Iron-sulfur clusters: why iron?

This communication addresses a simple question by means of density functional calculations: Why is iron used as the metal in iron-sulfur clusters? While there may be several answers to this question, it is shown here that one feature - the well-defined inner-sphere reorganization energy of self-exchange electron transfer - is very much favored in iron-sulfur clusters as opposed to metal substituted analogues of Mn, Co, Ni, and Cu. Furthermore, the conclusion holds for both 1Fe and 2Fe type iron-sulfur clusters. The results show that only iron provides a small inner-sphere reorganization energy of 21 kJ/mol in 1Fe (rubredoxin) and 46 kJ/mol in 2Fe (ferredoxin) models, whereas other metal ions exhibit values in the range 57-135 kJ/mol (1Fe) and 94-140 kJ/mol (2Fe). This simple result provides an important, although partial, explanation why iron alone is used in this type of clusters. The results can be explained by simple orbital rules of electron transfer, which state that the occupation of anti-bonding orbitals should not change during the redox reactions. This rule immediately suggests good and poor electron carriers.     

Solitary chemosensory cells: why do primary aquatic vertebrates need another taste system?

The taste-like system of solitary chemosensory cells (SCCs) has almost eluded scientific attention. This is particularly remarkable, since recent surveys have revealed that this system of epidermal cells is widespread and abundant among the anamniotic aquatic vertebrates. In the rocklings (Gadidae, Teleostei), high densities of SCCs occur at a specialized dorsal fin. Recent evidence from this model indicates that SCCs are narrowly tuned to dilutions of fish body mucus and bile. Thus, SCCs may sample the ambient water for the upstream presence of potential competitors or predators. However, in sea robins (Triglidae, Teleostei), SCCs seem to be involved in finding food. Information from many more species is needed to explain why SCCs and taste buds have been maintained in parallel for such a long evolutionary period of time - from the age of the agnathans to that of the most advanced teleost fishes.     

The timing of hibernation in Tasmanian echidnas: why do they do it when they do?

We investigated the patterns of hibernation and arousals in seven free-ranging echidnas Tachyglossus aculeatus setosus (two male, five female) in Tasmania using implanted temperature data loggers. All echidnas showed a ‘classical’ pattern of mammalian hibernation, with bouts of deep torpor interrupted by periodic arousals to euthermia (mean duration 1.04±0.05 (n=146). Torpor bout length increased as body temperature fell during the hibernation season, and became more variable as temperature rose again. Hibernation started in late summer (February 28±5 days, n=6) and males aroused just before the winter solstice (June 15±3 days, n=3), females that subsequently produced young aroused 40 days later (July 25±3, n=4) while females that did not produce young hibernated for a further two months (arousal Sept 27±5, n=7). We suggest that hibernation in Tasmanian echidnas can be divided into two phases, the first phase, marked by declining minimum body temperatures as ambient temperature falls, appears to be obligatory for all animals, while the second phase is ‘optional’ and is utilised to varying amounts by females. We suggest that early arousal and breeding is the favoured option for females in good condition, and that the ability to completely omit breeding in some years, and hibernate through to spring is an adaptation to an uncertain climate.     

Introduction: why do we need a science of well-being?

Introduction: why do we need a science of well-being?     

Why do Luehdorfia butterflies lay eggs in clusters?

Luehdorfia butterflies lay eggs in clusters. Clones of their host plants (Asiasarum and Heterotropa) are distributed pacthily among the understory of deciduous forests. Groups of Luehdorfia larvae often exhaust the clones and may wander over the forest floor seeking new clones. The highest mortality observed is during this wandering period. To elucidate why Luehdorfia butterflies lay eggs in clusters, a simulation experiment was made for hypothetical populations which lay eggs in clusters or singly. Field data on larval mortality, consumption, density of host clones and leaf weight for Luehdorfia japonica were incorporated into the model. The predictions of the simulation were: (1) When the egg density is low, the single egg type could leave many more pupae than the egg clustering type, but when the egg density is high, the former might leave smaller number of pupae than the latter; and (2) There are optimal sizes of egg clusters for different egg densities and the optimal size becomes larger as the egg density increased.     

The evolution of endothermy in terrestrial vertebrates: Who? When? Why?

Avian and mammalian endothermy results from elevated rates of resting, or routine, metabolism and enables these animals to maintain high and stable body temperatures in the face of variable ambient temperatures. Endothermy is also associated with enhanced stamina and elevated capacity for aerobic metabolism during periods of prolonged activity. These attributes of birds and mammals have greatly contributed to their widespread distribution and ecological success. Unfortunately, since few anatomical/physiological attributes linked to endothermy are preserved in fossils, the origin of endothermy among the ancestors of mammals and birds has long remained obscure. Two recent approaches provide new insight into the metabolic physiology of extinct forms. One addresses chronic (resting) metabolic rates and emphasizes the presence of nasal respiratory turbinates in virtually all extant endotherms. These structures are associated with recovery of respiratory heat and moisture in animals with high resting metabolic rates. The fossil record of nonmammalian synapsids suggests that at least two Late Permian lineages possessed incipient respiratory turbinates. In contrast, these structures appear to have been absent in dinosaurs and nonornithurine birds. Instead, nasal morphology suggests that in the avian lineage, respiratory turbinates first appeared in Cretaceous ornithurines. The other approach addresses the capacity for maximal aerobic activity and examines lung structure and ventilatory mechanisms. There is no positive evidence to support the reconstruction of a derived, avian-like parabronchial lung/air sac system in dinosaurs or nonornithurine birds. Dinosaur lungs were likely heterogenous, multicameral septate lungs with conventional, tidal ventilation, although evidence from some theropods suggests that at least this group may have had a hepatic piston mechanism of supplementary lung ventilation. This suggests that dinosaurs and nonornithurine birds generally lacked the capacity for high, avian-like levels of sustained activity, although the aerobic capacity of theropods may have exceeded that of extant ectotherms. The avian parabronchial lung/air sac system appears to be an attribute limited to ornithurine birds.     

Organellar genes: why do they end up in the nucleus?

Many mitochondrial and plastid proteins are derived from their bacterial endosymbiotic ancestors, but their genes now reside on nuclear chromosomes instead of remaining within the organelle. To become an active nuclear gene and return to the organelle as a functional protein, an organellar gene must first be assimilated into the nuclear genome. The gene must then be transcribed and acquire a transit sequence for targeting the protein back to the organelle. On reaching the organelle, the protein must be properly folded and modified, and in many cases assembled in an orderly manner into a larger protein complex. Finally, the nuclear copy must be properly regulated to achieve a fitness level comparable with the organellar gene. Given the complexity in establishing a nuclear copy, why do organellar genes end up in the nucleus? Recent data suggest that these genes are worse off than their nuclear and free-living counterparts because of a reduction in the efficiency of natural selection, but do these population-genetic processes drive the movement of genes to the nucleus? We are now at a stage where we can begin to discriminate between competing hypotheses using a combination of experimental, natural population, bioinformatic and theoretical approaches.     

Evidence for dynamic alteration in histone gene clusters of Caenorhabditis elegans: a topoisomerase II connection?

Chromatin integrity is maintained throughout the cell cycle through repair mechanisms and intrinsically by the ordered packaging of DNA in association with histone proteins; however, aberrant rearrangements within and between chromosomes do occur. The role of the nuclear matrix protein topoisomerase II (TopoII) in generating chromosome breakpoints has been a focus of recent investigations. TopoII preferentially binds in vitro to scaffold-associated regions (SARs) and is involved in many DNA processing activities that require chromosome untangling. SARs, biochemically defined DNA elements rich in A + T, have been proposed to serve as structural boundaries for chromatin loops and to delineate functional domains. In our investigation of gene compartmentalization in a eukaryotic genome, SAR-associated nucleotide motifs from Drosophila were mapped in the regions of three histone gene clusters in an in silico analysis of the genome of Caenorhabditis elegans. Sites with similarity to the 15 bp consensus for TopoII cleavage were found predominantly in A + T enriched intergenic regions. Reiteration of sites matching the TopoII core consensus led to the identification of a novel core histone gene on chromosome IV and provided evidence for duplication and inversion in each of the three histone gene clusters. Breakpoint analysis of DNA flanking reiterated regions revealed potential sites for TopoII cleavage and a base composition phenomenon suggestive of a trigger for inversion events.     

Comparative analyses in aquatic microbial ecology: how far do they go?

Methodological developments in recent years have led to an increase in empirical databases on the abundance and functions of aquatic microbes, now allowing synthesis studies. Most of these studies have adopted a comparative approach, such that comparative analyses are now available for most aspects of aquatic microbial food webs (more than 50 papers published in the last 15 years). Some of these analyses apparently yield conflicting results, introducing confusion and unnecessary disputes in the field. We briefly review the comparative analyses so far produced and we highlight generalities, show that some of the perceived discrepancies largely derive from partial analyses of a general underlying trend and formulate predictions based on these general trends that provide new avenues for research.     

Energy coupling in type II topoisomerases: why do they hydrolyze ATP?

Type II topoisomerases are essential enzymes in all cells. They help to solve the topological problems of DNA by passing one double helix through a transient break in another, in a reaction coupled to the hydrolysis of ATP. Members of one class of the enzymes, DNA gyrases, are configured to carry out an intramolecular reaction, removing positive supercoiling and introducing negative supercoiling into circular DNA using free energy derived from ATP hydrolysis. The nonsupercoiling class, including bacterial topoisomerase IV and eukaryotic topoisomerase II enzymes, can carry out both intra- and intermolecular reactions, and their primary role is the unlinking (decatenation) of daughter replicons before partition. In these enzymes, ATP hydrolysis is coupled to a reduction in DNA complexity (catenation, supercoiling, and knotting) below the level expected at equilibrium. This review discusses our current understanding of the mechanisms behind the coupling of the energy of ATP hydrolysis to topological changes catalyzed by both of these classes of enzyme.     

Amphibious fish: why do they leave water?

Summary Amphibious behaviour in fish has evolved separately many times since the first amphibious fishes, the rhipidistian crossopterygians, ventured onto land about 350 million years ago. This behaviour has resulted in the colonization and eventual domination by vertebrates of the terrestrial habitat. It is generally proposed that aquatic hypoxia, owing to metabolic oxygen consumption and organic decay, was the most important selective force in the evolution of air-breathing vertebrates (e.g. Randall et al., 1981). Modern amphibious fish species give an insight into the reasons for leaving and eventually abandoning the aquatic habitat. Amphibious fishes today leave the water for a variety of reasons associated with degradation of their aquatic habitat, or biotic factors within it.The possible causal factors which may elicit an emergence response are summarized in Fig. 1(a) and (b). Amphibious fish inhabiting closed systems, as typified by freshwater or intertidal pools, may leave water for any of the reasons detailed in Fig. 1(a). The relative importance of any one stimulus is likely to vary between different species. However, it is possible that in closed systems, adverse fluctuations in physico-chemical parameters will have a more important effect in eliciting amphibious behaviour than will biotic factors. In open systems, such as coastal waters or large freshwater bodies, effectively two routes of escape from adverse aquatic conditions are available to amphibious fish. They may move onto land, or alternatively they may move underwater to find better conditions. In such a system, where physico-chemical parameters remain relatively constant, abiotic factors are unlikely to have a significant influence on amphibious behaviour. The dominant stimulus in open systems is possibly the three-way interaction between predation, competition, and short-or long-term food availability (Fig. 1(b)).It is unlikely that any one of the factors discussed in this review will act alone in causing amphibious behaviour, and in this respect the available literature on fish leaving water is lacking. Much of it is fragmentary and partly anecdotal, and the limited amount of experimental work tends to concentrate on individual causal factors. There is evidently scope for detailed examination of emersion in a number of amphibious fishes, testing a matrix of environmental and biotic stimuli, in an attempt to determine in more detail the reasons for such behaviour.     

How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets

We analyzed 12 combined mitochondrial and nuclear gene datasets in seven orders of insects using both equal weights parsimony (to evaluate phylogenetic utility) and Bayesian methods (to investigate substitution patterns). For the Bayesian analyses we used relatively complex models (e.g., general time reversible models with rate variation) that allowed us to quantitatively compare relative rates among genes and codon positions, patterns of rate variation among genes, and substitution patterns within genes. Our analyses indicate that nuclear and mitochondrial genes differ in a number of important ways, some of which are correlated with phylogenetic utility. First and most obviously, nuclear genes generally evolve more slowly than mitochondrial genes (except in one case), making them better markers for deep divergences. Second, nuclear genes showed universally high values of CI and (generally) contribute more to overall tree resolution than mitochondrial genes (as measured by partitioned Bremer support). Third, nuclear genes show more homogeneous patterns of among-site rate variation (higher values of alpha than mitochondrial genes). Finally, nuclear genes show more symmetrical transformation rate matrices than mitochondrial genes. The combination of low values of alpha and highly asymmetrical transformation rate matrices may explain the overall poor performance of mitochondrial genes when compared to nuclear genes in the same analysis. Our analyses indicate that some parameters are highly correlated. For example, A/T bias was positively and significantly associated with relative rate and CI was positively and significantly associated with alpha (the shape of the gamma distribution). These results provide important insights into the substitution patterns that might characterized high quality genes for phylogenetic analysis: high values of alpha, unbiased base composition, and symmetrical transformation rate matrices. We argue that insect molecular systematists should increasingly focus on nuclear rather than mitochondrial gene datasets because nuclear genes do not suffer from the same substitutional biases that characterize mitochondrial genes.