Comparative analysis of barophily-related amino acid content in protein domains of Pyrococcus abyssi and Pyrococcus furiosus.

Amino acid substitution patterns between the nonbarophilic Pyrococcus furiosus and its barophilic relative P. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. Substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environment that led to the genetic code and diversified life.

A general framework of persistence strategies for biological systems helps explain domains of life.

The nature and cause of the division of organisms in superkingdoms is not fully understood. Assuming that environment shapes physiology, here we construct a novel theoretical framework that helps identify general patterns of organism persistence. This framework is based on Jacob von Uexküll's organism-centric view of the environment and James G.

Putative lateral inhibition in sensory processing for directional turns.

Computing targeted responses is a general problem in goal-directed behaviors. We sought the sensory template for directional turning in the predatory sea slug Pleurobranchaea californica, which calculates precise turn angles by averaging multiple stimulus sites on its chemotactile oral veil (Yafremava LS, Anthony CW, Lane L, Campbell JK, Gillette R. J Exp Biol 210: 561-569, 2007).

The origin and evolution of modern metabolism.

One fundamental goal of current research is to understand how complex biomolecular networks took the form that we observe today. Cellular metabolism is probably one of the most ancient biological networks and constitutes a good model system for the study of network evolution. While many evolutionary models have been proposed, a substantial body of work suggests metabolic pathways evolve fundamentally by recruitment, in which enzymes are drawn from close or distant regions of the network to perform novel chemistries or use different substrates.

Origins and evolution of modern biochemistry: insights from genomes and molecular structure.

The survey of components in living systems at different levels of organization enables an evolutionary exploration of patterns and processes in macromolecules, networks, and genomic repertoires. Here we discuss how phylogenetic strategies that generate intrinsically rooted phylogenies impact the evolutionary study of RNA and protein components of the macromolecular machinery that is responsible for biological function. We used these methods to generate timelines of discovery of components in systems, such as substructures in RNA molecules, architectures in proteomes, domains in multi-domain proteins, enzymes in metabolic networks, and protein architectures in proteomes.

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world.

The repertoire of protein architectures in proteomes is evolutionarily conserved and capable of preserving an accurate record of genomic history. Here we use a census of protein architecture in 185 genomes that have been fully sequenced to generate genome-based phylogenies that describe the evolution of the protein world at fold (F) and fold superfamily (FSF) levels. The patterns of representation of F and FSF architectures over evolutionary history suggest three epochs in the evolution of the protein world: (1) architectural diversification, where members of an architecturally rich ancestral community diversified their protein repertoire; (2) superkingdom specification, where superkingdoms Archaea, Bacteria, and Eukarya were specified; and (3) organismal diversification, where F and FSF specific to relatively small sets of organisms appeared as the result of diversification of organismal lineages.

Orienting and avoidance turning are precisely computed by the predatory sea-slug Pleurobranchaea californica McFarland.

Computing the direction and amplitude of orienting and avoidance turns is fundamental to prey pursuit and risk avoidance in motile foragers. We examined computation of turns in the predatory sea-slug Pleurobranchaea californica, observing orienting and aversive turn responses to chemotactile stimuli applied to the chemosensory oral veil. We made seven observations: (1) the relation of turn angle/stimulus site on the oral veil was linear; (2) turn amplitudes increased with stimulus strength; (3) turn responses markedly overshot the target stimulus; (4) responses to two simultaneous stimuli at different loci were averaged to an intermediate angle; (5) stimuli could induce sequential turns in which the angles of the first and third turns were similar, a form of working memory; (6) turn direction was affected by appetitive state, so that animals with higher feeding thresholds tended to avoid appetitive stimuli; and (7) avoidance turns induced by mildly noxious stimuli were computed similarly to orienting, while differing in direction.