Many biological mechanisms can be considered to be low-dimensional systems: their function is determined by molecular objects of reduced dimensionality. Bacterial photosynthesis is a very good ...example: the photosynthetic pathway is contained within nano-objects (vesicles) whose function is determined by the numbers and nanoscale organization of membrane proteins and by the ratios of the different types of protein that they contain. Systems biology has provided computational models for studying these processes, but there is a need for experimental platforms with which to test their predictions. This Invited Feature Article reviews recent work on the development of tools for the reconstruction of membrane processes on solid surfaces. Photochemical methods provide a powerful, versatile means for the organization of molecules and membranes across length scales from the molecular to the macroscopic. Polymer brushes are highly effective supports for model membranes and versatile functional and structural components in low-dimensional systems. The incorporation of plasmonic elements facilitates enhanced measurement of spectroscopic properties and provides an additional design strategy via the exploitation of quantum optical phenomena. A low-dimensional system that incorporates functional transmembrane proteins and a mechanism for the in situ measurement of proton transport is described.
A poly(glycerol monomethacrylate) (PGMA) macromolecular chain transfer agent has been utilized to polymerize benzyl methacrylate (BzMA) via reversible addition–fragmentation chain transfer ...(RAFT)-mediated aqueous emulsion polymerization. This formulation leads to the efficient formation of spherical diblock copolymer nanoparticles at up to 50% solids. The degree of polymerization (DP) of the core-forming PBzMA block has been systematically varied to control the mean particle diameter from 20 to 193 nm. Conversions of more than 99% were achieved for PGMA51–PBzMA250 within 6 h at 70 °C using macro-CTA/initiator molar ratios ranging from 3.0 to 10.0. DMF GPC analyses confirmed that relatively low polydispersities (M w/M n < 1.30) and high blocking efficiencies could be achieved. These spherical nanoparticles are stable to both freeze–thaw cycles and the presence of added salt (up to 0.25 M MgSO4). Three sets of PGMA51–PBzMA x spherical nanoparticles have been used to prepare stable Pickering emulsions at various copolymer concentrations in four model oils: sunflower oil, n-dodecane, n-hexane, and isopropyl myristate. A reduction in mean droplet diameter was observed via laser diffraction on increasing the nanoparticle concentration. Finally, the cis diol functionality on the PGMA stabilizer chains has been exploited to demonstrate the selective adsorption of PGMA51–PBzMA100 nanoparticles onto a micropatterned phenylboronic acid-functionalized planar surface. Formation of a cyclic boronate ester at pH 10 causes strong selective binding of the nanoparticles via the cis-diol groups in the PGMA stabilizer chains, as judged by AFM studies. Control experiments confirmed that minimal selective nanoparticle binding occurred at pH 4, or if the PGMA51 stabilizer block was replaced with a poly(ethylene glycol) PEG113 stabilizer block.
Summary
RenSeq is a NB‐LRR (nucleotide binding‐site leucine‐rich repeat) gene‐targeted, Resistance gene enrichment and sequencing method that enables discovery and annotation of pathogen resistance ...gene family members in plant genome sequences. We successfully applied RenSeq to the sequenced potato Solanum tuberosum clone DM, and increased the number of identified NB‐LRRs from 438 to 755. The majority of these identified R gene loci reside in poorly or previously unannotated regions of the genome. Sequence and positional details on the 12 chromosomes have been established for 704 NB‐LRRs and can be accessed through a genome browser that we provide. We compared these NB‐LRR genes and the corresponding oligonucleotide baits with the highest sequence similarity and demonstrated that ~80% sequence identity is sufficient for enrichment. Analysis of the sequenced tomato S. lycopersicum ‘Heinz 1706’ extended the NB‐LRR complement to 394 loci. We further describe a methodology that applies RenSeq to rapidly identify molecular markers that co‐segregate with a pathogen resistance trait of interest. In two independent segregating populations involving the wild Solanum species S. berthaultii (Rpi‐ber2) and S. ruiz‐ceballosii (Rpi‐rzc1), we were able to apply RenSeq successfully to identify markers that co‐segregate with resistance towards the late blight pathogen Phytophthora infestans. These SNP identification workflows were designed as easy‐to‐adapt Galaxy pipelines.
A quantitative investigation of the responses of surface-grown biocompatible brushes of poly(2-(methacryloyloxy)ethyl phosphorylcholine) (PMPC) to different types of salt has been carried out using ...ellipsometry, quartz crystal microbalance (QCM) measurements, and friction force microscopy. Both cations and anions of varying valency over a wide range of concentrations were examined. Ellipsometry shows that the height of the brushes is largely independent of the ionic strength, confirming that the degree of swelling of the polymer is independent of the ionic character of the medium. In contrast, QCM measurements reveal significant changes in mass and dissipation to the PMPC brush layer, suggesting that ions bind to phosphorylcholine (PC) groups in PMPC molecules, which results in changes in the stiffness of the brush layer, and the binding affinity varies with salt type. Nanotribological measurements made using friction force microscopy show that the coefficient of friction decreases with increasing ionic strength for a variety of salts, supporting the conclusion drawn from QCM measurements. It is proposed that the binding of ions to the PMPC molecules does not change their hydration state, and hence the height of the surface-grown polymeric brushes. However, the balance of the intra- and intermolecular interactions is strongly dependent upon the ionic character of the medium between the hydrated chains, modulating the interactions between the zwitterionic PC pendant groups and, consequently, the stiffness of the PMPC molecules in the brush layer.
A new cysteine-based methacrylic monomer (CysMA) was conveniently synthesized via selective thia-Michael addition of a commercially available methacrylate-acrylate precursor in aqueous solution ...without recourse to protecting group chemistry. Poly(cysteine methacrylate) (PCysMA) brushes were grown from the surface of silicon wafers by atom-transfer radical polymerization. Brush thicknesses of ca. 27 nm were achieved within 270 min at 20 °C. Each CysMA residue comprises a primary amine and a carboxylic acid. Surface zeta potential and atomic force microscopy (AFM) studies of the pH-responsive PCysMA brushes confirm that they are highly extended either below pH 2 or above pH 9.5, since they possess either cationic or anionic character, respectively. At intermediate pH, PCysMA brushes are zwitterionic. At physiological pH, they exhibit excellent resistance to biofouling and negligible cytotoxicity. PCysMA brushes undergo photodegradation: AFM topographical imaging indicates significant mass loss from the brush layer, while XPS studies confirm that exposure to UV radiation produces surface aldehyde sites that can be subsequently derivatized with amines. UV exposure using a photomask yielded sharp, well-defined micropatterned PCysMA brushes functionalized with aldehyde groups that enable conjugation to green fluorescent protein (GFP). Nanopatterned PCysMA brushes were obtained using interference lithography, and confocal microscopy again confirmed the selective conjugation of GFP. Finally, PCysMA undergoes complex base-catalyzed degradation in alkaline solution, leading to the elimination of several small molecules. However, good long-term chemical stability was observed when PCysMA brushes were immersed in aqueous solution at physiological pH.
Photosynthesis converts absorbed solar energy to a protonmotive force, which drives ATP synthesis. The membrane network of chlorophyll–protein complexes responsible for light absorption, ...photochemistry and quinol (QH2) production has been mapped in the purple phototrophic bacterium Rhodobacter (Rba.) sphaeroides using atomic force microscopy (AFM), but the membrane location of the cytochrome bc1 (cytbc1) complexes that oxidise QH2 to quinone (Q) to generate a protonmotive force is unknown. We labelled cytbc1 complexes with gold nanobeads, each attached by a Histidine10 (His10)-tag to the C-terminus of cytc1. Electron microscopy (EM) of negatively stained chromatophore vesicles showed that the majority of the cytbc1 complexes occur as dimers in the membrane. The cytbc1 complexes appeared to be adjacent to reaction centre light-harvesting 1-PufX (RC–LH1–PufX) complexes, consistent with AFM topographs of a gold-labelled membrane. His-tagged cytbc1 complexes were retrieved from chromatophores partially solubilised by detergent; RC–LH1–PufX complexes tended to co-purify with cytbc1 whereas LH2 complexes became detached, consistent with clusters of cytbc1 complexes close to RC–LH1–PufX arrays, but not with a fixed, stoichiometric cytbc1–RC–LH1–PufX supercomplex. This information was combined with a quantitative mass spectrometry (MS) analysis of the RC, cytbc1, ATP synthase, cytaa3 and cytcbb3 membrane protein complexes, to construct an atomic-level model of a chromatophore vesicle comprising 67 LH2 complexes, 11 LH1–RC–PufX dimers & 2 RC–LH1–PufX monomers, 4 cytbc1 dimers and 2 ATP synthases. Simulation of the interconnected energy, electron and proton transfer processes showed a half-maximal ATP turnover rate for a light intensity equivalent to only 1% of bright sunlight. Thus, the photosystem architecture of the chromatophore is optimised for growth at low light intensities.
•Cytbc1 complexes in Rba. sphaeroides membranes were labelled with gold nanobeads.•Biochemical, EM and AFM analyses show proximity of RC–LH1–PufX and cytbc1 complexes.•We constructed an atomic-level model of a membrane comprising all major complexes.•Computer simulations show that the membrane is optimised for low-light growth.
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•Aqueous fluoride extraction via lanthanum-loaded chelating resin is demonstrated.•The uptake mechanism changes, dependant on initial fluoride concentration.•Uptake from ...multi-component leachate occurs mainly via aluminium hydroxyfluoride precipitation.•Maximum uptake is greater than previously reported for similar metal-loaded resins.
Spent potlining (SPL) hazardous waste is a potentially valuable source of fluoride, which may be recovered through chemical leaching and adsorption with a selective sorbent. For this purpose, the commercially available chelating resin Purolite® S950+ was loaded with lanthanum ions, to create a novel ligand-exchange sorbent. The equilibrium fluoride uptake behaviour of the resin was thoroughly investigated, using NaF solution and a simulant leachate of SPL waste. The resin exhibited a large maximum defluoridation capacity of 187 ± 15 mg g−1 from NaF solution and 126 ± 10 mg g−1 from the leachate, with solution pH being strongly influential to uptake performance. Isotherm and spectral data indicated that both chemisorption and unexpected physisorption processes were involved in the fluoride extraction and suggested that the major uptake mechanism differed in each matrix. The resin demonstrates significant potential in the recovery of fluoride from aqueous waste-streams.
The integration of top-down (lithographic) and bottom-up (synthetic chemical) methodologies remains a major goal in nanoscience. At larger length scales, light-directed chemical synthesis, first ...reported two decades ago, provides a model for this integration, by combining the spatial selectivity of photolithography with the synthetic utility of photochemistry. This review describes attempts to realise a similar integration at the nanoscale, by employing near-field optical probes to initiate selective chemical transformations in regions a few tens of nm in size. A combination of near-field exposure and an ultra-thin resist yields exceptional performance: in self-assembled monolayers, an ultimate resolution of 9 nm (ca. λ/30) has been achieved. A wide range of methodologies, based on monolayers of thiols, silanes and phosphonic acids, and thin films of nanoparticles and polymers, have been developed for use on metal and oxide surfaces, enabling the fabrication of metal nanowires, nanostructured polymers and nanopatterned oligonucleotides and proteins. Recently parallel lithography approaches have demonstrated the capacity to pattern macroscopic areas, and the ability to function under fluid, suggesting exciting possibilities for surface chemistry at the nanoscale.
Lifshitz theory is widely used to calculate interfacial interaction energies and underpins established approaches to the interpretation of measurement data from experimental methods including the ...surface forces apparatus and the atomic force microscope. However, a significant limitation of Lifshitz theory is that it uses the bulk dielectric properties of the medium to predict the work of adhesion. Here, we demonstrate that a different approach, in which the interactions between molecules at surfaces and in the medium are described by a set of surface site interaction points (SSIPs), yields interaction free energies that are correlated better with experimentally determined values. The work of adhesion W(Lifshitz) between hydrocarbon surfaces was calculated in 260 liquids using Lifshitz theory and compared with interaction free energies ΔΔG calculated using the SSIP model. The predictions of these models diverge in significant ways. In particular, ΔΔG values for hydrocarbon surfaces are typically small and vary little, but in contrast, W(Lifshitz) values span 4 orders of magnitude. Moreover, the SSIP model yields significantly different ΔΔG values in some liquids for which Lifshitz theory predicts similar values of W(Lifshitz). These divergent predictions were tested using atomic force microscopy. Experimentally determined works of adhesion were closer to the values predicted using the SSIP model than Lifshitz theory. In mixtures of methanol and benzyl alcohol, even greater differences were found in the interaction energies calculated using the two models: the value of ΔΔG calculated using the SSIP model declines smoothly as the benzyl alcohol concentration increases, and values are well correlated with experimental data; however, W(Lifshitz) decreases to a minimum and then increases, reaching a larger value for benzyl alcohol than for methanol. We conclude that the SSIP model provides more reliable estimates of the work of adhesion than Lifshitz theory.
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