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Results for “Ribosome Profiling”

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PubMed2001

Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability.

Automated rRNA intergenic spacer analysis (ARISA) was used to characterise bacterial (B-ARISA) and fungal (F-ARISA) communities from different soil types. The 16S-23S intergenic spacer region from the bacterial rRNA operon was amplified from total soil community DNA for B-ARISA. Similarly, the two internal transcribed spacers and the 5.8S rRNA gene (ITS1-5.8S-ITS2) from the fungal rRNA operon were amplified from total soil community DNA for F-ARISA. Universal fluorescence-labeled primers were used for the PCRs, and fragments of between 200 and 1,200 bp were resolved on denaturing polyacrylamide gels by use of an automated sequencer with laser detection. Methodological (DNA extraction and PCR amplification) and biological (inter- and intrasite) variations were evaluated by comparing the number and intensity of peaks (bands) between electrophoregrams (profiles) and by multivariate analysis. Our results showed that ARISA is a high-resolution, highly reproducible technique and is a robust method for discriminating between microbial communities. To evaluate the potential biases in community description provided by ARISA, we also examined databases on length distribution of ribosomal intergenic spacers among bacteria (L. Ranjard, E. Brothier, and S. Nazaret, Appl. Environ. Microbiol. 66:5334-5339, 2000) and fungi.

Bacteria↗

PubMed2002

Identification and characterization of genes involved in the carcinogenesis of human squamous cell cervical carcinoma.

We utilized RT-PCR differential display and cDNA microarrays to identify cellular genes involved in the multi-step carcinogenesis of squamous cell cervical carcinoma. Thirty-eight cervical cancer patients in various stages of the disease and 5 non-cervical cancer patients were studied. Twenty-five cDNA clones were identified and these were subsequently demonstrated to be consistently over-expressed in squamous cell cervical carcinoma biopsies of various FIGO stages. To further evaluate the possible role that these genes may play in the progression of disease, we performed Northern blot analysis and RNA-RNA in situ hybridization studies using cervical cancer biopsies of various FIGO stages. Of particular interest are the 2 clones G32C4B and G30CC that have been identified to be the NADH dehydrogenase 4 gene and the gene that encodes ribosomal protein S12 respectively when compared to sequences available in the GenBank database. Increased expression of these 2 genes were detected in the matched normal tissues collected together with the late FIGO stages of cervical cancer biopsies. In comparison, upregulation of these 2 genes was not detected in cervical squamous epithelium collected from patients admitted for surgery for non-malignant conditions, suggesting that expression of these 2 genes may have altered in the adjacent histopathologically "normal" cervical squamous epithelial tissue from cervical cancer patients. The ribosomal protein S12 and the NADH dehydrogenase 4 genes may therefore be potentially useful as early pre-transformation diagnostic markers for human cervical cancer.

Biomarkers, Tumor↗

PubMed1997

Nocardioides pyridinolyticus sp. nov., a pyridine-degrading bacterium isolated from the oxic zone of an oil shale column.

A bacterial strain which is able to degrade pyridine was previously isolated from the oxic zone of an oil shale column and described as Pimelobacter sp. strain OS4T. However, Pimelobacter species have been transferred to the genera Nocardioides and Terrabacter. Strain OS4T was identified as a member of the genus Nocardioides on the basis of chemotaxonomic analysis and phylogenetic inference based on 16S ribosomal DNA (rDNA) sequence analysis. The G+C content of strain OS4T is 72.5 mol%. The cell wall peptidoglycan contains LL-diaminopimelic acid as the diamino acid. The predominant menaquinone is MK-8(H4). The cellular fatty acid profile of strain OS4T is similar to that of the genus Nocardioides. The 16S rDNA similarity of strain OS4T with previously described Nocardioides species is 94.5% +/- 0.7%, and a phylogenetic tree based on 16S rDNA sequences revealed a distinct lineage for strain OS4T within the evolutionary radiation enclosed by the genus Nocardioides. Therefore, on the basis of our data, we propose that strain OS4T should be placed in the genus Nocardioides as a member of a new species, Nocardioides pyridinolyticus. The type strain of the new species is strain OS4 (= KCTC 0074BP).

Base Composition↗

PubMed2004

The use of the polymerase chain reaction and restriction fragment length polymorphism technique associated with the classical morphology for characterization of Lymnaea columella, L. viatrix, and L. diaphana (Mollusca: Lymnaeidae).

The specific identification of Lymnaeid snails is based on a comparison of morphological characters of the shell, radula, renal and reproductive organs. However, the identification is complicated by dissection process, intra and interspecific similarity and variability of morphological characters. In the present study, polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP) techniques targeted to the first and second internal transcribed spacers (ITS1 and ITS2) rDNA and to the mitochondrial 16S ribosomal gene (16S rDNAmt) were used to differentiate the species Lymnaea columella, L. viatrix, and L. diaphana from some localities of Brazil, Argentina, and Uruguay as well as to verify whether the molecular results corroborates the classical morphological method.PCR-RFLP analysis of the ITS1, ITS2, and 16S using 12 restriction enzymes revealed characteristic patterns for L. columella and L. diaphana which were concordant with the classical morphology. On the other hand, for L. viatrix populations a number of 1 to 6 profiles were generated while morphology provided the species pattern results.

Animals↗

PubMed2007

Global analysis of differentially expressed genes in androgen-independent prostate cancer.

Progression to androgen independent (AI) is the main cause of death in prostate cancer, and the mechanism is still unclear. By reviewing the expression profiles of 26 prostate cancer samples in a holistic view, we found a group of genes differentially expressed in AI compared with androgen-dependent groups (P-value<0.01, t-test). Focusing on apoptosis, proliferation, hormone and angiogenesis, we found a group of genes such as thioredoxin domain containing 5 , tumor necrosis factor receptor superfamily, member 10a , ribosomal protein S19 and Janus kinase 2 upregulated in AI prostate cancer, could play important roles in the transition from AD to AI and could be biomarkers of prognosis.

Androgen Antagonists↗

PubMed1977

Alteration of 5S RNA conformation by ribosomal proteins L18 and L25.

The effects of ribosomal proteins L18, L25 and L5 on the conformation of 5S RNA have been studied by circular dichroism and temperature dependent ultraviolet absorbance. The circular dichroism spectrum of native 5S RNA is characterized in the near ultraviolet by a large positive band at 267 nm and a small negative band at 298 nm. The greatest perturbation in the spectrum was produced by protein L18 which induced a 20% increase in the 267 nm band and no change in the 298 nm band. By contrast, protein L25 caused a small decrease in both bands. No effect was observed with protein L5. Simultaneous binding of proteins L18 and L25 resulted in CD changes equivalent to the sum of their independent effects. The UV absorbance thermal denaturation profile of the 5S RNA L18 complex lacked the pre-melting behavior characteristic of 5S RNA. Protein L25 had no effect on the 5S RNA melting profile. We concluded that protein L18 increases the secondary, and possible the tertiary structure of 5S RNA, and exerts a minor stabilizing effect on its conformation while protein L25 causes a small decrease in 5S RNA secondary structure. The implications of these findings for ribosome assembly and function are discussed.

Chemical Phenomena↗

PubMed2004

Antitumor efficacy of intermittent treatment schedules with the rapamycin derivative RAD001 correlates with prolonged inactivation of ribosomal protein S6 kinase 1 in peripheral blood mononuclear cells.

The orally bioavailable rapamycin derivative RAD001 (everolimus) targets the mammalian target of rapamycin pathway and possesses potent immunosuppressive and anticancer activities. Here, the antitumor activity of RAD001 was evaluated in the CA20948 syngeneic rat pancreatic tumor model. RAD001 demonstrated dose-dependent antitumor activity with daily and weekly administration schedules; statistically significant antitumor effects were observed with 2.5 and 0.5 mg/kg RAD001 administered daily [treated tumor versus control tumor size (T/C), 23% and 23-30%, respectively], with 3-5 mg/kg RAD001 administered once weekly (T/C, 14-36%), or with 5 mg/kg RAD001 administered twice weekly (T/C, 36%). These schedules were well tolerated and exhibited antitumor potency similar to that of the cytotoxic agent 5-fluorouracil (T/C, 23%). Moreover, the efficacy of intermittent treatment schedules suggests a therapeutic window allowing differentiation of antitumor activity from the immunosuppressive properties of this agent. Detailed biochemical profiling of mammalian target of rapamycin signaling in tumors, skin, and peripheral blood mononuclear cells (PBMCs), after a single administration of 5 mg/kg RAD001, indicated that RAD001 treatment blocked phosphorylation of the translational repressor eukaryotic initiation factor 4E-binding protein 1 and inactivated the translational activator ribosomal protein S6 kinase 1 (S6K1). The efficacy of intermittent treatment schedules was associated with prolonged inactivation of S6K1 in tumors and surrogate tissues (> or =72 h). Furthermore, detailed analysis of the dose dependency of weekly treatment schedules demonstrated a correlation between antitumor efficacy and prolonged effects (> or =7 days) on PBMC-derived S6K1 activity. Analysis of human PBMCs revealed that S6K1 also underwent a concentration-dependent inactivation after RAD001 treatment ex vivo (>95% inactivation with 20 nM RAD001). In contrast, human PBMC-derived eukaryotic initiation factor 4E-binding protein 1 was present predominantly in the hypophosphorylated form and was unaffected by RAD001 treatment. Taken together, these results demonstrate a correlation between the antitumor efficacy of intermittent RAD001 treatment schedules and prolonged S6K1 inactivation in PBMCs and suggest that long-term monitoring of PBMC-derived S6K1 activity levels could be used for assessing RAD001 treatment schedules in cancer patients.

Animals↗

PubMed1995

PCR amplification of intergenic spacers in the ribosomal DNA of Drosophila melanogaster reveals high levels of turnover in length and copy-number of spacers in geographically separated populations.

A recently described PCR-based method for the analysis of intergenic spacer (IGS) length variation in the ribosomal (r) DNA of Drosophila melanogaster was used to analyse the distribution of IGS length variants in the rDNA of a number of recently collected D. melanogaster populations. One group of populations, from Europe and North Africa, was shown to have low intrapopulation IGS length variation following maintenance of massed populations in the laboratory for an extended period. However, a greater degree of IGS profile variability was detected at a number of levels in the majority of laboratory-maintained isofemale lines from two of these populations plus a second group of populations which were collected more recently from the eastern coast of Australia; all of which were immediately divided into isofemale lines following collection. Interestingly, PCR analysis of pooled DNA extracts from 30 individuals of either sex showed almost identical PCR profiles from each of the Australian populations. These preliminary results are discussed with regard to the possible combinations of forces (natural selection, neutral drift and genomic molecular drive) on the patterns of IGS length variation.

Animals↗

PubMed2002

Who eats what? Classifying microbial populations based on diurnal profiles of rRNA levels.

Identifying the relationships between various bacterial populations and the substrates they consume is central to the understanding of population dynamics and to the development of process control in activated sludge. However, linking a heterotrophic population to its activity in situ is difficult because ribosomal RNA (rRNA) techniques, while allowing the rapid identification of populations, provide little information about their heterotrophic activity. Activated sludge models describe biodegradation kinetics by classifying substrates into two types: readily and slowly degradable substrates. Assuming that bacterial populations specialize in degrading one type of substrate, their growth rate should be affected differently if the COD loading rate varies diurnally as for a municipal activated sludge system. Modeling results suggested that the growth rates of populations consuming readily degradable substrates vary according to variations in COD loading rate. On the other hand, the growth rates of populations consuming slowly degradable substrates do not change despite the variation in COD loading rate. Since the cellular rRNA level is positively correlated with the growth rate, we hypothesized that the rRNA levels of some populations in municipal activated sludge should increase throughout the day, while they should stay constant for other populations. This hypothesis was verified by monitoring the rRNA level of Acinetobacter (a model population consuming readily degradable substrates) and Gordonia (a model population consuming slowly degradable substrates) in the mixed liquor of a full-scale municipal activated sludge reactor for three weeks.

Bacteria↗

PubMed2004

Pharmacogenomic profiling of the PI3K/PTEN-AKT-mTOR pathway in common human tumors.

The protein synthetic machinery is activated by a variety of genetic alterations during tumor progression and represents an attractive target for cancer therapy. The mammalian target of rapamycin (mTOR) plays an important role in regulating protein translation through phosphorylation of p70 S6 kinase 1 (S6K1), a protein involved in ribosome biogenesis, and 4E-BP1 (eIF-4E binding protein), a translation repressor. It has been shown that mTOR has a direct linkage to the phosphatidylinositol-3'-kinase (PI3K)/PTEN-AKT survival pathway. Recent studies have demonstrated that mTOR inhibition by rapamycin or its analogues have remarkable activity against a wide range of human cancers in vitro and in human tumor xenograft models. Phase I clinical evaluations also suggested an anti-tumor effect of rapamycin analogue such as CCI-779. The clinical challenge for the application of this class of anticancer drug is the ability to prospectively identify which tumors will be sensitive to mTOR inhibition. Recent studies have identified cellular markers that are associated with the in vitro activity of rapamycin or CCI-779. However, there have been no reports on how these cellular markers are expressed together in human tumor specimen. In this study, multiple components of the PI3K/PTEN-AKT-mTOR pathway were evaluated by immunohistochemistry in tissue arrays containing 124 tumors from 8 common tumor types. The results show variable expression of all the signaling proteins. For example, mTOR expression was low in brain tumors, but high in the rest of tumors. High levels of 4E-BP1 were seen in colonic adenocarcinoma and low levels in lymphoma. Phospho-AKT (p-AKT) and phospho-S6K1 (p-S6K1) were the only proteins that had significantly correlated protein expression (rs=0.51, p<0.001). Since low PTEN, high p-AKT and high p-S6K1 expression render tumors sensitive to mTOR inhibition in vitro, these criteria were used to model tumor sensitivity. Overall, 26% of tumors (32/124) are predicted to be sensitive to mTOR inhibition, with variable rates for different tumors (melanoma 0% vs ovarian 41%). This is the first report on the PI3K/PTEN-AKT-mTOR pathway in common human tumors and evaluation of the coordinated expression of different signaling proteins. This study should provide a useful tool for selecting future targeted phase II and III clinical trials in the development of this exciting class of agents.

Adaptor Proteins, Signal Transducing↗

PubMed2004

[Study of collections of Mycobacterium non-tuberculosis by a restriction test of the amplified fragment spacer sequence 16S-23S of ribosomal DNA].

Fifty mycobacterial cultures were studied by restriction analysis of the amplified fragment of spacer sequence 16S-23S of ribosomal DNA. The following types were identified: M. tuberculosis complex, M. avium, M. intracellulare, M. scrofulaceum, M. kansasii, M. gordonae, M. ulcerans, M. fortuitum, M. smegmatis. The genetic heterogeneity of M. fortuitum was detected. The strains under study belong to 5 patterns: M. fortuitum I, M. fortuitum II, M. fortuitum X, M. fortuitum Y, M. fortuitum Z. The pattern characteristics for M. ulcerans (the size of a CPR product was 370 pn; the characteristics of the enzyme HaeIII-induced restriction profile was 214/155 pn) were obtained.

DNA Primers↗

PubMed1991

Formation and release of vesicles from the basal surfaces of rat eye non-pigmented ciliary epithelial cells: a novel secretory mechanism?

When rat ciliary body is processed by high pressure freezing and freeze substitution, numerous membrane-bound vesicle profiles are seen in the vitreous associated with the pars plana and in the valleys between the ciliary processes. They consist of a homogeneously distributed fine granular matrix and varying numbers of ribosome-like structures. The mechanism by which these vesicles are secreted appears to follow an apocrine-type pattern, albeit at the basal cell surface. Matrix material accumulates between the basal plasma membrane of non-pigmented ciliary epithelial cells and a cortical layer of cytoskeletal components; the blebs thus formed protrude through a discontinuity in the basal lamina and, by a progressive narrowing of the neck region, are eventually pinched off, giving rise to free vesicles. Under conventional aqueous chemical fixation conditions, most of these vesicles are washed away or their contents solubilized and extracted, which accounts for their not having been identified hitherto as genuine morphological structures. They are nonetheless apparent, albeit in reduced numbers and mostly empty. Such vesicles are also observed in tissue processed according to several other chemical fixation techniques, namely, conventional fixation in the presence of the cationic dye ruthenium hexamine trichloride, simultaneous glutaraldehyde/osmium tetroxide fixation, and microwave fixation. In the latter instance, comparable vesicle preservation to that obtained by high pressure freezing/freeze substitution may be achieved if fixation is followed by cryoprotection, plunge freezing, and freeze substitution instead of conventional post-fixation and dehydration procedures.

Animals↗

PubMed1996

In vivo angiogenesis in adult rat skeletal muscle: early changes in capillary network architecture and ultrastructure.

The individual structural stages in capillary growth have been identified during development and under pathological circumstances in adults (wound healing, tumors), but there are no data to indicate whether these steps are similar when angiogenesis is induced in a fully differentiated microvascular bed in normal, uninjured adult skeletal muscle. In this study changes in capillary ultrastructure were correlated with capillary density and network morphology to elucidate the sequelae of angiogenesis in adult rat extensor digitorum longus (EDL) muscle whose activity was increased by stimulation at 10 Hz (8 h/day). This resulted in an increased capillary/fiber (C/F) ratio (based on staining for alkaline phosphatase) after 4 days; by 7 days C/F ratio was increased further, by approximately 50%. The ultrastructure of capillary endothelium in both the EDL and extensor hallucis proprius (EHP) was similar to control muscles after 2 days of stimulation, whereas endothelial cells in some capillaries in muscle stimulated for 4 days revealed signs of metabolic activation such as proliferation of organelles (Golgi apparatus, endoplasmic reticulum, ribosomes and mitochondria) and fewer pinocytic vesicles. Luminal surfaces were often irregular with numerous pseudopodial processes. Basement membranes were always present but amorphous regions were observed, particularly near pericyte processes. Unusually small capillary profiles, with either a slit-like lumen or with cisternae but no lumen, probably represented capillary sprouts. The interstitium contained increased collagenous and granular extracellular matrix surrounding capillaries, and numerous activated fibroblasts which were closely apposed to many capillaries. Capillary growth in EHP was also evaluated by confocal microscopy using whole mounts. The complex pattern of vessels underwent remodelling between 2 and 7 days of stimulation, resulting in more tortuous capillaries with numerous sprouts and loops. These combined observations suggest that angiogenesis may occur by a combination of sprouting, intussusceptive growth and elongation; also, that activation of endothelial cells occurs at the same time as disturbance of basement membranes during the earliest phase of growth and remodelling of the capillary bed. These changes are postulated to occur in connection with increased shear stress and/or capillary wall tension, which have been demonstrated previously.

Age Factors↗

PubMed1987

Opposite responses of rabbit and human globin mRNAs to translational inhibition by cap analogues.

The translational efficiency of an mRNA may be determined at the step of translational initiation by the efficiency of its interaction with the cap binding protein complex. To further investigate the role of these interactions in translational control, we compare in vitro the relative sensitivities of rabbit and human alpha- and beta-globin mRNAs to translational inhibition by cap analogues. We find that rabbit beta-globin mRNA is more resistant to translational inhibition by cap analogues than rabbit alpha-globin mRNA, while in contrast, human beta-globin mRNA is more sensitive to cap analogue inhibition than human alpha-globin mRNA. This opposite pattern of translational inhibition by cap analogues of the rabbit and human alpha- and beta-globin mRNAs is unexpected as direct in vivo and in vitro comparisons of polysome profiles reveal parallel translational handling of the alpha- and beta-globin mRNAs from these two species. This discordance between the relative translational sensitivities of these mRNAs to cap analogues and their relative ribosome loading activities suggests that cap-dependent events may not be rate limiting in steady-state globin translation.

Animals↗

PubMed1995

Phenotypic and molecular characteristics of Aeromonas salmonicida subsp. salmonicida isolated in southern and northern Finland.

Aeromonas salmonicida subsp. salmonicida causes outbreaks of furunculosis in salmonid fish. Furunculosis was first detected in Finland in 1986 on fish farms located on the Finnish coast of the Bothnian Bay. Molecular methods, SDS-PAGE, ribotyping, randomly amplified polymorphic DNA (RAPD) and plasmid profile analysis as well as phenotypic characteristics (biochemical characteristics, maximum growth temperature, pigment and elastase production) were used both for typing the strains and to study the possible routes of transmission of the organism to Finland and the spread of infection within Finland from 1986 to 1993. Ribopattern analysis of chromosomal DNA digested with SmaI, BglI, PstI and ClaI of 28 Finnish strains and eight foreign strains (Denmark, Sweden, Norway or Canada) showed that all Finnish strains and the Swedish strain originating from the Swedish coast of the Bothnian Bay had identical ribopatterns. All other foreign strains had distinct, unique ribotypes except for the second Swedish strain studied, the ribotype of which was identical with that of one Danish strain. RAPD typing, based on the results of two arbitrary primers, yielded 15 types for the Finnish strains. Except for both Danish strains, which had the RAPD type which was identical with that of one Finnish strain, the foreign strains had RAPD patterns differing from those of the Finnish strains. Plasmid profile typing and RAPD profile typing did not correlate. Ribotyping with four different enzymes proved to be the most sensitive method for studying genetically homogeneous Aer. salmonicida subsp. salmonicida. Ribopattern analysis showed that the infection which first started in 1984/1985 on the Swedish coast of the Bothnian Bay may have been transmitted to Finland where the first outbreaks occurred in 1986. The strains infecting Finnish fish farms were very homogeneous, with most differences seen, for example, in maximum growth temperature, plasmid profiles and the RAPD profiles of the strains.

Aeromonas↗

PubMed2004

Diversity and ecology of soil fungal communities: increased understanding through the application of molecular techniques.

Fungi fulfil a range of important ecological functions, yet current understanding of fungal biodiversity in soil is limited. Direct DNA extraction from soil, coupled with polymerase chain reaction amplification and community profiling techniques, has proved successful in investigations of bacterial ecology and shows great promise for elucidating the taxonomic and functional characteristics of soil fungal communities. These community profiling techniques include denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), single-strand conformation polymorphism (SSCP), terminal restriction fragment length polymorphism (T-RFLP), amplified rDNA restriction analysis (ARDRA), amplified ribosomal intergenic spacer analysis (ARISA) and cloning, and are generally coupled with DNA sequencing. The techniques and their potential limitations are discussed, along with recent advances that have been made possible through their application in soil fungal ecology. It is unlikely that a single approach will be universally applicable for assessing fungal diversity in all soils or circumstances. However, judicious selection of the methodology, keeping the experimental aims in mind, and the exploitation of emerging technologies will undoubtedly increase our understanding of soil fungal communities in the future.

Biodiversity↗

PubMed1997

Use of polymerase chain reaction-based single strand conformational polymorphism and denaturing gradient gel electrophoresis methods for detection of sequence variation of ribosomal DNA of Trypanosoma cruzi.

Polymerase chain reaction (PCR) was used to amplify the V1 region of the small sub-unit (18S) ribosomal DNA gene from representative strains of Trypanosoma cruzi. In order to screen for sequence variation, amplification products were subsequently analysed by single strand conformational polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) techniques. SSCP could not detect sequence variation within T. cruzi, although electrophoretic profiles were clearly distinct from both Leishmania donovani and Leishmania braziliensis. DGGE could differentiate strains of T. cruzi and it appears that there are at least 2 18S V1 sequences of this multi-gene family within each strain examined, contrasting with Leishmania spp. where only 1 was identified. This is the first application of PCR-linked SSCP and DGGE analysis for differentiating parasitic protozoa.

Animals↗

PubMed1995

PCR-ribotyping of type isolates of currently accepted Exophiala and Phaeococcomyces species.

Portion of the ribosomal repeat of the type strains of the genera Exophiala and Phaeococcomyces were subjected to RFLP analysis. The amplicon length of the small subunit rRNA, the fragment NS1-NS24, was found to vary between 1800 to 3200 nucleotides. In contrast, the length of the fragment ITS1-ITS4 comprising the internal transcribed spacers (ITS1 and ITS2) was found to be constant at 600 nucleotides. Analysis of restriction profiles confirmed the synonymy of Exophiala dermatitidis and Mycotorula schawaii. Torula bergeri and Sporotrichum gougerotii were found to be identical to Phaeoannellomyces elegans, but different from their alleged synonym E. castellanii. A phenogram is presented.

DNA, Ribosomal↗