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Results for “Ribosome Profiling”

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PubMed2004

Platelet transcriptome: the application of microarray analysis to platelets.

Human blood platelets are intimately involved in the regulation of thrombosis, inflammation, and wound repair. These cells retain megakaryocyte-derived cytoplasmic mRNA and functionally intact protein translational capabilities, although very little is known about normal or pathological mRNA profiles. Microarray analysis has demonstrated a clear and reproducible molecular signature unique to platelets. There is a relative paucity of expressed transcripts compared with those found in other eukaryotic cells, most likely related to mRNA decay in these anucleate cells. In contrast, a complementary methodology for transcript profiling (serial analysis of gene expression [SAGE]) demonstrates that 89% of tags represent mitochondrial (mt) transcripts (enriched in 16S and 12S ribosomal RNAs), presumably related to persistent mt-transcription in the absence of nuclear-derived transcripts. The abundance of nonmitochondrial SAGE tags parallels relative expression for the most abundant transcripts as determined by microarray analysis, establishing the concordance of both techniques for platelet profiling. These observations establish the validity of transcript analysis as a tool for identifying novel platelet genes that may regulate normal and pathologic platelet (and/or megakaryocyte) functions. The potential application of platelet-specific microarrays in scientific and clinical settings related to platelet production, cardiovascular, and cerebrovascular diseases is reviewed.

Animals↗

PubMed2006

Reduced gene expression of clustered ribosomal proteins in Diamond-Blackfan anemia patients without RPS19 gene mutations.

Diamond-Blackfan anemia (DBA) is a rare congenital pure red cell aplasia occasionally presenting physical anomalies. Ribosomal protein S19 gene (RPS19) is one of the causative genes for DBA; however, the pathologic mechanism of erythroblastopenia and abnormal morphology has not been clarified. To assess the pathophysiology of DBA, the gene expression profile of 2 representative patients carrying no RPS19 mutations was compared with that of aplastic anemia (AA) patients, assessed by the microarray analyses. The K-mean clustering analysis revealed the significant categorization of 28 ribosomal protein (RP) genes into a small set of group (994 genes) (P=2.39E-17), all of which were expressed at lower levels in DBA than in AA patients. RPS19 was categorized into the set of low expressing genes in DBA patients. No mutations were determined in the promoter and coding sequences of top 10 RP genes expressed at the levels over 1.2 of the AA/DBA ratio, in 3 DBA patients. These results indicated that the lower expression of RP gene group, even without the mutation, was a distinctive feature of DBA from AA, although the study number was small. The reduced RP gene expression, by itself, may suggest an underlying mechanism of the constitutional anemia.

Adult↗

PubMed1999

Methanotroph diversity in landfill soil: isolation of novel type I and type II methanotrophs whose presence was suggested by culture-independent 16S ribosomal DNA analysis.

The diversity of the methanotrophic community in mildly acidic landfill cover soil was assessed by three methods: two culture-independent molecular approaches and a traditional culture-based approach. For the first of the molecular studies, two primer pairs specific for the 16S rRNA gene of validly published type I (including the former type X) and type II methanotrophs were identified and tested. These primers were used to amplify directly extracted soil DNA, and the products were used to construct type I and type II clone libraries. The second molecular approach, based on denaturing gradient gel electrophoresis (DGGE), provided profiles of the methanotrophic community members as distinguished by sequence differences in variable region 3 of the 16S ribosomal DNA. For the culturing studies, an extinction-dilution technique was employed to isolate slow-growing but numerically dominant strains. The key variables of the series of enrichment conditions were initial pH (4. 8 versus 6.8), air/CH(4)/CO(2) headspace ratio (50:45:5 versus 90:9:1), and concentration of the medium (1x nitrate minimal salts [NMS] versus 0.2x NMS). Screening of the isolates showed that the nutrient-rich 1x NMS selected for type I methanotrophs, while the nutrient-poor 0.2x NMS tended to enrich for type II methanotrophs. Partial sequencing of the 16S rRNA gene from selected clones and isolates revealed some of the same novel sequence types. Phylogenetic analysis of the type I clone library suggested the presence of a new phylotype related to the Methylobacter-Methylomicrobium group, and this was confirmed by isolating two members of this cluster. The type II clone library also suggested the existence of a novel group of related species distinct from the validly published Methylosinus and Methylocystis genera, and two members of this cluster were also successfully cultured. Partial sequencing of the pmoA gene, which codes for the 27-kDa polypeptide of the particulate methane monooxygenase, reaffirmed the phylogenetic placement of the four isolates. Finally, not all of the bands separated by DGGE could be accounted for by the clones and isolates. This polyphasic assessment of community structure demonstrates that much diversity among the obligate methane oxidizers has yet to be formally described.

Base Sequence↗

PubMed2003

Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications.

The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed.

Agriculture↗

PubMed1982

The neuronal architecture of the anteroventral cochlear nucleus of the cat in the region of the cochlear nerve root: horseradish peroxidase labelling of identified cell types.

Golgi impregnations of the posterior part of the cat's anteroventral cochlear nucleus have revealed two types of neurons, bushy cells with short bush-like dendrites and stellate cells with long, tapered processes; Nissl stains have revealed globular and multipolar cell bodies with dispersed and clumped ribosomal patterns, respectively. In the present study, we injected horseradish peroxidase into the trapezoid body. Ipsilaterally, retrograde, diffuse labelling of neurons, presumably through damaged fibers, yielded Golgi-like profiles of numerous bushy cells with typical dendrites and with thick axons projecting toward the trapezoid body. Stellate cells were almost never labelled in this way. Anterograde diffuse labelling of thick axons demonstrated calyx endings in the contralateral medial nucleus of the trapezoid body. In the electron-microscope, the perikarya of diffusely-filled bushy neurons were found to have the dispersed ribosomal pattern and the kinds of synaptic endings typical of globular cells, including large profiles of end-bulbs from cochlear nerve axons. After injections restricted to the medial trapezoid nucleus, granularly-labelled cells in the cochlear nucleus were almost completely confined to the contralateral side; Nissl counterstaining showed them to be globular cells in the posterior part of the anteroventral cochlear nucleus. After larger injections, involving surrounding regions of the superior olivary complex, granular labelling occurred throughout the ventral cochlear nucleus on both sides. There is also evidence that stellate cells in Golgi impregnations correspond to multipolar cell bodies in Nissl stains. We conclude that bushy cells typically correspond to globular cells, which receive end-bulbs from the cochlea and send thick axons to the contralateral medial trapezoid nucleus, where they form calyces on principal cells. Principal cells, in turn, are known to project to the lateral superior olive and to one of the nuclei of origin of the crossed olivo-cochlear bundle, which feeds back to the cochlea. In this circuit, correlations between synaptic patterns and particular physiological signal transfer characteristics can be suggested. These could be related to binaural intensity interactions in the lateral superior olive and to a regulatory loop involving the olivo-cochlear bundles.

Animals↗

PubMed2000

Direct profiling of the yeast dynamics in wine fermentations.

We present a method to directly characterize the yeast diversity present in wine fermentations by employing denaturing gradient gel electrophoresis (DGGE) of polymerase chain reaction (PCR)-amplified 26S ribosomal RNA (rRNA) genes. PCR-DGGE of a portion of the 26S rRNA gene was shown to distinguish most yeast genera associated with the production of wine. With this method the microbial dynamics in several model wine fermentations were profiled. PCR-DGGE provided a qualitative assessment of the yeast diversity in these fermentations accurately identifying populations as low as 1000 cells ml(-1). PCR-DGGE represents an attractive alternative to traditional plating schemes for analysis of the microbial successions inherent in the fermentation of wine.

Ecosystem↗

PubMed1996

PCR-RFLP analysis of the large subunit (23S) ribosomal RNA genes of Campylobacter jejuni.

Forty-seven strains of Campylobacter jejuni were examined by PCR-RFLP analysis of 23S rRNA genes. Seven different molecular profiles were detected by a combination of HpaII AluI and DdeI digest analysis. Most (83%) strains, including those with different Penner serotypes and from different hosts, had the same molecular profiles. The high level of conservation apparent within the 23S rDNA sequences confirmed their value as targets in species-specific PCR identification assays but not for subtypic discrimination within Camp. jejuni.

Campylobacter jejuni↗

PubMed1998

Further observations on the gap-junction-rich cells in the deep muscular plexus of the rat small intestine.

Interstitial cells forming many large gap junctions in the region of the deep muscular plexus of the rat small intestine were studied by electron microscopy and by three-dimensional cell models reconstructed from serial ultrathin sections. Two different profiles of cells were observed. Cells of the first profile are characterized by an elongated cell shape and by less electron-dense cytoplasm, containing many mitochondria, well-developed Golgi apparatus and free ribosomes. They mainly connect with smooth muscle cells of the main circular layer. In a three-dimensional cell model, the total area of the gap junctions occupies 1.3% of the cell surface. Cells of the second profile are characterized by the frequent occurrence of slender cytoplasmic processes, higher electron-dense cytoplasm, containing mitochondria, Golgie apparatus and well-developed rough endoplasmic reticulum, and numerous caveolae on the cell membrane. In this cell model, gap junctions occupy 0.8% of the cell surface. The ratio of gap junctions with the same profile of cells to the total gap junction area is 37.7%, which is more than three times greater than the 9.9% in cells of the first profile. These cells were closely associated with nerve terminals. It is likely that these cells with different profiles constitute subtypes with each other and cooperate for regulation of intestinal motility via the transmission of nerve signals.

Animals↗

PubMed2006

Transcriptional regulators of ribosomal biogenesis are increased in the unloaded heart.

Mechanical unloading of the rat heart increases both protein synthesis and protein degradation. The transcriptional mechanism underlying increased protein synthesis during atrophic remodeling is not known. The aim of this study was to identify transcriptional regulators and the gene expression profile regulating protein synthesis in the unloaded rat heart and in the unloaded failing human heart. We measured DNA binding activity, transcript levels, and protein expression of transcriptional regulators of protein synthesis in a model of atrophic remodeling induced by heterotopic transplantation of the rat heart (duration 1 and 7 days). Using microarray analysis and quantitative RT-polymerase chain reaction, we found an increase in c-myc-regulated gene expression including an induction of ribosomal subunit messenger RNA's (RPS 10, RPL 21) and rRNA (18S). Consistent with the gene expression profile, DNA binding activity of c-myc and the nuclear protein concentration of its coactivator, upstream binding factor (UBF), increased in the atrophied heart whereas protein levels of the c-myc inhibitor MAD1 decreased. We found the same increase of ribosomal subunit messenger RNA and rRNA in 21 paired samples of failing human hearts obtained before and after left ventricular assist device treatment (mean duration: 157+/-31 days). In summary, mechanical unloading increases c-myc activity and c-myc-regulated gene expression in the rat heart. Changes in transcript levels of genes regulating ribosomal biogenesis in the unloaded rat heart resemble those found in the unloaded failing human heart. We concluded c-myc and c-myc-regulated gene expression are transcriptional regulators of protein synthesis during atrophic remodeling of the heart.

Animals↗

PubMed1990

A single base change at 726 in 16S rRNA radically alters the pattern of proteins synthesized in vivo.

A single base change in 16S rRNA (C-726 to G) was constructed by site-directed mutagenesis and cloned into the multicopy plasmid pKK3535 (generating pKK726G) which contains the complete rrnB operon from Escherichia coli. The mutant 16S rRNA was found predominantly in the 30S subunit fraction but was present in the 70S ribosomes. Protein analyses of the free 30S subunits revealed a decrease in the levels of ribosomal proteins S2 and S21 while the composition of the 70S ribosomes was as the wild-type. Transformants of pKK726G were temperature sensitive for growth, although the mutant ribosomes themselves were translationally active in vivo at 37 and 42 degrees C. Two-dimensional gel electrophoresis of the proteins translated in vivo revealed an altered protein profile which included novel proteins, changes in the levels of normal proteins, and the presence of heat shock proteins (HSPs) at 30 degrees C. Inactivation of the host encoded wild-type ribosomes coincided with a significant decrease in the synthesis of the HSPs. We therefore believe the induction of the HSPs to be a secondary response by the cells to the presence of the abnormal proteins.

Base Sequence↗

PubMed1987

Calcium-dependent regulation of protein synthesis at translational initiation in eukaryotic cells.

Evidence that Ca2+ may serve as a physiologic regulator of post-transcriptional protein synthesis was recently reported (Brostrom, C. O., Bocckino, S. B., Brostrom, M. A., and Galuska, E. M. (1986) Mol. Pharmacol. 29, 104-111). To evaluate further the role of Ca2+ in translation, the polysomal contents of Ca2+-depleted and -restored GH3 pituitary cells were compared. Ca2+ depletion of intact cells with 1 mM EGTA resulted in the disappearance of polysomes and an accumulation of 80 S monosomes and ribosomal subunits typical of slowed rates of initiation. Ca2+ repletion rapidly (minutes) restored cellular polysomal contents with an accompanying accumulation of 43 S preinitiation complex (40 S.eukaryotic initiation factor 2.Met-tRNAf.GTP). Comparable polysomal profiles were found for Ca2+-depleted and -restored cells exposed to cycloheximide which apparently slowed polypeptide chain elongation to rate-limiting values in the overall translation process. Ribosomal transit times for both Ca2+-depleted and -restored cells were identical, indicating that elongation is not directly affected by the cation. Transit times were extended in parallel as a function of increasing cycloheximide concentration. Lysates of GH3 cells exhibited incorporation that was proportional to the polysomal contents derived from the original intact cell preparations. Such lysates did not possess the ability to initiate new peptide synthesis and were not affected by Ca2+ or EGTA. Ca2+-depleted cells exposed to cycloheximide provided lysates with identical elongation activity to that of lysates prepared from either comparably treated or control Ca2+-restored cells. Ca2+ is proposed to regulate translation in intact cells through modulation of the rate of initiation rather than either polypeptide chain elongation or termination.

Animals↗

PubMed2006

Cumulative effects of short-term polymetal contamination on soil bacterial community structure.

In this study we evaluated the short-term effects of copper, cadmium, and mercury, added singly or in combination at different doses, on soil bacterial community structure using the bacterial automated ribosomal intergenic spacer analysis (B-ARISA) fingerprinting technique. Principal-component analysis of B-ARISA profiles allowed us to deduce the following order of impact: (Cu + Cd + Hg) >> Hg > or = Cd > Cu. These results demonstrated that there was a cumulative effect of metal toxicity. Furthermore, the trend of modifications was consistent with the "hump-backed" relationships between biological diversity and disturbance described by Giller et al. (K. E. Giller, E. Witler, and S. P. McGrath, Soil Biol. Biochem. 30:1389-1414, 1998).

Bacteria↗

PubMedDate not supplied

Enteral nutrition and microflora in pediatric Crohn's disease.

BACKGROUND: Exclusive enteral nutrition (EN) is an established primary therapy for pediatric Crohn's disease (CD). The mechanism of action of such treatment is still conjectural. The aim of the present study was to investigate if EN-induced remission is associated with modification of the fecal microflora in CD. METHODS: Stool samples were collected from 5 healthy children and adolescents over a period of 3 months, and from 9 children and adolescents with active CD. To induce disease remission, children with CD received a course of exclusive EN for 8 weeks with a polymeric formula (Modulen IBD, Nestlè). At the end of the course of exclusive EN, children returned to a free diet but continued to take 40% of the daily caloric intake as polymeric formula. Fecal microflora was analyzed by 16S ribosomal DNA polymerase chain reaction and temperature gradient gel electrophoresis (TGGE) with direct visual comparison of band profiles of PCR products. RESULTS: In 8 of 9 children, the exclusive EN alone induced disease remission. In 1 child, it was necessary to add steroids to the exclusive EN course to achieve remission. In all children with CD, analysis of gel band distribution revealed profound modification of the fecal microflora after exclusive EN. Variations of band distribution corresponding to different bacterial species were observed also in children on partial EN and required time to achieve stability of the band profile. In contrast, control healthy children showed a host-specific and stable TGGE profile over time. CONCLUSION: These data suggest that a possible mechanism of action of EN in inducing disease remission in CD is the capacity of modification of gut microflora. Possible explanations of such capacity are both low residue and prebiotic properties of the polymeric liquid formula.

Adolescent↗

PubMed1991

Double-labeling in situ hybridization analysis of mRNAs for carbonic anhydrase II and myelin basic protein: expression in developing cultured glial cells.

We applied in situ hybridization to analyze the location and the developmental changes in the distribution of the transcripts for carbonic anhydrase II (CAII) and myelin basic protein (MBP) in mouse primary cultured glial cells. Both mRNAs were localized to the oligodendrocyte using double-labeling in situ hybridization. No evidence for CAII transcripts in astrocytes was obtained, indicating that CAII is expressed only by oligodendrocytes in normal rodent glia. As early as 48 h after plating, CAII and MBP mRNAs are present in a few, small round cells. Message is present 2-4 days before levels of these proteins can be detected in similar primary glial cultures. The intensity of labeling for MBP and CAII mRNA positive cells increases significantly during the second week but then decreases after the end of the third week. Only the oligodendrocyte perikaryon and a few processes are positive during the first week. In contrast, at 14 days, a large number of cell processes in addition to the cell bodies are heavily stained for both mRNAs. Both mRNAs could be detected far away from the cell body, up to 250 microns in some cell processes. Some segments on a cell process accumulate higher levels of mRNA than other areas. These areas may correspond to the accumulation of free ribosomes and to starting points for the membrane sheets elaborated by cultured oligodendrocytes. The developmental profile for timing and distribution of these two messages mimics closely their in situ pattern.

Animals↗

PubMed2004

Gene expression in the cyanobacterium Anabaena sp. PCC7120 under desiccation.

The N2-fixing cyanobacterium Anabaena sp. PCC7120 showed an inherent capacity for desiccation tolerance. A DNA microarray covering almost the entire genome of Anabaena was used to determine the genome-wide gene expression under desiccation. RNA was extracted from cells at intervals starting from early to late desiccation. The pattern of gene expression in DNA fragments was categorized into seven types, which include four types of up-regulated and three types of down-regulated fragments. Validation of the data was carried out by RT-PCR on selected up-regulated DNA fragments and was consistent with the changes in mRNA levels. Our conclusions regarding desiccation tolerance for Anabaena sp. PCC7120 are as follows: (i) Genes for osmoprotectant metabolisms and the K+ transporting system are up-regulated from early to mid-desiccation; (ii) genes induced by osmotic, salt, and low-temperature stress are up-regulated under desiccation; (iii) genes for heat shock proteins are up-regulated after mid-desiccation; (iv) genes for photosynthesis and the nitrogen-transporting system are down-regulated during early desiccation; and (v) genes for RNA polymerase and ribosomal protein are down-regulated between the early and the middle phase of desiccation. Profiles of gene expression are discussed in relation to desiccation acclimation.

Anabaena↗

PubMed2004

Structural polarity and dynamics of male germline stem cells in the milkweed bug (Oncopeltus fasciatus).

The male germline stem cells (GSCs) of the milkweed bug present an extraordinary structural polarity that is, to our knowledge, unequalled by any other type of stem cells. They consist of a perikaryon and numerous projections arising from the cell pole directed toward the apical cells, the proposed niche of the GSCs. The projections can traverse a considerable distance until their terminals touch the apical cells. From hatching until death, the GSC projections undergo conspicuous changes, the sequence of which has been deduced from observations of all developmental stages. Projection formation starts from lobular cell protrusions showing trabecular ingrowths of the cell membrane. Finger-like projections result from a process of growth and "carving out". The newly formed projections contain mostly only free ribosomes other than a few mitochondria. A stereotyped degradation process commences in the projection terminals: profiles of circular, often concentric, cisternae of rough endoplasmic reticulum appear and turn into myelin bodies, whereas mitochondria become more numerous. The cytoplasm vesiculates, lysosomal bodies appear, and mitochondria become swollen. At the same time, the projection terminals are segregated by transverse ingrowths of the cell membrane. Finally, autophagic vacuoles and myelin bodies fill the segregated terminals, which then rupture. Simultaneously, new projections seem to sprout from the perikaryon of the GSCs. These dynamics, which are not synchronized among the GSCs, indicate that a novel type of signal exchange and transduction between the stem cells and their niche is involved in the regulation of asymmetric versus symmetric division of GSCs.

Animals↗

PubMed2003

Validation of reference genes for transcription profiling in the salmon louse, Lepeophtheirus salmonis, by quantitative real-time PCR.

The salmon louse Lepeophtheirus salmonis, a marine ectoparasitic copepod that feeds on salmonids, cause huge financial losses in the aquaculture industry through fish mortality, reduced growth and therapeutic costs. Detailed knowledge about the salmon louse life cycle, at the functional molecular level, is of fundamental importance to evaluate alternative therapeutic or prophylactic strategies. In quantitative real-time PCR, a powerful technique in biological studies of differentially expressed genes, the transcription level of a regulated gene can be measured relative to an unregulated reference "housekeeping" gene. In the present study we validate candidate reference genes for transcription profiling throughout the life cycle of the salmon louse. Our results show that the structural ribosomal protein S20 (RPS20) and the translation elongation factor 1alpha (eEF1alpha) are valid as reference genes showing less than two fold variation in transcript levels. The frequently used reference gene glyceraldehyde-3-phosphate dehydrogenase (GAPDH), however, is up to six fold regulated during the L. salmonis life cycle. Furthermore our results indicated that 18S RNA, although constitutively expressed, is not a convenient reference gene for relative quantification of most transcripts.

Animals↗

PubMed2000

Isolation and characterization of an avian isolate of Encephalitozoon hellem.

Members of the phylum Microspora are a group of unusual, obligate intracellular eukaryotic parasites that infect a wide range of hosts. However, there are a limited number of microsporidial infections reported in avian hosts, and no parasite species has been defined as an avian pathogen. A microsporidian organism was recovered from the droppings of a clinically normal peach-faced lovebird (Agapornis roseicollis) and established in in vitro culture. Intermittent parasite spore shedding was documented over a 2-month period using calcofluor M2R staining of cloacal swabs. The organism was identified as Encephalitozoon hellem based on protein and antigenic profiles and molecular sequencing of the small subunit and internal transcribed spacer regions of the ribosomal RNA gene.

Animals↗