was studied. It was shown that cauloside C, theasaponine and stichoposide A in concentrations of 7.5 gamma/ml inhibited multiplication of the yeast cells by 65, 10 and 90 per cent respectively. The summation RNA of the yeast cells is divided into 3 zones on Sephadex G-100. The glycosides induced no pronounced changes in the chromotographic profile of RNA. Biosynthesis of the transport and ribosomal RNA were inhibited to the same extent. Triterpen glycosides inhibited the biosynthesis of RNA at the stage of 14C-uridine in corporation into the nucleotide pool of the yeast cells.

Cells, Cultured↗
PubMed2001

Isolate PM1 populations are dominant and novel methyl tert-butyl ether-degrading bacterial in compost biofilter enrichments.

The gasoline additive MTBE, methyl tert-butyl ether, is a widespread and persistent groundwater contaminant. MTBE undergoes rapid mineralization as the sole carbon and energy source of bacterial strain PM1, isolated from an enrichment culture of compost biofilter material. In this report, we describe the results of microbial community DNA profiling to assess the relative dominance of isolate PM1 and other bacterial strains cultured from the compost enrichment. Three polymerase chain reaction (PCR)-based profiling approaches were evaluated: denaturing gradient gel electrophoresis (DGGE) analysis of 230 bp 16S rDNA fragments; thermal gradient gel electrophoresis (TGGE) analysis of 575 bp 16S rDNA fragments; and non-denaturing polyacrylamide gel electrophoresis of 300-1,500 bp fragments containing 16S/23S ribosomal intergenic transcribed spacer (ITS) regions. Whereas all three DNA profiling approaches indicated that PM1-like bands predominated in mixtures from MTBE-grown enrichments, ITS profiling provided the most abundant and specific sequence data to confirm strain PM1's presence in the enrichment. Moreover, ITS profiling did not produce non-specific PCR products that were observed with T/DGGE. A further advantage of ITS community profiling over other methods requiring restriction digestion (e.g. terminal restriction fragment length polymorphisms) was that it did not require an additional digestion step or the use of automated sequencing equipment. ITS bands, excised from similar locations in profiles of the enrichment and PM1 pure culture, were 99.9% identical across 750 16S rDNA positions and 100% identical across 691 spacer positions. BLAST comparisons of nearly full-length 16S rDNA sequences showed 96% similarity between isolate PM1 and representatives of at least four different genera in the Leptothrix subgroup of the beta-Proteobacteria (Aquabacterium, Leptothrix, Rubrivivax and Ideonella). Maximum likelihood and parsimony analyses of 1,249 nucleotide positions supported isolate PM1's position in a separate lineage within the Leptothrix subgroup.

Bacteria↗
PubMed1982

Ribosomal proteins of sea urchin eggs. II. Taxonomical differences.

Ribosomal proteins from unfertilized eggs of three sea urchin species. Pseudocentrotus depressus, Hemicentrotus pulcherrimus, and Anthocidaris crassispina, were analyzed. Species-specific differences were observed in the profiles of large subunit proteins on two-dimensional slab gels, though the number of ribosomal proteins and the molecular weights of their counterparts were the same. The small subunit proteins revealed similarities in the electrophoretic profiles and in the phosphorylation patterns among these three species.

Animals↗
PubMed1990

Purification and characterization of a novel factor which stimulates rat ribosomal gene transcription in vitro by interacting with enhancer and core promoter elements.

Previous studies in our laboratory have characterized a 174-base-pair (bp) enhancer sequence in the rat ribosomal DNA spacer region that exhibits all of the characteristics of a polymerase (Pol) II enhancer. Further studies showed that at least half of the enhancer activity resides in a 37-bp motif (E1) within the 174-bp spacer sequence that is located between positions -2.183 and -2.219 kilobase pairs upstream of the initiation site. To identify the factor(s) that binds specifically to the 37-bp enhancer domain, we fractionated whole-cell extract from rat adenocarcinoma ascites cells by chromatography on a series of columns, including an oligodeoxynucleotide affinity column. The final preparation contained two polypeptides of molecular weights 79,400 and 89,100 and was completely devoid of RNA Pol I activity. Electrophoretic mobility shift analysis showed that the polypeptides in the purified preparation (designated E1BF) interacted with both the enhancer element and the core promoter. To determine whether each polypeptide can separately bind to the core promoter and the enhancer, the individual components were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, renatured, and subjected to gel retardation analysis. This experiment demonstrated that both polypeptides interacted with the two cis-acting sequences. The specificity of the binding was demonstrated by competition with unlabeled 37-bp and core promoter fragments and lack of competition with nonspecific DNAs in the mobility shift assay. The 37-bp enhancer as well as the downstream sequence of the core promoter were protected by E1BF in the DNase I footprinting assay. Addition of E1BF to limiting amounts of fraction DE-B, which contains all factors essential for Pol I-directed transcription, resulted in three- to fourfold stimulation of ribosomal DNA transcription. Comparison of molecular weights and footprinting profiles did not reveal any relationship between E1BF and other Pol I trans-acting factors.

Animals↗
PubMed2006

Staying alive in adversity: transcriptome dynamics in the stress-resistant dauer larva.

In response to food depletion and overcrowding, the soil nematode Caenorhabditis elegans can arrest development and form an alternate third larval stage called the dauer. Though nonfeeding, the dauer larva is long lived and stress resistant. Metabolic and transcription rates are lowered but the transcriptome of the dauer is complex. In this study, distribution analysis of transcript profiles generated by Serial Analysis of Gene Expression (SAGE) in dauer larvae and in mixed developmental stages is presented. An inverse relationship was observed between frequency and abundance/copy number of SAGE tag types (transcripts) in both profiles. In the dauer profile, a relatively greater proportion of highly abundant transcripts was counterbalanced by a smaller fraction of low to moderately abundant transcripts. Comparisons of abundant tag counts between the two profiles revealed relative enrichment in the dauer profile of transcripts with predicted or known involvement in ribosome biogenesis and protein synthesis, membrane transport, and immune responses. Translation-coupled mRNA decay is proposed as part of an immune-like stress response in the dauer larva. An influence of genomic region on transcript level may reflect the coordination of transcription and mRNA turnover.

Acclimatization↗
PubMed1977

Ribosomes, membranes and organelles during meiosis in angiosperms.

Evidence is presented from both observational and analytical techniques indicating profound changes to take place in the ribosome population during male and female meiosis in some flowering plants. During microsporogenesis these appear to involve the elimination of the major part of the ribosome complement early in the meiotic prophase, and its subsequent restoration by the disintegration in the tetrad cytoplasm of 'nucleoloids', themselves synthesized in the nucleus during late prophase. In female tissue the process is essentially similar except for differences in the restoration of the ribosome population. Immediately before the eradication of the ribosomes in both sexes, a sizeable proportion of the meiocyte cytoplasm is encapsulated by double, or multiple unit membrane profiles. Significantly this cytoplasm remains unaffected by the agents responsible for the degredation of the ribosome population. These events are also reflected in the organelle populations where cycles of dedifferentiation and redifferentiation take place. In view of evidence from other organisms, it is considered unlikely that these cycles are in any way a prerequisite of meiosis, but more a characteristic of cells undergoing major changes of phase, where a cytoplasmic 'clean-up' is required before the next stage of growth may begin.

Acid Phosphatase↗
PubMed2025

The chloroplast 16S rRNA dimethyltransferase BrPFC1 is required for Brassica rapa development under chilling stress.

Chloroplast ribosomal RNA (Ch-rRNA) methylation is critical for plant development and response to low temperatures. Several Ch-rRNA methyltransferases and their catalytic modes, as well as biological relevance, have been reported in model plant species. However, Ch-rRNA methyltransferases and their functional significance remain poorly characterized in crops, including leafy vegetables such as Chinese cabbage. In this study, we screened an EMS-mutagenized Chinese cabbage population and identified a yellow inner leaf (yif) mutant. This mutant develops yellowing inner leaves with reduced chlorophyll accumulation and ultrastructure-impaired chloroplasts under low-temperature conditions. Genetic analysis revealed a premature termination mutation in BrPFC1, encoding the chloroplast-localized 16S rRNA dimethyltransferase. The BrPFC1 mutation (yif) disrupts the dimethylation of 16S rRNA. The cold-sensitive phenotype of the yif mutant can be explained by temperature-dependent defects in the maturation and assembly of chloroplast ribosomes at 4°C. Through integrated analysis of chloroplast and nuclear transcriptomes coupled with translational profiling at 25°C and 4°C, we established that low temperature preferentially upregulates transcripts encoding nuclear-derived ribosomal proteins, while defective 16S rRNA specifically compromises the translational efficiency of chloroplast-encoded photosynthetic complex and ribosomal protein at 4°C. These findings establish rRNA modification by BrPFC1 as a critical regulatory layer for optimizing chloroplast translational efficiency at 4°C, providing mechanistic insights into post-translational adaptation strategies in Chinese cabbage.

Chloroplasts↗
PubMed1993

Molecular subtyping by genome and plasmid analysis of Campylobacter jejuni serogroups O1 and O2 (Penner) from sporadic and outbreak cases of human diarrhoea.

Ribosomal RNA gene patterns, randomly amplified polymorphic genomic DNA (RAPD) profiles and plasmid profiles were used to discriminate between 28 strains of Campylobacter jejuni serogroups O1 and O2 (Penner). Most isolates were biotype I (Lior). The strains were representative isolates from a UK school outbreak of enteritis (7 cases) and from 21 sporadic human cases of enteritis in 4 countries. The molecular techniques discriminated to various degrees between strains in each of the serogroups. The outbreak strains were homogeneous in most molecular features but a variety of types was detected amongst the isolates from the sporadic cases. Five groups of two or more strains with identical ribopatterns were identified and within each, strains from different patients were homogenous with respect to serogroup. RAPD profile typing based on numerical analysis generally matched ribotyping. Plasmid profiling overall gave least discrimination but was useful in separating some strains similar in other features. We concluded that optimal discrimination of C. jejuni could best be achieved using a combination of phenotypic and genotypic properties. Hae III ribotyping was the single most discriminatory and reproducible technique investigated. Several strains of C. jejuni from sporadic infections had similar molecular profiles which have potential for general typing purposes.

Bacterial Typing Techniques↗
PubMed1992

Unbalanced ribosome assembly in Saccharomyces cerevisiae expressing mutant 5 S rRNAs.

Mutant 5 S rRNA genes were expressed in Saccharomyces cerevisiae to further define the function of the ribosomal 5 S RNA. RNA synthesis and utilization were assayed using previously constructed markers which have been shown to be functionally neutral and easily detected by gel electrophoresis. Most mutations were found not to affect the growth rate because they were poorly expressed or could be accommodated effectively in the ribosomal structure. Two of the mutants, Y5A99U56U57 and Y5U90i5 adversely affected cell growth as well as protein synthesis in vitro. Polyribosome profiles in both of these mutants were substantially shorter, and an analysis of the ribosomal subunit composition revealed a significant imbalance with a 25-35% excess in 40 S subunits. Kinetic analyses of RNA labeling indicated very low cellular levels of mutant RNA either because it was poorly expressed (Y5U90i5) or rapidly degraded before being incorporated into mature 60 subunits (Y5A99U56U57). The results suggest that the 5 S RNA is required for the assembly of stable ribosomal 60 S subunits and raise the possibility that this RNA or, more likely, its corresponding ribonucleoprotein complex is critical for subunit assembly or even RNA processing.

Base Sequence↗
PubMedDate not supplied

Identification of Cannabis sativa L. (Cannabaceae) using restriction profiles of the Internal Transcribed Spacer II (ITS2).

The paper describes the construction of a restriction profile of the Internal Transcribed Spacer II (ITS2) of Cannabis sativa L. Nuclear Ribosomal DNA, using digestion by a selected number of restriction endonucleases. The method was evaluated for false positives and it is suggested that it could be used to identify suspected Cannabis samples, by comparing their restriction profiles with the restriction profile of known Cannabis material.

Cannabis↗
PubMed2006

Variation in microbial community composition and culturability in the rhizosphere of Leucanthemopsis alpina (L.) Heywood and adjacent bare soil along an alpine chronosequence.

We compared the size, culturability, diversity, and dominant species similarity of the bacterial communities of Leucanthemopsis alpina (L.) Heywood rhizosphere and adjacent bare soil (interspace) along a chronosequence of soil development time (5, 50, and 70 years) in the forefield of the Dammaglacier (Switzerland). We found no evidence that the size of the bacterial community was significantly affected by either soil age or the presence of L. alpina. In contrast, the proportion of the bacterial community that could be cultured on nonselective agars, and which was taken as an indication of the proportion of r-selected populations, was significantly higher in the 50- and 70-year-old soils than in the 5-year-old soil, and was also significantly higher in the rhizosphere of L. alpina at all time points. RDA indicated significant correlations between the increased culturability of the bacterial community over time and increasing concentrations of labile N, and between the increased culturability in the rhizosphere and increased concentrations of labile C and N. HaeIII-amplified ribosomal DNA (rDNA) restriction analysis of a library of 120 clones of 16S rDNA revealed 85 distinct phylotypes. Hurlbert's probability of interspecific encounter (PIE) values derived from this library ranged from 0.95 to 1.0, indicating a very high genetic diversity. There was no significant difference in the PIE values of rhizosphere and interspace communities. Detrended correspondence analysis (DCA) of 16S ribosomal RNA (rRNA) denaturing gradient gel electrophoresis (DGGE) community profiles clearly distinguished the rhizosphere from the interspace community in the 5-year-old soils and also clearly distinguished between these communities and the rhizosphere and interspace communities of the 50- and 70-year-old soils. However, 16S rRNA DGGE revealed little difference between rhizosphere and interspace communities in the 50- and 70-year-old soils. The relative similarity of the 16S rRNA profiles strongly reflected labile carbon and nitrogen availability. Overall, our results suggest that improved C and N availability in the rhizosphere of L. alpina increases the size of r-selected bacterial species populations, but that the influence of L. alpina depends on soil age, being maximal in the youngest soils and minimal in the oldest. The reduced influence of L. alpina in the older soils may reflect a feedback between improved nutrient availability and reduced rhizodeposition.

Bacteria↗
PubMed1997

Long-term follow-up of autoantibody profiles in black female lupus patients and clinical comparison with Caucasian and Asian patients.

The aim was to determine whether the autoantibody profile in Black female lupus patients is associated with clinical subsets, fluctuates over time and/or reflects disease activity. A clinical comparison with Caucasian and Asian patients matched for age of onset and disease duration was also undertaken. Up to seven serial bleeds from Black female lupus patients who had been followed up for periods of 3.15 yr were tested for antibodies to Ro/SSA, La SSB. Sm, RNP and ribosomal P using ELISA research assays. Significant differences in both clinical and serological profiles between the ethnic groups were found. Varying aspects of disease activity were linked to anti-DNA (renal, cardiovascular, global score), anti-ribosomal P (musculoskeletal, haematology) and anti-Sm (general) antibodies. There are differences in clinical and serological profiles amongst systemic lupus erythematosus patients of different ethnic origin. However, using the BILAG system, relatively few antibodies were found to reflect disease activity accurately in serial measurements.

Adult↗