Caught between two Allee effects: Trade-off between reproduction and predation risk

Reproductive activities are often associated with conspicuous morphology or behaviour that could be exploited by predators. Individuals can therefore face a trade-off between reproduction and predation risk. Here we use simple models to explore population-dynamical consequences of such a trade-off for populations subject to a mate-finding Allee effect and an Allee effect due to predation. We present our results in the light of populations that belong to endangered species or pests and study their viability and resilience. We distinguish several qualitative scenarios characterized by the shape and strength of the trade-off and, in particular, identify conditions for which the populations survive or go extinct. Reproduction can be so costly that the population always goes extinct. In other cases, the population goes extinct only over a certain range of low, intermediate or high levels of reproductive activities. Moreover, we show that predator removal (e.g. in an attempt to save an endangered prey species) has the least effect on populations with low cost of reproduction in terms of predation and, conversely, predator addition (e.g. to eradicate a pest) is most effective for populations with high predation cost of reproduction. Our results indicate that a detailed knowledge of the trade-off can be crucial in applications: for some trade-off shapes, only intermediate levels of reproductive activities might guarantee population survival, while they can lead to extinction for others. We therefore suggest that the fate of populations subject to the two antagonistic Allee effects should be evaluated on a case-by-case basis. Although the literature offers no quantitative data on possible trade-off shapes in any taxa, indirect evidence suggests that the trade-off and both Allee effects can occur simultaneously, e.g. in the golden egg bug Phyllomorpha laciniata.     

Caught between two proteins: a mycobacterial inhibitor challenges the mold

Elucidating the target or mechanism of action of potential drugs in the discovery pipeline is an integral component of most programs. For antibacterial compounds, generation of resistant mutants followed by whole genome sequencing has often been successful in uncovering the proteins involved in regulating compound activation, uptake, efflux and importantly, target processes. When this process succeeds, we are quick to declare a target. In a study reported by Sing and Dhar et al. (in press), the combination of resistant mutant generation, whole genome sequencing and recombineering to identify the target of a Mycobacterium tuberculosis growth inhibitor, pointed to a mechanism involving a scaffolding protein, Wag31, involved in polar elongation of mycobacterial cells. Time‐lapse microscopy and electron microscopy confirmed the view that this inhibitor resulted in interruption of nascent cell wall biosynthesis. However, co‐expression as well as regulated titration of the putative Wag31 target demonstrated that the wild‐type allele was dominant and showed no synergy with the inhibitor. The most plausible explanation from their results was that this inhibitor interfered with the interaction of Wag31 with one of its interacting partners in the elongation complex.     

Caught in the act

Femtobiology freeze-frames crucial split seconds of chemical reactions to investigate how enzymes function. The potential prize from this knowledge could be new avenues for drug development or ways to produce clean energy.Along with replication and mutability, living beings are set apart from the mineral background they inhabit by their metabolism—their ability to catalyse chemical reactions. Since Linus Pauling first proposed that these reactions are made possible by enzymes that recognize and bind tightly to their substrates at a crucial transition point [1], it has become increasingly clear that understanding these reactions requires details of the precise molecular alignments that take place at the level of femtoseconds (10⁻¹⁵s).This transition state is the ‘point of no return'' for colliding molecules in a chemical reaction. Beyond it, the reactants inevitably go on to form new products; before it, the reaction does not take place. It lasts for tens to hundreds of femtoseconds, when the molecules are at a state of maximum energy from which they will fall either towards completing the reaction, or with equal likelihood, away from it. The role of the enzyme is to enable the molecules to negotiate this energy summit and to reach the point of completing the reaction.Many processes, including protein folding and the splitting of water during photosynthesis, pass through more than one transition state. Unravelling them all is a challenging task, but the potential prizes are great and might include the ability to harness reactions to produce carbon-neutral energy, for example, by mimicking or exploiting photosynthesis. There are also great therapeutic possibilities, as cell replication in cancer or metabolic processes in pathogens could be halted by intervening at transition states to block key reactions.This therapeutic avenue was first explored in 1986 by Richard Wolfenden, now at the University of North Carolina at Chapel Hill, USA, who calculated that conformational changes in the active site of an enzyme at the transition state should enable it to bind to the reactants with huge strength to overcome the energy barrier [2]. This, in turn, suggested that suitably designed analogues, mimicking the reactants at the transition state, could intervene by binding to the enzyme during that brief window, thus rendering the enzyme ineffective.However, the technologies needed to gather information about transition states have only become available during the past decade. The principle technology in use is X-ray absorption spectroscopy (XAS), which is combined with an ultra-fast laser in an arrangement known as a ‘pump probe''. This setup determines the geometrical shape of the approaching molecular orbitals and the distribution of electrostatic charge around them. The XAS provides information about charge distribution, whilst the pump probe yields details of the geometrical structure during the crucial femtoseconds of the transition state.The pump probe splits a short laser pulse into two separate pulses by a timescale corresponding to the period of the relevant molecular vibrations. The first pulse—the pump—excites the sample, whereas the second pulse—the probe—measures the changes caused by the first. This information can be used to determine the structural details of the transition state, thus enabling the hunt for suitable analogues. Vern Schramm''s laboratory at the Albert Einstein College of Medicine of Yeshiva University, in New York, USA, is doing exactly this. “Our approach gives geometry and electrostatic information for the transition state,” Schramm explained. “We can use computational approaches to compare these to large numbers of related molecules to see which best mimic the transition state.” Schramm''s team has already applied this to develop a drug that targets Plasmodium falciparum—the protozoan parasite that causes malaria. The drug blocks the crucial purine pathway with a transition-state analogue [3]. Plasmodium is a purine auxotroph, meaning that it cannot manufacture the molecule directly. Instead, the parasite makes purines indirectly, through an enzyme called purine nucleoside phosphorylase that synthesizes a purine precursor called hypoxanthine. Schramm''s transition analogue, BCX4945, binds to the active site of the enzyme at the transition state and so blocks its action, starving the parasite of purine.…the potential prizes are great and might include the ability to harness reactions to produce carbon-neutral energy, for example, by mimicking or exploiting photosynthesisIn trials, BCX4945 cleared P. falciparum infection in night monkeys of the Aotus genus—a model close to that of human malarial infection. But there was some re-emergence of the parasite at reduced levels after a few days, similar to the pattern observed with conventional anti-malarial drugs. The drug has been licensed to BioCryst Pharmaceuticals, which is providing it to third parties, under license, for clinical trials. “One such party is now evaluating the drug for a go/no-go decision to go forward into a small-controlled human trial,” commented Schramm. We expect that party to make that decision by mid-2013.”Meanwhile, Schramm has planned laboratory studies to determine the exact mechanism of drug action, off-target effects and the efficiency of different drug combinations in night monkeys, as well as the rate of resistance formation in the parasite to BCX4945. However, he is having trouble finding funding for the research, as the eventual treatment would require more than three doses per day, making it difficult to deploy in regions that suffer from malaria and have poor health infrastructure. Nevertheless, Schramm is convinced that the drug has great potential because of its low toxicity and different mode of action, which starves the parasite. It has certainly demonstrated that transition-state analogues can work.In the meantime, Schramm''s group is targeting human immunodeficiency virus (HIV), which has also resisted attempts to develop satisfactory therapies that are both effective and have acceptably low side effects. The aim is to inhibit the HIV-1 protease that cleaves newly synthesized polypeptides to enable the virus particles to become infectious and invade new cells. HIV protease inhibitors have been used for years, but resistant strains of HIV have emerged. Schramm believes that a transition-state analogue might overcome this problem of resistance. “We recently solved the transition-state structures of HIV protease native and drug-resistant enzymes,” he said. “Surprisingly, the transition states are identical. Thus, the resistance does not come from altered transition-state structure. The result shows that if a transition-state analogue can be found for the reaction, it should efficiently inhibit both the native and resistant enzymes.”Although such an approach holds great promise, there are significant challenges for developing drugs that mimic transition states. One is that solving the structure of the transition state itself is not sufficient, as the analogues might still not be suitable for use in humans. Kinases, for example, perform a wide variety of signalling and other functions by transferring phosphate groups. “In kinases, we understand the transition states, but biologically compatible mimics of the transition state have not been achieved,” Schramm said.Even when biologically compatible, effective mimics are available, they might still prove inappropriate owing to unanticipated effects on other pathways. Schramm also pointed out that an inhibitor can be too powerful, irrespective of its mode of action. “Some human targets are essential and it will be harmful to cause complete inhibition for long periods. An example is the target of statins, HMGCoA reductase, which is the pacemaker enzyme for cholesterol, but also for all other steroid hormones,” he explained. This biochemical knowledge of the target is crucial for using transition-state analogues, Schramm noted. “When the target is unique to a pathogen, for example, their use is ideal. But when the target is a host enzyme, for example in cancer, animal experiments are essential to show that the analogue has the desired effect with limited toxicity.”Femtobiology is not only focused on identifying transition-state analogues for drug development; researchers are also digging into photosynthesis, given its potential for yielding carbon-neutral fuels and electric power. Photosynthesis involves two photoreactions that harvest light to energize electrons through a plethora of associated enzymes and co-factors. The crucial first step is carried out by photosystem 2 (PS2), which uses light energy to split two water molecules into oxygen and four electrons. The electrons are transferred to the Calvin cycle in which they convert carbon dioxide into carbohydrates.…the technologies needed to gather information about transition states have only become available during the past decadeThe water-splitting part of PS2 is the crucial component for solar energy conversion because it is the engine of the whole system and the key to its high efficiency [4]. “Understanding the water-splitting reaction and identifying the various reaction steps and intermediates is of key importance and will be very important for the development of new and efficient artificial systems,” explained Villy Sundstrom, whose team at Lund University in Sweden works on solar energy conversion research.The water splitting occurs in a cluster of four manganese ions and one calcium ion in a five-state cycle. To analyse the process accurately requires elucidating the precise structure of each stage, each of which lasts for only a short period. An important step forward was made in 2011, with the production of a model of the complex in the ground S1-state by X-ray crystallography at a resolution of 1.9 Å [5]. This still left the great challenge of determining the structure of the transient S2-, S3- and S4-states, but provided essential information that stimulated further work on the structure of the S2-state [6]. The study of the S2-state, by Khandavalli Lakshmi and colleagues at The Baruch ‘60 Center for Biochemical Solar Energy Research in Troy, New York, USA, involved the use of PS2 isolated from three species—two cyanobacteria and spinach. The researchers trapped the oxygen-evolving complex (OEC) in the S2-intermediate-state by low temperature illumination.Lakshmi''s team used a technique called two-dimensional hyperfine sublevel correlation spectroscopy to detect weak magnetic interactions between the manganese cluster of the S2-state and the surrounding protons. “The major breakthrough of the 1.9 Å X-ray crystal structure [of the S1-state] is that it identifies all of the amino acid ligands of the Mn₄Ca-oxo cluster and four water molecules that are directly coordinated to the metal ions,” Lakshmi said. This helped the team with their detective work in locating all the structural units within 5 Å of the Mn₄Ca-oxo cluster that might be involved. “This leads to several likely candidates that include amino acid ligands that are directly co-ordinated to the cluster, amino acid side chains that are not co-ordinated to the cluster, two water molecules that are co-ordinated to the manganese ion, two water molecules that are co-ordinated to the Ca²⁺ ion and nine water molecules that form a hydrogen bond network in the vicinity of the Mn₄Ca-oxo cluster in the crystal structure,” Lakshmi explained.…biochemical knowledge of the target is crucial for using transition-state analogues…One of the interesting findings was that the S2-states of the three organisms studied were almost indistinguishable. “In an unexpected but welcome surprise, we observe that the hyperfine spectra of the S2-state of the OEC of PSII from Thermosynechococcus vulcanus, the PsbB variant of Synechocystis PCC 6803 and spinach are identical,” Lakshmi said. “This suggests that the OEC of PSII is highly conserved in the three species”.There is still some way to go to unravel all S-states of PS2, Lakshmi conceded. “There are several open questions on the fate of the water molecules in the S-states that warrant immediate attention,” she said. These include the precise location and binding of the substrate water molecules, the oxidation state of the manganese ions that ligate the substrate water molecules and precise geometry of the Mn₄Ca-oxo cluster.In parallel with the structural and functional analysis of the S-states of PS2, research has been ongoing into artificial systems that use catalysts other than the Mn₄Ca-oxo for water splitting. Such systems had only achieved levels of efficiency usually two orders of magnitude lower than PS2 itself, in terms of the rate of oxygen production. But a major advance uses a ruthenium catalyst to achieve water oxidation rates similar to PS2 [7]. There is just one important caveat: the catalyst does not use light to drive the oxidation, it uses an acidic solution of ammonium cerium nitrate, a compound of the rare earth metal cerium. However, the team believes that the high rates of oxidation achieved with the ruthenium catalyst could lead to water oxidation technology based on more abundant elements, such as the first-row metals rather than rare earth ones. In the future, they hope that the knowledge gained about these artificial catalysts and how they work will pave the way to the light-driven generation of molecular hydrogen by water splitting.Whilst the ultimate aims of directly harnessing photosynthesis for human benefit, and the creation of an artificial system that rivals the water-splitting efficiency of PS2 would be huge steps forward with profound implications for energy production, the end is a long way off. In the meantime, the growing interest in split-second moments at the catalytic centres of many enzymes continues to enhance our knowledge of the metabolism and lays the groundwork for progress in drug development, energy production and other areas.     

Caspase-8 and Bid: Caught in the act between death receptors and mitochondria

Mitochondria play a central role in maintaining cells alive, but are also important mediators of cell death. The main event in mitochondrial signalling and control of apoptosis is the permeabilisation of the outer mitochondrial membrane and the release of pro-apoptotic proteins into the cytosol from the mitochondrial intermembrane space. With respect to death receptor-mediated apoptosis, the activation of the mitochondrial pathway is required for apoptosis induction in cells which are described as “type II” cells whereas “type I” cells do not require it. In type I cells, activation of the extrinsic pathway is sufficient to induce apoptosis. This review deals with the events that enable cell death in type II cells, i.e., the signals that lead from death receptor stimulation to permeabilisation of the outer mitochondrial membrane. Caspase-8 and Bid are the known procurers of the death signal in this part of the apoptotic pathway. Currently many exciting new findings are emerging concerning the regulation of caspase-8 and Bid function and activation. We will take you on a journey through these new developments and point out what we consider the major unknowns in this field. We end our review on an up-to-date discussion of the determinants of the type I-type II cell distinction. This article is part of a Special Issue entitled Mitochondria: the deadly organelle.     

Morphological definition of a case of 'usual' interstitial pneumonia

A 61-year-old Caucasian female complained of shortness of breath, fever, and a period of rapid weight loss. After routine studies, the patient underwent an open lung biopsy in order to define the characteristics of the interstitial lung disease, and initiate appropriate therapeutic intervention. Typical fibrotic and cellular proliferation were evident in the parenchyma, as determined by standard light microscopy. However, in a correlated study using light microscopy of plastic embedded tissue, as well as scanning and transmission electron microscopy, a major proliferating cell type was identified as a type II pneumocyte. These cells were the predominant lining cells of the alveoli and clearly protruded into and limited available respiratory air spaces. The predominance of type II pneumocytes in the pathogenesis of certain respiratory diseases requires that a better explanation be sought for this phenomenon.     

Rethinking the boundaries of Kawasaki disease: toward a revised case definition

This paper describes the historical evolution of the Kawasaki disease (KD) case definition and its limitations for identification and treatment of children at risk for coronary artery aneurysms (CAA). The dominant view of pathogenesis is that an unknown agent infects infants and children, who then develop the signs of KD. Some of the infected infants and children then develop CAA, and a few die from myocardial infarction. Because the etiologic agent remains unknown, diagnosis of KD relies on observation and recognition of the clinical signs that comprise the KD case definition criteria. This approach has been successful in identifying and treating many children at risk for CAA. Unfortunately, however, it has delayed the effective treatment of children who fail to meet the KD case definition criteria but who, nevertheless, develop CAA. The original case definition was developed before the general acceptance of CAA as sequelae of KD, the availability of the echocardiogram, and effective treatment with intravenous immunoglobulin. Despite an evolution in awareness, detection, and treatment of possible CAA sequela, the case definition has not been altered so as to incorporate this knowledge. Our investigation explores the transformation of the case definition from an epidemiological instrument to a diagnostic tool. We urge the construction of a more sensitive KD case definition that includes signs and laboratory findings associated with CAA.     

Analysis of the link between a definition of sustainability and the life cycle methodologies

Purpose

It has been claimed that in order to assess the sustainability of products, a combination of the results from a life cycle assessment (LCA), social life cycle assessment (SLCA) and life cycle costing (LCC) is needed. Despite the frequent reference to this claim in the literature, very little explicit analysis of the claim has been made. The purpose of this article is to analyse this claim.

Methods

An interpretation of the goals of sustainability, as outlined in the report Our Common Future (WCED 1987), which is the basis for most literature on sustainability assessment in the LCA community, is presented and detailed to a level enabling an analysis of the relation to the impact categories at midpoint level considered in life cycle (LC) methodologies.

Results

The interpretation of the definition of sustainability as outlined in Our Common Future (WCED 1987) suggests that the assessment of a product's sustainability is about addressing the extent to which product life cycles affect poverty levels among the current generation, as well as changes in the level of natural, human and produced and social capital available for the future population. It is shown that the extent to which product life cycles affect poverty to some extent is covered by impact categories included in existing SLCA approaches. It is also found that the extent to which product life cycles affect natural capital is well covered by LCA, and human capital is covered by both LCA and SLCA but in different ways. Produced capital is not to any large extent considered in any of the LC methodologies. Furthermore, because of the present level of knowledge about what creates and destroys social capital, it is difficult to assess how it relates to the LC methodologies. It is also found that the LCC is only relevant in the context of a life cycle sustainability assessment (LCSA) if focusing on the monetary gains or losses for the poor. Yet, this is an aspect which is already considered in several SLCA approaches.

Conclusions

The current consensus that LCSA can be performed through combining the results from an SLCA, LCA and LCC is only partially supported in this article: The LCSA should include both an LCA and an SLCA, which should be expanded to better cover how product life cycles affect poverty and produced capital. The LCC may be included if it has as a focus to asses income gains for the poor.     

A new definition and properties of the similarity value between two protein structures

Knowledge regarding the 3D structure of a protein provides useful information about the protein’s functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein’s atoms and concentrate on the number of protein’s atoms to be compared. This defines a new measure, called the weighted similarity value (WSV), adding physical properties to geometrical properties. We also show that our results are in good agreement with the results obtained by TM-SCORE and DALILITE. WSV can be of use in protein classification and in drug discovery.