Complexity can enhance stability in competitive systems

Empirical observations often indicate that complexity enhances stability, while most theoretical studies, such as May's (1972) classic paper, point to the opposite. Despite the wide generality of these latter theoretical analyses, our examination of the well-known competitive Lotka–Volterra system reveals that increasing complexity (measured in terms of connectance) can enhance species coexistence and persistence in model communities (measured in terms of their feasibility and stability). The high feasibility and stability found for tightly interconnected competitive subsystems might provide an explanation for the clumped structure in food webs.     

Interactions of substrates at the surface of P450s can greatly enhance substrate potency

Cytochrome P450s are a superfamily of heme containing enzymes that use molecular oxygen and electrons from reduced nicotinamide cofactors to monooxygenate organic substrates. The fatty acid hydroxylase P450BM-3 has been particularly widely studied due to its stability, high activity, similarity to mammalian P450s, and presence of a cytochrome P450 reductase domain that allows the enzyme to directly receive electrons from NADPH without a requirement for additional redox proteins. We previously characterized the substrate N-palmitoylglycine, which found extensive use in studies of P450BM-3 due to its high affinity, high turnover number, and increased solubility as compared to fatty acid substrates. Here, we report that even higher affinity substrates can be designed by acylation of other amino acids, resulting in P450BM-3 substrates with dissociation constants below 100 nM. N-Palmitoyl-l-leucine and N-palmitoyl-l-methionine were found to have the highest affinity, with dissociation constants of less than 8 nM and turnover numbers similar to palmitic acid and N-palmitoylglycine. The interactions of the amino acid side chains with a hydrophobic pocket near R47, as revealed by our crystal structure determination of N-palmitoyl-l-methionine bound to the heme domain of P450BM-3, appears to be responsible for increasing the affinity of substrates. The side chain of R47, previously shown to be important in interactions with negatively charged substrates, does not interact strongly with N-palmitoyl-l-methionine and is found positioned at the enzyme-solvent interface. These are the tightest binding substrates for P450BM-3 reported to date, and the affinity likely approaches the maximum attainable affinity for the binding of substrates of this size to P450BM-3.     

Substitution with selenomethionine can enhance the stability of methionine-rich proteins.

The availability of a series of phage T4 lysozymes with up to 14 methionine residues incorporated within the protein has made it possible to systematically compare the effect on protein stability of selenomethionine relative to methionine. Wild-type lysozyme contains two fully buried methionine residues plus three more on the surface. The substitution of these methionine residues with selenomethionine slightly stabilizes the protein. As more and more methionine residues are substituted into the protein, there is a progressive loss of stability. This is, however, increasingly offset in the selenomethionine variants, ultimately resulting in a differential increase in melting temperature of about 7 degrees C. This increase, corresponding to about 0.25 kcal/mol per substitution, is in reasonable agreement with the difference in the solvent transfer free energy between the two amino acids.     

Consumers can enhance ecosystem productivity and stability in changing environments

There is increasing interest in the impacts of pulsed resource inputs (e.g., seasonal fluctuations in primary production) on ecosystem properties. However, theoretical models have focused on the ecosystem role of consumers only in stable environments. We investigated how the consumption rate affects ecosystem properties when resource supplies are pulsed using a simple model with numerical simulations. We initially investigated how primary production responds to resource supply shortages under various consumption rates and found that a vigorous consumer attenuates a rapid reduction in primary production. We next examined ecosystem properties under pulsed resource supplies. Intermediate consumption enhances primary production. The consumption rate that maximizes productivity differs for producers and consumers in a given resource supply environment, irrespective of the pattern of pulsation. The enhancement of primary production and the maximization of secondary production occur simultaneously in a stable environment but are not always the same when the resource supply is pulsed. We also investigated the variability of primary production and found that intermediate consumption rates reduce its coefficient of variation. In addition, we found that consumers with either very low or very high consumption rates are vulnerable to extinction when resource supplies are pulsed. Therefore, consumers with intermediate consumption rates contribute not only to the enhancement and stabilization of primary production but also to the stability of the consumer population itself.     

High potency silencing by single-stranded boranophosphate siRNA

In RNA interference (RNAi), double-stranded short interfering RNA (ds-siRNA) inhibits expression from complementary mRNAs. Recently, it was demonstrated that short, single-stranded antisense RNA (ss-siRNA) can also induce RNAi. While ss-siRNA may offer several advantages in both clinical and research applications, its overall poor activity compared with ds-siRNA has prevented its widespread use. In contrast to the poor gene silencing activity of native ss-siRNA, we found that the silencing activity of boranophosphate-modified ss-siRNA is comparable with that of unmodified ds-siRNA. Boranophosphate ss-siRNA has excellent maximum silencing activity and is highly effective at low concentrations. The silencing activity of boranophosphate ss-siRNA is also durable, with significant silencing up to 1 week after transfection. Thus, we have demonstrated that boranophosphate-modified ss-siRNA can silence gene expression as well as native ds-siRNA, suggesting that boranophosphate-modified ss-siRNAs should be investigated as a potential new class of therapeutic agents.     

Small molecules enhance the potency of natural antimicrobial peptides

The skin-associated microbiome plays an important role in general well-being and in a variety of treatable skin conditions. In this regard, endogenous antimicrobial peptides have both a direct and indirect role in determining the composition of the microbiota. We demonstrate here that certain small molecular species can amplify the antimicrobial potency of naturally occurring antimicrobial peptides. In this study, we have used niacinamide, a form of vitamin B3 naturally found in foods and widely used in cosmetic skincare products, and two of its structural analogs, to investigate their cooperativity with the human antimicrobial peptide LL37 on the bacterium Staphylococcus aureus. We observed a clear synergistic effect of niacinamide and, to some extent, N-methylnicotinamide, whereas isonicotinamide showed no significant cooperativity with LL37. Adaptively biased molecular dynamics simulations using simplified model membrane substrates and single peptides revealed that these molecules partition into the headgroup region of an anionic bilayer used to mimic the bacterial membrane. The simulated effects on the physical properties of the simulated model membrane are well correlated with experimental activity observed in real biological assays despite the simplicity of the model. In contrast, these molecules have little effect on zwitterionic bilayers that mimic a mammalian membrane. We conclude that niacinamide and N-methylnicotinamide can therefore potentiate the activity of host peptides by modulating the physical properties of the bacterial membrane, and to a lesser extent through direct interactions with the peptide. The level of cooperativity is strongly dependent on the detailed chemistry of the additive, suggesting an opportunity to fine-tune the behavior of host peptides.     

Immobilization of invertase via carbohydrate moiety on chitosan to enhance its thermal stability

A new technique using chitosan as support for covalent coupling of invertase via carbohydrate moiety improved the activity and thermal stability of immobilized invertase. The best preparation of immobilized invertase retained 91% of original specific activity (412 U mg^–1). The half-life at 60°C was increased from 2.3 h (free invertase) to 7.2 h (immobilized invertase). In contrast, the immobilization of invertase via protein moiety on chitosan or using Sepharose as support resulted in less thermostable preparations. Additionally, immobilization of invertase on both supports caused the optimal reaction pH to shift from 4.5 to 2.5 and the substrate (sucrose) concentration for maximum activity to increase from 0.5 M to 1.0 M.     

Competition for RISC binding predicts in vitro potency of siRNA

Short interfering RNAs (siRNA) guide degradation of target RNA by the RNA-induced silencing complex (RISC). The use of siRNA in animals is limited partially due to the short half-life of siRNAs in tissues. Chemically modified siRNAs are necessary that maintain mRNA degradation activity, but are more stable to nucleases. In this study, we utilized alternating 2′-O-methyl and 2′-deoxy-2′-fluoro (OMe/F) chemically modified siRNA targeting PTEN and Eg5. OMe/F-modified siRNA consistently reduced mRNA and protein levels with equal or greater potency and efficacy than unmodified siRNA. We showed that modified siRNAs use the RISC mechanism and lead to cleavage of target mRNA at the same position as unmodified siRNA. We further demonstrated that siRNAs can compete with each other, where highly potent siRNAs can compete with less potent siRNAs, thus limiting the ability of siRNAs with lower potency to mediate mRNA degradation. In contrast, a siRNA with low potency cannot compete with a highly efficient siRNA. We established a correlation between siRNA potency and ability to compete with other siRNAs. Thus, siRNAs that are more potent inhibitors for mRNA destruction have the potential to out-compete less potent siRNAs indicating that the amount of a cellular component, perhaps RISC, limits siRNA activity.     

Extracellular nucleotides enhance agonist potency at the parathyroid hormone 1 receptor

Parathyroid hormone (PTH) activates the PTH/PTH-related peptide receptor (PTH1R) on osteoblasts and other target cells. Mechanical stimulation of cells, including osteoblasts, causes release of nucleotides such as ATP into the extracellular fluid. In addition to its role as an energy source, ATP serves as an agonist at P2 receptors and an allosteric regulator of many proteins. We investigated the effects of concentrations of extracellular ATP, comparable to those that activate low affinity P2X7 receptors, on PTH1R signaling. Cyclic AMP levels were monitored in real-time using a bioluminescence reporter and β-arrestin recruitment to PTH1R was followed using a complementation-based luminescence assay. ATP markedly enhanced cyclic AMP and β-arrestin signaling as well as downstream activation of CREB. CMP – a nucleotide that lacks a high energy bond and does not activate P2 receptors – mimicked this effect of ATP. Moreover, potentiation was not inhibited by P2 receptor antagonists, including a specific blocker of P2X7. Thus, nucleotide-induced potentiation of signaling pathways was independent of P2 receptor signaling. ATP and CMP reduced the concentration of PTH (1–34) required to produce a half-maximal cyclic AMP or β-arrestin response, with no evident change in maximal receptor activity. Increased potency was similarly apparent with PTH1R agonists PTH (1–14) and PTH-related peptide (1–34). These observations suggest that extracellular nucleotides increase agonist affinity, efficacy or both, and are consistent with modulation of signaling at the level of the receptor or a closely associated protein. Taken together, our findings establish that ATP enhances PTH1R signaling through a heretofore unrecognized allosteric mechanism.     

Competition potency of siRNA is specified by the 5'-half sequence of the guide strand

Small-interfering RNAs (siRNAs) execute specific cellular gene silencing by exploiting the endogenous RNA interference (RNAi) pathway. Therefore, excess amounts of siRNAs can saturate cellular RNAi machineries. Indeed, some siRNAs saturate the RNA-induced silencing complex (RISC) and competitively inhibit silencing by other siRNAs. However, the molecular feature of siRNAs that specifies competition potency has been undetermined. While previous reports suggested a correlation between the competition potency and silencing efficiency of siRNAs, we found that the silencing efficiency was insufficient to explain the competition potency. Instead, we show that the nucleotide sequence of the 5′-half of the guide strand determines the competition potency of an siRNA. Our finding provides important information for understanding the mechanistic basis of competition in combinatorial RNAi treatment.     

Solid polymeric microparticles enhance the delivery of siRNA to macrophages in vivo

Therapeutics based on small interfering RNA (siRNA) have a great clinical potential; however, delivery problems have limited their clinical efficacy, and new siRNA delivery vehicles are greatly needed. In this report, we demonstrate that submicron particles (800–900 nm) composed of the polyketal PK3 and chloroquine, termed as the PKCNs, can deliver tumor necrosis factor-α (TNF-α) siRNA in vivo to Kupffer cells efficiently and inhibit gene expression in the liver at concentrations as low as 3.5 μg/kg. The high delivery efficiency of the PKCNs arises from the unique properties of PK3, which can protect siRNA from serum nucleases, stimulate cell uptake and trigger a colloid osmotic disruption of the phagosome and release encapsulated siRNA into the cell cytoplasm. We anticipate numerous applications of the PKCNs for siRNA delivery to macrophages, given their high delivery efficiency, and the central role of macrophages in causing diseases such as hepatitis, liver cirrhosis and chronic renal disease.     

Modulation of angiogenesis with siRNA inhibitors for novel therapeutics

Cancer and many other serious diseases are characterized by the uncontrolled growth of new blood vessels. Recently, RNA interference (RNAi) has reinvigorated the therapeutic prospects for inhibiting gene expression and promises many advantages over binding inhibitors, including high specificity, which is essential for targeted therapeutics. This article describes the latest developments using small-interfering RNA (siRNA) inhibitors to downregulate various angiogenic and tumor-associated factors, both in cell-culture assays and in animal disease models. The majority of research efforts are currently focused on understanding gene function, as well as proof-of-concept for siRNA-mediated anti-angiogenesis. The prospects for siRNA therapeutics, both advantages and looming hurdles, are evaluated.     

Developmental canalization can enhance species survival

We investigate the behavior of haploid, asexual populations undergoing an evolutionary process. Each individual is endowed with a genotype, and one of several possible developmental mechanisms mapping this genotype onto a phenotype. We show that various properties of the mapping itself have important consequences for the survival of the groups. The populations which are most successful, both alone (but in a changing environment) as well as in competition against other groups (for which the mapping is different) consist of organisms where gene expression is characterized by pleiotropism, polygenic inheritance, and some amount of canalization (i.e. error damping). These same features lead to the appearance of patterns of punctuated equilibrium during evolution. Punctuated evolution was sometimes observed even in the absence of stabilizing selection; it then arose solely from the internal developmental constraints.     

Subthreshold olfactory stimulation can enhance sweetness

The impact of olfactory perception on sweetness was explored in a model solution using odorants at subthreshold concentrations. First, the impact of 6 odorants, previously described in the literature as congruent with sweetness, was investigated at suprathreshold level in a sucrose solution. Ethyl butyrate and maltol were selected as they had the highest and the lowest sweetness-enhancing properties, respectively. Second, the impact on sweetness of the 2 odorants was investigated at subthreshold concentrations. A system delivering a continuous liquid flow at the same sucrose level, but with varying odorant concentrations, was used. At a subthreshold level, ethyl butyrate but not maltol significantly enhanced the sweetness of the sucrose solution. This study highlights that olfactory perception induced by odorants at a subthreshold level can significantly modulate taste perception. Finally, contrary to results observed with ethyl butyrate at suprathreshold levels, at subthreshold levels, the intensity of sweetness enhancement was not proportional to ethyl butyrate concentration.     

Marine reserves can enhance ecological resilience

The goals of ecosystem‐based management (EBM) include protecting ecological resilience, the magnitude of a perturbation that a community can withstand and remain in a given state. As a tool to achieve this goal, no‐take marine reserves may enhance resilience by protecting source populations or reduce it by concentrating fishing in harvested areas. Here, we test whether spatial management with marine reserves can increase ecological resilience compared to non‐spatial (conventional) management using a dynamic model of a simplified fish community with structured predation and competition that causes alternative stable states. Relative to non‐spatial management, reserves increase the resilience of the desired (predator‐dominated) equilibrium state in both stochastic and deterministic environments, especially under intensive fishing. As a result, spatial management also increases the feasibility of restoring degraded (competitor‐dominated) systems, particularly if combined with culling of competitors or stock enhancement of adult predators.