PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Ribosome Profiling”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 577 records · Page 32Linked to original sources
PubMed2005

Expression profiling and validation of reference gene candidates in immune relevant tissues and cells from Atlantic salmon (Salmo salar L.).

The expression levels of three commonly used housekeeping genes, EF1-alpha, RPS20 and Beta-Actin, were examined in seven different tissues and leucocytes from non-stimulated Atlantic salmon (Salmo salar L.). The tissues analysed by quantitative real-time PCR were gill, liver, intestine, muscle, spleen, head kidney leucocytes (HKL) and peripheral blood leucocytes (PBL). The experiments were performed to investigate the transcriptional stability within and between tissues and leucocytes and between individuals. For all tissues and leucocytes, an appropriate reference gene was identified except for muscle tissue. HKL were used as a calibrator and the expression of EF1-alpha varied maximally 2.5-fold in five out of the six tissues and leucocytes investigated relative to the expression of 18S rRNA. The RPS20 gene was more intermediate and varied at least by a factor of two and maximally by a 20-fold factor. Beta-Actin was generally the most regulated gene showing high variations for gill (5.8x) and spleen tissue (10.3x) relative to the calibrator. A suitable reference gene for muscle tissue was not found since the expression varied between 8.3- and 25-fold for the three genes compared to the calibrator. By comparing the expression results of the non-stimulated tissues and leucocytes using the Normfinder programme, it was further shown that EF1-alpha was the most stably expressed gene both between individuals and the different tissues/leucocytes. Stimulation with lipopolysaccharide (LPS) of TO cells and HKL from Atlantic salmon was additionally performed to reveal whether an immune stimulating agent would change the expression level of EF1-alpha, RPS20 and Beta-Actin. LPS stimulation of cells revealed that RPS20 and EF1-alpha were least regulated by the LPS treatment in the TO cells relative to 18S rRNA, but in HKL, Beta-Actin was the most appropriate gene. However, the variations were overall maximally two-fold in LPS-stimulated TO cells and HKL, which make all three genes suitable as reference genes in this case. A further experiment showed that no RT- and/or PCR inhibitors were present in the non-stimulated tissues and cells, indicating true transcriptional differences.

Actins↗
PubMed1992

Post-hatching developmental changes in the ultrastructure of the duodenal absorptive epithelial cells in 1, 10 and 60-d-old chickens, with special reference to mitochondria.

1. Post-hatching developmental changes in the ultrastructure, cell area and histological RNA content of duodenal absorptive epithelial cells were observed in 1, 10 and 60-d-old White Leghorn (WL) and broiler (BR) chickens, with special reference to the mitochondria (Mt). 2. Epithelial cells in 1-d-old WL and BR had a well-developed Golgi area and a dense cluster of rod type Mt near the cell surface and at the infranuclear region. In BR, cells included well developed profiles of endoplasmic reticulum but fewer supranuclear vacuoles than those of WL, in which numerous free ribosomes were also found. Some Mt in BR showed a bud-like protrusion from the main body (tadpole type Mt). These suggest that the fine structural maturation of the epithelial cells in WL is involved in the process of cell maturation but epithelial cells of BR have almost matured at hatching. 3. In 10-d-old WL and BR, supranuclear vacuoles had disappeared and Mt increased in number. In WL, in addition to a decrease in free ribosomes, Mt developed to the tadpole type and further to dumbbell type ones. In BR, Mt also aggregated at the perinuclear region and some of them had developed from dumbbell shapes to a thick doughnut type. These findings indicate that epithelial cells in both breeds are more developed ultrastructurally than those in 1-d-old and that epithelial cells in BR are more activated for digestive and absorptive functions than those in WL. 4. In 60-d-old WL and BR, Mt showed various types with thinner matrices than 10-d-old, suggesting that the cell structure and function had reached a stable state. 5. BR revealed higher values for cell area and RNA content than WL at every age and RNA content of both breeds were maximal at 10 d, followed by 60 d. 6. Mt changed their shapes from rod type to tadpole type. The latter then developed to doughnut type via dumbbell type, related to an increase of epithelial cell functions. 7. Epithelial cells of BR are thus more highly activated than WL cells at each age and reach morphological and physiological maturation around 10 d.

Animals↗
PubMed2003

Metschnikowia santaceciliae, Candida hawaiiana, and Candida kipukae, three new yeast species associated with insects of tropical morning glory.

A new haplontic heterothallic species of Metschnikowia and two related asexual yeast species were discovered in morning glory flowers and associated insects. Metschnikowia santaceciliae came from Conotelus (Coleoptera: Nitidulidae) and other insect species associated with flowers of Ipomoea indica (purple morph) in Costa Rica. Candida hawaiiana and Candida kipukae were found in I. indica (syn. I. acuminata) and its insects in Hawai'i, and the former was also isolated in a specimen of Conotelus collected on Merremia tuberosa (Convolvulaceae) in Costa Rica. The three species have nearly identical physiological profiles, typical of the genus Metschnikowia. The sequences of the D1/D2 domains of their large subunit ribosomal DNA confirm that the species belong to the Metschnikowia clade, even though they share a very low degree of inter-relatedness. M. santaceciliae is a sister species to Metschnikowia continentalis. C. kipukae is a basal member of the large-spored Metschnikowia subclade, and C. hawaiiana has a weak affinity to Metschnikowia agaves. Two of the three species appear to be endemic. The type cultures are: Metschnikowia santaceciliae, strains UWO(PS)01-517a1=CBS 9148=NRRL Y-27475 (h(+, holotype) and UWO(PS)01-520a1=CBS 9149=NRRL Y-27476 (h-, isotype); Candida hawaiiana, strain UWO(PS)91-698.3=CBS 9146=NRRL Y-27473; Candida kipukae, strain UWO(PS)00-669.2=CBS 9147=NRRL Y-27474.

Animals↗
PubMed2001

Absence of Dbp2p alters both nonsense-mediated mRNA decay and rRNA processing.

Dbp2p, a member of the large family of DEAD-box proteins and a yeast homolog of human p68, was shown to interact with Upf1p, an essential component of the nonsense-mediated mRNA decay pathway. Dbp2p:Upf1p interaction occurs within a large conserved region in the middle of Upf1p that is largely distinct from its Nmd2p and Sup35/45p interaction domains. Deletion of DBP2, or point mutations within its highly conserved DEAD-box motifs, increased the abundance of nonsense-containing transcripts, leading us to conclude that Dbp2p also functions in the nonsense-mediated mRNA decay pathway. Dbp2p, like Upf1p, acts before or at decapping, is predominantly cytoplasmic, and associates with polyribosomes. Interestingly, Dbp2p also plays an important role in rRNA processing. In dbp2Delta cells, polyribosome profiles are deficient in free 60S subunits and the mature 25S rRNA is greatly reduced. The ribosome biogenesis phenotype, but not the mRNA decay function, of dbp2Delta cells can be complemented by the human p68 gene. We propose a unifying model in which Dbp2p affects both nonsense-mediated mRNA decay and rRNA processing by altering rRNA structure, allowing specific processing events in one instance and facilitating dissociation of the translation termination complex in the other.

Blotting, Northern↗
PubMed1993

Restriction fragment length polymorphisms of medicinal plants and crude drugs. II. Analysis of Glehnia littoralis of different geographical origin.

Total DNA was extracted from leaves of Glehnia littoralis belonging to various geographical strains with different furanocoumarin composition, and digested with restriction enzymes. Hybridization of digoxigenin-labeled probe containing rice ribosomal DNA to the digested DNA showed no difference in the restriction fragment length polymorphism (RFLP) profiles among the plants of different geographical origin. It is concluded that genetic diversity among the geographical strains of G. littoralis is so narrow as to be incapable of detecting RFLPs using rDNA as a probe.

DNA↗
PubMed1987

Effects of bilateral vagotomy on the ultrastructure of the cardiac ganglia in the monkey (Macaca fascicularis).

This study describes the effects of bilateral vagotomy on the ultrastructure of the cardiac ganglia of the monkey (Macaca fascicularis). One to three days after bilateral vagotomy there is widespread glycogen accumulation in the cytoplasm of the principal cardiac neurons. This is associated with distension of the granular endoplasmic reticulum and the loss of ribosomes from the cisternae. Between five and ten days after operation, about 10% of the neuronal profiles show an overall increase in electron density and intense darkening of the dendrites. From twenty one to twenty eight days postoperatively, the majority of the neuronal profiles have pale cytoplasm with reduction in granular endoplasmic reticulum and polyribosomes. The plasma membrane of the neuron is ruffled over the major portion of its surface. The satellite cells, which are reactive throughout the course of the experiments, exhibit a phagocytic capacity at this stage by removing portions of the neuronal cytoplasm. Vacuolation of the neuronal cytoplasm to a variable degree occurs in a small number of profiles between five to twenty eight days. The results suggest that bilateral vagotomy causes a widespread disturbance in the metabolic activity of the cardiac neurons. This is followed by transneuronal degenerative changes that are of a prolonged nature.

Animals↗
PubMed1994

Comparative study of 2',5'-oligoadenylate (2-5A) synthetase in control and Alzheimer's disease (AD) cells.

The properties of 2-5A synthetase, an interferon (IFN)-inducible enzyme that catalyzes the synthesis of a natural nucleic acid with 2',5'-phosphodiester linkage, were investigated using extracts prepared from fibroblasts derived from AD and age/sex-matched controls. Significant differences were found in kinetic parameters as well as activator requirements for the synthetase from the two sources. Fractionation of control and AD total lysates, the postribosomal supernatants, and the ribosomal salt washes, by gel filtration or by glycerol gradient centrifugation, also revealed a substantially different profile of elution of the enzyme. These results further support an altered 2-5A synthetase gene expression in AD cells.

2',5'-Oligoadenylate Synthetase↗
PubMed2006

DNA probes for the rapid identification of medically important Candida species using a multianalyte profiling system.

Recently, a new flow cytometric technology to detect multiple DNA target sequences in a single microtiter well plate was developed [multianalyte profiling (MAP) System, Luminex Corp., Austin, TX]. DNA probes, directed to the internal transcribed spacer 2 region of ribosomal DNA, were therefore designed to detect and differentiate PCR amplicons from six medically important Candida species using this system. Each probe was covalently linked to one of 100 available microsphere (bead) sets. Biotinylated PCR amplicons were then hybridized to the complementary probe on each bead set. Bound amplicons were detected fluorometrically using a streptavidin-linked reporter dye, R-phycoerythrin. Specific hybridization was noted for all six Candida species probes (mean sample-to-background ratio+/-standard error: Candida albicans, 58.7+/-1.2; Candida tropicalis, 53.2+/-3.8; Candida glabrata, 46.9+/-2.1; Candida parapsilosis, 59.9+/-1.6; Candida krusei, 54.7+/-3.7 vs. 0.9+/-0.03 for all heterologous Candida species DNA targets and vs. 1.0+/-0.1 for samples containing water instead of DNA; P < 0.001). The limit of test sensitivity was 0.5 pg of DNA. A sample could be processed and analyzed within 1 h post-PCR amplification. Therefore, the multianalyte profiling system was rapid, sensitive and specific for the detection and differentiation of the most medically important species of Candida.

Candida↗
PubMed1998

Identification of bacterial isolates obtained from intestinal contents associated with 12,000-year-old mastodon remains.

Mastodon (Mammut americanum) remains unearthed during excavation of ancient sediments usually consist only of skeletal material, due to postmortem decomposition of soft tissues by microorganisms. Two recent excavations of skeletal remains in anoxic sediments in Ohio and Michigan, however, have uncovered organic masses which appear to be remnants of the small and large intestines, respectively. Macrobotanical examinations of the composition of these masses revealed assemblages of plant material radiocarbon dated to approximately 11,500 years before the present and thought to be incompletely digested food remains from this extinct mammal. We attempted to cultivate and identify bacteria from the intestinal contents, bone-associated sediments, and sediments not in proximity to the remains using a variety of general and selective media. In all, 295 isolates were cultivated, and 38 individual taxa were identified by fatty acid-methyl ester (FAME) profiles and biochemical characteristics (API-20E). The taxonomic positions of selected enteric and obligately anaerobic bacteria were confirmed by 16S ribosomal DNA (rDNA) sequencing. Results indicate that the intestinal and bone-associated samples contained the greatest diversity of bacterial taxa and that members of the family Enterobacteriaceae represented 41% of all isolates and were predominant in the intestinal masses and sediments in proximity to the skeleton but were uncommon in the background sediments. Enterobacter cloacae was the most commonly identified isolate, and partial rDNA sequencing revealed that Rahnella aquatilis was the correct identity of strains suggested by FAME profiles to be Yersinia enterocolitica. No Bacteroides spp. or expected intestinal anaerobes were recovered. The only obligate anaerobes recovered were clostridia, and these were not recovered from the small intestinal masses. Microbiological evidence from this study supports other, macrobotanical data indicating the intestinal origin of these masses. Whether these organisms are direct descendants of the original intestinal microbiota, however, cannot be established.

Animals↗
PubMed2002

Selective growth of mucolytic bacteria including Clostridium perfringens in a neonatal piglet model of total parenteral nutrition.

BACKGROUND: Compromised barrier function and intestinal inflammation are common complications of total parenteral nutrition (TPN). OBJECTIVE: We tested the hypothesis that the lack of enteral nutrients in TPN might select commensal or pathogenic bacteria that use mucus as a substrate, thereby weakening the protection provided by the intestinal mucus layer. DESIGN: Ileal microbiota profiles of piglets fed by total enteral nutrition (TEN; n = 6) or TPN (n = 5) were compared with the use of 16S ribosomal DNA polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis and with a PCR-based method developed to specifically measure Clostridium perfringens concentrations. Ileal bacteria from TEN and TPN piglets were also examined for their ability to grow on mucin or sulfated monosaccharides. RESULTS: Bacterial community structure was equally complex in the ileum of TEN and TPN piglets, but profiles clustered according to mode of nutrition. Sixty-two percent of total mucus-associated bacteria (100 colonies tested) in TPN compared with 33% of mucus-associated bacteria (100 colonies tested) in TEN ileal samples grew on mucin. Bacteria capable of using sulfated monosaccharides were also enriched in TPN samples. C. perfringens, an opportunistic pathogen, was specifically enriched in the TPN ileum (P < 0.05). These results were corroborated by cultivation-based studies that showed rapid growth of C. perfringens on mucin-based substrates. CONCLUSIONS: Mucolytic potential is widespread among intestinal bacteria. Mucolytic bacteria in general and C. perfringens in particular were selected when enteral nutrients were withheld in this TPN piglet model. Similar enrichment processes may occur in humans nourished by TPN and may thereby contribute to intestinal dysfunction.

Animals↗
PubMed1977

Analysis of rabbit brain polysomal poly (A+) mRNA by DNA excess hybridization.

DNA sequence representation in rabbit brain mRNA was examined by DNA excess hybridization. purified polysomal poly (A+) mRNA was labeled in vitro with [3H] dimethyl sulfate and reacted at DNA: RNA ratios of 5000 : 1 and 30 000 : 1. Poly(A+) mRNA hybridizied mainly to nonrepeated DNA with a smaller kinetic component which was complementary to repeated DNA sequences. The latter component was not due to nuclear or ribosomal RNA contamination. Poly(A-) RNA purified from brain polysomes hybridized to excess DNA as a single repeated component. Thermal denaturation profiles of the RNA - DNA hybrids indicated a high degree of fidelity in base pairing.

Animals↗
PubMed1996

PairWise and SearchWise: finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames.

DNA translation frames can be disrupted for several reasons, including: (i) errors in sequence determination; (ii) RNA processing, such as intron removal and guide RNA editing; (iii) less commonly, polymerase frameshifting during transcription or ribosomal frameshifting during translation. Frameshifts frequently confound computational activities involving homologous sequences, such as database searches and inferences on structure, function or phylogeny made from multiple alignments. A dynamic alignment algorithm is reported here which compares a protein profile (a residue scoring matrix for one or more aligned sequences) against the three translation frames of a DNA strand, allowing frameshifting. The algorithm has been incorporated into a new package, WiseTools, for comparison of biological sequences. A protein profile can be compared against either a DNA sequence or a protein sequence. The program PairWise may be used interactively for alignment of any two sequence inputs. SearchWise can perform combinations of searches through DNA or protein databases by a protein profile or DNA sequence. Routine application of the programs has revealed a set of database entries with frameshifts caused by errors in sequence determination.

Algorithms↗
PubMed2002

A novel strategy by the action of ricin that connects phenotype and genotype without loss of the diversity of libraries.

We present a novel strategy for connection of phenotype and genotype in vitro that can be used for the selection of functional proteins even at room temperature. The strategy involves generation of a stable complex between a ribosome, an mRNA, and its translated protein, without removal of the termination codon, as a result of the action of the ricin A chain during translation. We demonstrate the potential selection capacity of this novel strategy by isolating such complexes that contain newly synthesized streptavidin and glutathione-S-transferase (GST) using appropriate ligands. The technique requires no transfection, no chemical synthesis, no ligation, and no removal of the termination codon. Thus our novel "Ribosome-Inactivation Display System (RIDS)" should provide, without loss of the pool population, a reliable, simple, and robust selection system for in vitro evolution of the properties of proteins in a predictable direction by a combination of randomization and appropriate selection strategies.

Gene Expression Profiling↗
PubMed2002

Global gene expression profiles of the cyanobacterium Synechocystis sp. strain PCC 6803 in response to irradiation with UV-B and white light.

We developed a transcript profiling methodology to elucidate expression patterns of the cyanobacterium Synechocystis sp. strain PCC 6803 and used the technology to investigate changes in gene expression caused by irradiation with either intermediate-wavelength UV light (UV-B) or high-intensity white light. Several families of transcripts were altered by UV-B treatment, including mRNAs specifying proteins involved in light harvesting, photosynthesis, photoprotection, and the heat shock response. In addition, UV-B light induced the stringent response in Synechocystis, as indicated by the repression of ribosomal protein transcripts and other mRNAs involved in translation. High-intensity white light- and UV-B-mediated expression profiles overlapped in the down-regulation of photosynthesis genes and induction of heat shock response but differed in several other transcriptional processes including those specifying carbon dioxide uptake and fixation, the stringent response, and the induction profile of the high-light-inducible proteins. These two profile comparisons not only corroborated known physiological changes but also suggested coordinated regulation of many pathways, including synchronized induction of D1 protein recycling and a coupling between decreased phycobilisome biosynthesis and increased phycobilisome degradation. Overall, the gene expression profile analysis generated new insights into the integrated network of genes that adapts rapidly to different wavelengths and intensities of light.

Adenosine Triphosphate↗
PubMed1974

Analytical study of microsomes and isolated subcellular membranes from rat liver. IV. Biochemical, physical, and morphological modifications of microsomal components induced by digitonin, EDTA, and pyrophosphate.

Isopycnic equilibration and sedimentation rate studies of rat liver microsomes led previously to the assignment of microsomal constituents into group a1 (monoamine oxidase), group a2 (5'-nucleotidase, alkaline phosphodiesterase I, alkaline phosphatase and cholesterol), group a3 (galactosyltransferase), group b (NADH cytochrome c reductase, NADPH cytochrome c reductase, aminopyrine demethylase, cytochrome b(5) and P 450), and group c (glucose 6-phosphatase, esterase, nucleoside diphosphatase, beta-glucuronidase and glucuronyltransferase). Confirmation and extension of the assignment into groups has been obtained by studying the differential effect of the reagents digitonin, EDTA, and PPi. Digitonin specifically affected the equilibrium density only of the group a2 and (to a lesser extent) group a3, and not of groups b and c under conditions which preserved the structure-linked latency of nucleoside diphosphatase and galactosyltransferase. Within experimental error the rate of sedimentation of all microsomal constituents was unaffected. The morphological appearance under the electron microscope was indistinguishable from that of nondigitonin-treated microsomes, except that a few smooth membranes (< 10%) exhibited broken-looking profiles. Treatment of microsomes with EDTA or PPi detached a substantial part of RNA and released protein in excess over the amount accountable for by detachment of ribosome constituents. This detachment was confirmed by electron microscopy. EDTA and PPi decreased markedly the equilibrium density and the density dispersion of groups b and c, due mainly to the uncoating of rough elements. EDTA and PPi shifted slightly the distribution profiles of groups a towards lower densities, possibly as a result of the release of adsorbed proteins. The combination of EDTA and digitonin, used subsequently, rendered the average equilibrium density of group a2 higher than that of groups b and c. Dense subfractions were thus enriched in constituents of group a2 and showed mainly broken-looking vesicles under the electron microscope. The import of our results on the biochemical and enzymic properties of the subcellular components of the microsome fractions is discussed.

Animals↗
PubMed1985

Polyamine depletion results in impairment of polyribosome formation and protein synthesis before onset of DNA synthesis in mitogen-activated human lymphocytes.

Lymphocytes, exposed to mitogens in culture, show enhanced protein and RNA synthesis before the onset of DNA synthesis. Inhibition by DL-alpha-difluoromethylornithine of polyamine synthesis in phytohaemagglutinin-activated human lymphocytes resulted in a suppression of protein synthesis, which was evident before the initiation of DNA synthesis. The mitogen-induced increase in the incorporation of [3H]thymidine into DNA was subsequently inhibited in parallel with the activity of thymidine kinase in the polyamine-depleted cells. Ultraviolet absorbance measurement of the ribosomes after sucrose gradient centrifugation revealed a suppression of polyribosome formation that coincided with the decrease in the rate of protein synthesis. The disturbance in the polysomal profiles did not appear to be due to a shortage of mRNA, since the synthesis of poly(A)-rich mRNA was reduced less than that of rRNA after inhibiting polyamine synthesis. Entry of both the pre-existing and newly synthesized ribosomal subunits into polysomal structures was found to be impaired. These results thus suggest an important role for polyamines in the initiation step of protein synthesis.

DNA↗
PubMed2006

Cochlear damage induces GAP-43 expression in cholinergic synapses of the cochlear nucleus in the adult rat: a light and electron microscopic study.

Recent studies suggest a potential for activity-dependent reconstruction in the adult mammalian brainstem that exceeds previous expectations. We found that a unilateral cochlear lesion led within 1 week to a rise of choline acetyltransferase (ChAT) immunoreactivity in the ventral cochlear nucleus of the affected side, matching the lesion-induced expression of growth-associated protein 43 (GAP-43) previously described. The rise of both ChAT and GAP-43 immunoreactivity was reflected in the average density of the staining. Moreover, the number of light-microscopically identifiable boutons increased in both stains. GAP-43-positive boutons could, by distinct ultrastructural features, regularly be identified as presynaptic endings. However, GAP-43 immunoreactivity was not only found in presynaptic endings with a classical morphology, but also in profiles that suggest morphological dynamic structures by showing filopodia, assemblages of pleomorphic vesicles, large vesicles (diameter up to 200 nm) fusing with the presynaptic plasma membrane close to synaptic contacts, small dense-core vesicles (diameter about 80 nm) and presynaptic ribosomes. Moreover, we observed perforated synapses as well as GAP-43 immunoreactivity condensed in rafts, both indicative of growing or changing neuronal connections. Classical and untypical ultrastructural profiles that contained GAP-43 also contained ChAT. We conclude that there is extensive deafness-induced GAP-43-mediated synaptic plasticity in the cochlear nucleus, and that this plasticity is predominantly, if not exclusively, based on cholinergic afferents.

Acetylcholine↗