Biomedical subjects
T H Jukes
Publications and source records attributed to T H Jukes.
Well-being and productivity.
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Numerical classification of coding sequences.
DNA sequences coding for protein may be represented by counts of nucleotides or codons. A complete reading frame may be abbreviated by its base count, e.g. A76C158G121T74, or with the corresponding codon table, e.g. (AAA)0(AAC)1(AAG)9 ... (TTT)0. We propose that these numerical designations be used to augment current methods of sequence annotation. Because base counts and codon tables do not require revision as knowledge of function evolves, they are well-suited to act as cross-references, for example to identify redundant GenBank entries. These descriptors may be compared, in place of DNA sequences, to extract homologous genes from large databases. This approach permits rapid searching with good selectivity.
Today's non-Orwellian animal farm.
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Antioxidants, nutrition, and evolution.
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Recent evidence for evolution of the genetic code.
The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.
Who has spoken for science?
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Evolutionary nucleotide replacements in DNA.
With the increasing availability of analytical information on mRNA molecules, it is now possible to compare homologous nucleotide sequences from different organisms and to draw conclusions about their evolution. Such comparisons have shown that silent changes in codons occur more frequently than nucleotide replacements that produce changes in amino acid sequences (code-altering changes). Furthermore, there is an important difference between amino acid sequence comparisons and nucleotide sequence comparisons. The former show only differences in amino acid residues, but the latter show several types of differences when corresponding codons are compared. Single-base replacements may be degenerate (silent) or expressed as amino acid replacements. Two-base codon changes may be degenerate, single-base changes, or be visible as such. Three-base codon changes may be degenerate (involving serine), simulate either single-base or two-base changes or be visible as such. All nine types of change are found in comparisons of genes from the viruses phi X174 and G4. The relative numbers of these nine types as based on all possible interchanges between all 61 amino acid codons were listed by Holmquist et al. and are shown in Table 1. We discuss these results in the light of the significance of nucleotide changes in molecular evolution.
Carcinogens in food and the Delaney clause.
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The Viking Mission: implications for life on Mars.
The results of the Viking Biology experiments are best explained by non-biological phenomena: The interaction of the reagents with the materials comprising the regolith. Conditions of water activity, temperature, availability of carbon sources and others in most regions of the planet are too extreme for survival and growth of any known Earth microorganisms. Although the possibility persists that some very unusual form of life is somewhere on that planet the evidence is best interpreted as negative. Even though there is no evidence for current life on Mars, whether or not life ever originated there is not known.
Neutral changes revisited.
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Dr. Best, insulin, and molecular evolution.
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Antibacterial agents in animal feeds.
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Statement regarding OSHA's proposed federal cancer policy.
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Living history: nutritional discoveries of the 1930's: introductory remarks.
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