Biomedical subjects

Anthony M Poole

Publications and source records attributed to Anthony M Poole.

4 recordsLinked to original sources

PubMed2003

Testing fundamental evolutionary hypotheses.

Sober and Steel (J. Theor. Biol. 218, 395-408) give important limits on the use of current models with sequence data for studying ancient aspects of evolution; but they go too far in suggesting that several fundamental aspects of evolutionary theory cannot be tested in a normal scientific manner. To the contrary, we show examples of how some alternatives to the theory of descent can be formulated in such a way that they lead to predictions that can be evaluated (and rejected). The critical factor is a logical formulation of the alternatives, even though not all possible alternatives can be tested simultaneously. Similarly, some of the limits using DNA sequence data can be overcome by other types of sequence derived characters. The uniqueness (or not) of the origin of life, though still difficult, is similarly amenable to the testing of alternative hypotheses.

Animals↗

PubMed2003

A search for H/ACA snoRNAs in yeast using MFE secondary structure prediction.

MOTIVATION: Noncoding RNA genes produce functional RNA molecules rather than coding for proteins. One such family is the H/ACA snoRNAs. Unlike the related C/D snoRNAs these have resisted automated detection to date. RESULTS: We develop an algorithm to screen the yeast genome for novel H/ACA snoRNAs. To achieve this, we introduce some new methods for facilitating the search for noncoding RNAs in genomic sequences which are based on properties of predicted minimum free-energy (MFE) secondary structures. The algorithm has been implemented and can be generalized to enable screening of other eukaryote genomes. We find that use of primary sequence alone is insufficient for identifying novel H/ACA snoRNAs. Only the use of secondary structure filters reduces the number of candidates to a manageable size. From genomic context, we identify three strong H/ACA snoRNA candidates. These together with a further 47 candidates obtained by our analysis are being experimentally screened.

Algorithms↗

PubMed2003

Prokaryote and eukaryote evolvability.

The concept of evolvability covers a broad spectrum of, often contradictory, ideas. At one end of the spectrum it is equivalent to the statement that evolution is possible, at the other end are untestable post hoc explanations, such as the suggestion that current evolutionary theory cannot explain the evolution of evolvability. We examine similarities and differences in eukaryote and prokaryote evolvability, and look for explanations that are compatible with a wide range of observations. Differences in genome organisation between eukaryotes and prokaryotes meets this criterion. The single origin of replication in prokaryote chromosomes (versus multiple origins in eukaryotes) accounts for many differences because the time to replicate a prokaryote genome limits its size (and the accumulation of junk DNA). Both prokaryotes and eukaryotes appear to switch from genetic stability to genetic change in response to stress. We examine a range of stress responses, and discuss how these impact on evolvability, particularly in unicellular organisms versus complex multicellular ones. Evolvability is also limited by environmental interactions (including competition) and we describe a model that places limits on potential evolvability. Examples are given of its application to predator competition and limits to lateral gene transfer. We suggest that unicellular organisms evolve largely through a process of metabolic change, resulting in biochemical diversity. Multicellular organisms evolve largely through morphological changes, not through extensive changes to cellular biochemistry.

Adaptation, Physiological↗

PubMed2002

The evolution of the ribonucleotide reductases: much ado about oxygen.

Ribonucleotide reduction is the only known biological means for de novo production of deoxyribonucleotides, the building blocks of DNA. These are produced from ribonucleotides, the building blocks of RNA, and the direction of this reaction has been taken to support the idea that, in evolution, RNA preceded DNA as genetic material. However, an understanding of the evolutionary relationships among the three modern-day classes of ribonucleotide reductase and how the first reductase arose early in evolution is still far off. We propose that the diversification of this class of enzymes is inherently tied to microbial colonization of aerobic and anaerobic niches. The work is of broader interest, as it also sheds light on the process of adaptation to oxygenic environments consequent to the evolution of atmospheric oxygen.

Allosteric Regulation↗