Observations on reticulocyte maturation.
Explore the source record for details and available documents.
Aging↗
SEARCH · Search PubMed
Results for “RNA Aggregation”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Role for Rab7 in maturation of late autophagic vacuoles.
The small GTP binding protein Rab7 has a role in the late endocytic pathway and lysosome biogenesis. The role of mammalian Rab7 in autophagy is, however, unknown. We have addressed this by inhibiting Rab7 function with RNA interference and overexpression of dominant negative Rab7. We show here that Rab7 was needed for the formation of preferably perinuclear, large aggregates, where the autophagosome marker LC3 colocalised with Rab7 and late endosomal and lysosomal markers. By electron microscopy we showed that these large aggregates corresponded to autophagic vacuoles surrounding late endosomal or lysosomal vesicles. Our experiments with quantitative electron microscopy showed that Rab7 was not needed for the initial maturation of early autophagosomes to late autophagic vacuoles, but that it participated in the final maturation of late autophagic vacuoles. Finally, we showed that the recruitment of Rab7 to autophagic vacuoles was retarded in cells deficient in the lysosomal membrane proteins Lamp1 and Lamp2, which we have recently shown to accumulate late autophagic vacuoles during starvation. In conclusion, our results showed a role for Rab7 in the final maturation of late autophagic vacuoles.
Animals↗
Short-term rescue by RNA injection of a mitotic arrest mutation that affects the preimplantation mouse embryo.
The mutation oligosyndactyly results in syndactyly, abnormal fusion and insertion of certain limb muscles, and diabetes insipidus in heterozygous mice. When homozygous the mutation is lethal; beginning at the blastocyst stage, the homozygous cells arrest in metaphase with intact spindles. The mutant phenotype cannot be corrected by forming aggregation chimeras with wild-type cells, suggesting that the mutation results in a cell autonomous lethal condition. Short-term rescue of the homozygous-induced mitotic arrest can be achieved, however, by cytoplasmic injection of polyadenylated RNA obtained from a rapidly dividing embryo-derived stem cell line.
Animals↗
Entropy-driven genome organization.
DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription "factories" in both pro- and eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.
Computer Simulation↗
Does water play a structural role in the folding of small nucleic acids?
Nucleic acid structure and dynamics are known to be closely coupled to local environmental conditions and, in particular, to the ionic character of the solvent. Here we consider what role the discrete properties of water and ions play in the collapse and folding of small nucleic acids. We study the folding of an experimentally well-characterized RNA hairpin-loop motif (sequence 5'-GGGC[GCAA]GCCU-3') via ensemble molecular dynamics simulation and, with nearly 500 micros of aggregate simulation time using an explicit representation of the ionic solvent, report successful ensemble folding simulations with a predicted folding time of 8.8(+/-2.0) micros, in agreement with experimental measurements of approximately 10 micros. Comparing our results to previous folding simulations using the GB/SA continuum solvent model shows that accounting for water-mediated interactions is necessary to accurately characterize the free energy surface and stochastic nature of folding. The formation of the secondary structure appears to be more rapid than the fastest ionic degrees of freedom, and counterions do not participate discretely in observed folding events. We find that hydrophobic collapse follows a predominantly expulsive mechanism in which a diffusion-search of early structural compaction is followed by the final formation of native structure that occurs in tandem with solvent evacuation.
Amino Acid Motifs↗
Modulation of lymphocyte nuclear matrix organization in vivo by 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole: an autoradiographic and immunofluorescence study.
Assembly of active nuclei in lymphocytes stimulated by mitogen is paralleled by the elaboration of a structurally and biochemically complex nuclear matrix (NM). To examine the dynamics of individual NM polypeptide components during blastogenesis, we have applied immunofluorescence labelling with anti-NM antibodies to concanavalin A-stimulated mouse splenocytes. Whereas peripherin and PI2 antigens did not reorganize during stimulation, labelling of PI1 and small nuclear ribonucleoprotein (snRNP) antigens increased markedly in intensity and redistributed in concert with the previously reported NM restructuring. Double-labelling showed, furthermore, that snRNPs and the internal staining component of PI1 were largely co-localized. As an approach to studying the role of RNA and RNA synthesis in NM organization, we have further examined the effects of the inhibitor of RNA synthesis, 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole (DRB), on NM antigen distribution. The rapid inhibition of 3H-uridine incorporation by DRB was accompanied by coordinate aggregation of snRNPs and of the internal PI1 component into large, brightly stained patches. Both 3H-uridine incorporation levels and antigen localization were readily reversed upon removal of DRB. We conclude that NM antigens behave independently during nuclear and NM assembly and that NM organization, as reflected by NM antigen distribution, is modulated by con A- and DRB-induced alterations in RNA synthesis. We propose, furthermore, that the PI1 antigen plays a role in RNA metabolism, and is possibly involved in RNA transport to the nuclear periphery.
Animals↗
Loss of E-cadherin-dependent cell-cell adhesion due to mutation of the beta-catenin gene in a human cancer cell line, HSC-39.
Detachment of cell-cell adhesion is indispensable for the first step of invasion and metastasis of cancer. This mechanism is frequently associated with the impairment of either E-cadherin expression or function. However, mechanisms of such abnormalities have not been fully elucidated. In this study, we demonstrated that the function of E-cadherin was completely abolished in the human gastric cancer cell line HSC-39, despite the high expression of E-cadherin, because of mutations in one of the E-cadherin-associated cytoplasmic proteins, beta-catenin. Although immunofluorescence staining of HSC-39 cells by using an anti-E-cadherin antibody (HECD-1) revealed the strong and uniform expression of E-cadherin on the cell surface, cell compaction and cell aggregation were not observed in this cell. Western blotting (immunoblotting) using HECD-1 exhibited a 120-kDa band which is equivalent to normal E-cadherin. Northern (RNA) blotting demonstrated a 4.7-kb band, the same as mature E-cadherin mRNA. Immunoprecipitation of metabolically labeled proteins with HECD-1 revealed three bands corresponding to E-cadherin, alpha-catenin, and gamma-catenin and a 79-kDa band which was apparently smaller than that of normal beta-catenin, indicating truncated beta-catenin. The 79-kDa band was immunologically identified as beta-catenin by using immunoblotting with anti-beta-catenin antibodies. Examination of beta-catenin mRNA by the reverse transcriptase-PCR method revealed a transcript which was shorter than that of normal beta-catenin. The sequencing of PCR product for beta-catenin confirmed deletion in 321 bases from nucleotides +82 to +402. Southern blotting of beta-catenin DNA disclosed mutation at the genomic level. Expression vectors of Beta-catenin were introduced into HSC-39 cells by transfection. In the obtained transfectants, E-cadherin-dependent cell-cell adhesiveness was recovered, as revealed by cell compaction, cell aggregation, and immunoflourescence staining. From these results, it was concluded that in HSC-39 cells, impaired cell-cell adhesion is due to mutations in beta-catenin which results in the dysfunction of E-cadherin.
Antibodies, Monoclonal↗
Significance of P-selectin expression in human glomerulonephritis.
OBJECTIVE: To examine the relationship between P-selectin expression and human glomerulonephritis. METHODS: P-selectin expression was investigated in renal biopsies of glomerulonephritis patients (n = 133) by immunohistochemical and in situ hybridization analyses. They were divided into three groups based on the degrees of cells proliferation or sclerosis. Group I: histological lesions in glomeruli are mild (n = 23); Group II: glomerular cells proliferation is prominent (n = 91); Group III: glomerular sclerosis is severe (n = 19). The Kruskal-Wallis test, Chisquare test and Spearman's correlation were used in our study. RESULTS: In normal controls, renal P-selectin expression was negative (n = 10). In glomerulonephritis, the up-regulated P-selectin expression on tubular epithelium was significantly higher than that on glomeruli and interstitium (P < 0.01). P-selectin was expressed predominantly on platelets in glomeruli, and glomerular P-selectin expression was more significantly up-regulated in Group II than in Group I or Group III (P < 0.05; and P < 0.01, respectively). There were strong correlations between the degree of tubulointerstitial lesions and the expression of P-selectin on tubular epithelium or within interstitium (rs = 0.395 and rs = 0.337, P < 0.01). Furthermore, P-selectin messenger RNA (mRNA) signals were also detected in the cytoplasm of glomerulus, tubular epithelial cells, interstitium and vascular endothelium. CONCLUSIONS: P-selectin might mediate intraglomerular platelets aggregation, activation and leukocyte accumulation in the early stages of human proliferative glomerulonephritis. The up-regulation of P-selectin in interstitium was associated with interstitial fibrosis and tubular atrophy and may contribute to the progression of glomerulonephritis.
Adult↗
Unusual polysomal aggregates in rat-liver preparations.
Explore the source record for details and available documents.
Animals↗
Serine specific transfer ribonucleic acids. 16. Aggregation of serine specific transfer ribonucleic acids.
Explore the source record for details and available documents.
Carbon Isotopes↗
Ribosome aggregates of the midgut of silkworm, Bombyx mori L.
Explore the source record for details and available documents.
Bombyx↗
Hepatitis C virus envelope proteins regulate CHOP via induction of the unfolded protein response.
Unfolded protein response (UPR) is a cellular adaptive response that functions to reduce stress caused by malfolded proteins in the endoplasmic reticulum (ER). UPR can be induced under physiological or pathological conditions and is responsible for the pathogenesis of many human diseases. Hepatitis C virus (HCV) is a single-stranded, positive-sense RNA virus causing chronic diseases. Its genome encodes two envelope proteins E1 and E2, which mature in the ER to form a noncovalently bound, native complex and disulfide aggregates and have previously been shown to induce expression of the molecular chaperone immunoglobulin heavy chain binding protein. In this study, we show that HCV envelope protein expression regulates another stress indicator CCAAT/enhancer-binding protein-homologous protein (CHOP). The ER-stress element and the activating transcription factor 4 element in the CHOP promoter were activated to a similar extent by HCV envelope protein expression. Using mouse embryonic fibroblasts deficient in the ER stress kinase RNA-activated protein kinase-like ER-resident kinase (PERK), we showed that PERK was necessary and sufficient for activating the CHOP promoter. Expression of HCV E1 and/or E2 also induced splicing of X-box binding protein 1 and transactivation of the unfolded protein response element, leading to the speculation that HCV E1 and E2 not only regulate the UPR but also ER-associated degradation.
DNA-Binding Proteins↗
Effect of elevated dietary tryptophan on protein synthesis in rat liver.
This study investigated whether rats force-fed for three days an elevated (1%) tryptophan diet compared to a control (0.2% tryptophan) diet had changes in hepatic protein metabolism. Earlier, we showed that a single administration of L-tryptophan to fasted rats caused a rapid increase in hepatic protein synthesis. In the present study rats force-fed a high tryptophan diet for 3 days and killed the fourth morning had increased rats of hapatic protein synthesis, cytochrome P-450 and b5 activities, in vitro nuclear RNA release (cell sap and nuclear effects) and nuclear envelope nucleoside triphosphatases activity compared to animals force-fed the control diet. We noted little or no change in hapatic total polyribosomal aggregation patterns or plasma and hepatic free amino acid levels.
Animals↗
Different mRNAs have different nuclear transit times in Dictyostelium discoideum aggregates.
Nuclear processing of mRNA precursors in differentiating multicellular Dictyostelium discoideum aggregates is markedly slower than in growing amoebae. Thus, we have been able to determine the time of nuclear processing of individual mRNA species in postaggregating cells by following the incorporation of 32PO4 into nuclear and cytoplasmic RNA complementary to cloned cDNAs. Precursors of mRNAs synthesized during both growth and differentiation remain in the nucleus for about 25 to 60 min. By contrast, typical mRNAs which are synthesized only by postaggregative cells have nuclear processing times between 50 and 100 min. Depending on the particular mRNA, between 20 and 60% of nuclear transcripts are converted into cytoplasmic mRNA. A third class of mRNAs are transcribed from a set of repetitive DNA segments and are expressed predominantly during differentiation. Nuclear precursors of these mRNAs are extensively degraded within the nucleus or very rapidly after transport to the cytoplasm. Those sequences that are stable in the cytoplasm exit from the nucleus only after a lag of over 2 h. Thus, mRNAs encoded by different genes that are subject to different types of developmental controls display different times of transit to the cytoplasm and different efficiencies of nuclear processing. Differential nuclear processing may contribute to the regulation of the level of individual cytoplasmic mRNAs.
Biological Transport↗
Elaboration of the messenger transport organizer pathway for localization of RNA to the vegetal cortex of Xenopus oocytes.
Previous studies demonstrated that there were two pathways, the messenger transport organizer (METRO) or early and the Vg1 or late, which function during stages 1 to 3 of oogenesis for the localization of RNAs at the vegetal cortex of Xenopus oocytes. In the present study we analyzed the properties of the METRO pathway, which localizes Xlsirt, Xcat2, and Xwnt11 RNAs to a specific region of the vegetal cortex during stage 1 of oogenesis. A combination of methodologies involving both fixed material and living oocytes was used to analyze RNA localization. We show that in early diplotene pre-stage 1 oocytes (25-50 microm in diameter) both endogenous and injected exogenous METRO RNAs translocated to multiple mitochondrial aggregates (pre-mitochondrial clouds) that surround the germinal vesicle (GV). However, by early stage 1 (diplotene oocytes, 50-200 microm), all three of the RNAs discriminated between the different clouds and translocated exclusively within the METRO of a single mitochondrial cloud. Therefore, in stage 1 diplotene oocytes there is a unique mechanism causing a change in the intrinsic property of the mitochondrial clouds which designates one of them as the RNA transport vehicle. During translocation through the cytoplasm Xlsirt and Xcat2 RNAs were detected associated with cytoplasmic particles of different morphologies. Additionally, we also found that the translocation of RNAs through the early or METRO pathway, unlike that of the late pathway, occurred in the absence of intact microtubule and actin microfilament cytoskeletal elements. This supports a cytoskeletal-independent model for localization of RNAs through the METRO pathway.
Actin Cytoskeleton↗
Expression of versican mRNA is developmentally regulated in the brain of the embryonic chick and the developing rat.
RNA prepared from the brains of chick embryos at 12 days of incubation contained a 12-kb transcript that hybridized with a cDNA probe for the aggregating proteoglycan versican. No transcripts were detected in the brains of newborn rats while, at 3 days of postnatal development, three sizes of transcripts were present. None were detected in the 6-day old brain and, at later stages, the smallest transcript predominated.
Animals↗
Prostaglandin E2 rapidly stimulates insulin-like growth factor-I gene expression in primary rat osteoblast cultures: evidence for transcriptional control.
Osteoblast-enriched (Ob) cultures isolated from fetal rat bone synthesize insulin-like growth factor-I (IGF-I), which functions as a locally acting growth and differentiation factor in the skeleton. Consistent with prior studies demonstrating that IGF-I production is enhanced in bone by agents that induce cAMP, prostaglandin E2 (PGE2) stimulates both cAMP synthesis and IGF-I mRNA in Ob cells. However, little is known about how cAMP regulates IGF-I expression in this or any other cell system. In rat tissues, multiple mechanisms influence levels of IGF-I mRNA, including transcription from two promoters, differential RNA splicing and stability, and alternative RNA polyadenylation. To determine how cAMP influences IGF-I gene expression in Ob cultures, we examined the responses of these cells to treatment with PGE2. PGE2 rapidly enhanced the accumulation of both large and small IGF-I transcripts, with increases in IGF-I mRNA detected within 2 h of treatment and persisting for 24 h. Analysis of precursor RNA by a highly specific and sensitive ribonuclease protection assay demonstrated a rise in nascent IGF-I mRNA within 30 min of exposure to PGE2, with a peak stimulation of 4-fold above control levels seen by 2 h and levels remaining elevated for up to 24 h. IGF-I transcripts in Ob cells were directed only by promoter 1, the more 5' of the two rat IGF-I gene promoters. As additionally assessed using the RNA polymerase II inhibitor 5,6-dichloro-1-beta-D-ribofuranosyl benzimidazole, PGE2 treatment had little effect on IGF-I mRNA stability. In aggregate, these studies show that in fetal rat Ob cultures, PGE2 enhances IGF-I gene expression primarily through transcriptional mechanisms that are limited to a single IGF-I gene promoter. Ob cells, therefore, may be an excellent model for determining how cAMP regulates IGF-I gene transcription.
Animals↗
Detection of HCV-RNA in paraffin-embedded liver biopsies from patients with autoimmune hepatitis.
BACKGROUND/AIMS: There may be a relationship between autoimmune hepatitis and viral infection. To examine this relationship, 19 patients with autoimmune hepatitis and/or chronic hepatitis C were studied. METHODS: Patients were selected initially on the basis of having autoantibodies (anti-nuclear, anti-smooth muscle, or anti-liver-kidney microsomal) in serum. Formalin-fixed, paraffin-embedded liver biopsies from these patients were tested for HCV-RNA by polymerase chain reaction. The biopsies were examined histologically to detect features suggestive of chronic hepatitis C or autoimmune hepatitis. The results were correlated with serum anti-HCV and HCV-RNA, and with response to steroid therapy. RESULTS: Five of the nineteen patients had detectable HCV-RNA in their liver biopsies. In two of three patients from whom serum was available, HCV-RNA was detectable. The remaining 14 patients were negative for HCV-RNA by tissue polymerase chain reaction. Serum was available from 11 of these patients, and serum HCV-RNA was negative in all. All of the three HCV-RNA-positive patients who were treated with steroids showed a partial response; tissue positivity for HCV-RNA was significantly higher in partial responders than in complete responders (60% vs 0%, p = 0.01). Severe portal and periportal inflammation with prominent plasma cells together with bridging parenchymal necrosis were seen more often in HCV-negative biopsies. Mild portal and periportal inflammation with portal lymphoid aggregates, apoptosis and spotty parenchymal necrosis were seen more in HCV-positive biopsies. CONCLUSIONS: These results show that hepatitis C virus can be detected in some patients with circulating autoantibodies. The ability to detect HCV-RNA in paraffin-embedded archival material provides a valuable addition to the battery of available HCV tests.
Adolescent↗