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.     

To be or not to be a good social partner?

Cooperation based in mutual benefit provides a perfect scenario to start selfish behaviors aimed to obtain greater benefit at the expense of the partner. Here we investigate if mutual benefit cooperation can be stable between individuals that cooperate with kindness (good partners) or if they will be displaced by other individuals that try to obtain more benefit with less cost (bad partners). Our model assumes an asymmetry between partners in such a way that one of them (actor) proposes the cooperation whereas the other (receiver) always accepts the offer. It also assumes that actors can choose the partner on the basis of their past experiences with the potential partners. With the help of a simple two-locus mathematical model we show that not only the gene that conditions the actor preference to choose good partners can increase in frequency but also the gene responsible of the good partner behavior.     

To be folded or to be unfolded?

The lack of ordered structure in “natively unfolded” proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a globular state. The expected average number of contacts per residue calculated from the amino acid sequence alone (using the average number of contacts for 20 amino acid residues in globular proteins) can be used as one of the simple indicators of natively unfolded proteins. The prediction accuracy for the sets of 80 folded and 90 natively unfolded proteins reaches 89% if the expected average number of contacts is used as a parameter and 83% in the case of hydrophobicity. An optimal set of artificial parameters for 20 amino acid residues obtained by Monte Carlo algorithm to maximally separate the sets of 90 natively unfolded and 80 folded proteins demonstrates the upper limit for prediction accuracy, which is 95%.     

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 be or not to be planktonic? Self‐inhibition of biofilm development

The transition between planktonic growth and biofilm formation represents a tightly regulated developmental shift that has substantial impact on cell fate. Here, we highlight different mechanisms through which bacteria limit their own biofilm development. The mechanisms involved in these self‐inhibition processes include: (i) regulation by secreted small molecules, which govern intricate signalling cascades that eventually decrease biofilm development, (ii) extracellular polysaccharides capable of modifying the physicochemical properties of the substratum and (iii) extracellular DNA that masks an adhesive structure. These mechanisms, which rely on substances produced by the bacterium and released into the extracellular milieu, suggest regulation at the communal level. In addition, we provide specific examples of environmental cues (e.g. blue light or glucose level) that trigger a cellular response reducing biofilm development. All together, we describe a diverse array of mechanisms underlying self‐inhibition of biofilm development in different bacteria and discuss possible advantages of these processes.     

Netrin-1 role in angiogenesis: To be or not to be a pro-angiogenic factor?

Angiogenesis designates the formation of new vessels from preexisting ones, and occurs mainly during development. Tight control of this process is a prerequisite to avoid excess/defect in angiogenesis that are the underlying causes of several diseases conditions. Growing lines of evidences have indicated that some guidance cues are involved in regulation of vascular system elaboration, in addition to their role during nervous system development. In this way, netrin-1 has been involved in control of angiogenesis. However, a controversy has emerged regarding its action, since it was concluded from different studies that this protein was either a pro or an anti-angiogenic factor. Thus, netrin-1 role is still unclear. The aim of this review is to propose clues to explain previously reported discrepancies, in light of the dependence receptors model. Indeed, netrin-1 could likely favor angiogenesis, notably by blocking apoptosis induced by its unbound UNC5B receptor.     

To be,or not to be,a non‐native freshwater fish?

We examine the evolving concept of what constitutes a non‐native (or alien) freshwater fish. In an attempt to distinguish between biogeographical and socio‐political perspectives, we review the patterns in the introduction and dispersal of non‐native fishes in Europe and North America, and especially the recent expansion of Ponto‐Caspian gobies in Europe. We assess patterns in the development of national policy and legislation in response to the perceived threat of non‐native fish introductions to native species and ecosystems. We review, and provide a glossary of, the terms and definitions associated with non‐native species. Finally, we discuss perspectives as regards the future treatment of naturalized species.     

Cellulose: To depolymerize… or not to?

Oxidation of the primary OH groups in cellulose is a pivotal reaction both at lab and industrial scale, leading to the value-added products, i.e. oxidized cellulose which have tremendous applications in medicine, pharmacy and hi-tech industry. Moreover, the introduction of carboxyl moieties creates prerequisites for further cellulose functionalization through covalent attachment or electrostatic interactions, being an essential achievement designed to boost the area of cellulose-based nanomaterials fabrication. Various methods for the cellulose oxidation have been developed in the course of time, aiming the selective conversion of the OH groups. These methods use: nitrogen dioxide in chloroform, alkali metal nitrites and nitrates, strong acids alone or in combination with permanganates or sodium nitrite, ozone, and sodium periodate or lead (IV) tetraacetate. In the case of the last two reagents, cellulose dialdehydes derivatives are formed, which are further oxidized by sodium chlorite or hydrogen peroxide to form dicarboxyl groups. A major improvement in the cellulose oxidation was represented by the introduction of the stable nitroxyl radicals, such as 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). However, a major impediment for the researchers working in this area is related with the severe depolymerisation occurred during the TEMPO-mediated conversion of CH₂OH into COOH groups. On the other hand, the cellulose depolymerisation represent the key step, in the general effort of searching for alternative strategies to develop new renewable, carbon-neutral energy sources. In this connection, exploiting the biomass feed stocks to produce biofuel and other low molecular organic compounds, involves a high amount of research to improve the overall reaction conditions, limit the energy consumption, and to use benign reagents. This work is therefore focused on the parallelism between these two apparently antagonist processes involving cellulose, building a necessary bridge between them, thinking how the reported drawbacks of the TEMPO-mediated oxidation of cellulose are heading towards to the biomass valorisation, presenting why the apparently undesired side reactions could be turned into beneficial processes if they are correlated with the existing achievements of particular significance in the field of cellulose conversion into small organic compounds, aiming the general goal of pursuing for alternatives to replace the petroleum-based products in human life.     

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.     

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.