Influence of lipids on the hydrophobic barrier within the pore of the TWIK-1 K2P channel

Several recent ion channel structures have revealed large side portals, or ‘fenestrations’ at the interface between their transmembrane helices that potentially expose the ion conduction pathway to the lipid core of the bilayer. In a recent study we demonstrated that functional activity of the TWIK-1 K2P channel is influenced by the presence of hydrophobic residues deep within the inner pore. These residues are located near the fenestrations in the TWIK-1 structure and promote dewetting of the pore by forming a hydrophobic barrier to ion conduction. During our previous MD simulations, lipid tails were observed to enter these fenestrations. In this addendum to that study, we investigate lipid contribution to the dewetting process. Our results demonstrate that lipid tails from both the upper and lower leaflets can occupy the fenestrations and partially penetrate into the pore. The lipid tails do not sterically occlude the pore, but there is an inverse correlation between the presence of water within the hydrophobic barrier and the number of lipids tails within the lining of the pore. However, dewetting still occurs in the absence of lipids tails, and pore hydration appears to be determined primarily by those side-chains lining the narrowest part of the pore cavity.     

Synthesis of N-alkyl substituted indolocarbazoles as potent inhibitors of human cytomegalovirus replication.

The synthesis and antiviral evaluation of unsymmetrical indolocarbazole derivatives of Arcyriaflavin A, substituted with a range of alkyl groups at the indole nitrogen, is described. Structure-activity relationships in this series against human cytomegalovirus (HCMV) replication in cell culture are reported. Compound 4b was identified as potent inhibitor of HCMV (IC(50)=19 nM), which retained activity against a range of HCMV strains including ganciclovir resistant isolates.     

Competition intensity at local versus regional spatial scales

Studies of competition intensity over natural (i.e. topographic) gradients often contradict the results from studies where artificial (i.e. fertilizer) gradients have been used. Why should the type of gradient matter? To explore the possibilities, we performed experiments to measure competition intensity experienced by tree seedlings from grass competitors across a natural resource gradient, and simultaneously across artificial soil nutrient (fertiliser) gradients. We measured various functional traits (i.e. specific leaf area, leaf area, leaf nitrogen content, δ¹⁵N, δ¹³C, RGR) to gain mechanistic insight into the nature of competition across these gradients. Competition intensity increased with increasing resource availability, unequivocally at the local scale (i.e. with fertilizer application) but not at the regional scale (i.e. across the natural productivity gradient). Our measurements of plant traits were generally consistent with measurements of competition intensity, and demonstrate that competition occurs even when resource levels are low. Competition mainly acted to reduce the growth of Eucalyptus seedlings. Functional (physiological) traits in the Eucalyptus seedlings were not strongly affected by competitors, with the possible exception of δ¹⁵N, which may effectively integrate information on soil nutrient, moisture and leaf processes.     

Populations evolving towards failure: costs of adaptation under competition at the range edge of an invasive perennial plant

Background: Species undergoing range expansion adapt to novel and stressful environments at range fronts. These adaptations of the edge populations may incur fitness costs. These costs may play a crucial role in stopping range expansion before absolute physiological and evolutionary limits were reached. Costs however have proven to be elusive. These may be specifically expressed under competition.

Aims: Here, we assessed the costs of adaptation in range-edge populations of an invasive plant by evaluating plant responses under competition.

Methods: We grew plants from range-centre and edge populations under competition treatments in a glasshouse. We predicted that plants from the range-edge would express lower reproductive efficiency under competition compared with centre population plants, and this would indicate a potentially maladaptive response.

Results: Under high competition, plants from the range-edge expressed lower reproductive efficiency relative to range-centre plants which supported our prediction. In addition, they were more heavily affected by competition.

Conclusions: Adaptation to novel environments at the range-edge has incurred a cost as a potentially maladaptive response under competition, which may contribute to the formation of the range-edge. This finding suggests that these costs likely form part of the classic trade-offs involved with stress-tolerance and may have effects on range evolution.     

Testing specialization hypothesis on a stress gradient

Specialization can allow plants to perform well in their home environments at the expense of poor performance in other habitats. A great difference in performance across habitats is observed as high phenotypic plasticity in performance traits and a by‐product of selection. However, phenotypic plasticity (particularly adaptive plasticity) can be an active response to the selection by allowing the maintenance of performance. Therefore, specialization and adaptive plasticity delineate two opposing strategies. The specialization hypothesis presents a non‐adaptive interpretation of plasticity and predicts that phenotypic plasticity of performance traits is greater in specialization to good habitats, whereas bad habitat specialists express low plasticity in performance traits. We tested the specialization hypothesis using plants adapted to extremely stressful mine‐site habitats (sites with highly acidic soil and heavy metal contamination). Seeds of five herbaceous species were collected from high stress (mine site) and low stress habitats. We established a glasshouse experiment where seedlings from high and low stress habitats were grown under near neutral pH and acid soil treatments. We compared performance trait plasticity (e.g. biomass) from high stress and low stress populations and found that there was no significant difference in performance traits between high and low stress populations across treatments. The overall result did not support the specialization hypothesis. Moreover, our results suggest that the species invaded the mine sites are either extreme generalists or the surrounding populations retain some stress tolerant genotypes that are capable of invading the mine sites.     

Two groups control light-induced schiff base deprotonation and the proton affinity of asp(85) in the Arg(82)His mutant of bacteriorhodopsin

Arg(82) is one of the four buried charged residues in the retinal binding pocket of bacteriorhodopsin (bR). Previous studies show that Arg(82) controls the pK(a)s of Asp(85) and the proton release group and is essential for fast light-induced proton release. To further investigate the role of Arg(82) in light-induced proton pumping, we replaced Arg(82) with histidine and studied the resulting pigment and its photochemical properties. The main pK(a) of the purple-to-blue transition (pK(a) of Asp(85)) is unusually low in R82H: 1.0 versus 2.6 in wild type (WT). At pH 3, the pigment is purple and shows light and dark adaptation, but almost no light-induced Schiff base deprotonation (formation of the M intermediate) is observed. As the pH is increased from 3 to 7 the M yield increases with pK(a) 4.5 to a value approximately 40% of that in the WT. A transition with a similar pK(a) is observed in the pH dependence of the rate constant of dark adaptation, k(da). These data can be explained, assuming that some group deprotonates with pK(a) 4.5, causing an increase in the pK(a) of Asp(85) and thus affecting k(da) and the yield of M. As the pH is increased from 7 to 10.5 there is a further 2.5-fold increase in the yield of M and a decrease in its rise time from 200 &mgr;s to 75 &mgr;s with pK(a) 9. 4. The chromophore absorption band undergoes a 4-nm red shift with a similar pK(a). We assume that at high pH, the proton release group deprotonates in the unphotolyzed pigment, causing a transformation of the pigment into a red-shifted "alkaline" form which has a faster rate of light-induced Schiff base deprotonation. The pH dependence of proton release shows that coupling between Asp(85) and the proton release group is weakened in R82H. The pK(a) of the proton release group in M is 7.2 (versus 5.8 in the WT). At pH < 7, most of the proton release occurs during O --> bR transition with tau approximately 45 ms. This transition is slowed in R82H, indicating that Arg(82) is important for the proton transfer from Asp(85) to the proton release group. A model describing the interaction of Asp(85) with two ionizable residues is proposed to describe the pH dependence of light-induced Schiff base deprotonation and proton release.     

“Active” and “passive” ecological restoration strategies in meta‐analysis

One of the means of creating a more robust methodology for ecological restoration involves reducing the gap between ecological theory and restoration practices. A common strategy to do so is using meta‐analysis to understand key drivers of restoration outcomes. “Active” and “passive” is a dichotomy often used to separate restoration strategies in such meta‐analyses. We investigate previously raised concerns about selection bias and subjective categorization of strategies. We promote a paired experimental design in future empirical research and propose the use of three categories of restoration strategy in lieu of “passive” and “active” to alleviate inconsistency in definitions and categorization.     

Optimal allocation of resources in response to shading and neighbours in the heteroblastic species, Acacia implexa

BACKGROUND AND AIMS: Heteroblasty is an encompassing term referring to ontogenetic changes in the plant shoot. A shaded environment is known to affect the process of heteroblastic development; however, it is not known whether crowded or high density growing conditions can also alter heteroblasty. Compound leaves of the shade-intolerant Acacia implexa allocate less biomass per unit photosynthetic area than transitional leaves or phyllodes and it is hypothesized that this trait will convey an advantage in a crowded environment. Compound leaves also have larger photosynthetic capture area - a trait known to be advantageous in shade. This studied tested the hypothesis that more compound leaves will be developed under shade and crowded environments. Furthermore, this species should undergo optimal allocation of biomass to shoots and roots given shaded and crowded environments. METHODS: A full factorial design of irradiance (high and low) and density levels (high, medium and low) on three populations sourced from varying rainfall regions (high, medium and low) was established under controlled glasshouse conditions. Traits measured include the number of nodes expressing a compound leaf, biomass allocation to shoots and roots, and growth traits. Key Results A higher number of nodes expressed a compound leaf under low irradiance and in high density treatments; however, there were no significant interactions across treatments. Phenotypes strongly associated with the shade avoidance syndrome were developed under low irradiance; however, this was not observed under high density. There was no significant difference in relative growth rates across light treatments, but growth was significantly slower in a crowded environment. Conclusions Heteroblastic development in Acacia can be altered by shade and crowded environments. In this experiment, light was clearly the most limiting factor to growth in a shaded environment; however, in a crowded environment there were additional limiting resources to growth.