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Results for “Ribosome Profiling”

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PubMed2003

Zoonotic genotypes of Blastocystis hominis detected in cattle and pigs by PCR with diagnostic primers and restriction fragment length polymorphism analysis of the small subunit ribosomal RNA gene.

Twenty two Blastocystis isolates from cattle and pigs were genotyped by PCR using diagnostic primers, and the homology among isolates was then confirmed by restriction fragment length polymorphism (RFLP) analysis of the small subunit ribosomal RNA gene. Two distinct genotypes, subtypes 1 and 3, were detected in one and two of the ten isolates from cattle, and three and one of the 12 isolates from pigs, respectively. The RFLP profiles of all isolates designated as subtype 1 and subtype 3 were identical to those of known ribodemes 1 and 2, respectively. We found that 31.8% (7/22) of isolates examined were zoonotic genotypes of Bastocystis hominis. However, 68.2% (15/22) of isolates were not amplified with any of the diagnostic primers, and the profiles of these isolates were different from any ribodemes of B. hominis reported previously. This study shows that Blastocystis organisms in cattle and pigs are a potential source of human infection.

Animals↗

PubMed1999

Ribosomal RNA expression in the developing rat olfactory bulb.

The rat olfactory bulb undergoes rapid postnatal growth, thus requiring the continuous production of new proteins. The present study examined the development of ribosomes, a key component in protein synthesis, in the bulb using an antibody specific to ribosomal RNA (Y10b). Furthermore, the potential role of afferent activity on patterns of Y10b immunoreactivity, as well as total RNA production (using incorporation of 3H-uridine) was examined by blocking an external naris on postnatal day 1 (P1). In control pups, Y10b was restricted to mitral cells at P2, with labeling expanding to include all layers by P10. Considerable increases in staining density were observed by P30. Although no differences in Y10b immunoreactive patterns were seen in naris-occluded animals 12-48 h after occlusion, or on P10 or P20, by P30, an apparent decrease in numbers of labeled profiles (presumably tufted cells) in the external plexiform layer was found. Furthermore, no changes were seen in levels of 3H-uridine incorporation. Despite the apparent insensitivity to naris closure, the results indicate that ribosome expression, as measured by Y10b immunoreactivity, undergoes rapid postnatal changes that parallel general patterns of growth in the rat olfactory bulb.

Animals↗

PubMed2002

Expression of ribosomal and translation-associated genes is correlated with a favorable clinical course in chronic lymphocytic leukemia.

B-cell chronic lymphocytic leukemia (B-CLL) is a heterogeneous disease with a highly variable clinical course. Recent studies have shown that CD38 surface expression on the malignant cell clone may serve as a prognostic marker in that CD38(+) patients with B-CLL are characterized by advanced disease stage, lesser responsiveness to chemotherapy, and shorter survival than CD38(-) patients. To further investigate the molecular phenotype of these 2 clinical subgroups, we compared the gene expression profiles of CD38(+) (n = 25) with CD38(-) (n = 45) B-CLL patients using oligonucleotide-based DNA chip microarrays representative of approximately 5600 genes. The results showed that B-CLLs display a common gene expression profile that is largely independent of CD38 expression. Nonetheless, the expression of 14 genes differed significantly between the 2 groups, including genes that are involved in the regulation of cell survival. Furthermore, unsupervised hierarchical cluster analysis of 76 B-CLL samples led to the separation of 2 major subgroups, comprising 20 and 56 patients. Clustering to the smaller group was due in part to the coordinate high expression of a large number of ribosomal and other translation-associated genes, including elongation factors. Importantly, we found that patients with high expression of translation factors were characterized by a more favorable clinical course with significantly longer progression-free survival and reduced chemotherapy requirements than the remaining patients (P <.05). Our data show that gene expression profiling can help identify B-CLL subtypes with different clinical characteristics. Furthermore, our results suggest a role of translation-associated genes in the pathogenesis of B-CLL.

ADP-ribosyl Cyclase↗

PubMed2004

Spatial distribution of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems.

Distribution profiles of marine crenarchaeota group I in the vicinity of deep-sea hydrothermal systems were mapped with culture-independent molecular techniques. Planktonic samples were obtained from the waters surrounding two geographically and geologically distinct hydrothermal systems, and the abundance of marine crenarchaeota group I was examined by 16S ribosomal DNA clone analysis, quantitative PCR, and whole-cell fluorescence in situ hybridization. A much higher proportion of marine crenarchaeota group I within the microbial community was detected in deep-sea hydrothermal environments than in normal deep and surface seawaters. The highest proportion was always obtained from the ambient seawater adjacent to hydrothermal emissions and chimneys but not from the hydrothermal plumes. These profiles were markedly different from the profiles of epsilon-Proteobacteria, which are abundant in the low temperatures of deep-sea hydrothermal environments.

Base Sequence↗

PubMed2003

Identification and characterization of mouse GTPBP3 gene encoding a mitochondrial GTP-binding protein involved in tRNA modification.

We report here the identification and characterization of mouse GTPBP3 encoding a mitochondrial GTPase. A full-length GTPBP3 cDNA has been isolated and the genomic organization of GTPBP3 has been elucidated. The mouse GTPBP3 gene containing 9 exons encodes a 486 residue protein with a strong homology to the GTPBP3-like proteins of bacteria, yeast, and other homologs, related to tRNA modification. The mouse GTPBP3 is ubiquitously expressed in various tissues, but abundantly in tissues with high metabolic rates including heart, liver, and brain. Surprisingly, this gene, unlike its human homolog, exhibited a low expression in skeletal muscle. Furthermore, immunofluorescence analysis of NIH3T3 cells expressing GTPBP3-GFP fusion protein demonstrated that the mouse Gtpbp3 localizes in mitochondrion. These observations suggest that the mouse Gtpbp3 is an evolutionarily conserved mitochondrial GTP-binding protein involved in the tRNA modification. Thus, it may modulate the translational efficiency and accuracy of codon-anticodon base pairings on the decoding region of mitochondrial ribosomes.

Amino Acid Sequence↗

PubMed2001

Detection of Plasmodium yoelii stage mRNA in BALB/c mice.

Relatively little information is available concerning the expression of parasite genes during the liver stage of Plasmodium infection, mostly because of low-level infection of host hepatocytes and the lack of purification techniques for the liver stage parasites. We have determined the optimal dosage of Plasmodium yoelii sporozoite inoculum and routes of inoculation, which are intravenous tail vein and the intrahepatic portal circulation. To determine which route was optimal, BALB/c mice were inoculated via 1 of these routes, and parasitemia was detected by reverse transcription polymerase chain reaction (RT-PCR) detecting both murine beta-actin and P. yoelii-specific 28S ribosomal RNA in the liver samples. Murine beta-actin was detected after 15 cycles of PCR, and its expression levels did not differ between treatment groups. However, P. yoelii-specific 28S ribosomal RNA gene product was detected after 15 cycles of PCR in animals inoculated via the tail vein but was not detected until 25 cycles in animals inoculated via the intrahepatic portal circulation. Experiments were then performed to identify the smallest inoculum required to initiate a liver stage infection that would yield sufficient parasite RNA for analysis. Inoculation with different doses of sporozoite inocula was followed by RT-PCR on the livers of the inoculated animals. The P. yoelii-specific 28S ribosomal RNA gene product was first detected in both treatment groups after 15 cycles, suggesting that both doses of sporozoite inocula provided relatively the same level of liver infection rate. We also have analyzed infected mouse liver for parasite-specific mRNA, which was detectable as early as 24 hr postinfection.

Animals↗

PubMed1978

Changes in the conformation and stability of 5 S RNA upon the binding of ribosomal proteins.

The binding of ribosomal proteins L25, L18, and L5 to 5 S RNA results in a conformational change and a destabilization of the 5 S RNA molecule. The changes observed in the near ultraviolet circular dichroism (CD) spectra and in the melting profiles indicate an increase in base stacking uith an accompanying increase in asymmetry of the bases and a decrease in the conformational stability of the 5 S RNA. These results are consistent with the interpretation that the binding of these proteins increases the stacking of specific single-stranded bases in 5 S RNA and aligns them in helical arrays, resulting in a conformation which facilitates base-pairing with nucleotide segment(s) of the ribosomal 23 S RNA or the transfer RNA (or both). The simple and precise difference CD method described here is potentially useful for studying subtle conformational changes of other nucleic acid-protein interactions.

Bacterial Proteins↗

PubMed2005

Microarray and real-time PCR analyses of gene expression in the honeybee brain following caffeine treatment.

To test the idea that caffeine might induce changes in gene expression in the honeybee brain, we contrasted the transcriptional profiles of control and caffeine-treated brains using high-throughput cDNA microarrays. Additional quantitative real-time PCR was performed on a subset of eight transcripts to visualize the temporal changes induced by caffeine. Genes that were significantly upregulated in caffeine-treated brains included those involved in synaptic signaling (GABA:Na symporter, dopamine D2R-like receptor, and synapsin), cytoskeletal modifications (kinesin and microtubule motors), protein translation (ribosomal protein RpL4, elongation factors), and calcium-dependent processes (calcium transporter, calmodulin- dependent cyclic nucleotide phosphodiesterase). In addition, our study uncovered a number of novel, caffeine-inducible genes that appear to be unique to the honeybee. Time-dependent profiling of caffeine-sensitive gene expression shows significant upregulation 1 h after treatment followed by moderate downregulation after 4 h with no additional changes occuring after 24 h. Our results provide initial evidence that the dopaminergic system and calcium exchange are the main targets of caffeine in the honeybee brain and suggest that molecular responses to caffeine in an invertebrate brain are similar to those in vertebrate organisms.

Animals↗

PubMed2006

Gene expression in head hair follicles plucked from men and women.

Characterizing gene expression in hair follicles can help to elucidate the hair growth cycle by delineating the genes and pathways involved in follicular growth and degeneration. The objectives of this study were to determine whether intact RNA could be extracted from a small number of plucked, unstaged hair follicles in sufficient quantity to conduct gene expression profiling, and to conduct global gene expression profiling. To this end, RNA was extracted from 1 to 3 unstaged follicles plucked from the scalp of 36 volunteers. The average quantifiable yield of RNA/follicle was 112.5 ng. Ribosomal ratios were lower than normally expected, but investigation indicated the RNA was intact. Ten of the samples were amplified and hybridized to Affymetrix genechips. On average, 2,567 of the total probe sets (8,500) were expressed in each sample; 1,422 were expressed in all 10 samples; 97 were significantly changed in one gender compared to the other, and 41 had high levels of interindividual variability. This study demonstrates that RNA of sufficient quantity and quality to use in microarray hybridizations can be obtained from as little as a single plucked human hair follicle. Genes expressed in all individuals are probably related to follicular growth and could form a starting set for developing signatures of toxicant exposure. The differentially expressed genes could be involved in producing gender and interindividual differences in hair growth.

Adult↗

PubMed1996

Variation within the internal transcribed spacer (ITS) of ribosomal DNA genes of intermediate snail hosts within the genus Bulinus (Gastropoda: Planorbidae).

Species within the genus Bulinus are responsible for transmission of schistosomes within the Schistosoma haematobium group. In order to provide a molecular insight into the species relationships within the genus, genetic variation between species representing the four species groups was assayed by Polymerase Chain Reaction (PCR) amplification of the ribosomal Internal Transcribed Spacer (ITS) region followed by Restriction Fragment Length Polymorphism (RFLP) analysis of this product with six restriction enzymes. This PCR-RFLP methodology detected considerable variation within the ITS region indicating that restriction profiles will be useful as genetic markers for identification purposes. The complete ITS1 spacer was sequenced for B. globosus, B. cernicus and B. truncatus. There were numerous nucleotide differences between taxa mainly insertions and deletions. Nucleotide divergence was calculated between species from the restriction profiles: the B. truncatus/tropicus complex and B. reticulatus group were most similar which were in turn more closely related to the B. africanus group than to the B. forskalii group. The nucleotide divergence between the species groups is substantial and questions the placement of these groups within the same genus.

Animals↗

PubMed1984

Quantitative analysis of rough endoplasmic reticulum approaches to the cell membrane in the secretory ameloblast of the rat incisor.

The distribution of approaches of rough endoplasmic reticulum to the cell membrane within the supranuclear region of the secretory ameloblast of the rat incisor was quantitated using a Zeiss MOP-3. In ameloblasts cut in cross section, most of these approaches appear as circular profiles representing cross sections of elongated cisternae, which are aligned parallel to the long axis of the cell. Because of their position, orientation, and distribution of ribosomes, these approaches were consistent with the appearance of subsurface cisternae. Using cross-sectioned ameloblasts, the lengths of apposed plasma membranes either between or within rows of cells were measured from electron micrographs. Along these lengths, matched approaches of rough endoplasmic reticulum from opposite sides of the apposed plasma membranes were counted. Approaches from either side that were unmatched were also counted. Thirteen percent of the approaches were matched between rows of ameloblasts, and 13.5% of the approaches were matched within rows, demonstrating no significant difference between the two sites. Furthermore, mathematical analysis showed that the theoretical probability of two approaches coinciding is 17%. The experimental values are not statistically different from the theoretical probability, and it is concluded that the matching of rough endoplasmic reticulum approaches to the plasma membrane, or subsurface cisternae, occurs at random.

Ameloblasts↗

PubMed1987

Ultrastructure of degenerative changes following ricin application to feline dental pulps.

The ultrastructure of degenerative changes within the ipsilateral trigeminal ganglion, and partes caudalis and interpolaris of the spinal trigeminal nucleus in the cat is described following the application of the potent toxin ricin to the tooth pulps of unilateral maxillary and mandibular posterior teeth, including the cuspids. Survival times ranged from 6 to 10 days. Typical changes identified within the ipsilateral trigeminal ganglion included myelin fragmentation and 'compartmentalization' of the axoplasm of medium-sized myelinated axons, while small myelinated and unmyelinated axons underwent a more variable response ranging from electron-lucent to electron-dense changes. The affected cell body was characterized by the presence of swollen, electron-lucent mitochondria, a reduction of cytoplasmic ribosomes and a filamentous hyperplasia. Other changes often included an eccentric nucleus and satellite cell proliferation. Degenerative changes often occurred in isolated elements surrounded by normal profiles, suggesting specificity of ricin within the trigeminal ganglion. Changes within brainstem axons showed both an electron-dense and a lucent, fragmenting type of axonal alteration. Terminal changes ranged from electron-dense to lucent and also included filamentous hyperplasia and 'hyperglycogenesis'. The altered axonal knobs contained round synaptic vesicles that were presynaptic to dendritic profiles and postsynaptic to terminals containing flattened synaptic vesicles. The above brainstem alterations were identified specifically in the following areas: ventrolateral, medial and dorsomedial pars interpolaris; the ventrolateral and mid-dorsal to dorsomedial areas of the marginalis and outer substantia gelatinosa layers of pars caudalis; and in ventral pockets corresponding to lamina V of the medullary dorsal horn. Dense alterations within terminals containing flattened synaptic vesicles that are typically presynaptic to primary afferents in these areas were rare findings, but along with vacuolization of dendritic profiles suggest a trans-synaptic effect possibly due to the exocytosis of ricin. The results are discussed in relation to different reports of dental projections and with regards to patterns of transganglionic degeneration.

Animals↗

PubMed2004

Identification of a novel cytokine-like transcript differentially expressed in avian gammadelta T cells.

Chicken represents a species with a high frequency of gammadelta T cells in peripheral blood, suggesting an important function. To elucidate the genes specific for the avian gammadelta T cells, the suppression subtractive hybridization (SSH) between gammadelta and alphabeta T cells was used. The SSH library, which was successfully enriched for the TCR gamma and delta (both V and C region) sequences, provided gammadelta T-cell-specific genes, including, for example, the ribosomal proteins, signaling and structural molecules, and molecules related to transcription and translation. Among these genes, a clone named KK34 was shown to match the PFAM profile for IL-5 and to have 19.5% amino acid identity to the human interleukin 5 protein. Clone KK34 had lower sequence homology, from 5.4% to 15.6%, to other short-chain four-helix bundle superfamily members IL-3, IL-4, IL-13 and GM-CSF. The hydrophobic signal peptide sequence and the presence of cysteines needed for the interchain disulfide bonds were found to be conserved between clone KK34 and mammalian IL-5 proteins. Clone KK34 transcript expression was studied by RT-PCR, Northern blotting and in situ hybridization and it was confirmed to be expressed in avian gammadelta T cells. We propose that this clone, KK34, may represent the first nonmammalian IL-5, supporting the findings that gammadelta T cells are important in the development of allergy.

Amino Acid Sequence↗

PubMed1995

Down-regulation of ornithine decarboxylase by an increased degradation of the enzyme during gastrulation of Xenopus laevis.

The present study was designed to analyze the regulation of the levels of the polyamines and their biosynthetic enzymes during embryonic development of Xenopus laevis. The activity of ornithine decarboxylase (ODC), a rate-controlling enzyme in polyamine biosynthesis, is elevated until, during gastrulation, there is a precipitous drop in activity. This is not attributable to a decrease in ODC mRNA content and polysome profiles reveal no apparent decrease in ODC message associated with polysomes. ODC synthesis seems to be maintained at a low, relatively constant rate until neurulation whereupon ribosome loading of ODC mRNA increases. During gastrulation the rate of ODC degradation increases dramatically, which can account for the decrease in ODC. S-Adenosylmethionine decarboxylase (AdoMetDC), another rate-controlling enzyme in polyamine biosynthesis, shows a low and constant activity from cleavage to neurulation. Subsequently, the AdoMetDC activity increases dramatically. The changes in AdoMetDC activity parallel the changes in AdoMetDC mRNA levels, suggesting a transcriptional control of AdoMetDC expression during this development period. The activities of ODC and AdoMetDC produce a steady increase in putrescine and spermidine content of the embryo. The spermine content also increases until gastrulation, but then decreases until the tailbud stage.

Adenosylmethionine Decarboxylase↗

PubMed2006

Cloning and expression pattern of peroxisome proliferator-activated receptor alpha in the thicklip grey mullet Chelon labrosus.

Aquatic organisms living in coastal and estuarine areas are exposed to diverse contaminants which can cause peroxisome proliferation. Peroxisome proliferators are agonists of peroxisome proliferator-activated receptors (PPARs), members of the nuclear receptor superfamily. We have recently demonstrated expression of the three PPAR isoforms in liver of mullet Chelon labrosus and other fish species by immunohistochemistry. The goal of the present study was first to clone PPARalpha and second to investigate its expression pattern in various tissues of mullet. PCR-based screening of mullet cDNA with PPARalpha specific degenerate primers resulted in amplification, subcloning and sequencing of a 1090 bp cDNA fragment (AY618315) that encodes mullet PPARalpha and exhibits highest amino acid identity to fish Sparus aurata PPARalpha (90%). Semi-quantitative RT-PCR was used to characterize the expression of PPARalpha in brain, muscle, liver, spleen, gill, heart and female gonad of juvenile and adult male and female mullet. For this, mullet 18S-rRNA (AY825252), beta-actin (AY836368) and elongation factor alpha (AY836369) were cloned and used as internal reference for RT-PCR. Expression of PPARalpha was detected in all tissues, was highest in liver and lowest in adult male and female muscle.

Actins↗

PubMed2000

Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain.

Expressed sequence tag (EST) analysis was conducted using a complementary DNA (cDNA) library made from the brain mRNA of channel catfish (Ictalurus punctatus). As part of our transcriptome analysis in catfish to develop molecular reagents for comparative functional genomics, here we report analysis of 1201 brain cDNA clones. Of the 1201 clones, 595 clones (49.5%) were identified as known genes by BLAST searches and 606 clones (50.5%) as unknown genes. The 595 clones of known gene products represent transcripts of 251 genes. These known genes were categorized into 15 groups according to their biological functions. The largest group of known genes was the genes involved in translational machinery (21.4%) followed by mitochondrial genes (6.2%), structural genes (3.1%), genes homologous to sequences of unknown functions (2.3%), enzymes (2.7%), hormone and regulatory proteins (2.5%), genes involved in immune systems (2.1%), genes involved in sorting, transport, and metal metabolism (1.8%), transcriptional factors and DNA repair proteins (1.6%), proto-oncogenes (1.2%), lipid binding proteins (1.2%), stress-induced genes (0.7%), genes homologous to human genes involved in mental diseases (0.6%), and development or differentiation-related genes (0.3%). The number of genes represented by the 606 clones of unknown genes is not known at present, but the high percentage of clones showing no homology to any known genes in the GenBank databases may indicate that a great number of novel genes exist in teleost brain.

Animals↗

PubMed1983

Localization of GTP-stimulated core glycosylation to fused microsomes.

Purified rough microsomes from liver maximally incorporated N-acetyl-[3H]glucosamine into endogenous acceptors from UDP-N-acetyl-[3H]glucosamine substrate, providing the associated ribosomes were removed and 0.5 mM GTP was added. These conditions also led to the coalescence of microsomes into large fused membranes. By measurement of membrane profiles on electron micrographs, a correlation was observed between GTP-stimulated glycosylation and microsomal membrane length (r2 = 0.92). Membrane fusion was not observed in the absence of GTP, with sugar transfer inhibited by greater than 90% for acid-resistant acceptors (protein), and approximately 50% for acid-labile acceptors (lipid-linked intermediates). When radiolabeled acceptors were localized by electron microscope radioautography, high concentrations of silver grains (83 grains/100 microns membrane length) were observed over fused membranes with lower grain densities observed over unfused membranes in the same preparation (20 grains/100 microns). These studies directly link microsomal membrane fusion to GTP-stimulated core glycosylation. The observations extend the suggestion of Godelaine et al. (1979, Eur. J. Biochem. 96:17-26) that physiological levels of GTP promote the translocation of substrate across endoplasmic reticulum membranes which, we propose, occurs via a membrane fusion phenomenon.

Acetylglucosamine↗

PubMed2005

Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes.

MOTIVATION: Coordinate regulation of gene expression can provide information on gene function. To begin a large-scale analysis of Dictyostelium gene function, we clustered genes based on their expression in wild-type and mutant strains and analyzed their functions. RESULTS: We found 17 modes of wild-type gene expression and refined them into 57 submodes considering mutant data. Annotation analyses revealed correlations between co-expression and function and an unexpected correlation between expression and function of genes involved in various aspects of chemotaxis. Co-regulation of chemotaxis genes was also found in published data from neutrophils. To test the predictive power of the analysis, we examined the phenotypes of mutations in seven co-regulated genes that had no published role in chemotaxis. Six mutants exhibited chemotaxis defects, supporting the idea that function can be inferred from co-expression. The clustering and annotation analyses provide a public resource for Dictyostelium functional genomics.

Animals↗