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At least 73 records · Page 4Linked to original sources
PubMed1995

AMBER chest radiography and patient dose measurements.

PURPOSE: Improved chest imaging has been reported with the usage of AMBER (advanced multiple-beam equalization radiography) equipment but with a higher patient radiation dose compared with conventional chest radiography. Most studies, however, describe dose measurements from phantoms. This study presents a comparison of radiation dose measurements in 57 patients for p.a. projections from an AMBER unit with and without an extra Cu filtration and from a formerly used conventional Siemens chest stand. MATERIAL AND METHODS: Dose measurements were performed with thermoluminescence dosimetry. Entrance surface doses were recorded from 5 dosimeters, placed on the patient's back. Four were placed over the upper and lower lung fields, respectively, and 1 over the mediastinal area. The dose values were then compared with the values obtained from the conventional chest stand and from the measurements with the extra filtration on the AMBER system. RESULTS: The mean entrance dose for the mediastinal area was 0.25 mSv (range 0.15-0.49). With the extra Cu filtration it was 0.16 mSv (0.07-0.29). For the lung fields the values were 0.19 mSv (0.07-0.44) and 0.10 mSv (0.02-0.31), respectively. For the conventional chest stand the entrance dose to the patient was 0.23 mSv. CONCLUSION: AMBER entrance surface doses for the p.a. projection without extra Cu filtration were comparable to the doses obtained with the formerly conventional Siemens chest stand and were well within European recommendations. With extra Cu filtration the AMBER entrance surface doses were reduced by a factor of almost 2.

Adult↗
PubMed1994

Amino acid racemization in amber-entombed insects: implications for DNA preservation.

DNA depurination and amino acid racemization take place at similar rates in aqueous solution at neutral pH. This relationship suggests that amino acid racemization may be useful in accessing the extent of DNA chain breakage in ancient biological remains. To test this suggestion, we have investigated the amino acids in insects entombed in fossilized tree resins ranging in age from <100 years to 130 million years. The amino acids present in 40 to 130 million year old amber-entombed insects resemble those in a modern fly and are probably the most ancient, unaltered amino acids found so far on Earth. In comparison to other geochemical environments on the surface of the Earth, the amino acid racemization rate in amber insect inclusions is retarded by a factor of >10(4). These results suggest that in amber insect inclusions DNA depurination rates would also likely be retarded in comparison to aqueous solution measurements, and thus DNA fragments containing many hundreds of base pairs should be preserved. This conclusion is consistent with the reported successful retrieval of DNA sequences from amber-entombed organisms.

Amber↗
PubMed2003

Coelomycetes in Dominican and Mexican amber.

Three species of fossil epiphyllous coelomycetes are described from Dominican and Mexican amber in the new genera, Asteromites gen. nov., Leptostromites gen. nov. and Leptothyrites gen. nov. Characters of the pycnidia and spores most closely resemble members of their extant respective genera, Leptostroma, Asteromella, and Leptothyrium, respectively. A. mexicanus sp. nov. occurs on a petal (possibly from a caesalpinoid legume such as Peltogyne) in Mexican amber. Leptostromites ellipticus sp. nov. occurs on a dicot leaf in Dominican amber, and Leptothyrites dominicanus sp. nov. on a monocot (grass?) leaf in Dominican amber.

Amber↗
PubMed2006

Comparing amber fossil assemblages across the Cenozoic.

To justify faunistic comparisons of ambers that differ botanically, geographically and by age, we need to determine that resins sampled uniformly. Our pluralistic approach, analysing size distributions of 671 fossilized spider species from different behavioural guilds, demonstrates that ecological information about the communities of two well-studied ambers is retained. Several lines of evidence show that greater structural complexity of Baltic compared to Dominican amber trees explains the presence of larger web-spinners. No size differences occur in active hunters. Consequently, we demonstrate for the first time that resins were trapping organisms uniformly and that comparisons of amber palaeoecosystem structure across deep time are possible.

Amber↗
PubMed1985

Amber, ochre and opal suppressor tRNA genes derived from a human serine tRNA gene.

Amber, ochre and opal suppressor tRNA genes have been generated by using oligonucleotide directed site-specific mutagenesis to change one or two nucleotides in a human serine tRNA gene. The amber and ochre suppressor (Su+) tRNA genes are efficiently expressed in CV-1 cells when introduced as part of a SV40 recombinant. The expressed amber and ochre Su+ tRNAs are functional as suppressors as demonstrated by readthrough of the amber codon which terminates the NS1 gene of an influenza virus or the ochre codon which terminates the hexon gene of adenovirus, respectively. Interestingly, several attempts to obtain the equivalent virus stock of an SV40 recombinant containing the opal suppressor tRNA gene yielded virus lacking the opal suppressor tRNA gene. This suggests that expression of an efficient opal suppressor derived from a human serine tRNA gene is highly detrimental to either cellular or viral processes.

Animals↗
PubMed1987

Novel amber suppressor tRNAs of mammalian origin.

Two amber suppressor tRNAs have been isolated from calf liver. They are different from previously identified naturally occurring amber suppressors of eukaryotes in so far as they are neither tRNATyr nor tRNAGln. They are leucine iso-acceptors and their nucleotide sequence indicates that they harbour a CAA and a CAG anticodon respectively. Both species are functional as amber suppressors as demonstrated by readthrough of the amber codon which terminates the 126 kd protein gene of tobacco mosaic virus RNA. The results bring new information in the discussion of codon-anticodon recognition and regulation of termination in eukaryotic protein synthesis.

Animals↗
PubMed1982

An amber mutation in the gene rpsA for ribosomal protein S1 in Escherichia coli.

An amber mutation has been induced in the gene rpsA (which codes for ribosomal protein S1) of Escherichia coli K-12 strain in the presence of an amber suppressor (supD) and mutations sueA, sueB and sueC that additively enhance the efficiency of suppression. That the amber mutation has occurred in the gene rpsA was confirmed by complementation with a plasmid which carried the wild-type allele of rpsA. The mutation is lethal in the absence of an amber suppressor, indicating that ribosomal protein S1 is indispensable to E. coli.

Bacteriophage lambda↗
PubMed1983

Intragenic localization of amber and temperature-sensitive rpoD mutations affecting RNA polymerase sigma factor of Escherichia coli.

A set of multi-copy plasmids carrying part or all of the rpoD gene of Escherichia coli have been used to localize several amber and temperature-sensitive mutations affecting RNA polymerase sigma factor. In contrast to the plasmid carrying a complete rpoD sequence, plasmids carrying part of rpoD could not complement any of the rpoD mutations tested. However, the mutants harboring some of the latter plasmids produced wild-type recombinants at high frequency, provided that they carry the recA+ gene. The results permitted us to localize the rpoD mutations into one of the three intragenic segments. Thus, the rpoD285(ts) mutation (Harris et al. 1978) was located on the 0.8 kilobase segment defined by the Bg/II and BamHI sites in the middle segment, and the amber mutation rpoD40 (Osawa and Yura 1980) in the N-terminal 0.8 kilobase segment. Four additional amber mutations were also identified and classified into one of the segments of rpoD. It was further revealed that plasmids carrying certain amber mutations (rpoD47 or rpoD63) in the C-terminal segment of rpoD render all rpoD mutants tested (including rpoD47 and rpoD63 mutants themselves) able to grow at the restrictive condition. It is suggested that the enhanced synthesis of incomplete sigma polypeptides encoded by rpoD47 or rpoD63 phenotypically suppresses the defects in sigma function at least partially.

Bacterial Proteins↗
PubMed1989

Replication of a human parvovirus nonsense mutant in mammalian cells containing an inducible amber suppressor.

When recombinant plasmids containing the entire adeno-associated virus (AAV) genome are transfected into permissive cells infected with a helper adenovirus, infectious AAV particles are efficiently generated. These plasmids can be used to generate mutant AAV genomes or recombinant AAV vectors. Packaging of mutant AAV genomes has required complementation with a second AAV plasmid in the transfection assay which may lead to generation of significant amounts of wild-type AAV recombinants. One approach to alleviate this problem was to generate conditional lethal mutants. We constructed an AAV plasmid recombinant having a nonsense mutation in the AAV rep gene by using oligonucleotide-directed mutagenesis to convert a serine codon to an amber codon. We show that this mutant AAV can be grown on monkey cell lines containing an inducible human serine tRNA amber suppressor. The amber suppression is quite efficient and yields a burst of mutant AAV particles at about 10% of the titer of wild-type AAV. The reversion frequency of the amber mutation appears to be less than 10(-5).

Animals↗
PubMed1993

Visualization of basal pleural space and lung with advanced multiple beam equalization radiography (AMBER).

During clinical use of AMBER (Advanced Multiple Beam Equalization Radiography) it was frequently felt that the basal lung and pleural space were better appreciated than with standard chest radiography. We aimed to quantify the amount of additional relevant anatomy seen in this part region and to review the normal radiographic anatomy. Four hundred patients without known chest disease were evaluated. Two groups of 200 patients (50% female) were studied with either AMBER or standard chest radiography (140 kVp, 180 cm FFD, Kodak Tmat G film, Lanex regular screen; for both techniques). Visualization of the pleural sinuses (in percent of the transverse thoracic diameter) and the basal pulmonary vessels (4-point scale) was evaluated by a panel of 3 radiologists. The shape of the sinus was traced if sufficiently visible and subjectively evaluated. A significantly (P < 0.05) larger segment of the dorsal (41 +/- 34%) and ventral (14 +/- 15%) sinuses was seen with the AMBER technique than with the standard technique (16 +/- 21% and 9 +/- 11%, respectively). Vessel visibility was also significantly (P < 0.001) better with AMBER (3.2 +/- 0.6) than with the standard technique (1.9 +/- 0.6). The dorsal sinus showed alternatively a curved or pointed configuration.

Adult↗
PubMedDate not supplied

Improved AMBER torsional parameters for the N-N rotational barrier in diacylhydrazines.

The structure and rotational barrier for substituted diacylhydrazines are of significant interest given the role this functionality plays in peptidomimetics and ecdysone agonists, the latter of which have application as extremely selective insecticides. Ab initio calculations show that the lowest energy conformations are typically nonplanar with essentially perpendicular nitrogen lone pairs. Molecular mechanics calculations using the AMBER force field in MacroModel yield minima and rotational barriers that are both quantitatively and qualitatively inconsistent with the ab initio results. In this work the AMBER N-N rotational barriers for all configurations of the parent, methyl and di-methyl substituted diformylhydrazines have been fitted to MP2/6-31 + G relative energies. The resulting AMBER torsional parameters have been validated by calculating the rotational barriers for N-t-butyl substituted diformylhydrazine, dibenzoylhydrazine and an azadipeptide. In each case the new AMBER rotational barriers compare favorably with the corresponding MP2 calculated rotational barriers.

Ecdysone↗
PubMed2003

Adaptation of an orthogonal archaeal leucyl-tRNA and synthetase pair for four-base, amber, and opal suppression.

Recently, it has been shown that an amber suppressor tRNA/aminoacyl-tRNA synthetase pair derived from the tyrosyl-tRNA synthetase of Methanococcus jannaschii can be used to genetically encode unnatural amino acids in response to the amber nonsense codon, TAG. However, we have been unable to modify this pair to decode either the opal nonsense codon, TGA, or the four-base codon, AGGA, limiting us to a 21 amino acid code. To overcome this limitation, we have adapted a leucyl-tRNA synthetase from Methanobacterium thermoautotrophicum and leucyl tRNA derived from Halobacterium sp. NRC-1 as an orthogonal tRNA-synthetase pair in Escherichia coli to decode amber (TAG), opal (TGA), and four-base (AGGA) codons. To improve the efficiency and selectivity of the suppressor tRNA, extensive mutagenesis was performed on the anticodon loop and acceptor stem. The two most significant criteria required for an efficient amber orthogonal suppressor tRNA are a CU(X)XXXAA anticodon loop and the lack of noncanonical or mismatched base pairs in the stem regions. These changes afford only weak suppression of TGA and AGGA. However, this information together with an analysis of sequence similarity of multiple native archaeal tRNA sequences led to efficient, orthogonal suppressors of opal codons and the four-base codon, AGGA. Ultimately, it should be possible to use these additional orthogonal pairs to genetically incorporate multiple unnatural amino acids into proteins.

Anticodon↗
PubMedDate not supplied

Identification and repair of positive binding antibodies containing randomly generated amber codons from synthetic phage display libraries.

Phage display technology allows for the rapid isolation and characterization of monoclonal antibodies that have vast potential for therapeutic and diagnostic applications. However, the panning process, which utilizes a host strain that suppresses termination by the amber codon, has an inherent bias toward clones containing randomly generated amber stop codons, complicating identification of positive binding antibodies when the antibody genes are finally expressed in a nonsupressor host. Here, we perform biopanning against a Histone 2A peptide using streptavidin- or anti-biotin-coated beads. After four rounds, a dominant clone is characterized but contains a spurious amber stop codon. A protocol is given that readily corrects the amber codon, allowing for soluble antibody production once the phagemid is transformed into a nonsuppressor bacterial strain. This work also highlights the ability to isolate antibodies against a protein antigen by using only a small peptide (15 amino acids) representing a portion of the antigen.

Amino Acid Sequence↗
PubMed1997

Transfer RNA-mediated suppression of amber stop codons in transgenic Arabidopsis thaliana.

An artificial amber suppressor tRNA(Leu) gene (supL) was physically linked to a mutated gus reporter gene, p35S-gus(amL), which was inactivated by an amber stop codon (amL). Upon introduction into Arabidopsis thaliana, the presence of the supL gene was found to be correlated with cytotoxic effects observed during tissue culture and in mature plants. Those primary transformants that displayed cytotoxic symptoms were shown by X-Glu staining to express GUS as a result of amber stop codon suppression in vivo. Phenotypically normal lines were found by RT-PCR to express supL. GUS activity above background level was barely detectable in these plants, indicating a low level expression of supL. However, the remaining suppressor activity was still sufficient to transactivate an amber-mutated male sterility gene, pA9-barnase(amL1) when combined within the same plant by crossing. The suppressor tRNA(Leu) gene may thus be used in transgenic plants for gene transactivation.

Bacterial Proteins↗
PubMed1993

[The determination of the surface and organ doses in the AMBER system. Advanced Multiple Beam Equalization Radiography].

Surface and organ doses were determined by means of thermoluminescence dosimetry with the Alderson-Rando phantom and the patient, for the AMBER thoracic imaging system, sensitivity class 400, and the conventional grid screen stand, sensitivity class 200. The dose on entering the body, which varied according to object-dependent modulation of x-ray intensity, was 140 microGy for the mediastinum and 96 microGy for the lung in p.a. AMBER takes, and hence was comparable with the entrance dose of 132 microGy with the conventional grid screen stand. In lateral takes the entrance doses were lower with the AMBER system (302 microGy) than with conventional takes (593 microGy). Exposure of the gonads at the AMBER system for p.a. thoracic takes was lower than at the screen grid stand in females (4-6 microGy). More unfavourable values were measured for the gonad exposure in males (2-0.8 micrograms).

Humans↗
PubMed1989

Construction, stable transformation, and function of an amber suppressor tRNA gene in Drosophila melanogaster.

Drosophila melanogaster strains with a stably incorporated amber suppressor tRNA gene have been generated. A tRNATyr gene was site specifically mutated to produce an anticodon sequence that recognizes the amber codon and then introduced into Drosophila by using P-element-mediated transformation. Transformants from four integration events were recovered. Two integrations resulted in both male and female sterility, whereas the other two resulted in male sterility but female fertility. Strains derived from the two female-fertile integration events were shown to have a low level of amber-suppressing activity by their ability to suppress an amber mutation in a chloramphenicol acetyltransferase gene.

Animals↗
PubMed1989

Rapid detection of ultraviolet-induced reversion of an amber mutation in mouse L cells.

An amber codon (TAG) was introduced into the N-terminal coding region of the murine H-2Kb gene. The mutant gene was transfected into mouse L cells, and a clone containing a single unrearranged chromosomally integrated copy of the mutant gene was mutagenized with 254-nm UV radiation. Surviving cells were scored for surface expression of H-2Kb protein with in situ immunoperoxidase staining. Revertants were detected at a frequency of 3 X 10(-6) at a dose of 40 J/m2 (3-5% survival). Revertant genes, cloned by plasmid rescue, contained the expected thymine-to-cytosine transitions at the amber codon. These data show that revertants can be rapidly detected in mammalian cells without selection and provide a basis for the development of mammalian cell lines that could be used to study mutational phenomena. During this study the steady-state level of mRNA was reduced in L cells carrying the amber mutant H-2Kb gene compared with L cells containing a wild-type or revertant H-2Kb gene. This reduction was shown not to be due to transcriptional differences, suggesting that the amber mutation decreases stability of the H-2Kb mRNA.

Amino Acid Sequence↗
PubMed2004

Complete set of orthogonal 21st aminoacyl-tRNA synthetase-amber, ochre and opal suppressor tRNA pairs: concomitant suppression of three different termination codons in an mRNA in mammalian cells.

We describe the generation of a complete set of orthogonal 21st synthetase-amber, ochre and opal suppressor tRNA pairs including the first report of a 21st synthetase-ochre suppressor tRNA pair. We show that amber, ochre and opal suppressor tRNAs, derived from Escherichia coli glutamine tRNA, suppress UAG, UAA and UGA termination codons, respectively, in a reporter mRNA in mammalian cells. Activity of each suppressor tRNA is dependent upon the expression of E.coli glutaminyl-tRNA synthetase, indicating that none of the suppressor tRNAs are aminoacylated by any of the twenty aminoacyl-tRNA synthetases in the mammalian cytoplasm. Amber, ochre and opal suppressor tRNAs with a wide range of activities in suppression (increases of up to 36, 156 and 200-fold, respectively) have been generated by introducing further mutations into the suppressor tRNA genes. The most active suppressor tRNAs have been used in combination to concomitantly suppress two or three termination codons in an mRNA. We discuss the potential use of these 21st synthetase-suppressor tRNA pairs for the site-specific incorporation of two or, possibly, even three different unnatural amino acids into proteins and for the regulated suppression of amber, ochre and opal termination codons in mammalian cells.

Amino Acyl-tRNA Synthetases↗