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C B Lawrence

Publications and source records attributed to C B Lawrence.

At least 55 records · Page 3Linked to original sources
PubMed1988

Chemical modification as a tool for analysis of messenger RNA secondary structure in ribonucleoprotein particles.

Chemical modification of unpaired bases is demonstrated in this study to be a reliable method for determining the conformation of nucleotides in mRNA. The modified nucleotides are identified by primer extension using reverse transcriptase. We have used this procedure to compare the structure of limited regions of SV40 T-antigen mRNA in solution, in nonpolysome-bound cytoplasmic messenger ribonucleoprotein particles, and in nuclear ribonucleoprotein complexes. The results indicate that SV40 T-antigen mRNA adopts a specific structure both in solution and when complexed with cellular proteins. The structures adopted by the mRNA in solution and in native cellular protein particles are very similar.

Antigens, Polyomavirus Transforming↗
PubMed1988

Definition and identification of homology domains.

A method is described for identifying and evaluating regions of significant similarity between two sequences. The notion of a 'homology domain' is employed which defines the boundaries of a region of sequence homology containing no insertions or deletions. The relative significance of different potential homology domains is evaluated using a non-linear similarity score related to the probability of finding the observed level of similarity in the region by chance. The sensitivity of the method is demonstrated by simulating the evolution of homology domains and applying the method to their detection. Several examples of the use of homology domain identification are given.

Algorithms↗
PubMed1988

The effects of reserpine upon the cardiac enlargement of copper deficiency.

Copper (Cu) deficiency, induced in rats by suckling from Cu-deficient dams and by offering a semisynthetic low-Cu diet from weaning, resulted in cardiac enlargement. This enlargement was not due to accumulation of excess fluid in the heart but was characterized by mitochondrial hypertrophy as demonstrated by electron microscopy and biochemical studies. Administration of reserpine limited the extent of cardiac enlargement; however, heart total noradrenaline (NA), unchanged by Cu deficiency, was significantly reduced by reserpine. It was concluded that cardiac enlargement in Cu deficiency was not directly related to NA concentration. An alteration in cardiac energy status, however, was suggested by reduction in activity of the nonheme iron-dependent enzyme, succinic dehydrogenase.

Age Factors↗
PubMed1987

Genetic relatedness of human DNA polymerase beta and terminal deoxynucleotidyltransferase.

The Protein Identification Resource (PIR) protein sequence data bank was searched for sequence similarity between known proteins and human DNA polymerase beta (Pol beta) or human terminal deoxynucleotidyltransferase (TdT). Pol beta and TdT were found to exhibit amino acid sequence similarity only with each other and not with any other of the 4750 entries in release 12.0 of the PIR data bank. Optimal amino acid sequence alignment of the entire 39-kDa Pol beta polypeptide with the C-terminal two thirds of TdT revealed 24% identical aa residues and 21% conservative aa substitutions. The Monte Carlo score of 12.6 for the entire aligned sequences indicates highly significant aa sequence homology. The hydropathicity profiles of the aligned aa sequences were remarkably similar throughout, suggesting structural similarity of the polypeptides. The most significant regions of homology are aa residues 39-224 and 311-333 of Pol beta vs. aa residues 191-374 and 484-506 of TdT. In addition, weaker homology was seen between a large portion of the 'nonessential' N-terminal end of TdT (aa residues 33-130) and the first region of strong homology between the two proteins (aa residues 31-128 of Pol beta and aa residues 183-280 of TdT), suggestive of genetic duplication within the ancestral gene. On the basis of nucleotide differences between conserved regions of Pol beta and TdT genes (aligned according to optimally aligned aa sequences) it was estimated that Pol beta and TdT diverged on the order of 250 million years ago, corresponding roughly to a time before radiation of mammals and birds.

Amino Acid Sequence↗
PubMed1986

Studies on the effect of copper deficiency on rat liver mitochondria. III. Effects on adenine nucleotide translocase.

Liver mitochondria from Cu-deficient rats exhibit impaired State 3 respiration (oxygen consumption in the presence of exogenous ADP) compared with Cu-adequate controls, whereas State 4 respiration (oxygen consumption after depletion of exogenous ADP) and ADP/O are unaffected. In view of previous observations (Davies, N.T., Lawrence, C.B., Mills, C.F. and Nicol, F. (1985) Biochim. Biophys. Acta 809, 351-361) it seemed that a decline in cytochrome c oxidase activity (EC 1.9.3.1) could not fully account for these findings. Cu deficiency resulted in a significant decline (40%, P less than 0.01) in [14C]ADP uptake by liver mitochondria which suggests there is a reduced activity of the adenine nucleotide translocase. The reduced translocase activity was not associated with any marked change in fatty-acid composition of either intact mitochondria or inner mitochondrial membranes. Inhibitor titrations with the irreversible inhibitor carboxyatractyloside showed that 'Cu-deficient' mitochondria required the same concentration of inhibitor to produce 100% inhibition of State 3 respiration as control mitochondria, suggesting that the amount of functional translocase enzyme present is unaffected. When the translocase assay was allowed to proceed until equilibrium was established between external and internal nucleotides, it was apparent that the exchangeable adenine nucleotide pool of Cu-deficient mitochondria was 36% lower than in controls. Analysis of mitochondria for their ATP, ADP and AMP contents showed that, whereas the AMP content was unaffected, ATP and ADP contents were 39 and 40% lower, respectively, which resulted in a significantly reduced pool of total adenine nucleotides (ATP + ADP + AMP) and a reduced 'energy charge' [(ATP + 0.5 ADP)/(ATP + ADP + AMP)]. These results are discussed in relation to current concepts of the regulation and control of mitochondrial respiration.

Adenine Nucleotides↗
PubMed1986

A novel, simple and rapid method for the isolation of mitochondria which exhibit respiratory control, from rat small intestinal mucosa.

A method is described for the isolation of functional mitochondria from rat intestinal mucosa. Its novel feature is the removal of mucus from the initial homogenate by treatment with DEAE-cellulose. The preparations exhibited acceptable ADP:O ratios, high State-3 respiration rates, and respiratory control ratios in excess of 3 when succinate, beta-hydroxybutyrate, glutamate/malate and glutamine were test substrates.

Animals↗
PubMed1986

Data structures for DNA sequence manipulation.

Two data structures designated Fragment and Construct are described. The Fragment data structure defines a continuous nucleic acid sequence from a unique genetic origin. The Construct defines a continuous sequence composed of sequences from multiple genetic origins. These data structures are manipulated by a set of software tools to simulate the construction of mosaic recombinant DNA molecules. They are also used as an interface between sequence data banks and analytical programs.

Base Sequence↗
PubMed1985

Comparative sequence analysis as a tool for studying the secondary structure of mRNAs.

Analysis of phylogenetically conserved secondary structure has been important in the development of models for the secondary structure of structural RNAs. In this paper, we apply this type of analysis to several families of informational RNAs to evaluate its usefulness in developing secondary structure models for mRNAs and mRNA precursors. We observed many conserved helices in all mRNA groups analyzed. Three criteria were used to identify potential helices which were not conserved solely because of coding sequence constraints, and may therefore be important for the structure and function of the RNA. These results suggest that this approach will be useful in deriving secondary structure models for informational RNAs when used in conjunction with other complementary techniques, and in designing experiments to determine the functional significance of conserved base pairing interactions.

Actins↗
PubMed1985

Studies on the effects of copper deficiency on rat liver mitochondria. I. Changes in mitochondrial composition.

As part of an investigation of the lesions of copper (Cu) deficiency a study was undertaken of the copper, iron, cytochrome and fatty acid composition of liver mitochondria from Cu deficient and Cu-adequate control rats. Cu concentrations were significantly decreased in whole liver, liver mitochondria and in blood plasma. Total iron was significantly increased in whole liver but remained at the normal level in mitochondria. Cytochrome c oxidase (EC 1.9.3.1) and its component cytochromes a and a3 were significantly reduced in liver mitochondria from Cu-deficient rats, whereas there was no effect on the concentration of cytochromes b, c1 and c. Evidence from comparisons between cytochrome c oxidase activity and the amount of enzyme present, as assessed from the mitochondrial cytochrome a and a3 content, suggests that in addition to an absolute loss of enzyme, Cu-deficiency adversely affects the efficiency of the residual enzyme. Severe Cu deficiency had no effect on 'ageing' or 'swelling' properties of liver mitochondria, indicating no marked effects on fatty acid composition. Fatty acid analyses demonstrated a slight but significant increase in docosapentenoic acid (22:5) of Cu-deficient mitochondria, but since this represents a minor component there was no change observed in the 'unsaturation index'. It was concluded that, in contrast to previous reports, Cu deficiency of the severity reported did not have a deleterious effect on the integrity and permeability of the inner mitochondrial membrane as exemplified by any qualitative modification of fatty acid constitution per se.

Animals↗
PubMed1985

Studies on the effects of copper deficiency on rat liver mitochondria. II. Effects on oxidative phosphorylation.

Effects of dietary copper deficiency in rats on respiratory enzymes of isolated rat liver mitochondria have been studied. After 2 weeks of Cu-depletion, cytochrome c oxidase (EC 1.9.3.1) activity had declined by 42% and between 4 and 8 weeks exhibited between 20 and 25% of the activity of control mitochondria. Activities of NADH cytochrome c reductase (EC 1.6.99.3) and succinate cytochrome c reductase (EC 1.3.99.1), were unaffected initially but declined by 32 and 46%, respectively, after 8 weeks of Cu-depletion. After 4 weeks there was a significant (34%) decline in succinate supported state 3 respiration with only a modest (18%) decline in state 4 respiration. The ADP:O ratio was unaffected by Cu-depletion after 6 and 8 weeks of dietary Cu-restriction. State 3 respiration was significantly reduced after 6 weeks when glutamate/malate or beta-hydroxybutyrate were used as substrates, whereas state 4 respiration and ADP:O ratios were unaffected. The fall in state 3 respiration was of sufficient magnitude at 8 weeks to cause a significant decline in the respiratory control ratio with all substrates. Comparisons between the relative activities of cytochrome c oxidase and reductase activities in Cu-deficient preparations, the relatively specific effect of the deficiency on state 3 respiration with all substrates tested and the ability to increase significantly oxygen consumption in excess of maximal state 3 respiration by the uncoupler 2,4-dinitrophenol suggest that the defect in Cu-deficient mitochondria cannot be attributed solely to the decreased activity of cytochrome c oxidase.

3-Hydroxybutyric Acid↗
PubMed1985

Analysis of repetitive sequence elements containing tRNA-like sequences.

Several repetitive sequence elements from diverse species share extensive sequence homology with tRNA molecules. Analysis of the tRNA-like sequences within these elements suggest that they have originated from authentic tRNA sequences. Elements containing tRNA-like sequences can be divided into three distinct groups whose members share extensive sequence homology, have similar sequence organization and have unique species distribution. We suggest that these three groups represent independent examples of retroposon families that have originated from tRNAs.

Animals↗
PubMed1984

A universal model for the secondary structure of 5.8S ribosomal RNA molecules, their contact sites with 28S ribosomal RNAs, and their prokaryotic equivalent.

The phylogenetic approach (ref. 1) has been utilized in construction of a universal 5.8S rRNA secondary structure model, in which about 65% of the residues exist in paired structures. Conserved nucleotides primarily occupy unpaired regions. Multiple compensating base changes are demonstrated to be present in each of the five postulated helices, thereby forming a major basis for their proof. The results of chemical and enzymatic probing of 5.8S rRNAs (ref. 13, 32) are fully consistent with, and support, our model. This model differs in several ways from recently proposed 5.8S rRNA models (ref. 3, 4), which are discussed. Each of the helices in our model has been extended to the corresponding bacterial, chloroplast and mitochondrial sequences, which are demonstrated to be positionally conserved by alignment with their eukaryotic counterparts. This extension is also made for the base paired 5.8S/28S contact points, and their prokaryotic and organelle counterparts. The demonstrated identity of secondary structure in these diverse molecules strongly suggests that they perform equivalent functions in prokaryotic and eukaryotic ribosomes.

Animals↗
PubMed1982

Noradrenaline concentrations in gut muscle and mucosa of the copper-deficient steer and rat.

1. Noradrenaline (NA) concentrations in the duodenum and colon of copper-deficient and Cu-adequate steers and rats were determined. 2. In Cu-deficient steers exhibiting diarrhoea, there were significant decreases (P less than 0.05) in duodenal and colonic muscle NA concentrations. Duodenal and colonic mucosal NA concentrations in the steer were also diminished by Cu deficiency but this effect was not statistically significant. 3. Rat intestinal musculature had a higher NA concentration than that of the steer. Rat duodenal muscle NA was not influenced by Cu deficiency, but increased markedly with age. 4. It is suggested that the decline in NA concentration of cattle musculature in copper deficiency may have a role to play in the aetiology of diarrhoea in such animals.

Animals↗
PubMed1982

Adenovirus type 2 fiber mRNA synthesis: no evidence for a cytoplasmic processing pathway.

Adenovirus type 2 fiber mRNA exists in several forms in the cytoplasm which differ in the presence or absence of extra 5'-leader segments (L. T. Chow and T. R. Broker, Cell 15:497-510, 1978). We have investigated the possibility that forms possessing extra leader segments serve as precursors to the mature form in the cytoplasm. Pulse-labeled fiber mRNA became considerably shorter (150 to 250 bases) during a chase; however, most of the pulse-labeled species failed to hybridize to DNA fragments known to encode extra leader segments. Moreover, the entire decrease in size appeared to be due to extensive shortening of the polyadenylic acid tail. Mature-sized fiber mRNA was synthesized normally in cells infected with the nondefective adenovirus type 2-simian virus 40 hybrid virus Ad2+ND5, in which the region encoding the extra leader segments is deleted. These results indicate that the additional 5'-leader segments present in wild-type adenovirus type 2 fiber mRNA are not required for the production of mature fiber mRNA and that species that possess them are not cytoplasmic precursors to the mature form.

Adenoviruses, Human↗
PubMed1981

Expression of adenovirus type 2 late genes in HeLa cells infected with adenovirus type 2 or adenovirus type 2-simian virus 40 hybrid viruses.

The relative levels of expression of the five 3'-coterminal mRNA families encode in the 16.4 to 99 map unit transcription unit of adenovirus type 2 (Ad2) are determined in part by the frequency of utilization of five possible polyadenylation sites. The possibility that polyadenylation frequencies at these sites may be regulated was tested by examining the expression of the fiber (polypeptide IV) gene in cells infected with nondefective (ND) Ad2-simian virus 40 hybrid viruses which express a sixth late mRNA family. Both the relative rate of fiber protein synthesis and the relative abundance of fiber mRNA were normal in cells infected with the hybrid viruses Ad2+ND1, Ad2+ND2, or Ad2+ND4.

Adenoviruses, Human↗
PubMed1980

Activation of an internal initiation site for protein synthesis during in vitro translation.

The major mRNA for adenovirus 2 polypeptide pVIII sediments at 18S as assayed by in vitro translation in the messenger-dependent rabbit reticulocyte lysate system. However, a small amount of messenger activity for pVIII sediments at abut 27S, coincident with the mRNA for 100 K. Isolation and fractionation of poly(A) containing RNA following in vitro translation of 27S 100 K mRNA demonstrated the appearance of an 18S messenger activity for pVIII, which is approximately the size of the authentic mRNA for this protein. Partial degradation of 27S 100 K mRNA with alkali or ribonuclease T1 also results in activation of an 18S messenger activity for pVIII suggesting that in vitro messenger activity for pVIII associated with 27S RNA is due to degradation of 100 K mRNA during translation in the cell-free system.

Adenoviridae↗