Development of tacrine clusters as positively cooperative systems for the inhibition of acetylcholinesterase

The synthesis of four tetra-tacrine clusters where the tacrine binding units are attached to a central scaffold via linkers of variable lengths is described. The multivalent inhibition potencies for the tacrine clusters were investigated for the inhibition of acetylcholinesterase. Two of the tacrine clusters displayed a small but significant multivalent inhibition potency in which the binding affinity of each of the tacrine binding units increased up to 3.2 times when they are connected to the central scaffold.     

Interactions of Schwann cells with neurites and with other Schwann cells involve the calcium-dependent adhesion molecule,N-cadherin

During embryogenesis, Schwann cells interact with axons and other Schwann cells, as they migrate, ensheath axons, and participate in organizing peripheral nervous tissues. The experiments reported here indicate that the calcium-dependent molecule, N-cadherin, mediates adhesion of Schwann cells to neurites and to other Schwann cells. Cell cultures from chick dorsal root ganglia and sciatic nerves were maintained in media containing either 2mM Ca⁺⁺ or 0.2 mM Ca⁺⁺, a concentration that inactivates calcium-dependent cadherins. When the leading lamellae of Schwann cells encountered migrating growth cones in medium with 2 mM Ca⁺⁺, they usually remained extended, and the growth cones often advanced onto the Schwann cell upper surface. In the low Ca⁺⁺ medium, the frequency of withdrawal of the Schwann cell lamella after contact with a growth cone was much greater, and withdrawal was the most common reaction to growth cone contact in medium with 2 mM Ca⁺⁺ and anti-N-cadherin. Similarly, when motile leading margins of two Schwann cells touched in normal Ca⁺⁺ medium, they often formed stable areas of contact. N-cadherin and vinculin were co-concentrated at these contact sites between Schwann cells. However, in low Ca⁺⁺ medium or in the presence of anti-N-cadherin, interacting Schwann cells usually pulled away from each other in a behavior reminiscent of contact inhibition between fibroblasts. In cultures of dissociated cells in normal media, Schwann cells frequently were aligned along neurites, and ultrastructural examination showed extensive close apposition between plasma membranes of neurites and Schwann cells. When dorsal root ganglia explants were cultured with normal Ca⁺⁺, Schwann cells migrated away from the explants in close association with extending neurites. All these interactions were disrupted in media with 0.2 mM Ca⁺⁺. Alignment of Schwann cells along neurites was infrequent, as were extended close apposition between axonal and Schwann cell plasma membranes. Finally, migration of Schwann cells from ganglionic explants was reduced by disruption of adhesive contact with neurites. The addition of antibodies against N-cadherin to medium with normal Ca⁺⁺ levels had similar effects as lowering the Ca⁺⁺ concentration, but antibodies against the neuronal adhesive molecule, L1, had no effects on interactions between Schwann cells and neurites.     

30 years of free‐air carbon dioxide enrichment (FACE): What have we learned about future crop productivity and its potential for adaptation?

Free‐air CO₂ enrichment (FACE) allows open‐air elevation of [CO₂] without altering the microclimate. Its scale uniquely supports simultaneous study from physiology and yield to soil processes and disease. In 2005 we summarized results of then 28 published observations by meta‐analysis. Subsequent studies have combined FACE with temperature, drought, ozone, and nitrogen treatments. Here, we summarize the results of now almost 250 observations, spanning 14 sites and five continents. Across 186 independent studies of 18 C₃ crops, elevation of [CO₂] by ca. 200 ppm caused a ca. 18% increase in yield under non‐stress conditions. Legumes and root crops showed a greater increase and cereals less. Nitrogen deficiency reduced the average increase to 10%, as did warming by ca. 2°C. Two conclusions of the 2005 analysis were that C₄ crops would not be more productive in elevated [CO₂], except under drought, and that yield responses of C₃ crops were diminished by nitrogen deficiency and wet conditions. Both stand the test of time. Further studies of maize and sorghum showed no yield increase, except in drought, while soybean productivity was negatively affected by early growing season wet conditions. Subsequent study showed reduced levels of nutrients, notably Zn and Fe in most crops, and lower nitrogen and protein in the seeds of non‐leguminous crops. Testing across crop germplasm revealed sufficient variation to maintain nutrient content under rising [CO₂]. A strong correlation of yield response under elevated [CO₂] to genetic yield potential in both rice and soybean was observed. Rice cultivars with the highest yield potential showed a 35% yield increase in elevated [CO₂] compared to an average of 14%. Future FACE experiments have the potential to develop cultivars and management strategies for co‐promoting sustainability and productivity under future elevated [CO₂].     

强化产电微生物与电极间电子传递速率的研究进展

产电微生物是微生物燃料电池、电解池和电合成等微生物电化学技术(Microbial electrochemical technologies,METs)的研究基础.产电微生物与电极界面间的胞外电子传递(Extracellular electron transfer,EET)效率低以及生物被膜形成能力弱限制了METs在有机...     

高阶相互作用对宿主-寄生群落动态的影响

物种间相互作用是影响生物群落稳定性和多样性的重要因素。基于Lotka-Volterra竞争模型,通过构建多宿主种群的种内和种间高阶相互作用模型,研究宿主种群的间接竞争效应对寄生群落动态的影响机制。为有效地揭示高阶作用对种群动态的影响,通过对比宿主-寄生群落的现象模型以及机制模型,利用机制模型产生的合理数据集对现象模型中高阶项的参数进行拟合,进而探讨了高阶相互作用在群落动态中的作用。结果显示,完整的高阶相互作用模型在描述多宿主-寄生系统的群落动态中表现最优,而直接相互作用模型对群落动态的描述相对较差,即同时考虑种间和种内的高阶相互作用模型更加符合机制模型所描述的群落动态。此外,种内高阶作用和种间高阶作用产生不对称效应,宿主间的种间高阶作用对群落产生的影响较种内高阶作用更为显著。该研究结果在一定意义上丰富了宿主-寄生生物群落的稳定性研究,为理解物种间相互作用的多样性研究提供了依据。     

Evaluation of acyllysine isostere interactions with the aromatic pocket of the AF9 YEATS domain

Amide−π interactions, in which an amide interacts with an aromatic group, are ubiquitous in biology, yet remain understudied relative to other noncovalent interactions. Recently, we demonstrated that an electrostatically tunable amide−π interaction is key to recognition of histone acyllysine by the AF9 YEATS domain, a reader protein which has emerged as a therapeutic target due to its dysregulation in cancer. Amide isosteres are commonly employed in drug discovery, often to prevent degradation by proteases, and have proven valuable in achieving selectivity when targeting epigenetic proteins. However, like amide−π interactions, interactions of amide isosteres with aromatic rings have not been thoroughly studied despite widespread use. Herein, we evaluate the recognition of a series of amide isosteres by the AF9 YEATS domain using genetic code expansion to evaluate the amide isostere−π interaction. We show that compared to the amide−π interaction with the native ligand, each isostere exhibits similar electrostatic tunability with an aromatic residue in the binding pocket, demonstrating that the isosteres maintain similar interactions with the aromatic residue. We identify a urea-containing ligand that binds with enhanced affinity for the AF9 YEATS domain, offering a promising starting point for inhibitor development. Furthermore, we demonstrate that carbamate and urea isosteres of crotonyllysine are resistant to enzymatic removal by SIRT1, a protein that cleaves acyl post-translational modifications, further indicating the potential of amide isosteres in YEATS domain inhibitor development. These results also provide experimental precedent for interactions of these common drug discovery moieties with aromatic rings that can inform computational methods.     

Influences of species, latitudes and methodologies on estimates of phenological response to global warming

New analyses are presented addressing the global impacts of recent climate change on phenology of plant and animal species. A meta‐analysis spanning 203 species was conducted on published datasets from the northern hemisphere. Phenological response was examined with respect to two factors: distribution of species across latitudes and taxonomic affiliation or functional grouping of target species. Amphibians had a significantly stronger shift toward earlier breeding than all other taxonomic/functional groups, advancing more than twice as fast as trees, birds and butterflies. In turn, butterfly emergence or migratory arrival showed three times stronger advancement than the first flowering of herbs, perhaps portending increasing asynchrony in insect–plant interactions. Response was significantly stronger at higher latitudes where warming has been stronger, but latitude explained < 4% of the variation. Despite expectation, latitude was not yet an important predictor of climate change impacts on phenology. The only two previously published estimates of the magnitude of global response are quite different: 2.3 and 5.1 days decade⁻¹ advancement. The scientific community has assumed this difference to be real and has attempted to explain it in terms of biologically relevant phenomena: specifically, differences in distribution of data across latitudes, taxa or time periods. Here, these and other possibilities are explored. All analyses indicate that the difference in estimated response is primarily due to differences between the studies in criteria for incorporating data. It is a clear and automatic consequence of the exclusion by one study of data on ‘stable’ (nonresponsive) species. Once this is accounted for, the two studies support each other, generating similar conclusions despite analyzing substantially nonoverlapping datasets. Analyses here on a new expanded dataset estimate an overall spring advancement across the northern hemisphere of 2.8 days decade⁻¹. This is the first quantitative analysis showing that data‐sampling methodologies significantly impact global (synthetic) estimates of magnitude of global warming response.     

Effects of arginine on heat-induced aggregation of concentrated protein solutions

Arginine is one of the commonly used additives to enhance refolding yield of proteins, to suppress aggregation of proteins, and to increase solubility of proteins, and yet the molecular interactions that contribute to the role of arginine are unclear. Here, we present experiments, using bovine serum albumin (BSA), lysozyme (LYZ), and β-lactoglobulin (BLG) as model proteins, to show that arginine can enhance heat-induced aggregation of concentrated protein solutions, contrary to the conventional belief that arginine is a universal suppressor of aggregation. Results show that the enhancement in aggregation is caused only for BSA and BLG, but not for LYZ, indicating that arginine's preferential interactions with certain residues over others could determine the effect of the additive on aggregation. We use this previously unrecognized behavior of arginine, in combination with density functional theory calculations, to identify the molecular-level interactions of arginine with various residues that determine arginine's role as an enhancer or suppressor of aggregation of proteins. The experimental and computational results suggest that the guanidinium group of arginine promotes aggregation through the hydrogen-bond-based bridging interactions with the acidic residues of a protein, whereas the binding of the guanidinium group to aromatic residues (aggregation-prone) contributes to the stability and solubilization of the proteins. The approach, we describe here, can be used to select suitable additives to stabilize a protein solution at high concentrations based on an analysis of the amino acid content of the protein.     

Model-free analysis of binding at lipid membranes employing micro-calorimetric measurements

Based on universal thermodynamic principles (Schwarz in Biophys Chem 86:119–129, 2000) it is shown how measured enthalpy changes can be utilized to determine the relevant binding isotherm as well as the variation of the molar enthalpy change. This is carried out in a novel way involving multiple titration experiments whose evaluation requires no beforehand assumptions or models whatever. An appropriate specific model mechanism may be discussed afterwards and developed in view of the given experimental results. The pertinent procedure is demonstrated using micro-calorimetric data obtained in the case of the local anesthetic dibucaine as it associates with POPC liposomes. Mutual interactions of the bound ligand molecules could be described in terms of repulsive enthalpic and entropic activity coefficients. Apparently these are induced by electrostatic forces and by the finite size of binding sites, respectively.     

Linking herbivore-induced defences to population dynamics

1. Theoretical studies have shown that inducible defences have the potential to affect population stability and persistence in bi‐ and tritrophic food chains. Experimental studies on such effects of prey defence strategies on the dynamics of predator–prey systems are still rare. We performed replicated population dynamics experiments using the herbivorous rotifer Brachionus calyciflorus and four strains of closely related algae that show different defence responses to this herbivore. 2. We observed herbivore populations to fluctuate at a higher frequency when feeding on small undefended algae. During these fluctuations minimum rotifer densities remained sufficiently high to ensure population persistence in all the replicates. The initial growth of rotifer populations in this treatment coincided with a sharp drop in algal density. Such a suppression of algae by herbivores was not observed in the other treatments, where algae were larger due to induced or permanent defences. In these treatments we observed rotifer population densities to first rise and then decline. The herbivore went extinct in all replicates with large permanently defended algae. The frequency of herbivore extinctions was intermediate when algae had inducible defences. 3. A variety of alternative mechanisms could explain differential herbivore persistence in the different defence treatments. Our analysis showed the density and fraction of highly edible algal particles to better explain herbivore persistence and extinctions than total algal density, the fraction of highly inedible food particles or the accumulation of herbivore waste products or autotoxins. 4. We argue that the rotifers require a minimum fraction and density of edible food particles for maintenance and reproduction. We conjecture that induced defences in algae may thus favour larger zooplankton species such as Daphnia spp. that are less sensitive to shifts in their food size spectrum, relative to smaller zooplankton species, such as rotifers and in this way contributes to the structuring of planktonic communities.