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Query: UNIPROT:P06889 (Mol)
 630,302 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A test given by Moore and Goodman (1977) that checks the significance of a homology between protein sequences is generalized to any type of distance measure and to any classification of codon pairs or amino acids according to this measure. A normal distribution is shown to approximate satisfactorily the probability distribution underlying this test for the examples chosen, and supposedly for any distance measure. The test accordingly reduces to a simple standard procedure.
J Mol Evol 1978 Feb 21
PMID:Generalization and simplification of the Moore-Goodman test for significant of alignment homologies. 63 83

The process of determining the optimal phylogenetic tree from amino acid sequences or comparable data is divided into six stages. Particular attention is given both to the criteria that are used when testing for the optimal tree and the problem of determining the position of the original ancestor. Four types of criteria for evaluating the optimal tree are considered: 1. parsimony (fewest total changes), 2. path lengths from an ancestor to existing species, 3. subtracting the difference between each pair of species as measured on the tree and as compared directly with the data ("excess differences"), 4. Moore Residual Coefficient. These criteria are examined on a set of test data and some of the reasons for the differences among them are discussed. For example, the "average percent standard deviation" weights excess differences unequally in inverse proportion to the square of the observed differences. The Moore Residual Coefficient and the "excess differences" will not necessarily give a value of zero when there are no duplicated changes unless there can only be two states for each character (i.e. binary data). The path length and difference criteria (as well as the Moore Residual Coefficient) give unequal weighting to the individual branches of the tree by counting some branches more times than others. Particularly because of this some criteria will reject trees that are equally parsimonious and the criteria are said to be invalid. However the criterion of parsimony is insensitive in that it can give the same value for several basic networks and it does not specify the position of the original ancestor, the root of the tree. The importance is emphasised of stating a model and examining its predictions before a criterion is chosen to select the best network. The number of rooted trees that can be derived from a basic network (or unrooted tree) is described in relation to how detailed a description of the original ancestor is required. Four methods are described for determining the position of the root of the tree or original ancestor. Each method depends upon some additional information to that used in constructing the basic network and the method chosen will depend on this additional knowledge.
J Mol Evol 1976 Aug 03
PMID:Criteria for optimising phylogenetic trees and the problem of determining the root of a tree. 96 92

When Escherichia coli 50-S ribosomal subunits are treated with increasing concentrations of urea partial deproteination occurs. Furthermore, we observed that the number of sulfhydryl groups which react with Ellman's reagent is a sigmoidal function of the urea concentration. These results are similar to those previously reported for the 30-S subunit (Acharya, A.S. and Moore, P.B. (1973) J. Mol. Biol. 76, 207-221). For both subunits we identify the proteins which dissociate (split proteins) or are recoverable in a ribonucleoprotein particle (core proteins) under the action of 6 M urea in a buffer of moderate ionic strength.
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PMID:Characterization of the particles produced by exposure of ribosomal subunits to urea. 110 83

The regulation of glycolytic genes in response to carbon source in the yeast Saccharomyces cerevisiae has been studied. When the relative levels of each glycolytic mRNA were compared during exponential growth on glucose or lactate, the various glycolytic mRNAs were found to be induced to differing extents by glucose. No significant differences in the stabilities of the PFK2, PGK1, PYK1, or PDC1 mRNAs during growth on glucose or lactate were observed. PYK::lacZ and PGK::lacZ fusions were integrated independently into the yeast genome at the ura3 locus. The manner in which these fusions were differentially regulated in response to carbon source was similar to that of their respective wild-type loci. Therefore, the regulation of glycolytic mRNA levels is mediated at the transcriptional level. When the mRNAs are ordered with respect to the glycolytic pathway, two peaks of maximal induction are observed at phosphofructokinase and pyruvate kinase. These enzymes (i) catalyze the two essentially irreversible steps on the pathway, (ii) are the two glycolytic enzymes that are circumvented during gluconeogenesis and hence are specific to glycolysis, and (iii) are encoded by mRNAs that we have shown previously to be coregulated at the translational level in S. cerevisiae (P. A. Moore, A. J. Bettany, and A. J. P. Brown, NATO ASI Ser. Ser. H Cell Biol. 49:421-432, 1990). This differential regulation of glycolytic mRNA levels might therefore have a significant influence upon glycolytic flux in S. cerevisiae.
Mol Cell Biol 1991 Oct
PMID:Yeast glycolytic mRNAs are differentially regulated. 192 48

The major membrane-associated or transmembrane isoforms of the neural cell adhesion molecule (NCAM) are generated by alternative splicing at the 3' end of the mRNA. Further diversity in NCAM structure is observed in the extracellular region of the polypeptide, where the insertion of additional amino acid residues can result from alternative splicing events occurring at the exon 7-exon 8 and exon 12-exon 13 junctions. Here we report the characterization of tissue-specific patterns of alternative splicing at the exon 12-exon 13 junction by using the polymerase chain reaction. Nine alternatively spliced sequences in rat heart between exon 12 and exon 13 were identified. Each sequence consisted of different combinations of the three small exons (15, 48, and 42 bp in length) and the AAG triplet that make up MSD1, the 108-bp muscle-specific sequence found in human skeletal muscle NCAM (G. Dickson, H.J. Gower, C. H. Barton, H. M. Prentice, V. L. Elsom, S. E. Moore, R. D. Cox, C. Quinn, W. Putt, and F. S. Walsh, Cell 50:1119-1130, 1987). Although the rat equivalent of MSD1 (designated 15+ 48+ 42+ 3+) was detected in all ages of heart examined, it was only one of four or five major splice combinations at any given age. The only alternatively spliced sequence found in the exon 7-exon 8 junction of heart NCAM mRNA was the 30-bp variable alternatively spliced exon previously identified in rat brain. Twenty-seven NCAM forms with distinct sequences were found by analysis of individual NCAM transcripts from postnatal day 1 heart tissue for alternative splicing at the exon 7-exon 8 junction, the exon 12-exon 13 junction and the 3' end. Several combinations of splicing patterns in these three different regions of the gene appeared to be preferentially expressed. The observation that the expression of alternatively spliced forms of NCAM is developmentally regulated suggests a role for NCAM diversity in cardiac development.
Mol Cell Biol 1991 Mar
PMID:At least 27 alternatively spliced forms of the neural cell adhesion molecule mRNA are expressed during rat heart development. 199 15

The adenovirus 294R protein of E4 ORF 6 forms a physical and functional complex with the 496R protein product of E1b. The E4 294R ORF 6 protein also functions in parallel with the E4 116R ORF 3 protein in viral late protein synthesis. We have examined the roles of these three proteins and the protein complex in viral late protein synthesis and late message metabolism, by comparing the phenotypes of E4 294R-, E4 116R-, and E1b 496R- mutants to those of a series of double mutants. Our data indicate that the 294R and 116R proteins act in parallel to permit the accumulation of normal levels of unprocessed late viral RNA in the nucleus of infected cells. Both 294R and 496R function in parallel with the 116R protein in viral nuclear RNA accumulation, but do so to different degrees, suggesting that 294R and 496R may have roles apart from the functional complex in mediating accumulation of viral messages in the nucleus, or that they have nonequivalent roles within the complex. Our results are also consistent with a role for the 496R/294R protein complex in mediating efficient transport of late messages from the nucleus to the cytoplasm and/or in maintaining the stability of those messages on reaching the cytoplasm, as suggested previously (S. Pilder, M. Moore, J. Logan, and T. Shenk, 1986, Mol. Cell. Biol. 6, 470-476). Finally the 116R protein seems to act in parallel with the complex to permit normal viral DNA replication.
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PMID:Interaction of adenoviral E4 and E1b products in late gene expression. 213 59

The Z-DNA motif polydeoxythymidylic-guanylic [d(TG)].polydeoxyadenylic-cytidylic acid [d(AC)], present throughout eucaryotic genomes, is capable of readily forming left-handed Z-DNA in vitro and has been shown to promote homologous recombination. The effects of simian virus 40 T-antigen-dependent substrate replication upon the stimulation of recombination conferred by the Z-DNA motif d(TG)30 were analyzed. Presence of d(TG)30 adjacent to a T-antigen-binding site I can stimulate homologous recombination between nonreplicating plasmids, providing that T antigen is absent, in both simian CV-1 cells and human EJ cells (W. P. Wahls, L. J. Wallace, and P. D. Moore, Mol. Cell. Biol. 10:785-793). It has also been shown elsewhere that the presence of d(TG)n not adjacent to the T-antigen-binding site can stimulate homologous recombination in simian virus 40 molecules replicating in the presence of T antigen (P. Bullock, J. Miller, and M. Botchan, Mol. Cell. Biol. 6:3948-3953, 1986). However, it is demonstrated here that d(TG)30 nine base pairs distant from a T-antigen-binding site bound with T antigen does not stimulate recombination between either replicating or nonreplicating substrates in somatic cells. The bound T antigen either prevents the d(TG)30 sequence from acquiring a recombinogenic configuration (such as left-handed Z-DNA), or it prevents the interaction of recombinase proteins with the sequence by stearic hindrance.
Mol Cell Biol 1990 Feb
PMID:Homologous recombination enhancement conferred by the Z-DNA motif d(TG)30 is abrogated by simian virus 40 T antigen binding to adjacent DNA sequences. 215 23

Cells of the hemopoietic system arise by proliferation and differentiation of progenitor cells. This process begins with multipotential stem cells which can self-renew and also undergo progressive differentiation to progenitor cells committed to particular lineages, ultimately yielding mature blood cells (D. Metcalf and M. A. S. Moore, Haematopoietic Cells, 1971). Early commitment of lymphoid progenitors is generally believed to separate the lymphoid lineage from the myeloid and erythroid lineages, whose progenitors are separated late in differentiation (Metcalf and Moore, 1971). We recently developed a derivative of Moloney murine leukemia virus (M-MuLV) in which the enhancer sequences from simian virus 40 were substituted into the M-MuLV long terminal repeat. This recombinant virus (delta Mo + SV M-MuLV) induces pre-B and B lymphoid leukemia with long latency after inoculation of 2-day-old NIH Swiss mice (R. Hanecak, P. K. Pattengale, and H. Fan, J. Virol. 62:2427-2436, 1988). In this report, we describe the derivation of a permanent, virus-producing cell line with the phenotypic characteristics of mature macrophages from a B-cell-derived lymphoblastic lymphoma induced by delta Mo + SV M-MuLV. Comparison studies of immunoglobulin heavy-chain gene rearrangements and also delta Mo + SV M-MuLV proviral integration sites confirmed that the macrophage cell line was derived from the original B-lymphoblastic lymphoma. Moreover, inoculation of the macrophage cell line into animals resulted in histiocytic sarcomas of the macrophage type, thus reflecting stable conversion of B-lymphoid tumor cells to the macrophage phenotype. These results suggest a closer relationship between lymphoid and myeloid cells than previously believed.
Mol Cell Biol 1989 May
PMID:Differentiation in vitro of a leukemia virus-induced B-cell lymphoma into macrophages. 254 61

Gene amplification in human tumor cells is frequently mediated by extrachromosomal elements (e.g., double minute chromosomes [DMs]). Recent experiments have shown that DMs can be formed from smaller, submicroscopic circular precursors referred to as episomes (S. M. Carroll, M. L. DeRose, P. Gaudray, C. M. Moore, D. R. Needham-Vandevanter, D. D. Von Hoff and G. M. Wahl, Mol. Biol. 8:1525-1533, 1988). To investigate whether episomes are generally involved as intermediates in gene amplification, we determined whether they mediate the amplification of the mdr1 gene, which when overexpressed engenders cross resistance to multiple lipophilic drugs. A variety of methods including electrophoresis of undigested DNAs in high-voltage gradients, NotI digestion, and production of double-strand breaks by gamma irradiation were used to distinguish between mdr1 sequences amplified on submicroscopic circular molecules and those amplified within DMs or chromosomal DNA. The gamma-irradiation procedure provides a new method for detecting and determining the size of circular molecules from 50 kilobases (kb) to greater than 1,000 kb. These methods revealed that some of the amplified mdr1 genes in vinblastine-resistant KB-V1 cells are contained in supercoiled circular molecules of approximately 600 and approximately 750 kb. Analysis of the replication of these molecules by a Meselson-Stahl density shift experiment demonstrated that they replicate approximately once in a cell cycle. The data lend further support to a model for gene amplification in which DMs are generally formed from smaller, autonomously replicating precursors.
Mol Cell Biol 1989 Jan
PMID:Autonomously replicating episomes contain mdr1 genes in a multidrug-resistant human cell line. 264 29

Several hepatotoxic agents with varied chemical mechanisms of toxicity (acetaminophen, diquat, and CCl4) depress membrane calcium pumps and/or enhance the permeability of membranes to calcium. To probe the relevance of these findings to maintenance of calcium homeostasis after toxins in vivo, we measured the activity of glycogen phosphorylase a, as an index of cytosolic free [Ca2+], in freeze-clamped liver samples obtained at several times after the toxin dose. Both acetaminophen and diquat caused significant increases of phosphorylase a activity, and activity remained elevated for several hours after the dose. Significantly, the administration prior to diquat of desferrioxamine, which offers protection against the liver necrosis and depression of microsomal Ca2+ accumulation observed after diquat alone (Tsokos-Kuhn et al., Mol Pharmacol 34: 209-214, 1988), decreased phosphorylase activation. Activation of phosphorylase was observed also after CCl4 administration, as previously reported by Long and Moore (Biochem Pharmacol 35: 4131-4137, 1986). We conclude that perturbations in liver membrane Ca2+ regulation observed after administration of these hepatotoxins in vivo correlate directly with phosphorylase a activity, thereby providing additional in vivo evidence for an alteration of Ca2+ homeostasis early in the development of the liver damage produced by these chemicals.
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PMID:Evidence in vivo for elevation of intracellular free Ca2+ in the liver after diquat, acetaminophen, and CCl4. 278 60


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