To model or not to model?

In theory, the combination of mathematical modeling with experimental studies can be a powerful and compelling approach to understanding cell biology. In practice, choosing appropriate problems, identifying willing and able collaborators, and publishing the resulting research can be remarkably challenging. To provide perspective on the question of whether and when to combine modeling and experiments, a panel of experts at the 2010 ASCB Annual Meeting shared their personal experiences and advice on how to use modeling effectively.     

To charge or not to charge?

The ability to engineer proteins with increased thermostability will profoundly broaden their practical applications. Recent experimental results show that optimization of charge-charge interactions on the surface of proteins can be a useful strategy in the design of thermostable enzymes. Results also indicate a possibility that such optimized interactions provide structural determinants for enhanced stability of proteins from thermophilic organisms. In this article, the general strategy for design of thermostable proteins and perspectives for future studies are discussed.     

To check or not to check? The application of meiotic studies to plant breeding

Understanding the barriers that prevent pairing and recombination of the chromosomes from two parental species is important for crop improvement strategies. It had been generally thought that plants do not possess checkpoint mechanisms during meiosis. However, recent data may question this assumption and suggest that exploitation of such mechanisms could be crucial to breeding.     

To be or not to be ubiquitinated?

Levels of p21, a cyclin-dependent kinase (CDK) inhibitor, are controlled in part at the post-translational level by protein degradation. Although the signaling pathways leading to p21 degradation have not yet been fully elucidated, it is evident that p21 ubiquitination is an essential factor in its degradation. We discuss that, with the only notable exception of ornithine decarboxylase, ubiquitination appears to be a prerequisite for proteasomal degradation rather than an unnecessary byproduct of such proteolysis.     

Monoamine oxidase: To B or not to B?

That the enzyme, monoamine oxidase (E.C. 1.4.3.4. amine: O₂ oxidoreductase, MAO) exists in multiple forms was first suggested by Johnston (1) who studied the effects of the irreversible inhibitor clorgyline on MAO. It has been proposed that MAO can be classified into two types, A and B, according to their inhibitor sensitivity and substrate specificity. Type A MAO was found to be solely responsible for the deamination of 5-hydroxytryptamine (5-HT) and shows high sensitivity to clorgyline, while type B MAO metabolizes 2-phenethylamine (PEA) and benzylamine (BA) and is less sensitive to clorgyline. Subsequently, it was shown that type B MAO is highly sensitive to the irreversible inhibitor deprenyl (2).Recently, the “multiple forms” concept has been questioned (3–5) mainly because of increasing evidence which is contradictory to some earlier findings. As an alternative, another hypothesis was put forward insinuating that MAO is an enzyme with multiple binding sites but only one molecular entity (3,4,6,7). This account will focus on some experimental findings accumulated mainly since 1978 and which, although equivocal, strongly support the “one molecular entity” hypothesis of MAO.     

Control of nucleosome movement: To space or not to space nucleosomes?

A key feature of ATP-dependent chromatin remodeling complexes is how they control the ability of the complex to translocate along DNA within the context of a nucleosome. Although these complexes generally initiate DNA translocation near the dyad axis of the nucleosome, the progression and eventual termination is regulated in quite distinct ways. The best studies examples of these are the ISWI type which has strong extranucleosomal DNA dependent activity or the SWI/SNF type which has no linker DNA requirement. Recent data provide more insights into the mechanism of regulation of DNA translocation by the ISWI type complexes and how the structure of the ISWI-nucleosome complex changes during chromatin remodeling.     

To freeze or not to freeze? An evolutionary perspective on the cold-hardiness strategies of overwintering ectotherms

We address the question of whether freeze-tolerance, freeze-avoidance, or mixed strategy represents the best adaptation for overwintering ectotherms to endure severe winter. To this end, we develop an optimization fitness model that takes into account different physiological parameters such as energetic level, the physiological stress associated with each strategy, and climatic variables. The results show that the freeze-tolerance strategy is strongly dependent on a low sensitivity to the number of freezing days and on a capacity to reduce stress associated with freezing. This strategy is also favored when the initial energetic level is low compared to the freeze-avoidance strategy, which is favored by a high initial energetic level, a low stress associated with the supercooling, and a low sensitivity of this strategy to climatic conditions. From a theoretical point of view, the mixed strategy permits survival in harsher environments but requires the optimization of all parameters involved in both cold-hardiness strategies. However, the mixed strategy shows energetic advantages in variable environments allowing animals to resist the harshest periods. From the model results, it appears that the physiological processes developed by ectotherms to reduce these stresses might be a key to understanding the evolution of the cold-hardiness strategies.     

To be or not to be rhythmic? A review of studies on organisms inhabiting constant environments

Abstract

Circadian clocks are endogenous time keeping mechanisms that drive near 24-h behavioural, physiological and metabolic rhythms in organisms. It is thought that organisms possess circadian clocks to facilitate coordination of essential biological events to the external day and night (extrinsic advantage) so as to enhance Darwinian fitness. However, on Earth, there are a number of habitats that are not subject to such robust daily cycling of geo-physical factors. Do organisms living under such conditions exhibit rhythmic behaviours that are driven by endogenous circadian clocks? We attempt to critically survey studies of rhythms (or the lack of them) in organisms living in a range of constant environments. Many such organisms do show rhythms in behaviour and/or physiological variables. We suggest that such presence of rhythms may be indicative of an underlying clock that facilitates, (a) internal synchrony among rhythms, and (b) temporal partitioning of incompatible cellular processes (intrinsic advantage). We then highlight reasons that limit our interpretations about the presence (or absence) of clocks in such organisms living under constant conditions, and suggest possible methods to conclusively test whether or not rhythms in these organisms are driven by endogenous circadian clocks with the hope that it may enhance our understanding of circadian clocks in organisms under constant environments.     

The somatopause: to treat or not to treat?

There is much evidence that some aspects of ageing are similar to those observed in selective hormone deficiencies during adulthood. Replacement therapy in hypogonadism and/or growth hormone (GH) deficiency in adulthood is very successful in reversing the related clinical symptomatology. However, preliminary studies of GH treatment in the normal elderly have been largely disappointing: an increase in muscle mass is only accompanied by improved muscle strength if exercise is also increased during this period. No real benefit of GH therapy, additional to that of exercise, has been reported. Epidemiological studies indicate a relationship between high-normal insulin-like growth factor-I levels and cancer development. No definitive answers can presently be given regarding the safety of long-term GH therapy in otherwise healthy individuals during the somatopause.