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At least 253 records · Page 14Linked to original sources
PubMed2006

Amber from western Amazonia reveals Neotropical diversity during the middle Miocene.

Tertiary insects and arachnids have been virtually unknown from the vast western Amazonian basin. We report here the discovery of amber from this region containing a diverse fossil arthropod fauna (13 hexapod families and 3 arachnid species) and abundant microfossil inclusions (pollen, spores, algae, and cyanophyceae). This unique fossil assemblage, recovered from middle Miocene deposits of northeastern Peru, greatly increases the known diversity of Cenozoic tropical-equatorial arthropods and microorganisms and provides insights into the biogeography and evolutionary history of modern Neotropical biota. It also strengthens evidence for the presence of more modern, high-diversity tropical rainforest ecosystems during the middle Miocene in western Amazonia.

Amber↗
PubMed2005

First identifiable Mesozoic harvestman (Opiliones: Dyspnoi) from Cretaceous Burmese amber.

Two inclusions in a piece of Upper Cretaceous (Albian) Burmese amber from Myanmar are described as a harvestman (Arachnida: Opiliones), Halitherses grimaldii new genus and species. The first Mesozoic harvestman to be named can be referred to the suborder Dyspnoi for the following reasons: prosoma divided into two regions, the posterior formed by the fusion of the meso- and metapeltidium; palp lacking a terminal claw, with clavate setae, and tarsus considerably shorter than the tibia. The bilobed, anteriorly projecting ocular tubercle is reminiscent of that of ortholasmatine nemastomatids. The status of other Mesozoic fossils referred to Opiliones is briefly reviewed.

Amber↗
PubMed1998

Staphylococcus succinus sp. nov., isolated from Dominican amber.

Two bacterial isolates, designated AMG-D1T and AMG-D2, were recovered from 25-35-million-year-old Dominican amber. AMG-D1T and AMG-D2 biochemically most closely resemble Staphylococcus xylosus; they differ physiologically from other staphylococci. Fatty acid analysis and comparisons with extensive databases were unable to show relatedness to any specific taxon. Moreover, AMG-D1T and AMG-D2 contain tuberculostearic acid and meso-diaminopimelic acid, characteristic of the G + C-rich coryneform bacteria, as opposed to L-lysine characteristic of staphylococci. AMG-D1T and AMG-D2 have a G + C ratio of 35 mol%. Phylogenetic analysis with the 16S rRNA gene indicated that AMG-D1T and AMG-D2 were most closely related to Staphylococcus equorum, S. xylosus, Staphylococcus saprophyticus and other novobiocin-resistant staphylococci. Stringent DNA-DNA hybridization studies with AMG-D1T revealed similarities of 38% with S. equorum, 23% with S. xylosus and 6% with S. saprophyticus. The results indicate that AMG-D1T and AMG-D2 represent a novel species, which was named Staphylococcus succinus sp. nov. The type strain of the new species is AMG-D1 (ATCC 700337).

Amber↗
PubMed2006

A fossil bee from Early Cretaceous Burmese amber.

The bee fossil record is fragmentary, making it difficult to accurately estimate the antiquity of bee-mediated pollination. Here, we describe a bee fossil [Melittosphex burmensis (new species), Melittosphecidae (new family)] from Early Cretaceous Burmese amber (approximately 100 million years before the present). The fossil provides insights into the morphology of the earliest bees and provides a new minimum date for the antiquity of bees and bee-mediated pollination.

Amber↗
PubMed1991

Amber mutation creates a diagnostic MaeI site in the androgen receptor gene of a family with complete androgen insensitivity.

We have discovered in the X-linked androgen receptor gene a single nucleotide substitution that is the putative cause of complete androgen insensitivity (resistance) in a family with affected individuals in 2 generations. Earlier studies on the family indicated co-segregation of mutant phenotype and the RFLPs at the loci DXS1 and DXYS1. The mutation is an adenine-to-thymine transversion in exon 8 that changes the sense of codon 882 from lysine to an amber (UAG) translation termination signal. The substitution creates a recognition sequence for the restriction endonuclease MaeI: this permits ready recognition of hemizygotes and heterozygotes after amplification of genomic exon 8 by the polymerase chain reaction. The mutation predicts the synthesis of a truncated receptor that lacks 36 amino acids at the carboxy terminus of its 252-amino acid androgen-binding domain. The cultured genital skin fibroblasts of the one affected patient examined have normal levels of androgen receptor mRNA, but negligible androgen-receptor binding activity. These results accord with a variety of data from spontaneous and artificial mutations indicating that all portions of the steroid binding domain contribute to normal steroid binding by a steroid receptor.

Amino Acid Sequence↗
PubMed1984

The Schizosaccharomyces pombe sup3-i suppressor recognizes ochre, but not amber codons in vitro and in vivo.

The inefficient suppressor sup3-i of the fission yeast Schizosaccharomyces pombe is an ochre suppressor. Sup3-i was derived from the efficient serine inserting UGA suppressor sup3-e. The cloning and sequencing of the sup3-i gene indicate that the suppressor is different from the parent sup3-e by a C----T substitution in the sequence coding for the middle position of the anticodon. In vitro translation assays supplemented with purified sup3-i tRNA and programmed with Xenopus globin mRNAs lead to the accumulation of a readthrough product in response to UAA termination signals, but not in response to UGA termination codons. Transformation of Saccharomyces cerevisiae nonsense mutant strains with plasmid DNA carrying the S. pombe sup3-i gene, led to ochre, but not amber or UGA suppression in vivo.

Alleles↗
PubMed2006

Thixotrophy property of hydrogels to evaluate the cell growing on the inside of the material bulk (Amber effect).

The realization of injectable hydrogels is one of the most challenging aims of biomedical research. Most injectable hydrogels are obtained by photopolymerization in situ. A hydrogel which is able to pass through a needle without losing its structure once crosslinked would be of great interest for several biomedical applications. In this work, hyaluronane and alginate-based 50% hydrogels were synthesized, their thixotrophic behavior was verified and their mechanical properties (G' and G'') were determined before and after the passage through the needle. A morphological analysis by scanning electron microscopy (SEM) was also performed in order to evaluate the effect of the passage of the hydrogel through the needle on the morphological structure of the material. The thixotrophic property of these hydrogels is used to realize a cell-containing material that supports cell proliferation and growth permitting in vivo engineering of new tissues. In fact, thixotrophic hydrogel can be sucked together with cell suspension and in this way cells remain entrapped inside the hydrogel structure (Amber effect). A comparison of the cell growth using this technique with the classical seeding technique (cell seeding onto the hydrogel) was performed. A different behavior was found between hyaluronane and alginate-based hydrogels.

Humans↗
PubMed2005

The Amber biomolecular simulation programs.

We describe the development, current features, and some directions for future development of the Amber package of computer programs. This package evolved from a program that was constructed in the late 1970s to do Assisted Model Building with Energy Refinement, and now contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.

Algorithms↗
PubMed2004

Distinguish protein decoys by using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model.

Recent works have shown the ability of physics-based potentials (e.g., CHARMM and OPLS-AA) and energy minimization to differentiate the native protein structures from large ensemble of non-native structures. In this study, we extended previous work by other authors and developed an energy scoring function using a new set of AMBER parameters (also recently developed in our laboratory) in conjunction with molecular dynamics and the Generalized Born solvent model. We evaluated the performance of our new scoring function by examining its ability to distinguish between the native and decoy protein structures. Here we present a systematic comparison of our results with those obtained with use of other physics-based potentials by previous authors. A total of 7 decoy sets, 117 protein sequences, and more than 41,000 structures were evaluated. The results of our study showed that our new scoring function represents a significant improvement over previously published physics-based scoring functions.

Computational Biology↗
PubMed2004

Physical scoring function based on AMBER force field and Poisson-Boltzmann implicit solvent for protein structure prediction.

A well-behaved physics-based all-atom scoring function for protein structure prediction is analyzed with several widely used all-atom decoy sets. The scoring function, termed AMBER/Poisson-Boltzmann (PB), is based on a refined AMBER force field for intramolecular interactions and an efficient PB model for solvation interactions. Testing on the chosen decoy sets shows that the scoring function, which is designed to consider detailed chemical environments, is able to consistently discriminate all 62 native crystal structures after considering the heteroatom groups, disulfide bonds, and crystal packing effects that are not included in the decoy structures. When NMR structures are considered in the testing, the scoring function is able to discriminate 8 out of 10 targets. In the more challenging test of selecting near-native structures, the scoring function also performs very well: for the majority of the targets studied, the scoring function is able to select decoys that are close to the corresponding native structures as evaluated by ranking numbers and backbone Calpha root mean square deviations. Various important components of the scoring function are also studied to understand their discriminative contributions toward the rankings of native and near-native structures. It is found that neither the nonpolar solvation energy as modeled by the surface area model nor a higher protein dielectric constant improves its discriminative power. The terms remaining to be improved are related to 1-4 interactions. The most troublesome term is found to be the large and highly fluctuating 1-4 electrostatics term, not the dihedral-angle term. These data support ongoing efforts in the community to develop protein structure prediction methods with physics-based potentials that are competitive with knowledge-based potentials.

Algorithms↗
PubMed1993

An amber mutation of prion protein in Gerstmann-Sträussler syndrome with mutant PrP plaques.

We found an amber mutation in the open reading frame of the prion protein (PrP) gene. The codon 145 mutation (tyrosine to stop) was recognized on a PrP allele of a patient with Alzheimer-type clinical course. Pathologic examination revealed many amyloid plaques and neurofibrillary changes. However, the amyloid plaques in this patient were not composed of beta/A4 protein, but of PrP. Both wild and mutant PrP alleles were detected in the cerebral mRNA; however, only C-terminal truncated PrP was detected in the kuru plaques. We herein present evidence that only mutant PrP aggregates to make kuru plaques in the central nervous system.

Adult↗
PubMed1991

Amber codon suppression: the in vivo and in vitro analysis of two C-hordein genes from barley.

A 1420 bp genomic fragment (lambda-hor1-17) encompassing a Hor-1 gene encoding a C-hordein polypeptide is presented. The deduced amino acid sequence is 261 residues long. It comprises a 20 amino acid signal peptide, unique NH2- and COOH-terminal regions and a coding region comprised of pentapeptide (PQQPY) and octapeptide (PQQPFPQQ) repeat motifs. The 431 bp of 5' non-coding region contains a 'TATA box' at -105, a 'CACA box' (-181 to -201) and a -300 prolamin element. In the 3' non-coding region there are two putative polyadenylation signals located 88 and 142 bp downstream of the stop codon. The structure of lambda-hor1-17 is compared with that of another gene (lambda-hor1-14) encoding a C-hordein polypeptide, which contains an amber codon interrupting the ORF. A functional assay in which the 5' non-coding regions of the two genes were fused to the beta-glucuronidase (GUS) gene demonstrated that both genes were transcriptionally active and that circa 430 bp of the C-hordein promoters were sufficient to drive the expression of the GUS gene in developing barley endosperms. It also demonstrated that both promoters had transcriptional efficiencies comparable with that of the 35S CaMV promoter. The in vitro translation of the coding region of lambda-hor1-14 in the wheat germ system showed that the premature stop codon could be partially suppressed. The suppression was also demonstrated in a transient expression assay in vivo using isolated barley endosperms.

Amino Acid Sequence↗
PubMed1979

Isolation and properties of a plasmid which expresses the E. coli Su+7 amber suppressor tRNA gene.

The gene of the amber suppressor tRNA derived from tRNATry, Su+7, has been inserted into a col E1-derived vehicle by selecting for its expression. Despite selection for a suppressor phenotype, and the plasmid's stable presence at ca. 180 copies cell during balanced growth, the level mature tRNA maintained by the gene is less than that of the normal haploid tRNATry locus in the bacterial chromosome. Transfer RNA genes, both the plasmid Su+7 gene and chromosomal tRNA's are expressed during inhibition of protein synthesis. During, e.g. chloramphenicol inhibition, Su-7 and Su+7 tRNA can be elevated similarly in the plasmid-containing cell; Su+7 reaches levels of molecules/cell which ordinarily characterize a major tRNA. The recombinant plasmid, but not the cloning vehicle alone, has a more general effect on tRNA levels; accumulation of tRNA from three chromosomal tRNA loci including tRNATry, continues during extensive isoleucine limitation. The plasmid therefore contains a locus which probably alters the relaxed-stringent circuit, whose effect is disseminated to at least 3 widely separated loci.

Chromosome Mapping↗
PubMed1980

High efficiency temperature-sensitive amber suppressor strains of Escherichia coli K12: isolation of strains with suppressor-enhancing mutations.

Two independent high efficiency ts amber suppressor strains have been isolated as derivatives of a well-characterized supD ts suppressor strain (Oeschger and Woods, 1976). The mutations which raise suppressor activity have been shown by Hfr mapping to be distinct from each other and the supD locus. One of the isolates provides up to 100% efficient suppressor activity at low temperatures.

Chromosome Mapping↗
PubMed1986

Amber nonsense mutations in regulatory and structural genes of the nitrogen control circuit of Neurospora crassa.

Neurospora crassa possesses a set of nitrogen-regulated enzymes whose expression requires a lifting of nitrogen catabolite repression and specific induction. The nit-2 gene is a major regulatory locus which appears to act in a positive way to turn on the expression of these nitrogen-related enzymes whereas the nit-4 gene appears to mediate nitrate induction of nitrate and nitrite reductase. The nit-3 gene specifies nitrate reductase and is subject to control by both nit-2 and nit-4. Many new nit-2, nit-3, and nit-4 mutants were isolated in order to obtain amber nonsense mutations in these loci which were suppressible by the suppressor gene, Ssu-1. A nit-2 nonsense mutant was isolated which has altered regulatory properties for control of nitrate reductase. L-amino acid oxidase, and uricase, and which may encode a truncated regulatory protein. Four nit-3 nonsense mutations were isolated, each of which completely lacks nitrate reductase activity, which is restored to markedly different levels by suppression with Ssu-1. Studies of heat activation and thermal lability of nitrate reductase suggest a qualitative alteration of the enzyme occurs in two of the Ssu-1 nit-3 strains.

Genes↗
PubMed1993

PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus).

DNA from 30-million-year-old amber preserved termites (Mastotermes electrodominicus) was PCR amplified with nuclear ribosomal RNA small subunit primers and cloned into the TA vector (INVITROGEN). We obtained several classes of recombinant clones as a result. Authentic Mastotermes electrodominicus clones were identified. The source of other classes of clones was identified as contaminants of the ancient DNA template. Several of the clones appeared to be chimeric in structure with half of the clone identical to the termite sequence and the other half identical to contaminant sequences. The phenomenon of PCR jumping was identified as a possible source for the chimeric clones.

Animals↗