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 163 records · Page 9Linked to original sources
PubMed1980

Regulation of RNA polymerase synthesis. Conditional lethal amber mutations in the beta subunit gene.

Amber mutations in the rpoB gene specifying the beta subunit of RNA polymerase coupled with conditional amber suppressors were used to restrict the synthesis of core RNA polymerase in strains of Escherichia coli. Such a restriction stimulated transcription of genetic units containing RNA polymerase subunit genes. Within the L10 transcription unit (genetic structure: promotor (PL10), rplJ (L10), rplL (L7/L12), attenuator, rpoB (beta), rpoC (beta'), terminator), the initiation of transcription at the promotor was enhanced and termination at the transcription attenuator was relaxed. Transcription of the genetic unit containing the rpoA gene (alpha) was also enhanced. In the strain containing a non-polar amber mutation, the synthesis rate of the beta' subunit protein during the restriction correlated with the level of transcription of the beta and beta' genes. In contrast, synthesis of L7/L12 ribosomal protein remained essentially unaltered in spite of the elevated levels of L10-L7/L12 mRNA.

DNA-Directed RNA Polymerases↗
PubMed1993

[Evaluation of bronchiectasia with AMBER and high-resolution computerized tomography. Prospective study of a group of 50 patients].

The authors compared the diagnostic value of AMBER and HRCT in the evaluation of bronchiectasis. A series of 50 patients with conventional X-ray findings suggestive of this condition (increased pulmonary markings, loss of pulmonary volume and segmental cysts) were submitted to HRCT. In all the patients with bronchiectasis (25/50), AMBER showed increased pulmonary markings in one or more localizations, while loss of pulmonary volume was observed in 22 cases and segmental cysts in 8. The positive predictive value (PPV) of these findings was 50% for increased markings, 59% for the loss of pulmonary volume, 64% for the association of the former two signs and finally 100% for segmental cysts. The false-positive cases were due to bronchial wall thickening and to areas of peribronchial fibrosis. On the basis of their findings, the authors conclude that, except for the finding of segmental cysts, AMBER does not allow the unquestionable diagnosis of bronchiectasis to be made due to its low PPV (64%) and that further studies with HRCT are therefore required.

Bronchiectasis↗
PubMed1993

Identity of Saccharomyces cerevisiae tRNA(Trp) is not changed by an anticodon mutation that creates an amber suppressor.

A C35-->T mutation in an Escherichia coli tRNA(Trp) gene creates an amber suppressor which efficiently inserts glutamine in response to UAG codons in vivo (Soll, L., and Berg, P. (1969) Nature 223, 1340-1342). We have introduced the same change in a yeast tRNA(Trp) gene and demonstrated that the tRNA acts as an efficient amber suppressor in vivo. Amino acid sequence analyses were performed on chitinase produced by cells carrying the corresponding gene with a UAG codon at position 8 of the mature protein plus the mutant tRNA(Trp) gene. In contrast to comparable experiments with E. coli, tryptophan is inserted at a frequency > or = 80% by the yeast suppressor tRNA(Trp). Furthermore, in vitro charging experiments with the mutant tRNA(Trp) reveal no detectable increase in glutamine acceptor activity results from the C35-->T transition. The identity elements in E. coli tRNA(Gln) are well characterized (Jahn, M., Rogers, J., and Soll, D. (1991) Nature 352, 258-260). Sequence comparisons of the tRNA(Trp) and tRNA(Gln) molecules from E. coli reveal that the amber suppressor tRNA(Trp) has four of five identity elements required for glutaminyl-tRNA synthetase recognition. A similar comparison in the yeast system shows only two of the five potential identity elements are present. We conclude that, in spite of substantial structural similarities between yeast and E. coli aminoacyl-tRNA synthetases, fundamental differences can exist with regard to tRNA recognition.

Amino Acyl-tRNA Synthetases↗
PubMed2004

Bulk carbon, oxygen, and hydrogen stable isotope composition of recent resins from amber-producing Hymenaea.

Resins of Hymenaea, an angiosperm tree genus known to be a copious resin producer and a major source of amber since the Oligo-Miocene, were collected from a wide range of tropical environments from Latin America and Africa, and analyzed for their carbon, hydrogen, and oxygen stable isotope composition. The average value for delta13C in the resins was found to be -27.0+/-1.3 per thousand, which is very similar to the values reported for resins in other studies. Delta18O values for the Hymenaea resins averaged +11.2+/-1.6 per thousand, or about 20 per thousand more depleted than normal plant cellulose. DeltaD values of the resins ranged from -196 to -319 per thousand, with an average of -243+/-30 per thousand. Rough estimates suggest a fractionation of -200 to -210 per thousand between the resins and the environmental water. This value is similar to the -200 per thousand value observed for the fractionation between other plant lipids and environmental water. The present study suggests that the stable isotope composition of fossil resins (amber) has the potential to provide information on ancient environmental waters.

Amber↗
PubMed2004

Micrococcus luteus -- survival in amber.

A growing body of evidence now supports the isolation of microorganisms from ancient materials. However, questions about the stringency of extraction methods and the genetic relatedness of isolated organisms to their closest living relatives continue to challenge the authenticity of these ancient life forms. Previous studies have successfully isolated a number of spore-forming bacteria from organic and inorganic deposits of considerable age whose survival is explained by their ability to enter suspended animation for extended periods of time. However, despite a number of putative reports, the isolation of non-spore-forming bacteria and an explanation for their survival have remained enigmatic. Here we describe the isolation of non-spore-forming cocci from a 120-million-year-old block of amber, which by genetic, morphological, and biochemical analyses are identified as belonging to the bacterial species Micrococcus luteus. Although comparison of 16S rRNA sequences from the ancient isolates with their modern counterparts is unable to confirm the precise age of these bacteria, we demonstrate, using complementary molecular and cell biological techniques, evidence supporting the view that these (and related modern members of the genus) have numerous adaptations for survival in extreme, nutrient-poor environments, traits that will assist in this bacteria's persistence and dispersal in the environment. The bacteria's ability to utilize succinic acid and process terpine-related compounds, both major components of natural amber, support its survival in this oligotrophic environment.

Amber↗
PubMed2005

A fossil Aspergillus from Baltic amber.

A piece of Baltic amber (Tertiary, Eocene) contains an inclusion of a springtail (Collembola) which is overgrown by an Aspergillus species. The fossil fungus is described as A. collembolorum sp. nov. The excellent mode of preservation of the numerous conidiophores is remarkable and can be explained by sporulation in liquid resin. This is the second report of a fossil Aspergillus, the first being from Dominican amber.

Amber↗
PubMed2002

Amber: the organic gemstone.

Resins are produced by woody plants on a worldwide basis. We have found several distinct classes of modern diterpenoid resins based phenomenologically on the solid-state (13)C NMR spectra of the bulk material. Resin fossilizes over millions of years into a robust material sometimes called amber. We have characterized several hundred samples of fossil resin by solid-state (13)C NMR spectroscopy. We can relate one globe-spanning group of fossil resins to the modern genus Agathis, based on spectral evolution over time. A second large group has not been related with certainty to specific modern plants. Fossil resins from Europe fall into two categories, the famous Baltic ambers and another that resembles the Agathis group. Fossil resins from the Americas and Africa are closely related to the modern genus Hymenaea. Based on spectral distinctions, fossil resin found in an archaeological context sometimes can be assigned to a specific geographical origin on the basis of its (13)C NMR spectrum.

Amber↗
PubMed2006

A microworld in Triassic amber.

Amber provides an effective medium for conservation of soft-bodied microorganisms, but finds older than 135 million years are very rare and have not so far contained any microbial inclusions. Here we describe 220-million-year-old droplets of amber containing bacteria, fungi, algae and protozoans that are assignable to extant genera. These inclusions provide insight into the evolution and palaeoecology of Lower Mesozoic microorganisms: it seems that the basal levels of food webs of terrestrial communities (biocoenoses) have undergone little or no morphological change from the Triassic to the Recent.

Amber↗
PubMed2002

Spirochete and protist symbionts of a termite (Mastotermes electrodominicus) in Miocene amber.

Extraordinary preservation in amber of the Miocene termite Mastotermes electrodominicus has led to the discovery of fossil symbiotic microbes. Spirochete bacteria and wood-digesting protists were identified in the intestinal tissue of the insect. Fossil wood (xylem: developing vessel-element cells, fibers, pit connections), protists (most likely xylophagic amitochondriates), an endospore (probably of the filamentous intestinal bacterium Arthromitus = Bacillus), and large spirochetes were seen in thin section by light and transmission electron microscopy. The intestinal microbiota of the living termite Mastotermes darwiniensis, a genus now restricted to northern Australia, markedly resembles that preserved in amber. This is a direct observation of a 20-million-year-old xylophagus termite fossil microbial community.

Amber↗
PubMed2005

Cellular fine structures and histochemical reactions in the tissue of a cypress twig preserved in Baltic amber.

A twig of a cypress plant preserved for ca. 45 Myr in Baltic amber was analysed by light and electron microscopy. Cross-sections of the whole plant showed an almost intact tissue of the entire stem and leaves, revealing, to our knowledge, the oldest and most highly preserved tissue from an amber inclusion reported so far. The preparations are based on a new technique of internal imbedding, whereby the hollow spaces within the inclusion are filled with synthetic resin which stabilizes the cellular structures during the sectioning procedure. Cytological stains applied to the sections reacted with cell walls and nuclei. A strong green auto-fluorescence of the cuticle and the resin canals in the leaves was observed. Transmission electron micrographs revealed highly preserved fine structures of cell walls, membranes and organelles. The results were compared with taxonomically related recent Glyptostrobus and Juniperus plants.

Amber↗
PubMed1995

Revival and identification of bacterial spores in 25- to 40-million-year-old Dominican amber.

A bacterial spore was revived, cultured, and identified from the abdominal contents of extinct bees preserved for 25 to 40 million years in buried Dominican amber. Rigorous surface decontamination of the amber and aseptic procedures were used during the recovery of the bacterium. Several lines of evidence indicated that the isolated bacterium was of ancient origin and not an extant contaminant. The characteristic enzymatic, biochemical, and 16S ribosomal DNA profiles indicated that the ancient bacterium is most closely related to extant Bacillus sphaericus.

Amber↗
PubMed1995

The use of the AMBER force field in conformational analysis of carbohydrate molecules: determination of the solution conformation of methyl alpha-lactoside by NMR spectroscopy, assisted by molecular mechanics and dynamics calculations.

The solution conformation of methyl alpha-lactoside has been studied through nmr spectroscopy and molecular mechanics calculations using the assisted model building with energy refinement (AMBER) force field. The nmr data have included nuclear Overhauser effect (NOE) measurements both in the laboratory and rotating frames, longitudinal relaxation times, and homonuclear and heteronuclear coupling constants. The steady-state and transient NOEs have been interpreted in terms of an ensemble average distribution of conformers, making use of the complete relaxation matrix approach. The molecular mechanics calculations have been performed at two dielectric constants [epsilon = 1*r and 80 Debyes (D)] in an exhaustive way, and have been complemented with specific calculations at intermediate epsilon values. Relaxed energy maps and adiabatic surfaces have been generated for the different dielectric constants. The probability distribution of conformers has been estimated from these steric energy maps. Molecular dynamics simulations in vacuo have also been performed. The experimental results indicate that the beta (1-->4)-glycosidic linkage shows some fluctuations among three low energy regions, although spends ca. 85% of its time in the region close to the global minimum. It is shown that the overestimation of the electrostatic contributions in AMBER is responsible for the failure of this force field to explain the experimental results when used at low dielectric constant (epsilon < 20 D). The matching between the expected and observed facts increases for epsilon > 40 D. Different conditions have been tested to perform temperature constant molecular dynamics simulations in vacuo, which have indicated that, when used without explicit solvent, this force field should only be employed in a qualitatively way when analyzing dynamical properties of oligosaccharides.

Carbohydrate Conformation↗
PubMed2004

Development and testing of a general amber force field.

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.

Nucleic Acids↗
PubMed2006

Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides.

Based on the AMBER polarizable model (ff02), we have re-optimized the parameters related to the main-chain (Phi, Psi) torsion angles by fitting to the Boltzmann-weighted average quantum mechanical (QM) energies of the important regions (i.e., beta, P(II), alpha(R), and alpha(L) regions). Following the naming convention of the AMBER force field series, this release will be called ff02pol.rl The force field has been assessed both by energetic comparison against the QM data and by the replica exchange molecular dynamics simulations of short alanine peptides in water. For Ace-Ala-Nme, the simulated populations in the beta, P(II) and alpha(R) regions were approximately 30, 43, and 26%, respectively. For Ace-(Ala)(7)-Nme, the populations in these three regions were approximately 24, 49, and 26%. Both were in qualitative agreement with the NMR and CD experimental conclusions. In comparison with the previous force field, ff02pol.rl demonstrated good balance among these three important regions. The optimized torsion parameters, together with those in ff02, allow us to carry out simulations on proteins and peptides with the consideration of polarization.

Computer Simulation↗
PubMed2002

Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.

A theoretical and computational approach to ab initio structure prediction for polypeptides in water is described and applied to selected amino acid sequences for testing and preliminary validation. The method builds systematically on the extensive efforts applied to parameterization of molecular dynamics (MD) force fields, employs an empirically well-validated continuum dielectric model for solvation, and an eminently parallelizable approach to conformational search. The effective free energy of polypeptide chains is estimated from AMBER united atom potential functions, with internal degrees of freedom for both backbone and amino acid side chains explicitly treated. The hydration free energy of each structure is determined using the Generalized Born/Solvent Accessibility (GBSA) method, modified and reparameterized to include atom types consistent with the AMBER force field. The conformational search procedure employs a multiple copy, Monte Carlo simulated annealing (MCSA) protocol in full torsion angle space, applied iteratively on sets of structures of progressively lower free energy until a prediction of a structure with lowest effective free energy is obtained. Calibration tests for the effective energy function and search algorithm are performed on the alanine dipeptide, selected protein crystal structures, and united atom decoys on barnase, crambin, and six examples from the Rosetta set. Specific demonstration cases of the method are provided for the 8-mer sequence of Ala residues, a 12-residue peptide with longer side chains QLLKKLLQQLKQ, a de novo designed 16 residue peptide of sequence (AAQAA)3Y, a 15-residue sequence with a beta sheet motif, GEWTWDATKTFTVTE, and a 36 residue small protein, Villin headpiece. The Ala 8-mer readily formed an alpha-helix. An alpha-helix structure was predicted for the 16-mer, consistent with observed results from IR and CD spectroscopy and with the pattern in psi/straight phi angles of known protein structures. The predicted structure for the 12-mer, composed of a mix of helix and less regular elements of secondary structure, lies 2.65 A RMS from the observed crystal structure. Structure prediction for the 8-mer beta-motif resulted in form 4.50 A RMS from the crystal geometry. For Villin, the predicted native form is very close to the crystal structure, RMS values of 3.5 A (including sidechains), and 1.01 A (main chain only). The methodology permits a detailed analysis of the molecular forces which dominate various segments of the predicted folding trajectory. Analysis of the results in terms of internal torsional, electrostatic and van der Waals and the electrostatic and non-electrostatic contributions to hydration, including the hydrophobic effect, is presented.

Alanine↗
PubMed2003

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model.

The accuracy of model selection from decoy ensembles of protein loop conformations was explored by comparing the performance of the Samudrala-Moult all-atom statistical potential (RAPDF) and the AMBER molecular mechanics force field, including the Generalized Born/surface area solvation model. Large ensembles of consistent loop conformations, represented at atomic detail with idealized geometry, were generated for a large test set of protein loops of 2 to 12 residues long by a novel ab initio method called RAPPER that relies on fine-grained residue-specific phi/psi propensity tables for conformational sampling. Ranking the conformers on the basis of RAPDF scores resulted in selected conformers that had an average global, non-superimposed RMSD for all heavy mainchain atoms ranging from 1.2 A for 4-mers to 2.9 A for 8-mers to 6.2 A for 12-mers. After filtering on the basis of anchor geometry and RAPDF scores, ranking by energy minimization of the AMBER/GBSA potential energy function selected conformers that had global RMSD values of 0.5 A for 4-mers, 2.3 A for 8-mers, and 5.0 A for 12-mers. Minimized fragments had, on average, consistently lower RMSD values (by 0.1 A) than their initial conformations. The importance of the Generalized Born solvation energy term is reflected by the observation that the average RMSD accuracy for all loop lengths was worse when this term is omitted. There are, however, still many cases where the AMBER gas-phase minimization selected conformers of lower RMSD than the AMBER/GBSA minimization. The AMBER/GBSA energy function had better correlation with RMSD to native than the RAPDF. When the ensembles were supplemented with conformations extracted from experimental structures, a dramatic improvement in selection accuracy was observed at longer lengths (average RMSD of 1.3 A for 8-mers) when scoring with the AMBER/GBSA force field. This work provides the basis for a promising hybrid approach of ab initio and knowledge-based methods for loop modeling.

Algorithms↗
PubMed2001

Pathobiology of amber disease, caused by Serratia Spp., in the New Zealand grass grub, Costelytra zealandica.

Amber disease in the New Zealand grass grub (Costelytra zealandica) is caused by some strains of Serratia entomophila or Serratia proteamaculans (Enterobacteriaceae). When treated with pathogenic isolates, larvae ceased feeding within 48 h, developed an amber coloration after 72 h, and entered a long chronic phase without feeding. An acute dose of 2-4 x 10(4) pathogenic bacteria was sufficient to produce disease in 50% of treated larvae. Time to death was directly related to temperature. At 15 degrees C, infected larvae remained in a chronic, nonfeeding state for more than 4 months prior to death. Nonpathogenic isolates, lacking the disease-causing plasmid (pADAP), had no effect on either feeding or disease. Twenty-four hours after ingestion, bacteria were found predominantly in the hindgut and growth occurred primarily within the fermentation chamber and in the head section of the larvae. Nonpathogenic strains did not multiply in treated larvae. Treatment of diseased larvae with antibiotic eliminated Serratia cells from the insects but did not result in restoration of feeding or the dark gut characteristic of the healthy larva.

Animals↗
PubMed1975

Genetic properties of some amber-ochre supersuppressors in Saccharomyces cerevisiae.

21 amber-ochre supersuppressor alleles have been isolated in a strain of Saccharomyces cerevisiae. Their dominance-recessiveness, temperature sensitivity, allelism, intergenic and intragenic complementation properties and their effect on cell viability and colony growth rate have been characterized. They are compared with the yeast amber-ochre supersuppressors described by Inge-Vechtomov and Andrianova (1970a, b) and Hawthorne and Leupold (1974). The possible molecular basis of their suppressor activity is discussed in relation to their genetic properties.

Alleles↗