What is the function of neuronal AP‐3?

Neurotransmission requires the proper organization and rapid recycling of synaptic vesicles. Rapid retrieval has been suggested to occur either by kiss-and-stay or kiss-and-run mechanisms, whereas classical recycling is mediated by clathrin-dependent endocytosis. Molecular coats are key components in the selection of cargos, AP-2 (adaptor protein 2) playing a prominent role in synaptic vesicle endocytosis. Another coat protein, AP-3, has been implicated in synaptic vesicle biogenesis and in the generation of secretory and lysosomal-related organelles. In the present review, we will particularly focus on the recent data concerning the recycling of synaptic vesicles and the function of AP-3 and the v-SNARE (vesicular soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) TI-VAMP (tetanus neurotoxin-insensitive vesicle-associated membrane protein) in these processes. We propose that AP-3 plays an important regulatory role in neurons which contributes to the basal and stimulated exocytosis of synaptic vesicles.     

How common is the funnel‐like energy landscape in protein‐protein interactions?

The goal of this study is to verify the concept of the funnel-like intermolecular energy landscape in protein-protein interactions by use of a series of computational experiments. Our preliminary analysis revealed the existence of the funnel in many protein-protein interactions. However, because of the uncertainties in the modeling of these interactions and the ambiguity of the analysis procedures, the detection of the funnels requires detailed quantitative approaches to the energy landscape analysis. A number of such approaches are presented in this study. We show that the funnel detection problem is equivalent to a problem of distinguishing between distributions of low-energy intermolecular matches in the funnel and in the low-frequency landscape fluctuations. If the fluctuations are random, the decision about whether the minimum is the funnel is equivalent to determining whether this minimum is significantly different from a would-be random one. A database of 475 nonredundant cocrystallized protein-protein complexes was used to re-dock the proteins by use of smoothed potentials. To detect the funnel, we developed a set of sophisticated models of random matches. The funnel was considered detected if the binding area was more populated by the low-energy docking predictions than by the matches generated in the random models. The number of funnels detected by use of different random models varied significantly. However, the results confirmed that the funnel may be the general feature in protein-protein association.     

What is the mechanism of ParA‐mediated DNA movement?

The stable maintenance of low‐copy‐number plasmids requires active partitioning, with the most common mechanism in prokaryotes involving the ATPase ParA. ParA proteins undergo intricate spatiotemporal relocations across the nucleoid, dynamics that function to position plasmids at equally spaced intervals. This spacing naturally guarantees equal partitioning of plasmids to each daughter cell. However, the fundamental mechanism linking ParA dynamics with regular plasmid positioning has proved difficult to dissect. In this issue of Molecular Microbiology, Vecchiarelli et al. report on a time‐delay mechanism that allows a slow cycling between the nucleoid‐bound and unbound forms of ParA. The authors also propose a mechanism for plasmid movement that does not rely on ParA polymerization.     

What is the risk‐benefit ratio of long‐term antipsychotic treatment in people with schizophrenia?

The long‐term benefit‐to‐risk ratio of sustained antipsychotic treatment for schizophrenia has recently been questioned. In this paper, we critically examine the literature on the long‐term efficacy and effectiveness of this treatment. We also review the evidence on the undesired effects, the impact on physical morbidity and mortality, as well as the neurobiological correlates of chronic exposure to antipsychotics. Finally, we summarize factors that affect the risk‐benefit ratio. There is consistent evidence supporting the efficacy of antipsychotics in the short term and mid term following stabilization of acute psychotic symptoms. There is insufficient evidence supporting the notion that this effect changes in the long term. Most, but not all, of the long‐term cohort studies find a decrease in efficacy during chronic treatment with antipsychotics. However, these results are inconclusive, given the extensive risk of bias, including increasing non‐adherence. On the other hand, long‐term studies based on national registries, which have lower risk of bias, find an advantage in terms of effectiveness during sustained antipsychotic treatment. Sustained antipsychotic treatment has been also consistently associated with lower mortality in people with schizophrenia compared to no antipsychotic treatment. Nevertheless, chronic antipsychotic use is associated with metabolic disturbance and tardive dyskinesia. The latter is the clearest undesired clinical consequence of brain functioning as a potential result of chronic antipsychotic exposure, likely from dopaminergic hypersensitivity, without otherwise clear evidence of other irreversible neurobiological changes. Adjunctive psychosocial interventions seem critical for achieving recovery. However, overall, the current literature does not support the safe reduction of antipsychotic dosages by 50% or more in stabilized individuals receiving adjunctive psychosocial interventions. In conclusion, the critical appraisal of the literature indicates that, although chronic antipsychotic use can be associated with undesirable neurologic and metabolic side effects, the evidence supporting its long‐term efficacy and effectiveness, including impact on life expectancy, outweighs the evidence against this practice, overall indicating a favorable benefit‐to‐risk ratio. However, the finding that a minority of individuals diagnosed initially with schizophrenia appear to be relapse free for long periods, despite absence of sustained antipsychotic treatment, calls for further research on patient‐level predictors of positive outcomes in people with an initial psychotic presentation.     

Baculovirus‐induced tree‐top disease: how extended is the role of egt as a gene for the extended phenotype?

Many parasites alter host behaviour to enhance their chance of transmission. Recently, the ecdysteroid UDP‐glucosyl transferase (egt) gene from the baculovirus Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) was identified to induce tree‐top disease in L. dispar larvae. Infected gypsy moth larvae died at elevated positions (hence the term tree‐top disease), which is thought to promote dissemination of the virus to lower foliage. It is, however, unknown whether egt has a conserved role among baculoviruses in inducing tree‐top disease. Here, we studied tree‐top disease induced by the baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in two different host insects, Trichoplusia ni and Spodoptera exigua, and we investigated the role of the viral egt gene therein. AcMNPV induced tree‐top disease in both T. ni and S. exigua larvae, although in S. exigua a moulting‐dependent effect was seen. Those S. exigua larvae undergoing a larval moult during the infection process died at elevated positions, while larvae that did not moult after infection died at low positions. For both T. ni and S. exigua, infection with a mutant AcMNPV lacking egt did not change the position where the larvae died. We conclude that egt has no highly conserved role in inducing tree‐top disease in lepidopteran larvae. The conclusion that egt is a ‘gene for an extended phenotype’ is therefore not generally applicable for all baculovirus–host interactions. We hypothesize that in some baculovirus–host systems (including LdMNPV in L. dispar), an effect of egt on tree‐top disease can be observed through indirect effects of egt on moulting‐related climbing behaviour.     

What is the role of the second “structural” NADP+‐binding site in human glucose 6‐phosphate dehydrogenase?

Human glucose 6-phosphate dehydrogenase, purified after overexpression in E. coli, was shown to contain one molecule/subunit of acid-extractable "structural" NADP+ and no NADPH. This tightly bound NADP+ was reduced by G6P, presumably following migration to the catalytic site. Gel-filtration yielded apoenzyme, devoid of bound NADP+ but, surprisingly, still fully active. Mr of the main component of "stripped" enzyme by gel filtration was approximately 100,000, suggesting a dimeric apoenzyme (subunit Mr = 59,000). Holoenzyme also contained tetramer molecules and, at high protein concentration, a dynamic equilibrium gave an apparent intermediate Mr of 150 kDa. Fluorescence titration of the stripped enzyme gave the K d for structural NADP+ as 37 nM, 200-fold lower than for "catalytic" NADP+. Structural NADP+ quenches 91% of protein fluorescence. At 37 degrees C, stripped enzyme, much less stable than holoenzyme, inactivated irreversibly within 2 d. Inactivation at 4 degrees C was partially reversed at room temperature, especially with added NADP+. Apoenzyme was immediately active, without any visible lag, in rapid-reaction studies. Human G6PD thus forms active dimer without structural NADP+. Apparently, the true role of the second, tightly bound NADP+ is to secure long-term stability. This fits the clinical pattern, G6PD deficiency affecting the long-lived non-nucleate erythrocyte. The Kd values for two class I mutants, G488S and G488V, were 273 nM and 480 nM, respectively (seven- and 13-fold elevated), matching the structural prediction of weakened structural NADP+ binding, which would explain decreased stability and consequent disease. Preparation of native apoenzyme and measurement of Kd constant for structural NADP+ will now allow quantitative assessment of this defect in clinical G6PD mutations.     

Liquid‐based cytology: is this the way forward for cervical screening?

Liquid-based cytology (LBC) is currently being marketed as an alternative methodology to replace the conventional PAP smear in cervical cytology. A substantial body of literature exists in support of LBC, some of which is at least partially sponsored by product manufacturers. The majority of published literature in support of LBC employs Bethesda reporting terminology. In this study we have analysed published raw data and presented this in NHSCSP terminology. Claims relating to sensitivity, specificity and smear adequacy have then been considered with reference to this data. Our analysis of existing data does not support the nationwide implementation of LBC at present. Further studies are recommended in order to evaluate the place of this technology within the NHSCSP.     

Condition‐dependent immune defence in the Magpie: how important is ectoparasitism?

The immune system has high costs of maintenance and production and expression of immune function should be dependent on the condition of the individual. The fitness cost that parasites impose on hosts may then be reflected in the investment that hosts make in immunity. Little is known about sources and consequences of intra- and interspecific variation in the presence and size of organs of the immune system in relation to ectoparasitism. Variation in the presence and size of the bursa of Fabricius and spleen size was measured to assess potential relationships between immune defence, nutritional condition and ectoparasites in the Magpie Pica pica. We found three species of lice (Mallophaga), two species of louse flies (Hippoboscidae), and the larvae of a tick (Ixodidae) infecting magpies. Age explained a significant proportion of variation in prevalence and number of parasite species, first-year birds being more parasitized than adults. Spleen size increased with nutritional condition, and the level of ectoparasitism negatively affected nutritional condition. Only one species of lice (Philopterus picae) was involved; the negative effect of this species on nutritional condition was more pronounced in males than females. These results are consistent with the hypotheses of condition-dependent investment in the immune system and sexual differences in susceptibility to parasite effects. Ectoparasites may thus play a role in modulating the relationship between condition and immune defence. We also found evidence for an interaction between the bursa and the spleen. Magpies with bursa had larger spleens than those where it had atrophied. This interaction did not affect ectoparasitism or nutritional condition.     

Air‐core fiber or photonic‐crystal rod,which is more suitable for energetic femtosecond pulse generation and three‐photon microscopy at the 1700‐nm window?

Energetic femtosecond pulses at the 1700‐nm window are a prerequisite for deep‐tissue three‐photon microscopy (3PM). Soliton self‐frequency shift (SSFS) in photonic‐crystal (PC) rod has been the only technique to generate such pulses suitable for 3PM. Here we demonstrate through SSFS in an air‐core fiber, we can generate most energetic femtosecond soliton pulses at the 1700‐nm window, 5.2 times higher than that from PC rod. However, the air‐core soliton pulse width is 5.9 times longer than that of PC rod soliton. Based on comparative 3PM excited with both air‐core and PC rod solitons, we propose the more suitable source for 3PM. We further elucidate the challenge of generating shorter soliton pulses from air‐core fibers through numerical simulation.     

Extinction and time help drive the marine‐terrestrial biodiversity gradient: is the ocean a deathtrap?

The marine‐terrestrial richness gradient is among Earth's most dramatic biodiversity patterns, but its causes remain poorly understood. Here, we analyse detailed phylogenies of amniote clades, paleontological data and simulations to reveal the mechanisms underlying low marine richness, emphasising speciation, extinction and colonisation. We show that differences in diversification rates (speciation minus extinction) between habitats are often weak and inconsistent with observed richness patterns. Instead, the richness gradient is explained by limited time for speciation in marine habitats, since all extant marine clades are relatively young. Paleontological data show that older marine invasions have consistently ended in extinction. Simulations show that marine extinctions help drive the pattern of young, depauperate marine clades. This role for extinction is not discernible from molecular phylogenies alone, and not predicted by most previously hypothesised explanations for this gradient. Our results have important implications for the marine‐terrestrial biodiversity gradient, and studies of biodiversity gradients in general.     

Trade‐offs in evolutionary immunology: just what is the cost of immunity?

It has become increasingly clear that life-history patterns among the vertebrates have been shaped by the plethora and variety of immunological risks associated with parasitic faunas in their environments. Immunological competence could very well be the most important determinant of life-time reproductive success and fitness for many species. It is generally assumed by evolutionary ecologists that providing immunological defences to minimise such risks to the host is costly in terms of necessitating trade-offs with other nutrient-demanding processes such as growth, reproduction, and thermoregulation. Studies devoted to providing assessments of such costs and how they may force evolutionary trade-offs among life-history characters are few, especially for wild vertebrate species, and their results are widely scattered throughout the literature. In this paper we attempt to review this literature to obtain a better understanding of energetic and nutritional costs for maintaining a normal immune system and examine how costly it might be for a host who is forced to up-regulate its immunological defence mechanisms. The significance of these various costs to ecology and life history trade-offs among the vertebrates is explored. It is concluded that sufficient evidence exists to support the primary assumption that immunological defences are costly to the vertebrate host.     

What is the proximate cause for size‐dependent ecophysiological differences in vascular epiphytes?

Size-related variation in physiological parameters as diverse as photosynthetic capacity, abscisic acid relationships or the relative water deficit at stomatal closure have been reported for a large number of vascular epiphytes, but the proximate mechanism behind these observations has not been identified. We test four possible reasons for size-related changes in photosynthetic capacity, leaf-N content and specific leaf area: (i) plant size itself, (ii) plant age or developmental stage, (iii) previous nutrition, or (iv) previous water regime. A suite of study species and approaches were used: a 'natural experiment' with the orchid Polystachya foliosa; an experimental field study with another orchid, Dimerandra emarginata; and a study under controlled conditions with the tank bromeliad, Vriesea sanguinolenta. Neither size, age nor differences in water supply caused differences in leaf N and photosynthetic capacity, while low supply of nutrients yielded, and high supply with nutrients completely removed, size-related trends. The observed size-related trends are thus a consequence of in situ differences in nutrient acquisition. Arguably, the improved nutrient status of larger plants under natural conditions results from larger tanks, holding moisture for increasingly longer intervals, which allows longer periods of decomposition of detritus and of nutrient uptake.     

Perturbing mitosis for anti‐cancer therapy: is cell death the only answer?

Interfering with mitosis for cancer treatment is an old concept that has proven highly successful in the clinics. Microtubule poisons are used to treat patients with different types of blood or solid cancer since more than 20 years, but how these drugs achieve clinical response is still unclear. Arresting cells in mitosis can promote their demise, at least in a petri dish. Yet, at the molecular level, this type of cell death is poorly defined and cancer cells often find ways to escape. The signaling pathways activated can lead to mitotic slippage, cell death, or senescence. Therefore, any attempt to unravel the mechanistic action of microtubule poisons will have to investigate aspects of cell cycle control, cell death initiation in mitosis and after slippage, at single‐cell resolution. Here, we discuss possible mechanisms and signaling pathways controlling cell death in mitosis or after escape from mitotic arrest, as well as secondary consequences of mitotic errors, particularly sterile inflammation, and finally address the question how clinical efficacy of anti‐mitotic drugs may come about and could be improved.     

Post‐dispersal seed recovery by animals: is it a plant‐ or an animal‐driven process?

The ability of animals to find and consume hoarded seeds (i.e. seed recovery) is a key stage within the seed dispersal process. However, the ecology of seed recovery is still poorly understood. Here, we analyze the factors controlling seed recovery by scatter‐hoarding rodents in an oak‐dominated temperate forest. We examined the relative importance of intrinsic seed traits (i.e. plant‐driven) and extrinsic seed factors (i.e. animal‐driven) on the probability of seed recovery. We found that seed recovery is mainly driven by extrinsic seed factors, mostly related to animal behavior (pilfering frequency, microsite preference, predation risk, burial depth and cache size). Important intrinsic traits such as seed size, seed quality and seed‐drop timing were, on average, of lower significance in the probability of seed recovery (2.8‐times less important than extrinsic factors); only seed quality was an important intrinsic trait. On the other hand, larger and nutritionally more valuable seeds showed a removal–recovery tradeoff as they enhance seed removal and hoarding (increasing dispersal quality) but also favour seed recovery (increasing predation). We find that other mechanisms beyond seed traits (e.g. masting) are needed to decrease seed recovery and, thus, increase seed survival. We conclude that, as seed recovery is mostly driven by animal behavioural factors, it substantially differs from other previous stages of the seed dispersal process that are more dependent on seed traits. We argue that seed recovery needs further attention to advance our understanding of the ecology of seed dispersal and the role of secondary dispersers as a selective force for seeds.     

Extending the stress‐gradient hypothesis – is competition among animals less common in harsh environments?

The role of positive interactions has become widely accepted as a mechanism shaping community dynamics. Most empirical evidence comes from plant communities and sessile marine organisms. However, evidence for the relative role of positive interactions in organizing terrestrial animal communities is more limited, and a general framework that includes positive interactions among animals is lacking. The ‘stress gradient hypothesis’ (SGH) developed by plant ecologists predicts that the balance between positive and negative interactions will vary along gradients of biotic and abiotic stress, with positive interactions being more important in stressful environments. Paralleling the SGH, stress gradients for terrestrial herbivores could be equated to inverse primary productivity gradients, so we would expect positive interactions to prevail in more stressful, low productivity environments. However, this contradicts the typical view of terrestrial animal ecology that low primary productivity systems will foster intense competition for resources among consumers. Here we use alpine herbivores as a case study to test one of the predictions of the SGH in animal communities, namely the prevalence of positive interactions in low productivity environments. We identify potential mechanisms of facilitation and review the limited number of examples of interspecific interactions among alpine herbivores to assess the role of positive and negative interactions in structuring their communities. A meta‐analysis showed no clear trend in the strength and direction of interactions among alpine herbivores. Although studies were biased towards reporting significant negative inter actions, we found no evidence of competition dominating in harsh environments. Thus, our results only partially support the SGH, but directly challenge the dominant view among animal ecologists. Clearly, a sound theoretical framework is needed to include competition, positive and neutral interactions as potential mechanisms determining the structure of animal communities under differing environmental conditions, and the stress‐gradient hypothesis can provide a solid starting point.     

Where is the Evidence for Assessing Evidence‐Based Restoration? Comments on Ntshotsho et al. (2010)

In their article “Assessing the evidence base for restoration in South Africa,” Ntshotsho et al. attempt to determine whether restoration in South Africa is evidence based by reporting on 10 projects' baseline data collection, goal setting, and monitoring. However, their contribution suffers from two major constraints. First, they confuse assessing the evidence base with assessing whether restoration is evidence based. Truly, assessing the evidence base would entail a systematic review of the quantity and quality of information available as well as the conclusions supported, perhaps in a meta‐analytical framework. Determining if restoration is evidence based would require a survey of project managers to evaluate if they take decisions based on scientific information. Second, Ntshotsho et al. do not clearly distinguish successfully achieving restoration project goals from successfully restoring ecosystems. They largely focus on projects' socioeconomic goals without emphasizing that these goals are, by definition, secondary to ecological goals in determining restoration success. Thus, Ntshotsho et al. provide neither a sound assessment of the evidence base for restoration nor whether restoration is evidence based. To evaluate and encourage evidence‐based restoration in South Africa, we recommend a simple assessment of the basis on which restoration managers make decisions, identification of factors precluding evidence‐based decision‐making, and development of platforms to evaluate the data collected in restoration programs to generate an evidence base from which to make defendable decisions.     

Why does the magnitude of genotype‐by‐environment interaction vary?

Genotype‐by‐environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide‐ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps.     

Mitochondrial‐targeted catalase is good for the old mouse proteome,but not for the young: ‘reverse’ antagonistic pleiotropy?

Reactive oxygen species (ROS) are highly reactive oxygen‐containing molecules associated with aging and a broad spectrum of pathologies. We have previously shown that transgenic expression of the antioxidant enzyme catalase targeted to the mitochondria (mCAT) in mice reduces ROS, attenuates age‐related disease, and increases lifespan. However, it has been increasingly recognized that ROS also has beneficial roles in signaling, hormesis, stress response, and immunity. We therefore hypothesized that mCAT might be beneficial only when ROS approaches pathological levels in older age and might not be advantageous at a younger age when basal ROS is low. We analyzed abundance and turnover of the global proteome in hearts and livers of young (4 month) and old (20 month) mCAT and wild‐type (WT) mice. In old hearts and livers of WT mice, protein half‐lives were reduced compared to young, while in mCAT mice the reverse was observed; the longest half‐lives were seen in old mCAT mice and the shortest in young mCAT. Protein abundance of old mCAT hearts recapitulated a more youthful proteomic expression profile (P‐value < 0.01). However, young mCAT mice partially phenocopied the older wild‐type proteome (P‐value < 0.01). Age strongly interacts with mCAT, consistent with antagonistic pleiotropy in the reverse of the typical direction. These findings underscore the contrasting roles of ROS in young vs. old mice and indicate the need for better understanding of the interaction between dose and age in assessing the efficacy of therapeutic interventions in aging, including mitochondrial antioxidants.