Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Amber”

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.

At least 37 records · Page 2Linked to original sources
PubMedDate not supplied

Effect of terminal sterilization by irradiation on amber Type I and Type III glass containers containing veterinary oxytetracycline suspension.

The purpose of this study is to determine the effect of terminal sterilization by gamma irradiation on 500-mL amber Type I and Type III glass containers (bottles) containing oxytetracycline (OTC) (25% W/V) suspension formulated using 20% (W/V) phospholipids syrup. The formulation was developed for veterinary parenteral administration. The results of terminal sterilization were used to assess the acceptability for this suspension product. OTC is light-sensitive and needs to be stored in amber glass containers. Amber Type I and Type III glass containers were considered for this formulation during development. Type I is a highly resistant, borosilicate glass (oxidized glass). Type III, which is soda-lime glass (reduced glass, see Materials and Methods), may also be used for parenteral products. The amber Type I and Type III glass containers, containing the suspension, were irradiated at 20-40 kGy for 150 min. In order to determine the sterility of the suspension, ampoules of the biological indicator, Bacillus pumilus, were placed in a number of bottles of the suspension. The bottles with the biological indicators were then positioned among the rest of the production bottles as per a radiation dose-mapping study conducted at the sterilization facility. Potency determination and stability evaluations for OTC were performed using high pressure liquid chromatography (HPLC). The results indicate that the gamma irradiation dose of 20-40 kGy for 150 min was able to inactivate 10(6) Bacillus pumilus spores in ampoules. After gamma sterilization, OTC concentration, pH, particle size, endotoxins, and sterility were evaluated. The assay results were comparable for the suspension in amber Type I and Type III glass containers. Sterility and pyrogenicity were measured by the USP Membrane Filtration Method and USP Bacterial Endotoxins Test, respectively. The suspension in the amber Type III glass container was also chemically (HPLC) and physically (suspension mean particle size, viscosity, density, and syringeability) stable for at least 12 months at room temperature. However, amber Type I glass darkened following irradiation, leading to a substantial reduction in glass transparency. The appearance of amber Type III glass was acceptable. Thus, the "reduced" glass, such as soda-lime, was found to be much less susceptible to darkening than the highly oxidized borosilicate amber. Due to the potential aesthetic concerns with Type I glass, the amber Type III glass container was selected for this suspension formulation.

Chromatography, High Pressure Liquid↗
PubMed1994

The range of life in amber: significance and implications in DNA studies.

A survey of the major fossiliferous amber deposits is provided, including ages and various categories of life forms reported from each. The frequency of occurrence of the major groups of plants and animals in these amber deposits is also given. Thus far, DNA from four insect and one plant species has been extracted from amber fossils. In the case of the stingless bee in Dominican amber, evidence of reproducibility is provided, since two independent laboratories isolated DNA from six or more different specimens of the same insect. Amber sources for DNA studies are listed together with their advantages and disadvantages. The important points are the availability of desired pieces, the proper identification of the fossil, verification of the amber deposit, the cost involved, and the feasibility of causing damage to the specimen. The availability of several types of amber (Mexican, Dominican, Baltic, Chinese, Canadian, Siberian and Lebanese) at four major sources (academic collections, commercial dealers, private collections and amber mines) is discussed. The scientific implications of obtaining DNA from amber inclusions are presented.

Animals↗
PubMed1985

First identification of an amber nonsense mutation in Schizosaccharomyces pombe: major differences in the efficiency of homologous versus heterologous yeast suppressor tRNA genes.

In Saccharomyces cerevisiae ochre and opal, as well as amber mutations are known, whereas in the fission yeast Schizosaccharomyces pombe no amber alleles have been described. We have characterized trp1-566, an amber allele in the trp1 locus of S. pombe. The identification of trp1-566 as an amber allele is based on the following results: (a) The nonsense allele can be converted to an ochre allele by nitrosoguanidine mutagenesis. (b) trp1-566 is suppressed by a bona fide S. pombe amber suppressor tRNA, supSI. The supSI gene was obtained by primer-directed in vitro mutagenesis of a tRNASer from S. pombe. Unexpectedly, an S. cerevisiae amber suppressor tRNASer, supR21, transformed into S. pombe, failed to suppress trp1-566. Northern analysis of S. pombe transformants, containing supRL1 or S. cerevisiae tRNALeu or tRNATyr genes reveals that these genes are not transcribed in the fission yeast. As an additional tool for the analysis of nonsense mutations in S. pombe, we obtained by nitrosoguanidine mutagenesis two unlinked amber suppressor alleles, sup13 and sup14, which act on trp1-566.

Base Sequence↗
PubMed1999

Diversity of Microorganisms Isolated from Amber.

> Abstract Claims that organisms can be cultured from amber, if substantiated, would be significant contributions to our understanding of the evolution, tenacity, and potential spread of life. Three reports on the isolation of organisms from amber have been published. Cano and Borucki recently reported the isolation of Bacillus sphaericus and Lambert et al. have described a new species designated Staphylococcus succinus from 25-40 million year old Dominican amber. These characterized organisms were phylogenetically distant from extant relatives and the Staphylococcus sp. sufficiently far removed from other extant staphylococci to be considered a new species. Here we report the culture of bacteria from Dominican and previously untested 120 million year old Israeli (Lebanese lode) amber. Twenty-seven isolates from the amber matrix have been characterized by fatty-acid profiles (FAME) and/or 16S rRNA sequencing. We also performed a terminal restriction fragment pattern (TRF) analysis of the original amber before prolonged culture by consensus primer amplification of the 16S rRNA followed by restriction enzyme digestion of the amplicons. Sample TRFs were consistent with a sparse bacterial assemblage and included at least five of the isolated organisms. Finally, we microscopically mapped the internal topography of an amber slice.http://link.springer-ny.com/link/service/journals/00248/bibs/38n1p58.html

Journal Article↗
PubMed1982

An amber suppressor tRNA gene derived by site-specific mutagenesis: cloning and function in mammalian cells.

We describe the synthesis, cloning, expression, and in vivo function of a suppressor tRNA gene in mammalian cells. By using "primer-directed mutagenesis" on a Xenopus laevis tyrosine tRNA gene cloned into the recombinant single-strand phage M13mp5, we have generated an amber suppressor tRNA gene that has a nucleotide change--GTA leads to CTA--in the anticodon sequence. The suppressor (Su) tRNA gene was introduced into monkey kidney cells (CV-1) by using simian virus 40 (SV40) DNA as vector (SV40-tRNATyrSu+). CV-1 cells infected with virus containing the mutant, but not the wild-type, tRNA gene produce a functional amber suppressor tRNA as indicated by suppression of amber mutations in co-infecting adenovirus serotype 2-SV40 hybrids. Further evidence that suppression of these amber mutations is tRNA mediated was derived by isolation of total tRNA from CV-1 cells infected with the SV40-tRNATyr (Su+) recombinant and its use in demonstration of read through of an amber codon during in vitro translation of tobacco mosaic virus RNA in reticulocyte extracts. Interestingly, the amplification of an amber suppressor gene in CV-1 cells does not interfere with SV40 production, suggesting that suppression of amber codons may not be very deleterious to mammalian cell metabolism.

Animals↗
PubMed2001

The amber codon in the gene encoding the monomethylamine methyltransferase isolated from Methanosarcina barkeri is translated as a sense codon.

Each of the genes encoding the methyltransferases initiating methanogenesis from trimethylamine, dimethylamine, or monomethylamine by various Methanosarcina species possesses one naturally occurring in-frame amber codon that does not appear to act as a translation stop during synthesis of the biochemically characterized methyltransferase. To investigate the means by which suppression of the amber codon within these genes occurs, MtmB, a methyltransferase initiating metabolism of monomethylamine, was examined. The C-terminal sequence of MtmB indicated that synthesis of this mtmB1 gene product did not cease at the internal amber codon, but at the following ochre codon. Antibody raised against MtmB revealed that Escherichia coli transformed with mtmB1 produced the amber termination product. The same antibody detected primarily a 50-kDa protein in Methanosarcina barkeri, which is the mass predicted for the amber readthrough product of the mtmB1 gene. Sequencing of peptide fragments from MtmB by Edman degradation and mass spectrometry revealed no change in the reading frame during mtmB1 expression. The amber codon position corresponded to a lysyl residue using either sequencing technique. The amber codon is thus read through during translation at apparently high efficiency and corresponds to lysine in tryptic fragments of MtmB even though canonical lysine codon usage is encountered in other Methanosarcina genes.

Amino Acid Sequence↗
PubMed1980

Isolation and characterization of Escherichia coli dnaA amber mutants.

Specialized transducing phage lambda (formula, see text) dnaA-2 was mutagenized, and two derivatives designated lambda (formula) dnaA17(Am) and lambda (formula) dnaA452(Am) were obtained. They did not transduce such mutations as dnaA46, dnaA167, and dnaA5 when an amber suppressor was absent, but they did so in the presence of an amber suppressor. By contrast, they transduced the dna-806 and tna-2 mutations in the absence of an active amber suppressor. The dna-806 and tna-2 mutations are known to be located very close to the dnaA gene, but in separate cistrons. When ultraviolet light-irradiated uvrB cells were infected with the derivative phages and proteins specified by them were analyzed by gel electrophoresis, a 50,000-dalton protein was found to be specifically missing if an amber suppressor was absent. This protein was synthesized when an amber suppressor was present. The dnaA17(Am) mutation on the transducing phage genome was then transferred by genetic recombination onto the chromosome of an Escherichia coli strain carrying a temperature-sensitive amber suppressor supF6(Ts), yielding a strain which was temperature sensitive for growth and deoxyribonucleic acid replication. The temperature-sensitive trait was suppressed by supD, supE, or supF. We conclude that, most likely, the derivative phages acquired amber mutations in the dnaA gene whose product is a 50,000-dalton protein as identified by gel electrophoretic analysis.

Bacterial Proteins↗
PubMed1980

Suppression of murine retrovirus polypeptide termination: effect of amber suppressor tRNA on the cell-free translation of Rauscher murine leukemia virus, Moloney murine leukemia virus, and Moloney murine sarcoma virus 124 RNA.

The effect of suppressor tRNA's on the cell-free translation of several leukemia and sarcoma virus RNAs was examined. Yeast amber suppressor tRNA (amber tRNA) enhanced the synthesis of the Rauscher murine leukemia virus and clone 1 Moloney murine leukemia virus Pr200(gag-pol) polypeptides by 10- to 45-fold, but at the same time depressed the synthesis of Rauscher murine leukemia virus Pr65(gag) and Moloney murine leukemia virus Pr63(gag). Under suppressor-minus conditions, Moloney murine leukemia virus Pr70(gag) was present as a closely spaced doublet. Amber tRNA stimulated the synthesis of the "upper" Moloney murine leukemia virus Pr70(gag) polypeptide. Yeast ochre suppressor tRNA appeared to be ineffective. Quantitative analyses of the kinetics of viral precursor polypeptide accumulation in the presence of amber tRNA showed that during linear protein synthesis, the increase in accumulated Moloney murine leukemia virus Pr200(gag-pol) coincided closely with the molar loss of Pr63(gag). Enhancement of Pr200(gag-pol) and Pr70(gag) by amber tRNA persisted in the presence of pactamycin, a drug which blocks the initiation of protein synthesis, thus arguing for the addition of amino acids to the C terminus of Pr63(gag) as the mechanism behind the amber tRNA effect. Moloney murine sarcoma virus 124 30S RNA was translated into four major polypeptides, Pr63(gag), P42, P38, and P23. In the presence of amber tRNA, a new polypeptide, Pr67(gag), appeared, whereas Pr63(gag) synthesis was decreased. Quantitative estimates indicated that for every 1 mol of Pr67(gag) which appeared, 1 mol of Pr63(gag) was lost.

Kinetics↗
PubMed2005

Digital slot-scan charge-coupled device radiography versus AMBER and Bucky screen-film radiography: comparison of image quality in a phantom study.

PURPOSE: To evaluate the image quality and performance of a chest digital radiography system and to compare this with the image quality and performance of advanced multiple-beam equalization radiography (AMBER) and Bucky screen-film radiography systems. MATERIALS AND METHODS: The chest digital radiography system is a digital charge-coupled device (CCD) chest imaging unit that uses slot-scan technology. A contrast-detail test object was used in combination with a phantom that simulates the primary and scatter transmission for the lungs and mediastinum. Twelve phantom images were obtained with each modality (ie, CCD digital radiography and AMBER and Bucky screen-film radiography) and were judged by six observers. CCD digital radiography soft-copy reading was compared with AMBER hard-copy reading. To measure image quality, contrast-detail curves were constructed from the observer data. The Wilcoxon signed rank test was used for statistical analysis. RESULTS: For the lung configuration, contrast-detail curves showed lower threshold depth for hard-copy images obtained with CCD digital radiography than for those obtained with Bucky screen-film radiography. For hard-copy images, the difference between contrast-detail curves for CCD digital radiography and those for Bucky screen-film radiography was statistically significant (P < .006). No significant difference was found between CCD digital radiography and AMBER for hard-copy images obtained in either the lung or mediastinum configuration. For the lung configuration, a lower threshold depth was observed for CCD digital radiography soft-copy reading than for AMBER hard-copy reading, with significantly different contrast-detail curves for CCD digital radiography soft copy and AMBER hard copy (P < .006). No significant difference was found between either system for the mediastinum configuration. CONCLUSION: Contrast-detail curves indicate that image quality for the CCD chest system provides a digital alternative to AMBER and Bucky screen-film radiography.

Phantoms, Imaging↗
PubMedDate not supplied

Comparison of inter-observer reproducibility between conventional chest radiography and AMBER in the evaluation of silicosis.

The aims of this study were to test inter-observer and intraobserver agreement in the diagnosis of silicosis using conventional chest radiography and AMBER. One hundred and fifteen patients underwent chest x-rays and AMBER for the diagnosis of silicosis. Five readers blindly and independently evaluated the radiograms with standard ILO/UC classification scales. Reproducibility was assessed using ANOVA repeated measurements methods. AMBER showed a better technical quality of radiograms than conventional chest x-rays; interobserver reproducibility was high and similar (R = 0.75); intraobserver agreement between chest x-rays and AMBER was high ranging from 0.62 to 0.86 for the 5 readers. Notwithstanding the absence of standards for profusion classification, the interobserver reproducibility with AMBER was similar to that obtained with chest x-rays. Moreover, the intraobserver agreement in profusion scoring between AMBER and chest radiography was high, suggesting that AMBER and chest radiography provided similar information in the evaluation of silicosis.

Aged↗
PubMed1984

Amber dnaG mutation exerting a polar effect on the synthesis of RNA polymerase sigma factor in Escherichia coli.

Three amber mutants of Escherichia coli, dnaG9, dnaG24 and dnaG26, affected in the structural gene (dnaG) for "primase" have been isolated from a parental strain carrying a temperature-sensitive amber suppressor (supF-Ts6). These mutants grow at 30 degrees C but not at 42 degrees C since primase is essential for growth and is synthesized only at low temperatures. Chimeric plasmids carrying dnaG+ but no other chromosomal genes of E. coli complemented the amber mutations, and the plasmid carrying a part of dnaG lost the complementing activity. Beside, plasmids carrying a dnaG amber mutation complemented a temperature-sensitive dnaG mutation only in the presence of amber suppressor. One of the amber mutations, dnaG24 which maps proximal to the NH2-terminus of the dnaG gene, exerted a polar effect on the synthesis of RNA polymerase sigma factor in E. coli.

DNA Primase↗
PubMed1997

Physical mapping of a collection of Mael-generating amber mutations in the beta gene of Escherichia coli RNA polymerase and the functional effect of internal deletions constructed through their manipulation.

We report the fine mapping of 55 of our 95 amber mutations in the beta gene of Escherichia coli RNA polymerase by virtue of the unique MaeI restriction sites created by this subset of nonsense mutations (i.e. CTAG, where the amber codon is underlined). [The full data are reported in Supplementary Publication SUP 50181 (12 pages), which has been deposited at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1997) 321, 8-10.] The CTAG mutations, which have been positioned to within approx. 9-60 bp, are distributed almost along the entire length of the rpoB gene, the one exception being the interval 400-499. The lack of amber fragments for mutations within the 5' approx. 265 codons suggests lability of the extreme N-terminal region; further potential destabilizing 'signals' may be present in the non-conserved 'spacer' regions. The locations of four of the eleven rpoB amber mutations that are strongly polar on expression of the downstream rpoC gene have been determined through a combination of MaeI mapping, PCR amplification and DNA sequencing. Surprisingly, one such mutant carries two tandem CTAG sites but is viable with three of the nonsense suppressors tested. These polar amber sites define three different amino acids (Gln-31, Gln-83 and Trp-183) that fall within three sequence-conservation blocks in the N-terminal region. Six of the MaeI/Am (where MaeI/Am is an amber mutation generating a MaeI restriction site) rpoB alleles (Gln-83, Gln-276, Gln-327, Gln-618, Gln-649 and Trp-183) have been used to generate small in-frame deletions (31-100 codons) within conserved and non-conserved regions of the beta gene, and the properties of these deletion variants were assessed in vivo. The smallest deletion reported in this study removes 31 amino acids from the middle of a region common to the eubacterial/chloroplast subgroup of beta homologues, and our results strongly suggest beta(deltaQ618-Q649) is assembled into a holoenzyme form capable of transcriptional initiation in vivo.

Amino Acid Sequence↗
PubMed1982

Polyamine requirement for efficient translation of amber codons in vivo.

Multiplication of several amber mutants of bacteriophage T7 was decreased in two polyamine-deficient mutants of Escherichia coli K-12 carrying amber suppressors, relative to the multiplication of wild type bacteriophage T7 in the same hosts. In contrast the same T7 amber bacteriophages multiplied well in these strains when supplemented with polyamines. The requirement for polyamines for optimal translation of amber codons in vivo was confirmed by showing that infection of polyamine-depleted E. coli with bacteriophage T7 carrying an amber mutation in gene 1 resulted in an increased accumulation of the amber fragment of the gene 1 protein and a decreased accumulation of the full-length gene 1 protein compared with infection of an amine-supplemented culture. These results indicate that one important function of polyamines in vivo is concerned with protein translation and the protein-synthesizing ribosomal complex.

Codon↗
PubMed1979

Conditionally lethal amber mutations in the dnaA region of the Escherichia coli chromosome that affect chromosome replication.

Three amber mutations, dna-801, dna-803, and dna-806, were isolated by localized mutagenesis of the dnaA-oriC region of the chromosome from an Escherichia coli strain carrying temperature-sensitive amber suppressors. When the mutations were not suppressed at 42 degrees C, the cells did not grow and DNA synthesis was arrested. They were very closely linked to each other and to the dnaA46 mutation. The mutant phenotype of each strain was converted to the wild type by infecting the mutants with specialized transducing phase lambda i21 dnaA-2 but not with lambda i21 tna. Derivatives of lambda i21 dnaA-2, each of which carried the amber mutation dna-801 dna-803, or dna-806, converted the dnaA mutant phenotype to Dna+ but did not convert rhe amber mutants to the wild-type phenotype. E. coli uvrB cells were irradiated with ultraviolet light and infected with each of these phage strains. An analysis of proteins synthesized in the cells revealed that two proteins with molecular weights of 50,000 and 43,000 were specified by lambda i21 dnaA-2 but not by lambda i21 tna. When the ultraviolet-irradiated cells did not carry an amber suppressor, the derivative phage with the amber mutation invariably failed to produce the 43,000-dalton protein, but when the host cell carried supF (tyrT), the protein was produced. The 50,000-dalton protein was unaffected.

Bacterial Proteins↗
PubMed1998

Tetracycline-regulated suppression of amber codons in mammalian cells.

As an approach to inducible suppression of nonsense mutations in mammalian cells, we described recently an amber suppression system in mammalian cells dependent on coexpression of Escherichia coli glutaminyl-tRNA synthetase (GlnRS) along with the E. coli glutamine-inserting amber suppressor tRNA. Here, we report on tetracycline-regulated expression of the E. coli GlnRS gene and, thereby, tetracycline-regulated suppression of amber codons in mammalian HeLa and COS-1 cells. The E. coli GlnRS coding sequence attached to a minimal mammalian cell promoter was placed downstream of seven tandem tetracycline operator sequences. Cotransfection of HeLa cell lines expressing a tetracycline transactivator protein, carrying a tetracycline repressor domain linked to part of a herpesvirus VP16 activation domain, with the E. coli GlnRS gene and the E. coli glutamine-inserting amber suppressor tRNA gene resulted in suppression of the amber codon in a reporter chloramphenicol acetyltransferase gene. The tetracycline transactivator-mediated expression of E. coli GlnRS was essentially completely blocked in HeLa or COS-1 cells grown in the presence of tetracycline. Concomitantly, both aminoacylation of the suppressor tRNA and suppression of the amber codon were reduced significantly in the presence of tetracycline.

Acylation↗
PubMed1993

Advanced multiple beam equalization radiography (AMBER) combined with computed radiography. Preliminary evaluation.

The combined use of AMBER (Advanced Multiple Beam Equalization Radiography) and a digital storage phosphor (SP) radiography system was evaluated for chest radiography in a pilot study with 4 patients. Four image modes with different dose levels were compared: the SP in combination with an AMBER equalized exposure (SP/AMBER) and 3 nonequalized exposures with dose levels corresponding to the respective calculated AMBER lung dose (SP/lung field dose), the calculated AMBER mediastinal dose (SP/mediastinal dose) and the calculated AMBER average dose (SP/average dose). All image modes were matched for Hurter and Driffield characteristics and subjectively rated according to visibility of details. The improved signal-to-noise (S/N) ratio of SP/AMBER resulted in a better visualization of structures in the mediastinum and the basal lung where SP/lung field dose scored lowest. For the central lung no quality differences were seen between techniques. The compressed dynamic range of the SP/AMBER images was more easily displayed on the hard-copy film. The combination of AMBER with SP radiography promises to overcome the dynamic range limitations of digital displays while, at moderate doses, giving better S/N and image quality than standard SP technique.

Adult↗
PubMed2006

Applications of diamond crystal ATR FTIR spectroscopy to the characterization of ambers.

Diamond crystal ATR FTIR spectroscopy is a rapid technique with virtually no sample preparation which requires small sample amounts and showed potential in the study of ambers. FTIR spectra of ambers present discriminating patterns and can be used to distinguish amber from immature resins as copal, to determine local or Baltic origin of archaeological ambers and to detect most of the falsifications encountered in the amber commercialisation.

Amber↗
PubMed1990

Frameshift and double-amber mutations in the bacteriophage T4 uvsX gene: analysis of mutant UvsX proteins from infected cells.

The bacteriophage T4 uvsX gene encodes a 43 kDa, single-stranded DNA-dependent ATPase, double-stranded DNA-binding protein involved in DNA recombination, repair and mutagenesis. Mutants of uvsX have a DNA-arrest phenotype and reduced burst size. Western blot immunoassay of UvsX peptides made by a number of amber mutants revealed amber peptides ranging from 25-32 kDa. Wild-type UvsX protein was also detected in lysates of cells infected with uvsX amber mutants, suggesting that their mutations are suppressed by translational ambiguity. We investigated the effects of mutations near the 5' end of uvsX. A frameshift mutation was engineered at codon 33. Western immunoblots for UvsX protein demonstrated that the frameshift mutant expresses no detectable wild-type UvsX; instead, a 37 kDa reactive peptide was detected. In order to determine if this peptide represents truncated UvsX protein, the mutation was regenerated in the cloned uvsX gene and expressed in transformed Escherichia coli. Endopeptidase digestion of the 37 kDa protein from the cloned gene generated peptide fragments indistinguishable from those obtained from wild-type UvsX. A double-amber mutant of uvsX was also generated by oligonucleotide site-directed mutagenesis. No UvsX protein was detected in lysates of cells infected with the uvsXam64am67 double mutant. Plaque size and sensitivity to UV inactivation for both the double-amber and the frameshift mutants were indistinguishable from those of other uvsX mutants. Mutations in uvsY had no demonstrable effect on efficiency of plating or UV sensitivity of uvsX mutants. Thus, null mutants of uvsX are viable.

Adenosine Triphosphatases↗