Exploiting Organometallic Chemistry to Functionalize Small Cuprous Oxide Colloidal Nanocrystals.

The ligand chemistry of colloidal semiconductor nanocrystals mediates their solubility, band gap, and surface facets. Here, selective organometallic chemistry is used to prepare small, colloidal cuprous oxide nanocrystals and to control their surface chemistry by decorating them with metal complexes. The strategy is demonstrated using small (3-6 nm) cuprous oxide (Cu2O) colloidal nanocrystals (NC), soluble in organic solvents. Organometallic complexes are coordinated by reacting the surface Cu-OH bonds with organometallic reagents, M(C6F5)2, M = Zn(II) and Co(II), at room temperature. These reactions do not disrupt the Cu2O crystallinity or nanoparticle size; rather, they allow for the selective coordination of a specific metal complex at the surface. Subsequently, the surface-coordinated organometallic complex is reacted with three different carboxylic acids to deliver Cu-O-Zn(O2CR') complexes. Selective nanocrystal surface functionalization is established using spectroscopy (IR, 19F NMR), thermal gravimetric analyses (TGA), transmission electron microscopy (TEM, EELS), and X-ray photoelectron spectroscopy (XPS). Photoluminescence efficiency increases dramatically upon organometallic surface functionalization relative to that of the parent Cu2O NC, with the effect being most pronounced for Zn(II) decoration. The nanocrystal surfaces are selectively functionalized by both organic ligands and well-defined organometallic complexes; this synthetic strategy may be applicable to many other metal oxides, hydroxides, and semiconductors. In the future, it should allow NC properties to be designed for applications including catalysis, sensing, electronics, and quantum technologies.

Environment-independent distribution of mutational effects emerges from microscopic epistasis.

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, where the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global-epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is remarkably predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low.

Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments.

Adaptation is driven by the selection for beneficial mutations that provide a fitness advantage in the specific environment in which a population is evolving. However, environments are rarely constant or predictable. When an organism well adapted to one environment finds itself in another, pleiotropic effects of mutations that made it well adapted to its former environment will affect its success. To better understand such pleiotropic effects, we evolved both haploid and diploid barcoded budding yeast populations in multiple environments, isolated adaptive clones, and then determined the fitness effects of adaptive mutations in 'non-home' environments in which they were not selected. We find that pleiotropy is common, with most adaptive evolved lineages showing fitness effects in non-home environments. Consistent with other studies, we find that these pleiotropic effects are unpredictable: they are beneficial in some environments and deleterious in others. However, we do find that lineages with adaptive mutations in the same genes tend to show similar pleiotropic effects. We also find that ploidy influences the observed adaptive mutational spectra in a condition-specific fashion. In some conditions, haploids and diploids are selected with adaptive mutations in identical genes, while in others they accumulate mutations in almost completely disjoint sets of genes.

Wet spinning imogolite nanotube fibres: an in situ process study.

Imogolite nanotubes (INTs) form transparent aqueous liquid-crystalline solutions, with strong birefringence and X-ray scattering power. They provide an ideal model system for studying the assembly of one-dimensional nanomaterials into fibres, as well as offering interesting properties in their own right. Here, in situ polarised optical microscopy is used to study the wet spinning of pure INTs into fibres, illustrating the influence of process variables during extrusion, coagulation, washing and drying on both structure and mechanical properties. Tapered spinnerets were shown to be significantly more effective than thin cylindrical channels for forming homogeneous fibres; a result related to simple capillary rheology by fitting a shear thinning flow model. The washing step has a strong influence of structure and properties, combining the removal of residual counter-ions and structural relaxation to produce a less aligned, denser and more networked structure; the timescales and scaling behavior of the processes are compared quantitatively. Both strength and stiffness are higher for INT fibres with a higher packing fraction and lower degree of alignment, indicating the importance of forming a rigid jammed network to transfer stress through these porous, rigid rod assemblies. The electrostatically-stabilised, rigid rod INT solutions were successfully cross-linked using multivalent anions, providing robust gels, potentially useful in other contexts.

Epistasis and evolution: recent advances and an outlook for prediction.

As organisms evolve, the effects of mutations change as a result of epistatic interactions with other mutations accumulated along the line of descent. This can lead to shifts in adaptability or robustness that ultimately shape subsequent evolution. Here, we review recent advances in measuring, modeling, and predicting epistasis along evolutionary trajectories, both in microbial cells and single proteins. We focus on simple patterns of global epistasis that emerge in this data, in which the effects of mutations can be predicted by a small number of variables. The emergence of these patterns offers promise for efforts to model epistasis and predict evolution.

Matched Ligands for Small, Stable Colloidal Nanoparticles of Copper, Cuprous Oxide and Cuprous Sulfide.

This work applies organometallic routes to copper(0/I) nanoparticles and describes how to match ligand chemistries with different material compositions. The syntheses involve reacting an organo-copper precursor, mesitylcopper(I) [CuMes]z (z=4, 5), at low temperatures and in organic solvents, with hydrogen, air or hydrogen sulfide to deliver Cu, Cu2 O or Cu2 S nanoparticles. Use of sub-stoichiometric quantities of protonated ligand (pro-ligand; 0.1-0.2 equivalents vs. [CuMes]z ) allows saturation of surface coordination sites but avoids excess pro-ligand contaminating the nanoparticle solutions. The pro-ligands are nonanoic acid (HO2 CR1 ), 2-[2-(2-methoxyethoxy)ethoxy]acetic acid (HO2 CR2 ) or di(thio)nonanoic acid, (HS2 CR1 ), and are matched to the metallic, oxide or sulfide nanoparticles. Ligand exchange reactions reveal that copper(0) nanoparticles may be coordinated by carboxylate or di(thio)carboxylate ligands, but Cu2 O is preferentially coordinated by carboxylate ligands and Cu2 S by di(thio)carboxylate ligands. This work highlights the opportunities for organometallic routes to well-defined nanoparticles and the need for appropriate ligand selection.

Best Practices in Designing, Sequencing, and Identifying Random DNA Barcodes.

Random DNA barcodes are a versatile tool for tracking cell lineages, with applications ranging from development to cancer to evolution. Here, we review and critically evaluate barcode designs as well as methods of barcode sequencing and initial processing of barcode data. We first demonstrate how various barcode design decisions affect data quality and propose a new design that balances all considerations that we are currently aware of. We then discuss various options for the preparation of barcode sequencing libraries, including inline indices and Unique Molecular Identifiers (UMIs). Finally, we test the performance of several established and new bioinformatic pipelines for the extraction of barcodes from raw sequencing reads and for error correction. We find that both alignment and regular expression-based approaches work well for barcode extraction, and that error-correction pipelines designed specifically for barcode data are superior to generic ones. Overall, this review will help researchers to approach their barcoding experiments in a deliberate and systematic way.

Platinum deposition on functionalised graphene for corrosion resistant oxygen reduction electrodes.

Graphene-related materials are promising supports for electrocatalysts due to their stability and high surface area. Their innate surface chemistries can be controlled and tuned via functionalisation to improve the stability of both the carbon support and the metal catalyst. Functionalised graphenes were prepared using either aryl diazonium functionalisation or non-destructive chemical reduction, to provide groups adapted for platinum deposition. XPS and TGA-MS measurements confirmed the presence of polyethyleneglycol and sulfur-containing functional groups, and provided consistent values for the extent of the reactions. The deposited platinum nanoparticles obtained were consistently around 2 nm via reductive chemistry and around 4 nm via the diazonium route. Although these graphene-supported electrocatalysts provided a lower electrochemical surface area (ECSA), functionalised samples showed enhanced specific activity compared to a commercial platinum/carbon black system. Accelerated stress testing (AST) showed improved durability for the functionalised graphenes compared to the non-functionalised materials, attributed to edge passivation and catalyst particle anchoring.

Mutational robustness changes during long-term adaptation in laboratory budding yeast populations.

As an adapting population traverses the fitness landscape, its local neighborhood (i.e., the collection of fitness effects of single-step mutations) can change shape because of interactions with mutations acquired during evolution. These changes to the distribution of fitness effects can affect both the rate of adaptation and the accumulation of deleterious mutations. However, while numerous models of fitness landscapes have been proposed in the literature, empirical data on how this distribution changes during evolution remains limited. In this study, we directly measure how the fitness landscape neighborhood changes during laboratory adaptation. Using a barcode-based mutagenesis system, we measure the fitness effects of 91 specific gene disruption mutations in genetic backgrounds spanning 8000-10,000 generations of evolution in two constant environments. We find that the mean of the distribution of fitness effects decreases in one environment, indicating a reduction in mutational robustness, but does not change in the other. We show that these distribution-level patterns result from differences in the relative frequency of certain patterns of epistasis at the level of individual mutations, including fitness-correlated and idiosyncratic epistasis.

Effect of graphene flake size on functionalisation: quantifying reaction extent and imaging locus with single Pt atom tags.

Here, the locus of functionalisation on graphene-related materials and the progress of the reaction is shown to depend strongly on the starting feedstock. Five characteristically different graphite sources were exfoliated and functionalized using a non-destructive chemical reduction method. These archetypical examples were compared via a model reaction, grafting dodecyl addends, evaluated with TGA-MS, XPS and Raman data. A general increase in grafting ratio (ranging from 1.1 wt% up to 25 wt%) and an improvement in grafting stoichiometry (C/R) were observed as flake radius decreased. Raman spectrum imaging of the functionalised natural flake graphite identified that grafting is directed towards flake edges. This behaviour was further corroborated, at atomistic resolution, by functionalising the graphene layers with bipyridine groups able to complex single platinum atoms. The distribution of these groups was then directly imaged using aberration-corrected HAADF-STEM. Platinum atoms were found to be homogeneously distributed across smaller graphenes; in contrast, a more heterogeneous distribution, with a predominance of edge grafting was observed for larger graphites. These observations show that grafting is directed towards flake edges, but not necessary at edge sites; the mechanism is attributed to the relative inaccessibility of the inner basal plane to reactive moieties, resulting in kinetically driven grafting nearer flake edges. This phenomenology may be relevant to a wide range of reactions on graphenes and other 2d materials.

Scalable Sacrificial Templating to Increase Porosity and Platinum Utilisation in Graphene-Based Polymer Electrolyte Fuel Cell Electrodes.

Polymer electrolyte fuel cells hold great promise for a range of applications but require advances in durability for widespread commercial uptake. Corrosion of the carbon support is one of the main degradation pathways; hence, corrosion-resilient graphene has been widely suggested as an alternative to traditional carbon black. However, the performance of bulk graphene-based electrodes is typically lower than that of commercial carbon black due to their stacking effects. This article reports a simple, scalable and non-destructive method through which the pore structure and platinum utilisation of graphene-based membrane electrode assemblies can be significantly improved. Urea is incorporated into the catalyst ink before deposition, and is then simply removed from the catalyst layer after spraying by submerging the electrode in water. This additive hinders graphene restacking and increases porosity, resulting in a significant increase in Pt utilisation and current density. This technique does not require harsh template etching and it represents a pathway to significantly improve graphene-based electrodes by introducing hierarchical porosity using scalable liquid processes.

Binding affinity landscapes constrain the evolution of broadly neutralizing anti-influenza antibodies.

Over the past two decades, several broadly neutralizing antibodies (bnAbs) that confer protection against diverse influenza strains have been isolated. Structural and biochemical characterization of these bnAbs has provided molecular insight into how they bind distinct antigens. However, our understanding of the evolutionary pathways leading to bnAbs, and thus how best to elicit them, remains limited. Here, we measure equilibrium dissociation constants of combinatorially complete mutational libraries for two naturally isolated influenza bnAbs (CR9114, 16 heavy-chain mutations; CR6261, 11 heavy-chain mutations), reconstructing all possible evolutionary intermediates back to the unmutated germline sequences. We find that these two libraries exhibit strikingly different patterns of breadth: while many variants of CR6261 display moderate affinity to diverse antigens, those of CR9114 display appreciable affinity only in specific, nested combinations. By examining the extensive pairwise and higher order epistasis between mutations, we find key sites with strong synergistic interactions that are highly similar across antigens for CR6261 and different for CR9114. Together, these features of the binding affinity landscapes strongly favor sequential acquisition of affinity to diverse antigens for CR9114, while the acquisition of breadth to more similar antigens for CR6261 is less constrained. These results, if generalizable to other bnAbs, may explain the molecular basis for the widespread observation that sequential exposure favors greater breadth, and such mechanistic insight will be essential for predicting and eliciting broadly protective immune responses.

Defect-Free Single-Layer Graphene by 10 s Microwave Solid Exfoliation and Its Application for Catalytic Water Splitting.

Mass production of defect-free single-layer graphene flakes (SLGFs) by a cost-effective approach is still very challenging. Here, we report such single-layer graphene flakes (SLGFs) (>90%) prepared by a nondestructive, energy-efficient, and easy up-scalable physical approach. These high-quality graphene flakes are attributed to a novel 10 s microwave-modulated solid-state approach, which not only fast exfoliates graphite in air but also self-heals the surface of graphite to remove the impurities. The fabricated high-quality graphene films (∼200 nm) exhibit a sheet resistance of ∼280 Ω/sq without any chemical or physical post-treatment. Furthermore, graphene-incorporated Ni-Fe electrodes represent a remarkable ∼140 mA/cm2 current for the catalytic water oxidation reaction compared with the pristine Ni-Fe electrode (∼10 mA/cm2) and a 120 mV cathodic shift in onset potential under identical experimental conditions, together with a faradic efficiency of >90% for an ideal ratio of H2 and O2 production from water. All these excellent performances are attributed to extremely high conductivity of the defect-free graphene flakes.

Continuous Binder-Free Fibers of Pure Imogolite Nanotubes.

Imogolite nanotubes (INTs) display a range of useful properties and provide an ideal material system to study the assembly of nanomaterials into macroscopic fibers. A method of wet spinning pure, binder-free imogolite fibers has been developed using double-walled germanium imogolite nanotubes. The nanotube aspect ratio can be controlled during the initial synthesis and is critical to the spinning process. Fibers made from short nanotubes (<100 nm) have very low gel strengths, while dopes with longer nanotubes (500-1000 nm) are readily spinnable. The tensile behavior of the resulting imogolite nanotube fibers is strongly influenced by relative humidity (RH), with a modulus of 30 GPa at 10% RH compared to 2.8 GPa at 85% RH, as well as a change in failure mode. This result highlights the importance of inter-nanotube interactions in such assemblies and provides a useful strategy for further exploration. Interestingly, in the absence of a matrix phase, a degree of misorientation appears to improve load transfer between the individual INTs within the porous fiber, likely due to an increase in the number of interparticle contacts. Imogolite nanotubes are an appealing analogue to other nanotube fiber systems, and it is hoped that learnings from this system can also be used to improve carbon nanotube fibers.

Phenotypic and molecular evolution across 10,000 generations in laboratory budding yeast populations.

Laboratory experimental evolution provides a window into the details of the evolutionary process. To investigate the consequences of long-term adaptation, we evolved 205 Saccharomyces cerevisiae populations (124 haploid and 81 diploid) for ~10,000,000 generations in three environments. We measured the dynamics of fitness changes over time, finding repeatable patterns of declining adaptability. Sequencing revealed that this phenotypic adaptation is coupled with a steady accumulation of mutations, widespread genetic parallelism, and historical contingency. In contrast to long-term evolution in E. coli, we do not observe long-term coexistence or populations with highly elevated mutation rates. We find that evolution in diploid populations involves both fixation of heterozygous mutations and frequent loss-of-heterozygosity events. Together, these results help distinguish aspects of evolutionary dynamics that are likely to be general features of adaptation across many systems from those that are specific to individual organisms and environmental conditions.

Designing Structural Electrochemical Energy Storage Systems: A Perspective on the Role of Device Chemistry.

Structural energy storage devices (SESDs), designed to simultaneously store electrical energy and withstand mechanical loads, offer great potential to reduce the overall system weight in applications such as automotive, aircraft, spacecraft, marine and sports equipment. The greatest improvements will come from systems that implement true multifunctional materials as fully as possible. The realization of electrochemical SESDs therefore requires the identification and development of suitable multifunctional structural electrodes, separators, and electrolytes. Different strategies are available depending on the class of electrochemical energy storage device and the specific chemistries selected. Here, we review existing attempts to build SESDs around carbon fiber (CF) composite electrodes, including the use of both organic and inorganic compounds to increase electrochemical performance. We consider some of the key challenges and discuss the implications for the selection of device chemistries.

Understanding and controlling the covalent functionalisation of graphene.

Chemical functionalisation is one of the most active areas of graphene research, motivated by fundamental science, the opportunities to adjust or supplement intrinsic properties, and the need to assemble materials for a broad array of applications. Historically, the primary consideration has been the degree of functionalisation but there is growing interest in understanding how and where modification occurs. Reactions may proceed preferentially at edges, defects, or on graphitic faces; they may be correlated, uncorrelated, or anti-correlated with previously grafted sites. A detailed collation of existing literature data indicates that steric effects play a strong role in limiting the extent of reaction. However, the pattern of functionalisation may have important effects on the resulting properties. This article addresses the unifying principles of current graphene functionalisation technologies, with emphasis on understanding and controlling the locus of functionalisation.

Thermal Decomposition of Ternary Sodium Graphite Intercalation Compounds.

Graphite intercalation compounds (GICs) are often used to produce exfoliated or functionalised graphene related materials (GRMs) in a specific solvent. This study explores the formation of the Na-tetrahydrofuran (THF)-GIC and a new ternary system based on dimethylacetamide (DMAc). Detailed comparisons of in situ temperature dependent XRD with TGA-MS and Raman measurements reveal a series of dynamic transformations during heating. Surprisingly, the bulk of the intercalation compound is stable under ambient conditions, trapped between the graphene sheets. The heating process drives a reorganisation of the solvent and Na molecules, then an evaporation of the solvent; however, the solvent loss is arrested by restacking of the graphene layers, leading to trapped solvent bubbles. Eventually, the bubbles rupture, releasing the remaining solvent and creating expanded graphite. These trapped dopants may provide useful property enhancements, but also potentially confound measurements of grafting efficiency in liquid-phase covalent functionalization experiments on 2D materials.

Antibacterial Surfaces with Activity against Antimicrobial Resistant Bacterial Pathogens and Endospores.

Hospital-acquired bacterial infections are a significant burden on healthcare systems worldwide causing an increased duration of hospital stays and prolonged patient suffering. We show that polyurethane containing crystal violet (CV) and 3-4 nm zinc oxide nanoparticles (ZnO NPs) possesses excellent bactericidal activity against hospital-acquired pathogens including multidrug resistant Escherichia coli (E. coli), Pseudomonas aeruginosa, methicillin-resistant Staphylococcus aureus (MRSA), and even highly resistant endospores of Clostridioides (Clostridium) difficile. Importantly, we used clinical isolates of bacterial strains, a protocol to mimic the environmental conditions of a real exposure in the healthcare setting, and low light intensity equivalent to that encountered in UK hospitals (∼500 lux). Our data shows that ZnO NPs enhance the photobactericidal activity of CV under low intensity light even with short exposure times, and we show that this involves both Type I and Type II photochemical pathways. Interestingly, polyurethane containing ZnO NPs alone showed significant bactericidal activity in the dark against one strain of E. coli, indicating that the NPs possess both light-activated synergistic activity with CV and inherent bactericidal activity that is independent of light. These new antibacterial polymers are potentially useful in healthcare facilties to reduce the transmission of pathogens between people and the environment.

Quantification of blood-brain barrier transport and neuronal toxicity of unlabelled multiwalled carbon nanotubes as a function of surface charge.

Nanoparticles capable of penetrating the blood-brain barrier (BBB) will greatly advance the delivery of therapies against brain disorders. Carbon nanotubes hold great potential as delivery vehicles due to their high aspect-ratio and cell-penetrating ability. Studies have shown multiwalled carbon nanotubes (MWCNT) cross the BBB, however they have largely relied on labelling methods to track and quantify transport, or on individual electron microscopy images to qualitatively assess transcytosis. Therefore, new direct and quantitative methods, using well-defined and unlabelled MWCNT, are needed to compare BBB translocation of different MWCNT types. Using highly controlled anionic (-), cationic (+) and non-ionic (0) functionalized MWCNT (fMWCNT), we correlate UV-visible spectroscopy with quantitative transmission electron microscopy, quantified from c. 270 endothelial cells, to examine cellular uptake, BBB transport and neurotoxicity of unlabelled fMWCNT. Our results demonstrate that: (i) a large fraction of cationic and non-ionic, but not anionic fMWCNT become trapped at the luminal brain endothelial cell membrane; (ii) despite high cell association, fMWCNT uptake by brain endothelial cells is low (<1.5% ID) and does not correlate with BBB translocation, (iii) anionic fMWCNT have highest transport levels across an in vitro model of the human BBB compared to non-ionic or cationic nanotubes; and (iv) fMWCNT are not toxic to hippocampal neurons at relevant abluminal concentrations; however, fMWCNT charge has an effect on carbon nanotube neurotoxicity at higher fMWCNT concentrations. This quantitative combination of microscopy and spectroscopy, with cellular assays, provides a crucial strategy to predict brain penetration efficiency and neurotoxicity of unlabelled MWCNT and other nanoparticle technologies relevant to human health.