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 1,027 records · Page 57Linked to original sources
PubMed1976

Protein metabolism in transected peripheral nerves of the crayfish.

The significance of the protein metabolism in crayfish peripheral nerve was studied in relation the ability of crayfish motor axons to survive for over 200 days following axotomy. In contrast to frog peripheral nerves, the crayfish nerves appear to more closely resemble ganglia in their profiles of synthesis expressed on sodium dodecyl sulfate (SDS) gels, and have higher incorporation rates of [3H]leucine into protein than ganglia. Since anisomycin inhibits over 95% of protein synthesis in crayfish peripheral nerve, it was concluded that this local protein synthesis was dependent upon a eukaryotic ribosomal mechanism. Radioautography of isolated nerves reveals newly synthesized proteins in glial sheaths, and also within the axoplasm of large motor fibers. Based upon the data available at present, a hypothesis that the glia surrounding the axons are responsible for the local protein synthesis, and that some of these newly synthesized proteins are transported into the axon, is presented. Transection of crayfish peripheral nerves proximal to the neuron cell bodies produced a more than two-fold increase in [3H]leucine incorporation, but no significant changes in labeling profiles of the proteins on SDS gels. The data suggest that while an active local protein synthesis may be necessary for the maintenance of several crayfish motor axons, it is not a sufficient condition.

Animals↗
PubMed2005

Analysis of the genetic polymorphism of Paracoccidioides brasiliensis and Paracoccidioides cerebriformis "Moore" by random amplified polymorphic DNA (RAPD) and 28S ribosomal DNA sequencing--Paracoccidioides cerebriformis revisited.

Our purpose was to compare the genetic polymorphism of six samples of P. brasiliensis (113, 339, BAT, T1F1, T3B6, T5LN1), with four samples of P. cerebriformis (735, 741, 750, 361) from the Mycological Laboratory of the Instituto de Medicina Tropical de São Paulo, using Random Amplified Polymorphic DNA Analysis (RAPD). RAPD profiles clearly segregated P. brasiliensis and P. cerebriformis isolates. However, the variation on band patterns among P. cerebriformis isolates was high. Sequencing of the 28S rDNA gene showed nucleotide conservancy among P. cerebriformis isolates, providing basis for taxonomical grouping, and disclosing high divergence to P. brasiliensis supporting that they are in fact two distinct species. Moreover, DNA sequence suggests that P. cerebriformis belongs in fact to the Aspergillus genus.

Base Sequence↗
PubMed2006

Analysis of intergenic spacer region length polymorphisms to investigate the halophilic archaeal diversity of stromatolites and microbial mats.

Hamelin Pool in Western Australia is one of the two major sites in the world with active marine stromatolite formation. Surrounded by living smooth and pustular mats, these ancient laminated structures are associated with cyanobacterial communities. Recent studies have identified a wide diversity of bacteria and archaea in this habitat. By understanding and evaluating the microbial diversity of this environment we can obtain insights into the formation of early life on Earth, as stromatolites have been dated in the geological record as far back as 3.5 billion years. Automated ribosomal intergenic spacer analysis (ARISA) patterns were shown to be a useful method to genetically discriminate halophilic archaea within this environment. Patterns of known halophilic archaea are consistent, by replicate analysis, and the halophilic strains isolated from stromatolites have novel intergenic spacer profiles. ARISA-PCR, performed directly on extracted DNA from different sample sites, provided significant insights into the extent of previous unknown diversity of halophilic archaea within this environment. Cloning and sequence analysis of the spacer regions obtained from stromatolites confirmed the novel and broad diversity of halophilic archaea in this environment.

Archaea↗
PubMed1983

A change in isoaccepting leucine transfer RNA species in rat brain after prolonged ingestion of ethanol.

The effects of prolonged ethanol administration (10% ethanol-water solution as the sole drinking fluid for 6 to 14 weeks) on brain ribosomes and tRNA were studied in Sprague-Dawley rats. For comparison, liver ribosomes were also studied. The amounts of ribosomes in brain and liver and the proportion of the ribosomes in the form of polyribosomes were found to be essentially unaltered after 14 weeks of ethanol intake. In the brains of ethanol-treated animals, the total amount of unfractionated tRNA was slightly increased after 6 weeks. The acceptance of radioactive glutamic acid, leucine, methionine, phenylalanine, proline and serine by tRNA was also unaltered. When the activities of aminoacyl-tRNA synthetases specific for the six amino acids were studied in cross-over experiments, no changes were found. Comparison of the isoaccepting species of [14C]Met-, [14C]Leu- and [14C]Ser-tRNA by chromatography on benzoylated DEAE-cellulose revealed significant alteration in the chromatographic profile of [14C]Leu-tRNA derived from the brains of the alcohol-treated rats. These results suggest that prolonged intake of relatively small amounts of ethanol is accompanied in rats by essentially no alterations in total amounts of brain and liver ribosomes, brain tRNA, or activities of several aminoacyl-tRNA synthetases. As demonstrated by the leucine tRNAs, however, the quantitative distribution of isoaccepting tRNA species may change.

Alcoholism↗
PubMed2004

cDNA representational difference analysis of ileal Peyer's patches in lambs after oral inoculation with scrapie.

cDNA representational difference analysis (RDA) was used to study gene expression profiles in the ileal Peyer's patch of a lamb 1 week after oral inoculation with the scrapie agent. Twenty-five differentially expressed cDNA fragments were identified and cloned. Sequence analysis indicated seven novel gene sequences. Other clones shared sequence homology with genes encoding ribosomal and mitochondrial proteins, the translation initiation factor EIF4GII and the bovine pancreatic thread protein. Reverse Northern was used to confirm the differential expression in another four lambs inoculated with scrapie and the tissue distribution of the novel genes was examined using Northern blot analysis.

Administration, Oral↗
PubMed2002

Functional second genes generated by retrotransposition of the X-linked ribosomal protein genes.

We have identified a new class of ribosomal protein (RP) genes that appear to have been retrotransposed from X-linked RP genes. Mammalian ribosomes are composed of four RNA species and 79 different proteins. Unlike RNA constituents, each protein is typically encoded by a single intron- containing gene. Here we describe functional autosomal copies of the X-linked human RP genes, which we designated RPL10L (ribosomal protein L10-like gene), RPL36AL and RPL39L after their progenitors. Because these genes lack introns in their coding regions, they were likely retrotransposed from X-linked genes. The identities between the retrotransposed genes and the original X-linked genes are 89-95% in their nucleotide sequences and 92-99% in their amino acid sequences, respectively. Northern blot and PCR analyses revealed that RPL10L and RPL39L are expressed only in testis, whereas RPL36AL is ubiquitously expressed. Although the role of the autosomal RP genes remains unclear, they may have evolved to compensate for the reduced dosage of X-linked RP genes.

5' Flanking Region↗
PubMed2004

Insights into the evolution of the nucleolus by an analysis of its protein domain repertoire.

Recently, the first investigation of nucleoli using mass spectrometry led to the identification of 271 proteins. This represents a rich resource for a comprehensive investigation of nucleolus evolution. We applied a protocol for the identification of known and novel conserved protein domains of the nucleolus, resulting in the identification of 115 known and 91 novel domain profiles. The phyletic distribution of nucleolar protein domains in a collection of complete proteomes of selected organisms from all domains of life confirms the archaebacterial origin of the core machinery for ribosome maturation and assembly, but also reveals substantial eubacterial and eukaryotic contributions to nucleolus evolution. We predict that, in different phases of nucleolus evolution, protein domains with different biochemical functions were recruited to the nucleolus. We suggest a model for the late and continuous evolution of the nucleolus in early eukaryotes and argue against an endosymbiotic origin of the nucleolus and the nucleus. Supplementary material for this article can be found on the BioEssays website at http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html.

Archaeal Proteins↗
PubMed1982

Electron microscopic immunocytochemical localization of tyrosine hydroxylase in the area postrema of rat.

The ultrastructural morphology and specialized neuronal, vascular, and ventricular associations of tyrosine hydroxylase-labeled neurons are examined within the area postrema of rat brain. Specific antiserum to the purified enzyme is localized throughout the rostrocaudal and dorsoventral extent of the area postrema by means of the peroxidase-antiperoxidase technique. In all regions, peroxidase immunoreactivity for tyrosine hydroxylase is distributed throughout the cytoplasm of selectively labeled neuronal perikarya and processes. The perikarya contain a large nucleus, infolded nuclear membrane, numerous cytoplasmic organelles, and form axosomatic synapses with unlabeled terminals. The majority of the labeled processes are dendrites, which contain ribosomes, microtubules, mitochondria, and scattered vesicles. These dendrites are postsynaptic to unlabeled axon terminals and show membrane specializations with other labeled dendrites and perikarya. In contrast to dendrites, peroxidase-labeled profiles clearly distinguished as axons or axon terminals are sparse and never show membrane specializations with other neuronal or nonneuronal structures within the area postrema. Numerous large processes which could be either axons or dendrites are associated with blood vessels and the ventricular surface of the area postrema. With respect to blood vessels, processes are located either in direct apposition to the external glial membrane, or less frequently, within the perivascular space. The ventricular processes are either associated with blood vessels in the subpial space or distributed among the cilia and villi at the anterior margins of the area postrema. The neuronal and nonneuronal associations of the tyrosine hydroxylase-labeled processes are consistent with a receptor or chemosensor function for catecholamines in this circumventricular organ.

Animals↗
PubMed1985

Taxol-induced neuropathy: further ultrastructural studies of nerve fibre changes in situ.

Nerve fibre changes have been further monitored morphologically in rat sciatic nerves which had been locally injected with taxol, an antimitotic drug known to promote microtubule assembly. Taxol caused a slowly progressive accumulation of microtubules over a three week period of experimentation, the effect being more pronounced in Schwann cells. Schwann cells of myelinated fibres became detached from nodes of Ranvier and were applied to naked internodes as bulbous cells replete with microtubules and smooth endoplasmic reticulum (ER). In some cases, the smooth ER was believed to arise from rough ER after the displacement of ribosomes. These cells also contained myelin fragments from the original internodes. Microtubules displayed unique relationships with cytoplasmic membranes and were seen to exist as regular 22 nm microtubules, as obliquely sectioned profiles or as incomplete, trough-shaped structures. Internodes devoid of myelin were common, and naked axons covered only by basal lamina appeared swollen and invariably contained an abundance of microtubules. Schwann cells lacking axons had multilobate nuclei and possessed complex arrays comprising smooth ER membranes and microtubules. In areas where microtubules were absent, these membranes compacted to form intracellular myelin. Intermediate filaments existed in lower numbers than normal within both axons and Schwann cells. Arrested mitoses were occasionally seen and it is speculated that together with the immobilization of the cell by the over-abundant polymerization of tubulin, incomplete mitosis was an underlying cause for the observed lack of remyelination over the 21-day period of study. These results suggest that perturbations in microtubule synthesis might dramatically affect Schwann cell behaviour and myelin proliferation.

Alkaloids↗
PubMed2005

Adaptive responses to mitochondrial dysfunction in the rho degrees Namalwa cell.

Mitochondrial function depends on the synchronised expression of nuclear and mitochondrial-encoded genes. The expression of many nuclear genes is sensitive to the functional state of mitochondria. Mitochondria containing mutated mtDNA populations have been shown to withstand stress to a high level of tolerance. The prolonged survival of cells that are devoid of mitochondrial DNA is further evidence for the existence of this adaptive response. Yeast cells lacking the mitochondrial genome configure their pattern of nuclear gene expression to accommodate changes in nutrient availability and in response to different stress conditions. Little is known about the signalling pathways that mediate the adaptive response in mammalian cells with mitochondrial dysfunction. To gain a global perspective on adaptive responses in cells with mitochondrial dysfunction, we used Affymetrix microarray technology to compare the whole genome transcription profile of Namalwa cells (rho(+)) to that of a Namalwa cell depleted of mitochondrial DNA (rho degrees ). Our results demonstrate that rho degrees Namalwa induce genes encoding hypoxia target proteins, mitochondrial ribosomal proteins, transport channels, tRNA synthetases and enzymes of the glycolytic pathway and the fatty oxidation pathway suggesting that hypoxia and the ensuing cellular adaptations could play an important adaptive role in cells with mitochondrial dysfunction.

Adaptation, Physiological↗
PubMed2003

Developmentally programmed gene elimination in Euplotes crassus facilitates a switch in the telomerase catalytic subunit.

The primary function of telomerase is to maintain preexisting telomere tracts. In the ciliate Euplotes crassus, however, telomerase RNP structure and substrate recognition are altered during macronuclear development to facilitate de novo telomere addition. We found that E. crassus harbors three TERT genes encoding the telomerase catalytic subunit that not only vary in their nucleotide and predicted protein sequences, but also in their expression profiles. Expression of EcTERT-1 and -3 correlates with the requirement for telomere maintenance, while that of EcTERT-2 correlates with de novo telomere synthesis. All three genes appear to require ribosomal frameshifting for expression of catalytically active protein. The transcriptionally active form of EcTERT-2 exists only transiently in mated cells and is absent from the vegetative macronucleus. Thus, telomerase expression in Euplotes is controlled by unique regulatory mechanisms that culminate in a developmental switch to a different catalytic subunit with properties suited to de novo telomere addition.

Amino Acid Sequence↗
PubMed1997

Nosocomial outbreak of multi-resistant Acinetobacter baumannii on a surgical ward: epidemiology and risk factors for acquisition.

Between December 1994 and April 1995, a nosocomial outbreak caused by a multi-resistant Acinetobacter baumannii, occurred on a surgical ward in our hospital. The organism was isolated from 13 patients, eight of whom were infected whereas the others were colonized. Twelve isolates were compared by cell envelope protein electrophoretic profiles and AFLP, a recently described DNA fingerprinting method. Both methods indicated that this outbreak was caused by spread of a single strain, which was identified as A. baumannii by amplified ribosomal DNA fingerprinting (ARDRA). A case-control comparison was performed to identify risk factors associated with nosocomial acquisition of A. baumannii. Risk factors for cross-colonization were length of stay, surgery, wounds and treatment with broad-spectrum antibiotics. Cross-infection with A. baumannii among patients occurred despite implementation of stringent infection control measures. The outbreak was controlled after temporary closure of the surgical ward for disinfection purposes. Patients admitted on a general surgical ward colonized or infected with multi-resistant A. baumannii strains should alert the hospital infection control team, and prompt implementation of strict infection prevention measures to prevent further spread is advised.

Acinetobacter↗
PubMed2005

Pulmonary adenosquamous carcinoma in a dog.

A mass that developed in the lung of a 10-year-old mixed-breed dog was pathologically examined. Histopathological examination showed papillary and tubular growth of glandular epithelium-like cells in some areas and growth of squamous cells arranged in nests in other areas, showing coexistence of adenocarcinoma and squamous cell carcinoma in a lung tumour. Immunohistochemical staining with anti-keratin-cytokeratin antibody was strongly positive for cytoplasms in both components. Electron microscopically, the neoplastic cells of the adenocarcinoma component had features of glandular cells, with microvilli, numerous free ribosomes, large round secretory granules and intercellular desmosomes. Non-keratinized squamous cells had tonofilaments and intercellular desmosomes. These findings led to the diagnosis of primary adenosquamous carcinoma, which demonstrates phenotypic profiles characteristic of both epidermal keratinocytes and glandular epithelium.

Animals↗
PubMed2026

Insights into the regulatory roles of LIKE-HETEROCHROMATIN PROTEIN 1 and its targeting to different nuclear compartments modulated by NLS and the conserved domains in the moss Physcomitrium patens.

LIKE-HETEROCHROMATIN PROTEIN 1 (LHP1) is a polycomb group protein that exists in shared multiprotein complexes that harbor core PRC1 and PRC2 proteins. We previously characterized LHP1 in the moss Physcomitrium patens and showed that its function is closely linked with regulation of RNA metabolic processes and the protein is distributed in the nucleoplasm, subnuclear foci, and the nucleolus. To gain mechanistic insight into PpLHP1-mediated gene regulation, in the present study genome-wide changes in transcript profiles of genes affected by loss-of-PpLHP1 function were studied using pplhp1 mutants. RNA-seq analysis reveals a key role for PpLHP1 in regulating energy metabolic processes, ribosome-related pathways, stress signaling/responsive pathways, DNA transcription, etc. ChIP using H3K27me3 coupled with qRT-PCR shows that PpLHP1 suppresses transcription at 5S rRNA promoters and the untimely activation of genes regulating developmental transition by PRC2-dependent and independent mechanisms. To study how PpLHP1 finds its targets in different nuclear compartments and the roles of the multiple NLSs and the conserved domains in guiding the protein, FRAP and deletion studies were performed. These show that PpLHP1 is a mobile protein that diffuses freely in the nucleoplasmic space showing different retention times in the nucleolus, nucleoplasm, and the subnuclear foci indicating its differential affinity for targets at these sites. Expression of PpLHP1 fragments in protonema cells and its subsequent visualization under confocal microscope shows that localization of PpLHP1 to different subnuclear compartments is guided by the monopartite NLS2, CD, and CSD that also play a key role in promoting subnuclear foci formation in the nucleoplasm.

Bryopsida↗
PubMed1995

Phenotypic and genetic diversity of chlorine-resistant Methylobacterium strains isolated from various environments.

Strains of pink-pigmented facultative methylotrophs which were isolated previously from various environments and assigned tentatively to the genus Methylobacterium were characterized in comparison with authentic strains of previously known species of this genus. Most of the isolates derived from chlorinated water supplies exhibited resistance to chlorine, whereas 29 to 40% of the isolates from air, natural aquatic environments, and clinical materials were chlorine resistant. None of the tested authentic strains of Methylobacterium species obtained from culture collections exhibited chlorine resistance. Numerical analysis of phenotypic profiles showed that the test organisms tested were separated from each other except M. organophilum and M. rhodesianum. The chlorine-resistant isolates were randomly distributed among all clusters. The 16S ribosomal DNA (rDNA) sequence-based phylogenetic analyses showed that representatives of the isolates together with known Methylobacterium species formed a line of descent distinct from that of members of related genera in the alpha-2 subclass of the Proteobacteria and were divided into three subclusters within the Methylobacterium group. These results demonstrate that there is phenotypic and genetic diversity among chlorine-resistant Methylobacterium strains within the genus.

Bacterial Typing Techniques↗
PubMed2004

[Myiasis caused by Oestridae: serological and molecular diagnosis].

Myiasis-causing Oestridae (bot flies) infect several animal species world-wide, from palaearctic to subtropical/tropical areas. Oestrids affect livestock production causing abortion, reduced milk production, losses in weight and fertility, poor hide quality and an impairment of the host's immune system. In the last few years much research has been carried out on the immunology of these infestations, in order to acquire efficient and reliable diagnostic serological tools; the genome of the different species of Oestridae has been studied to further their molecular identification, taxonomy and phylogenesis. The immunodiagnostic methods for many myiasis causing Oestrids have proven to be a viable alternative to the clinical parasitological examination or the post-mortem examination. Numerous serological tests have been developed for the diagnosis of bovine hypodermosis caused by Hypoderma bovis and Hypoderma lineatum, and ELISAs using larval hypodermin C as the antigen are currently used on serum, individual and pooled milk samples to detect the presence of circulating anti-Hypoderma antibodies. In Italy the best period to sample the animals is November-January, since it is in this period that the antibody kinetics of the animals reaches a peak. Recently the efficacy of the ELISA test on pasteurized milk samples has been demonstrated, allowing the diagnosis of bovine hypodermosis also in areas where there is no information on the presence of the disease and the sampling of the animals is laborious. The cross-reactivity between Przhevalskiana silenus antigens and anti-Hypoderma antibodies led to assessing the usefulness of a simple and cost-effective ELISA for the diagnosis of goat warble fly infection. In particular, it has been demonstrated that infected goats display an antibody peak in November-December in blood and milk, thus making this period suitable for sampling. Although no extensive data is available on the immunology of sheep and goat oestrosis caused by Oestrus ovis, the efficacy of ELISA has been demonstrated by correlating serological results with clinical post-mortem examinations. No immunological techniques are currently used to diagnose gasterophilosis of equids and only one study reports the efficacy of ELISA for detecting anti-Gasterophilus antibodies in infected equids. Several studies have been conducted into the molecular characterization of the mitochondrial DNA (mtDNA)--in particular of the gene encoding for the cytochrome oxidase I (COI)--for many free-living and parasitic arthropods for diagnostic, taxonomic and phylogenetic purposes. As regards Oestridae causing myiasis, the first study features a PCR-RFLP assay of the most common Italian species (i.e. H. bovis, H. lineatum, Gasterophilus intestinalis, P. silenus, O. ovis), which showed clear genetic differences among the genera examined, but no inter-specific variation between the two species of Hypoderma considered. The molecular characterization of the most variable region of the COI gene (encoding for the region from E4 to the terminal COOH) was able to clearly differentiate H. bovis and H. lineatum. The E4-COOH region of the COI gene has been characterized for 18 oestrid species and from a taxonomical point of view, molecular data confirm the morphological classification, with the examined species divided into four subfamilies. New insights have also been gained on the molecular differentiation of the most common species of Hypoderma (i.e. H. bovis, H. lineatum, Hypoderma actaeon, Hypoderma diana and Hypoderma tarandi) and, in particular, the restriction enzyme BfaI, provides a diagnostic profile that can be used to simultaneously differentiate all the species examined. The characterization of the E4-COOH COI gene and the hypervariable region of the gene encoding for the ribosomal Isu revealed the identity of Hypoderma sinense as a new species, infecting cattle and yaks in China. Finally, the molecular analysis of the same mitochondrial and ribosomal regions showed that P. silenus, Przhevalskiana aegagri and Przhevalskiana crossii are morphotypes of the same species.

Animals↗
PubMed2003

Rapid identification of Trichophyton tonsurans by PCR-RFLP analysis of ribosomal DNA regions.

BACKGROUND: Culture morphology of Trichophyton (T.) tonsurans, an emerging pathogen of dermatophytosis in Japan, varies widely and species level identification is sometimes very difficult. Reliable molecular markers are expected to be introduced for their identification. OBJECTIVE: The present study was conducted to evaluate the efficacy of restriction fragment length polymorphism (RFLP) analysis of PCR amplified ribosomal (r) DNA including internal transcribed spacers (ITS), as an identification tool. METHODS: Total cellular DNA was extracted from 26 Japanese isolates of T. tonsurans, along with several taxa of the members in the T. mentagrophytes complex, T. rubrum, T. violaceum and Epidermophyton floccosum, using a mini-preparation method. PCR amplicons were digested with restriction enzymes Mva I or Hinf I, then electrophoresed on 5% polyacrylamide gel. RESULTS: The banding profiles were observed about 8 h from initiating DNA extraction. Intraspecies polymorphism was not detected among T. tonsurans isolates, and their profiles obtained using Mva I digestion were clearly different from those of the other dermatophyte species. The restriction profiles evaluated from nucleotide sequence of the regions by a computer analysis were compatible with the electrophoresed profiles on gel. CONCLUSION: PCR-RFLP analysis is a rapid and reliable tool for the identification of T. tonsurans.

Adolescent↗