title: On the origin and evolution of thermophily: Reconstruction of functional precambrian enzymes from ancestors of Bacillus

authors: Hobbs, Joanne K.

subjects: ancestral reconstruction

abstract: Thermophily is thought to be a primitive trait, characteristic of early forms of life on Earth, that has been gradually lost over evolutionary time. The genus Bacillus provides an ideal model for studying the evolution of thermophily as it is an ancient taxon and its contemporary species inhabit a range of thermal environments. The thermostability of reconstructed ancestral proteins has been used as a proxy for ancient thermal adaptation. The reconstruction of ancestral “enzymes” has the added advantages of demonstrable activity, which acts as an internal control for accurate inference, and providing insights into the evolution of enzymatic catalysis. Here, we report the reconstruction of the structurally complex core metabolic enzyme LeuB (3-isopropylmalate dehydrogenase, E. C. 1.1.1.85) from the last common ancestor (LCA) of Bacillus using both maximum likelihood (ML) and Bayesian inference. ML LeuB from the LCA of Bacillus shares only 76% sequence identity with its closest contemporary homolog, yet it is fully functional, thermophilic, and exhibits high values for kcat, kcat/KM, and ΔG‡ for unfolding. The Bayesian version of this enzyme is also thermophilic but exhibits anomalous catalytic kinetics. We have determined the 3D structure of the ML enzyme and found that it is more closely aligned with LeuB from deeply branching bacteria, such as Thermotoga maritima, than contemporary Bacillus species. To investigate the evolution of thermophily, three descendents of LeuB from the LCA of Bacillus were also reconstructed. They reveal a fluctuating trend in thermal evolution, with a temporal adaptation toward mesophily followed by a more recent return to thermophily. Structural analysis suggests that the determinants of thermophily in LeuB from the LCA of Bacillus and the most recent ancestor are distinct and that thermophily has arisen in this genus at least twice via independent evolutionary paths. Our results add significant fluctuations to the broad trend in thermal adaptation previously proposed and demonstrate that thermophily is not exclusively a primitive trait, as it can be readily gained as well as lost. Our findings also demonstrate that reconstruction of complex functional Precambrian enzymes is possible and can provide empirical access to the evolution of ancient phenotypes and metabolisms

text: On the origin and evolution of thermophily: Reconstruction of functional precambrian enzymes from ancestors of Bacillus Thermophily is thought to be a primitive trait, characteristic of early forms of life on Earth, that has been gradually lost over evolutionary time. The genus Bacillus provides an ideal model for studying the evolution of thermophily as it is an ancient taxon and its contemporary species inhabit a range of thermal environments. The thermostability of reconstructed ancestral proteins has been used as a proxy for ancient thermal adaptation. The reconstruction of ancestral “enzymes” has the added advantages of demonstrable activity, which acts as an internal control for accurate inference, and providing insights into the evolution of enzymatic catalysis. Here, we report the reconstruction of the structurally complex core metabolic enzyme LeuB (3-isopropylmalate dehydrogenase, E. C. 1.1.1.85) from the last common ancestor (LCA) of Bacillus using both maximum likelihood (ML) and Bayesian inference. ML LeuB from the LCA of Bacillus shares only 76% sequence identity with its closest contemporary homolog, yet it is fully functional, thermophilic, and exhibits high values for kcat, kcat/KM, and ΔG‡ for unfolding. The Bayesian version of this enzyme is also thermophilic but exhibits anomalous catalytic kinetics. We have determined the 3D structure of the ML enzyme and found that it is more closely aligned with LeuB from deeply branching bacteria, such as Thermotoga maritima, than contemporary Bacillus species. To investigate the evolution of thermophily, three descendents of LeuB from the LCA of Bacillus were also reconstructed. They reveal a fluctuating trend in thermal evolution, with a temporal adaptation toward mesophily followed by a more recent return to thermophily. Structural analysis suggests that the determinants of thermophily in LeuB from the LCA of Bacillus and the most recent ancestor are distinct and that thermophily has arisen in this genus at least twice via independent evolutionary paths. Our results add significant fluctuations to the broad trend in thermal adaptation previously proposed and demonstrate that thermophily is not exclusively a primitive trait, as it can be readily gained as well as lost. Our findings also demonstrate that reconstruction of complex functional Precambrian enzymes is possible and can provide empirical access to the evolution of ancient phenotypes and metabolisms

year: 2011

title: Scaling of spectral anisotropy with magnetic field strength in decaying magnetohydrodynamic turbulence

authors: Oughton, Sean

subjects: magnetohydrodynamics

abstract: Space plasmameasurements,laboratory experiments, and simulations have shown that magnetohydrodynamic(MHD)turbulence exhibits a dynamical tendency towards spectral anisotropy given a sufficiently strong background magnetic field. Here the undriven decaying initial-value problem for homogeneous MHDturbulence is examined with the purpose of characterizing the variation of spectral anisotropy of the turbulent fluctuations with magnetic field strength. Numerical results for both incompressible and compressible MHD are presented. A simple model for the scaling of this spectral anisotropy as a function of the fluctuating magnetic field over total magnetic field is offered. The arguments are based on ideas from reduced MHD (RMHD) dynamics and resonant driving of certain non-RMHD modes. The results suggest physical bases for explaining variations of the anisotropy with compressibility, Reynolds numbers, and spectral width of the (isotropic) initial conditions.

text: Scaling of spectral anisotropy with magnetic field strength in decaying magnetohydrodynamic turbulence Space plasmameasurements,laboratory experiments, and simulations have shown that magnetohydrodynamic(MHD)turbulence exhibits a dynamical tendency towards spectral anisotropy given a sufficiently strong background magnetic field. Here the undriven decaying initial-value problem for homogeneous MHDturbulence is examined with the purpose of characterizing the variation of spectral anisotropy of the turbulent fluctuations with magnetic field strength. Numerical results for both incompressible and compressible MHD are presented. A simple model for the scaling of this spectral anisotropy as a function of the fluctuating magnetic field over total magnetic field is offered. The arguments are based on ideas from reduced MHD (RMHD) dynamics and resonant driving of certain non-RMHD modes. The results suggest physical bases for explaining variations of the anisotropy with compressibility, Reynolds numbers, and spectral width of the (isotropic) initial conditions.

year: 1998

title: Putting Sylvia in her place: Ashton-Warner as New Zealand educational theorist

authors: Middleton, Sue

subjects: Sylvia Ashton-Warner

abstract: Sylvia Ashton-Warner, a New Zealand teacher, won international acclaim in the 1950s-1950s with her novels, autobiographies, and accounts of her educational theory. Blurring genres between fiction and autobiography, much of her writing was centred on the ‘creative teaching scheme’ she developed in Maori Schools. At the heart of the scheme was the idea that literacy was best achieved when children captioned their experiences of fear and sex, the two great (Freudian) drives. In Sylvia’s infant room, these erupted to the surface by means of captions (a child’s ‘key vocabulary’). I introduce Lefebvre’s idea of ‘rhythm analysis’, applying it first to the teaching scheme, then to the ‘system’ in which Ashton-Warner taught. With reference to extracts from Ashton-Warner’s Creative Teaching Scheme and Myself, I connect the rhythms of her life with her ‘theory.’ I identify Sylvia’s own ‘key words’ (violence and war; ghosts; sex and the kiss) and their rhythmic engagements and collisions with educational ‘authorities.’

text: Putting Sylvia in her place: Ashton-Warner as New Zealand educational theorist Sylvia Ashton-Warner, a New Zealand teacher, won international acclaim in the 1950s-1950s with her novels, autobiographies, and accounts of her educational theory. Blurring genres between fiction and autobiography, much of her writing was centred on the ‘creative teaching scheme’ she developed in Maori Schools. At the heart of the scheme was the idea that literacy was best achieved when children captioned their experiences of fear and sex, the two great (Freudian) drives. In Sylvia’s infant room, these erupted to the surface by means of captions (a child’s ‘key vocabulary’). I introduce Lefebvre’s idea of ‘rhythm analysis’, applying it first to the teaching scheme, then to the ‘system’ in which Ashton-Warner taught. With reference to extracts from Ashton-Warner’s Creative Teaching Scheme and Myself, I connect the rhythms of her life with her ‘theory.’ I identify Sylvia’s own ‘key words’ (violence and war; ghosts; sex and the kiss) and their rhythmic engagements and collisions with educational ‘authorities.’

year: 2009