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At least 73 records · Page 4Linked to original sources

Mutation of the p53 gene in human acute myelogenous leukemia.

Heterogeneity of p53 protein expression is seen in blast cells of patients with acute myelogenous leukemia (AML). p53 protein is detected in the blasts of certain AML patients but not in others. We have identified p53 protein variants with abnormal mobility on gel electrophoresis and/or prolonged half-life (t 1/2). We have sequenced the p53 coding sequence from primary blast cells of five AML patients and from the AML cell line (OCIM2). In OCIM2, a point mutation in codon 274 was identified that changes a valine residue to aspartic acid. A wild type p53 allele was not detected in these cells. Two point mutations (codon 135, cysteine to serine; codon 246, methionine to valine) were identified in cDNA from blasts of one AML patient. Both mutations were present in blast colonies grown from single blast progenitor cells, indicating that individual leukemia cells had sustained mutation of both p53 alleles. The cDNAs sequenced from blast samples of four other patients, including one with prolonged p53 protein t 1/2 and one with no detectable p53 protein, were fully wild type. Thus, the heterogeneity of p53 expression cannot be explained in all cases by genetic change in the p53 coding sequence. The prolonged t 1/2 of p53 protein seen in some AML blasts may therefore reflect changes not inherent to p53. A model is proposed in which mutational inactivation of p53, although not required for the evolution of neoplasia, would confer a selective advantage, favoring clonal outgrowth during disease progression.

Base Sequence↗

Molecular analysis of echovirus 13 isolates and aseptic meningitis, Spain.

Echovirus 13 (EV13), considered rare, was reported worldwide in 2000, mostly related to aseptic meningitis outbreaks. In Spain, 135 EV13 isolates were identified. The genetic relationships between 64 representative strains from Spain and other reported isolates from the United States, Germany, Italy, Japan, and Sweden were described by analyzing the partial sequence of the major capsid protein (VP1) gene. The strains from Spain were clearly identified as EV13 (79.5% similarity with the EV13 reference strain) and were grouped phylogenetically into two different clusters (by origination on either the Iberian Peninsula or Canary Islands). Isolates from Germany from 2000 clustered with the Canary Islands group. The isolates from other countries obtained before 2000 were genetically distant. Changes in EV13 coding sequence involved several differences in the C-terminal extreme of the VP1 protein. Part of the neutralizing antigenic site III has been described in this genome region in poliovirus and swine vesicular disease virus.

Amino Acid Sequence↗

Genetic instability in human mismatch repair deficient cancers.

Cancers showing microsatellite instability (MSI-H) are frequent tumors characterized by inactivating alterations of mismatch repair (MMR) genes that lead to an incapacity to recognize and repair errors that occur during DNA replication. These cancers can be inherited as in the human non-polyposis colorectal cancer syndrome, or can occur sporadically in 10-15% of colorectal, gastric and endometrial cancers. MSI-H tumors have different clinicopathological features compared to cancers without this phenotype, termed MSS, and the repertoire of genetic events involved in tumoral progression of both phenotypes is thought to be different. In MSI-H tumors, most of the genetic changes occur at both non-coding and coding microsatellites that are particularly prone to errors during replication due to their repetitive sequence. This mechanism appears to be the main "genetic pathway" by which functional changes with putative oncogenic effects are accumulated in these tumors.

Base Pair Mismatch↗

Global incorporation of unnatural amino acids in Escherichia coli.

The incorporation of amino acid analogs is becoming increasingly useful. Site-specific incorporation of unnatural amino acids allows the application of chemical biology to protein-specific investigations and applications. However, the global incorporation of unnatural amino acids allows for tests of proteomic and genetic code hypotheses. For example, the adaptation of organisms to unnatural amino acids may lead to new genetic codes. To understand and quantify changes from such perturbations, an understanding is required of the microbiological and proteomic responses to the incorporation of unnatural amino acids. Here we describe protocols to characterize the effects of such proteome-wide perturbations.

Amino Acids↗

Amino acid composition of proteins as a product of molecular evolution.

The average amino acid composition of proteins is determined by the genetic code and by random base changes in evolution. Small but significant deviations from expected composition can be explained by selective constraint on amino acid substitutions. In particular, the deficiency of arginine in proteins has been caused by constraint, during evolution, on fixation of mutations substituting arginine for other amino acids.

Amino Acids↗

Evolution of the mitochondrial genetic code. III. Reassignment of CUN codons from leucine to threonine during evolution of yeast mitochondria.

Yeast mitochondria use UUR as the sole leucine codons. CUN, universal leucine codons, are read as threonine by aberrant threonine tRNA with anticodon sequence (UAG). The reassignment of CUN codons to threonine during yeast mitochondrial evolution could have proceeded by the disappearance of CUN codons from the reading frames of messenger RNA, through mutation mainly to UUR leucine codons as a result of AT pressure. We suggest that this was accompanied by a loss of leucine-accepting ability of tRNA Leu(UAG). This tRNA could have then acquired threonine-accepting activity through the appearance of an additional threonyl-tRNA synthetase. CUN codons that subsequently appeared from mutations of various other codons would have been translated as threonine. This change in the yeast mitochondrial genetic code is likely to have evolved through a series of nondisruptive nucleotide substitutions that produced no widespread replacement of leucine by threonine in proteins as a consequence.

Adenine↗

Thermodynamics of living matter: physical foundations of biology.

All major functions of life are exerted by reversible conformational changes of living matter, the genetically coded, giant molecules of proteins, polynucleotides, and biological membranes. Only thermodynamics can answer the questions why these reversible actions occur, why they are inevitable, and what the physical foundations may be on which biology rests. Classical Gibbs-Helmholtz thermodynamics was found to be inapplicable to the interpretation of reactions in living matter, because copious flows of heat without exchange of work obscure the subtle bond-forming or bond-breaking energy transformations that are driving the actions of living matter. An alternative thermodynamic formulation that is universally applicable was developed and applied to numerical examples: formation of a diatomic molecule from the elements, and two conformational changes, a protein folding and the winding of a polynucleotide helix. The subtle energy transformations, bond-forming or bond-breaking, that were causing the two reactions of living matter to proceed in vitro forward or in reverse have been identified as the thermal work function delta Wto(T) and the chemical bond energy delta Ho0. Since the chemical bond energies and the heat capacities delta CoP(T) between reaction temperature and the absolute zero, unchangeable attributes of matter, were the only ingredients used for the treatment, the complexity of the reactions has been reduced--as far as effects and ultimate causes are concerned--to the simplicity of low temperature physics, a solid physical foundation for all biological and medical sciences.

Animals↗

A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution.

The tailoring of existing genetic systems to new uses is called genetic co-option. Mechanisms of genetic co-option have been difficult to study because of difficulties in identifying functionally important changes. One way to study genetic co-option in protein-coding genes is to identify those amino acid sites that have experienced changes in selective pressure following a genetic co-option event. In this paper we present a maximum likelihood method useful for measuring divergent selective pressures and identifying the amino acid sites affected by divergent selection. The method is based on a codon model of evolution and uses the nonsynonymous-to-synonymous rate ratio (omega) as a measure of selection on the protein, with omega = 1, < 1, and > 1 indicating neutral evolution, purifying selection, and positive selection, respectively. The model allows variation in omega among sites, with a fraction of sites evolving under divergent selective pressures. Divergent selection is indicated by different omega's between clades, such as between paralogous clades of a gene family. We applied the codon model to duplication followed by functional divergence of (i) the epsilon and gamma globin genes and (ii) the eosinophil cationic protein (ECP) and eosinophil-derived neurotoxin (EDN) genes. In both cases likelihood ratio tests suggested the presence of sites evolving under divergent selective pressures. Results of the epsilon and gamma globin analysis suggested that divergent selective pressures might be a consequence of a weakened relationship between fetal hemoglobin and 2,3-diphosphoglycerate. We suggest that empirical Bayesian identification of sites evolving under divergent selective pressures, combined with structural and functional information, can provide a valuable framework for identifying and studying mechanisms of genetic co-option. Limitations of the new method are discussed.

Amino Acids↗

Distribution and inheritance of beta-amylase alleles in north European barley varieties.

Allelic diversity and inheritance of polymorphic sites of the intron III-exon IV region of the seed specific beta-amylase gene Bmy1 were studied in a set of 55 barley accessions composed mainly of old Latvian and Scandinavian commercial varieties and three Hordeum spontaneum lines from Israel. A CAPS-marker was used for genotyping the C698 --> T polymorphism encoding alleles of beta-amylase with different thermostability. The genotype C698 which is diagnostic for a more thermostable isoform of the beta-amylase was detected in 13 of the investigated accessions. In most cases the origin of the C698 genotype could be traced back to the old Danish variety Binder in the pedigree. However, this genotype was lost in later varieties originating from Binder. A 6+1 bp deletion event in intron III of the beta-amylase gene was in all cases linked to the presence of the C698 mutation, while the repeat number of a microsatellite in intron III had no correlation to the presence of the C698 mutation. Sequence analysis revealed a number of haplotypes within exon IV that did not result in amino acid changes due to the degenerated genetic code.

Alleles↗

[The language of medicine].

The idiom of physicians has evolved from Latin to the genetic code, in parallel with a change in the paradigm of disease. From the end of the 18th century, disease was no longer attributed to a disturbance of the body equilibrium, but to a localised abnormality--of organs, cells and eventually genes. A further step in this direction is the proposed creation of physician-engineers to replace broken parts in the human machinery. Such blind reductionism fails to offer a solution for somatisation, a scourge of modern western societies. Even organ specialists should be able to revert to the holistic notion of 'disequilibrium' to account for unexplained symptoms. For the medical profession, an education in the humanities is no less important than that in science.

History of Medicine↗

[Analysis program for quantitative detection of chromosome aberrations using comparative genomic hybridization].

Comparative genomic hybridization (CGH) is a molecular cytogenetic method for the detection of chromosomal imbalances between a tumor and a normal genome. In order to produce quantitative and reproducible results, we developed an image analysis program that allows the detection and mapping of the genetic alterations. The result is represented as a CGH sum karyogram in which the genetic changes are documented as color coded-chromosomes. The aim of our investigation is to correlate the genotype with the phenotype on the basis of CGH sum karyograms and thus to achieve a genetic characterization that will supplement the morphological tumor description.

Cell Transformation, Neoplastic↗

[Age-dependent changes in connective tissue].

Alterations of the various connective tissues with aging are investigated by combined morphological and biochemical methods. The aging of connective tissues depends on aging of informational- and structural-macromolecules. Aging-dependent alterations of proteoglycans/GAG and collagen can be caused by changes in genetic information or in the cellular information-coded synthesis, but also by changes in the controls of the various metabolic processes of connective tissue cells. The activities of enzymes involved in the anabolism and the catabolism of proteoglycans/GAG and collagen show reductions with aging, but do not show age-specific variations. The aging of connective tissues is rather a dynamic process (with measurable metabolic parameters of the various connective tissue cells and their products) than a passive or so-called degenerative connective tissue process. The bradytrophy concept of connective tissue cannot be accepted any longer, because connective tissue cells partly have metabolic rates at the same level as parenchymal cells. Furthermore, parenchymal cells can synthesize and degrade mesenchymal structural macromolecules. Connective tissue aging is demonstrated on 3 organ groups: 1. on typical mesenchymal organs: aorta, cartilage and skin, 2. on organs, which are mainly composed by connective tissue: heart and lung, 3. on connective tissues of parenchymal organs: liver and kidney. These various organs exhibit some common basic processes but also differences in connective tissue aging, which are due to the different composition of proteoglycans/GAG and collagen types, and on structure and function. The aging of connective tissues is of special importance for the aging of organs. Besides alterations of cells and GAG, the very important aging fibrosis in several mesenchymal and parenchymal organs is demonstrated and discussed. The connective tissue aging of organs is one of the reasons why the frequency of diseases increases with aging and diseases are grafted more strongly on aging cells, tissues, organs and organisms.

Aging↗

The Drosophila ribosomal protein S6 gene includes a 3' triplication that arose by unequal crossing-over.

Ribosomal protein S6 (rpS6) is the major phosphoprotein of the small ribosomal subunit of eukaryotes and is phosphorylated in response to treatment with mitogens and other stimuli. We have examined the organization of the rpS6 gene of Drosophila melanogaster. Comparisons of a cDNA with genomic DNA identify a transcription unit including three exons. Two tandem repeats downstream of this transcription unit reiterate divergent copies of the third exon and flanking regions. Comparisons of these three repeats with respect to nucleotide base substitutions and deletions or insertions show clearly that they arose via a duplication and subsequent crossing-over between misaligned copies. Although no direct evidence exists that the downstream exons are transcribed, the maintenance of open reading frames in spite of extensive genetic changes is consistent with a protein-coding function.

Amino Acid Sequence↗

Physicochemical optimization in the genetic code origin as the number of codified amino acids increases.

We have assumed that the coevolution theory of genetic code origin (Wong JT, Proc Natl Acad Sci USA 72:1909-1912, 1975) is essentially correct. This theory makes it possible to identify at least 10 evolutionary stages through which genetic code organization might have passed prior to reaching its current form. The calculation of the minimization level of all these evolutionary stages leads to the following conclusions. (1) The minimization percentages increased linearly with the number of amino acids codified in the codes of the various evolutionary stages when only the sense changes are considered in the analysis. This seems to favor the physicochemical theory of genetic code origin even if, as discussed in the paper, this observation is also compatible with the coevolution theory. (2) For the first seven evolutionary stages of the genetic code, this trend is less clear and indeed is inverted when we consider the global optimisation of the codes due to both sense changes and synonymous changes. This inverse correlation between minimization percentages and the number of amino acids codified in the codes of the intermediate stages seems to favor neither the physicochemical nor the stereochemical theories of genetic code origin, as it is in the early and intermediate stages of code development that these theories would expect minimization to have played a crucial role, and this does not seem to be the case. However, these results are in agreement with the coevolution theory, which attributes a role to the physicochemical properties of amino acids that, while important, is nevertheless subordinate to the mechanism which concedes codons from the precursor amino acids to the product amino acids as the primary factor determining the evolutionary structuring of the genetic code. The results are therefore discussed in the context of the various theories proposed to explain genetic code origin.

Algorithms↗

Construction of interleukin-1 alpha mutants using unequal contamination of synthetic oligonucleotides.

Proteins without readily available three-dimensional structural data present a difficult problem in the exploration of structure/function relationships. Saturation mutagenesis using contaminated oligonucleotides can identify potentially interesting regions of such a protein. This technique, in which synthesized oligonucleotides contain low-level base substitutions, allows random mutations to be placed throughout a gene sequence. Using double-stranded cassettes, a region of the human interleukin-1 alpha gene has been altered using such mutagenic oligonucleotides. However, instead of contaminating both strands of the gene sequence at the same level, each strand of the insert was contaminated at a different level. Several recombinants were sequenced and the effects of the mutations on the activity of the proteins were examined. Contaminating the two oligonucleotides at different levels produced a significantly different distribution of nucleotide changes from that seen if both strands were contaminated at the same level. The observed distribution followed the average of the distributions for each of the two contamination levels. This resulted in roughly equal frequencies of 1 to 5 nucleotide changes per clone with very few clones containing the wild-type nucleotide sequence. This helped overcome the redundancy in the genetic code, resulting in a high frequency of amino acid changes, and allowed changes at every amino acid to be sampled in a small number of mutants. This procedure can allow a gene sequence to be screened rapidly by removing most wild-type sequences from analysis while making sure that there are many amino acid changes in the resultant mutants.

Amino Acid Sequence↗

Effects of habitat fragmentation and changes of dispersal behaviour after a recent population decline on the genetic variability of noncoding and coding DNA of a monogamous Malagasy rodent.

While interactions among demography, behaviour and genetic structure are well-documented for neutral genetic markers, the role of these parameters and the effects of genetic drift and selection are considerably less well understood in functional genes, such as the major histocompatibility complex (MHC). In this study, the consequences of habitat fragmentation and the effects of a current population decline on noncoding (mitochondrial DNA) and two coding MHC loci (DQA, DRB) with different functional importance were investigated in the small remnant subdivided population of the endangered Malagasy giant jumping rat (Hypogeomys antimena). Both neutral and selective markers revealed a significant genetic differentiation between the two remnant subpopulations. The FST values were much lower in the MHC DQA and DRB genes than in the mitochondrial data. The MHC DRB loci display the effects of both balancing selection (high sequence diversity, four times higher nonsynonymous than synonymous substitutions in the functionally important antigen-binding site positions, twice the average heterozygosity of individual amino acids at the positions identified as part of the antigen-binding site (ABS) than those outside the ABS and nonselective forces including genetic drift. Simultaneously with a current population decline offspring reduced their dispersal distances. No substantial effects were detected within the first 6 years of reduced gene flow in either mitochondrial or MHC markers.

Animals↗

Experts discuss findings on drug resistance.

John Mellors, MD, professor of medicine and chief of infectious diseases at the University of Pittsburgh, and Sharon Kemp, director of HIV Research for Virco UK in Cambridge, United Kingdom, answer questions about a study presented at the 5th International Workshop on HIV Resistance and Treatment Strategies, held in June in Scottsdale, AZ. The study found that a change at position 318 in the genetic code of HIV can make the virus highly resistant to treatment with non-nucleoside reverse transcription.

Anti-HIV Agents↗