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At least 1,207 records · Page 67Linked to original sources
PubMed2003

Nutrition and genetics: an expanding frontier.

The age of molecular biology began in 1953 with the discovery of the structure of DNA. By 1961 the genetic code for the translation of the sequence of bases in DNA to amino acids in proteins was underway, and a model for the genetic regulation of protein synthesis was proposed. My interest in the genetic regulation of nutrient metabolism began in that year during my sabbatical leave in the laboratory of Sir Hans Krebs at Oxford University. In the present article, I describe 2 episodes in my career during which I used genetic concepts to explain a nutritional phenomenon; the first episode occurred before doing the experimental work, and the second occurred after the experimental work was completed. My first brainstorm, which occurred in 1961, was to investigate the hypothesis that all of the fat-soluble vitamins act by the regulation of a cluster of genes. Unfortunately, I selected vitamin K as my model and discovered that it is the only fat-soluble vitamin that does not work in full or in part by the regulation of a set of genes. In 1967 I undertook a second problem, which was to determine the mode of action of polyunsaturated fatty acids in lowering plasma lipid concentrations in humans. We discovered that linoleic acid reduced the storage and enhanced the oxidation of fatty acids. The genetic interpretation of this study has come only recently: polyunsaturated fats have been shown to down-regulate enzymes that accomplish storage of fatty acids and to up-regulate genes that enhance fatty acid oxidation.

Animals↗
PubMed2006

[A research on TGFBI gene mutations in Chinese families with corneal dystrophies].

OBJECTIVE: To identify what kind of TGFBI gene mutation happening to Chinese patients with corneal dystrophies. METHODS: Three Chinese families with stromal corneal dystrophies and one Chinese family with Thiel-Behnke corneal dystrophies were studied, of whom three were Han race and another was Mongolia race in China. All members of families were examined clinically and their genomic DNAs were extracted from blood leukocytes. Thirteen exons in TGFBI gene were amplified by polymerase chain reaction (PCR) and directly sequenced for molecular analysis. RESULTS: Mutations in TGFBI gene were detected from all the patients with corneal dystrophy, but not found in normal subjects of families. The mutation R555W was found and identified from the family with granular corneal dystrophy; R555Q from the family with Thiel-Behnke corneal dystrophy; and R124H from the other two families with Avellino corneal dystrophy. CONCLUSION: The above study results show that the amino acids R124 and R555, if their genetic codes result from the mutations, play an important role in the pathogenesis of autosomal dominant corneal dystrophy of Chinese patients, and the molecular genetic analysis can improve the accuracy of diagnosing corneal dystrophy. In China, the mutation R555Q found in the family with Thiel-Behnke corneal dystrophy is reported for the first time.

Base Sequence↗
PubMed1990

The use of information theory to analyze genomic changes in neoplasia.

How the cell maintains and uses its heritable information may be a critical factor in neoplasia. For example, neoplastic development is thought to depend upon the interplay between random genomic instability and nonrandom selective forces. Information theory provides a means to analyze these processes. One may quantitate not only the amount and lability of information contained within a segment of genetic code, but also the genotypic heterogeneity and the degree of selection affecting a population of cells. In addition, it is theoretically possible to monitor genetic information as it is processed by cells during replication, transcription, and translation. These parameters could permit a detailed analysis of the evolutionary changes hypothesized to underlie neoplastic development.

Animals↗
PubMedDate not supplied

Molecular evolution: first enzymes, gases as substrates and genetic templates.

A fundamental problem in biology is the self-assembly of the first cells capable of growth and division under anoxic conditions on the Earth. Evolution proceeded by self-assembling and self-replicating cells that reproduced their own genetic information and also changed their genetic code over time. Was it also possible that some of the first proteins were catalytic and used gases as substrates and also acted as genetic templates? This paper explores the possibility that primitive protein enzymes used gases as their substrates, and reverse translation may have been a feature in the self-assembly of the first cell(s).

Cells↗
PubMedDate not supplied

Aligning amino acid sequences: comparison of commonly used methods.

We examined two extensive families of protein sequences using four different alignment schemes that employ various degrees of "weighting" in order to determine which approach is most sensitive in establishing relationships. All alignments used a similarity approach based on a general algorithm devised by Needleman and Wunsch. The approaches included a simple program, UM (unitary matrix), whereby only identities are scored; a scheme in which the genetic code is used as a basis for weighting (GC); another that employs a matrix based on structural similarity of amino acids taken together with the genetic basis of mutation (SG); and a fourth that uses the empirical log-odds matrix (LOM) developed by Dayhoff on the basis of observed amino acid replacements. The two sequence families examined were (a) nine different globins and (b) nine different tyrosine kinase-like proteins. It was assumed a priori that all members of a family share common ancestry. In cases where two sequences were more than 30% identical, alignments by all four methods were almost always the same. In cases where the percentage identity was less than 20%, however, there were often significant differences in the alignments. On the average, the Dayhoff LOM approach was the most effective in verifying distant relationships, as judged by an empirical "jumbling test." This was not universally the case, however, and in some instances the simple UM was actually as good or better. Trees constructed on the basis of the various alignments differed with regard to their limb lengths, but had essentially the same branching orders. We suggest some reasons for the different effectivenesses of the four approaches in the two different sequence settings, and offer some rules of thumb for assessing the significance of sequence relationships.

Amino Acid Sequence↗
PubMed2001

Degeneracy and complexity in biological systems.

Degeneracy, the ability of elements that are structurally different to perform the same function or yield the same output, is a well known characteristic of the genetic code and immune systems. Here, we point out that degeneracy is a ubiquitous biological property and argue that it is a feature of complexity at genetic, cellular, system, and population levels. Furthermore, it is both necessary for, and an inevitable outcome of, natural selection.

Animals↗
PubMed2004

Codon volatility as an indicator of positive selection: data from eukaryotic genome comparisons.

It has been suggested that codon volatility (the proportion of the point-mutation neighbors of a codon that encode different amino acids) can be used as an index of past positive selection. We compared codon volatility with patterns of synonymous and nonsynonymous nucleotide substitution in genome-wide comparisons of orthologous genes between three pairs of related genomes: (1) the protists Plasmodium falciparum and P. yoelii, (2) the fungi Saccharomyces cerevisiae and S. paradoxus, and (3) the mammals mouse and rat. Codon volatility was not consistently associated with an elevated rate of nonsynonymous substitution, as would be expected under positive selection. Rather, the most consistent and powerful correlate of elevated codon volatility was nucleotide content at the second codon position, as expected, given the nature of the genetic code.

Animals↗
PubMed1998

Combination of DMT-mononucleotide and Fmoc-trinucleotide phosphoramidites in oligonucleotide synthesis affords an automatable codon-level mutagenesis method.

BACKGROUND: Synthetic DNA has been used to introduce variability into protein-coding regions. In protocols that produce a few mutations per gene, the sampling of amino-acid sequence space is limited by the bias imposed by the genetic code. It has long been apparent that the incorporation of trinucleotides in the synthetic regime would circumvent this problem and significantly enhance the usefulness of the technique. RESULTS: A new method is described for the creation of codon-level degenerate oligodeoxyribonucleotides that combines conventional dimethoxytrityl (DMT) mononucleoside phosphoramidite chemistry with 9-fluorenylmethoxycarbonyl (Fmoc) trinucleotide phosphoramidites (whose synthesis is reported in the paper). The substoichiometric use of these Fmoc-trinucleotides in an automatable, solid-phase synthesis procedure afforded DNA fragments comprising the wild-type sequence and a controllable distribution of mutants within two- and three-codon stretches of DNA, within the multiple cloning site of the conventional cloning vector pUC19. CONCLUSIONS: DMT and Fmoc are compatible protecting groups in conventional oligonucleotide synthesis methods, resulting in controllable levels of codon-based mutagenesis.

Cloning, Molecular↗
PubMed1991

Synthesis of life in the lab? Defining a protoliving system.

The synthesis of a living system in the lab has been judged by a number of critics as partly attained by the proteinoid microsphere because of its primitive properties of metabolism, growth, and reproduction. These same critics, however, judge the organism as not alive, or as being 50 to 75 percent alive (Baltscheffsky and Jurka, 1984), owing to the absence of a nucleic acid genetic coding mechanism. The experiments in retracing evolution suggest, however, that the self-sequencing of amino acids was the evolutionary precursor of modern nucleic acid templating; the genetic memory is the molecule. The proteinoid microsphere is not a modern living system, but does represent at least a protoliving system (Fox and Dose, 1972). Berra (1990, p. 75) has commented on other difficulties in defining a protoliving system. In Berra's opinion, metabolism, reproduction, responsiveness to stimuli, and cellularity constitute or describe aliveness. These properties characterize proteinoid microspheres. A number of experiments demonstrate that amino acids in aminoacyl adenylates yield specific products, whereas nucleotides are without effect. For this and related reasons, especially the demonstrated self-sequencing of amino acids when they are warmed, resultant bio-functional properties of self-assembled microstructures, and demonstrated self-sequencing of amino acids in modern systems, the results appear to bridge from the chemical era to the biological period. All the above emerges from a departure in style of research (Young, 1984; Pauling and Zuckerkandl, 1972). The latter authors said, "It appears likely that biogenesis is the passage from a 'non-living system' existing in a large number of states to a 'living' system also existing in a large number of states."(ABSTRACT TRUNCATED AT 250 WORDS)

Nucleic Acids↗
PubMed1985

Theory of degenerate coding and informational parameters of protein coding genes.

The theory of degenerate coding is presented in a way enabling further application to molecular biology. There are two kinds of redundancy of a degenerate code. The first is due to the excess in codon length and the second to the code degeneracy. If the code is asymmetrically degenerate, the second kind of redundancy can be profitable for control of error rate. This control can be performed just by selective synonymous codon usage. Utilisation of the genetic code is partially influenced by this theoretical possibility. In particular the degree of error protectivity is well correlated with deviation from equiprobability in synonymous codon usage. The biological significance of this fact is discussed.

Animals↗
PubMed2003

Removing the redundancy from randomised gene libraries.

Amino acid substitution plays a vital role in both the molecular engineering of proteins and analysis of structure-activity relationships. High-throughput substitution is achieved by codon randomisation, which generates a library of mutants (a randomised gene library) in a single experiment. For full randomisation, key codons are typically replaced with NNN (64 sequences) or NN(G)(CorT) (32 sequences). This obligates cloning of redundant codons alongside those required to encode the 20 amino acids. As the number of randomised codons increases, there is therefore a progressive loss of randomisation efficiency; the number of genes required per protein rises exponentially. The redundant codons cause amino acids to be represented unevenly; for example, methionine is encoded just once within NNN, whilst arginine is encoded six times. Finally, the organisation of the genetic code makes it impossible to encode functional subsets of amino acids (e.g. polar residues only) in a single experiment. Here, we present a novel solution to randomisation where genetic redundancy is eliminated; the number of different genes equals the number of encoded proteins, regardless of codon number. There is no inherent amino acid bias and any required subset of amino acids may be encoded in one experiment. This generic approach should be widely applicable in studies involving randomisation of proteins.

Amino Acid Substitution↗
PubMed1996

Glutaminyl-tRNA synthetase: from genetics to molecular recognition.

Accurately aminoacylated tRNAs are an a priori requirement for translation of the genetic code. They are synthesized by the aminoacyl-tRNA synthetases which select both the correct amino acid and tRNA from a total of more than 400 possible combinations. Genetic, biochemical and structural studies have begun to reveal the mechanisms by which this specificity is achieved by Escherichia coli glutaminyl-tRNA synthetase (GlnRS). Sequence-specific interactions between GlnRS and tRNA(Gln) determine both the accuracy of tRNA selection and the efficiency of aminoacylation. Thus, amino acid recognition is tRNA-dependent. Consequently, while a noncognate tRNA may be recognized by GlnRS, the resulting tRNA-enzyme complex displays a considerably reduced affinity for glutamine compared to wild-type. This mechanism now provides a ready explanation as to why the majority of tRNA mischarging events, including those originally described over 25 years ago for GlnRS, impair cellular viability only to a limited degree.

Amino Acyl-tRNA Synthetases↗
PubMed2003

Genetic material in the early evolution of bacteria.

DNA and RNA are nucleic acids that cells and viruses use to produce copies of themselves. However, there is an immense paucity of knowledge on how these nucleic acids originated and changed as early bacteria became capable of growth and cell division. One possibility is that parallel evolution of the genetic code and protein synthesis was required for assembly of the first cells capable of growth and division. It is also possible that DNA-RNA duplices were intermediate genetic material in the early assembly of the first cells. These ideas will be discussed as well as other aspects of the assembly of the first cells on the Earth.

Bacteria↗
PubMed2001

A model for phylogenetic inference using structural and chemical covariates.

We investigated whether or not evolutionary change in DNA sequence data was homogeneous across different classes of base pairs. DNA sequences for eight protein-coding mitochrondrial genes were obtained for 38 vertebrate taxa from GenBank. Each nucleotide site in the alignment was classified according to a number of covariates, including its codon position, genetic code degeneracy, and hydrophobicity. The evolutionary transition matrix for each base was estimated by tracing implied character changes under parsimony on a known phylogenetic tree. Canonical variates analyses of the inferred transition matrices were performed for each gene to determine whether or not different classes of bases behaved similarly. We found five distinct clusters of transition matrices that could be roughly defined by combinations of codon position and degeneracy. This pattern was consistent among all genes. A stochastic model of rate variation based on the interaction of the covariates was developed to assess the statistical significance of the clusters. The five-group classification was found to explain significantly more sequence variation than did a codon only classification, a codon degeneracy classification, or a codon and degeneracy classification. The same five-group classification was found for all genes tested, suggesting a common process underlying the molecular evolution of the mitochondrial genome. These results confirm that there are classes of base pairs that evolve differently, and suggest that models of sequence evolution that incorporate covariate information may be useful in developing nucleotide substitution models that more accurately reflect evolutionary history.

Animals↗
PubMed2004

Regulation of RNA function by aminoacylation and editing?

The chemical modification of nucleic acids is a ubiquitous phenomenon. Aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a reaction essentially devoted to protein synthesis but it is used also as an emergency mechanism to recycle stalled ribosomes, and it is required for genome replication in some RNA viruses. In several aminoacyl-tRNA synthetases a correction mechanism known as editing is present to prevent aminoacylation errors. Genome data reveal a growing number of open reading frames encoding ARS-like proteins. This strongly suggests the existence of a widespread and nonconventional machinery for aminoacylation and editing. Here we review the different biological functions of aminoacylation and editing; also we propose an evolutionary scenario for the origin of these two reactions, and hypothesize an extant role for RNA charging and editing outside the genetic code.

Amino Acyl-tRNA Synthetases↗
PubMed2005

A Bayesian framework for SNP identification.

As evolutionary models for single-nucleotide polymorphisms (SNPs) become available, methods for using them in the context of evolutionary information and expert prior information is a necessity. We formulate a probability model for SNPs as a Bayesian inference problem. Using this framework we compare the individual and combined predictive ability of four evolutionary models of varying levels of specificity on three SNP databases (two specifically targeted at functional SNPs) by calculating posterior probabilities and generating Receiver Operating Characteristic (ROC) curves. We discover that none of the models do exceptionally well, in some cases no better than a random-guess model. However, we demonstrate that several properties of the Bayesian formulation improve the predictability of SNPs in the three databases, specifically the ability to utilize mixtures of evolutionary models and a prior based on the genetic code.

Bayes Theorem↗
PubMed2002

[From genetics to law, the viewpoint of the physician].

OF ALL SCIENCES: Genetics, science of the transmission of hereditary characteristics, is probably that which interferes most with the Law. However, it was not genetics that provoked the ideological, social and political upheaval at the end of the 19th and during the 20th century; it was the theory of evolution, which preceded the discovery of genetics that was to provide the substratum of evolution mechanisms. Most of the lethal ideologies of the 20th century were based on this. As was the case of eugenics, with the participation of scientists, legislators and judges. GENETIC ENGINEERING: The logical application of the theory of evolution and universality of the genetic code, led to the development of the genome program. Today, sequencing of the human genome is almost finished, but many years will be needed before details of the physiological genetic manifestations will be known. Genes themselves would not generally be concerned by patenting rules. However, there is an international tendency towards envisaging the patenting of genes. DEVELOPMENT OF GENETIC TESTS AND THEIR INCREASING USE FOR MEDICAL PURPOSES: Are among the ethical problems raised by genetics. Genetic diagnosis, conducted before embryo transfer is called "pre-implantation". This raises the problem of an eventual pre-implantation eugenic selection and therefore requires strict control. Reinforcement of the right to knowledge of genetic origins is also one of the socio-legal problems raised by the progress in genetics.

Attitude of Health Personnel↗
PubMed1977

The restriction of codon ambiguity on the basis of known variants.

The genetic code may be used to formulate the nucleotide sequence of a messenger RNA from the known amino acid sequence of a protein. Unfortunately, the degeneracy of the code means that there will be ambiguity in the nucleotide assignments in a third or more of the positions. A simple procedure is given that utilizes the information of known genetic variants to reduce that ambiguity. Problems associated with silent polymorphism are treated. The human alpha and beta hemoglobins are used to exemplify the technique. A total of 68 nucleotides in the two sequences are thereby made less ambiguous. One reduction leads to a nucleotide inconsistent with the result of the recently published beta hemoglobin sequence.

Base Sequence↗