Valency and bonding on a larger scaleIn molecular systems, valency describes the number of bonds an atom can make with its neighbors. Larger objects such as colloids can be linked together to make ...connected structures in which the number of connections, or valency, is controlled by the central object. Jones et al. review the two main approaches to creating stiff bonds, based on DNA-based materials synthesis. These approaches allow the construction of molecular-like objects from building blocks much larger than single atoms.Science, this issue 10.1126/science.1260901 For over half a century, the biological roles of nucleic acids as catalytic enzymes, intracellular regulatory molecules, and the carriers of genetic information have been studied extensively. More recently, the sequence-specific binding properties of DNA have been exploited to direct the assembly of materials at the nanoscale. Integral to any methodology focused on assembling matter from smaller pieces is the idea that final structures have well-defined spacings, orientations, and stereo-relationships. This requirement can be met by using DNA-based constructs that present oriented nanoscale bonding elements from rigid core units. Here, we draw analogy between such building blocks and the familiar chemical concepts of "bonds" and "valency" and review two distinct but related strategies that have used this design principle in constructing new configurations of matter.
The rapid expansion of next‐generation sequencing has yielded a powerful array of tools to address fundamental biological questions at a scale that was inconceivable just a few years ago. Various ...genome‐partitioning strategies to sequence select subsets of the genome have emerged as powerful alternatives to whole‐genome sequencing in ecological and evolutionary genomic studies. High‐throughput targeted capture is one such strategy that involves the parallel enrichment of preselected genomic regions of interest. The growing use of targeted capture demonstrates its potential power to address a range of research questions, yet these approaches have yet to expand broadly across laboratories focused on evolutionary and ecological genomics. In part, the use of targeted capture has been hindered by the logistics of capture design and implementation in species without established reference genomes. Here we aim to (i) increase the accessibility of targeted capture to researchers working in nonmodel taxa by discussing capture methods that circumvent the need of a reference genome, (ii) highlight the evolutionary and ecological applications where this approach is emerging as a powerful sequencing strategy and (iii) discuss the future of targeted capture and other genome‐partitioning approaches in the light of the increasing accessibility of whole‐genome sequencing. Given the practical advantages and increasing feasibility of high‐throughput targeted capture, we anticipate an ongoing expansion of capture‐based approaches in evolutionary and ecological research, synergistic with an expansion of whole‐genome sequencing.
Multicomponent nanocrystal superlattices represent an interesting class of material that derives emergent properties from mesoscale structure, yet their programmability can be limited by the ...alkyl-chain-based ligands decorating the surfaces of the constituent nanocrystals. Polymeric ligands offer distinct advantages, as they allow for more precise tuning of the effective size and 'interaction softness' through changes to the polymer's molecular weight, chemical nature, architecture, persistence length and surrounding solvent. Here we show the formation of 10 different binary nanocrystal superlattices (BNSLs) with both two- and three-dimensional order through independent adjustment of the core size of spherical nanocrystals and the molecular weight of densely grafted polystyrene ligands. These polymer-brush-based ligands introduce new energetic contributions to the interparticle potential that stabilizes various BNSL phases across a range of length scales and interparticle spacings. Our study opens the door for nanocrystals to become modular elements in the design of functional particle brush solids with controlled nanoscale interfaces and mesostructures.
Abstract
The spontaneous assembly of chiral structures from building blocks that lack chirality is fundamentally important for colloidal chemistry and has implications for the formation of advanced ...optical materials. Here, we find that purified achiral gold tetrahedron-shaped nanoparticles assemble into two-dimensional superlattices that exhibit planar chirality under a balance of repulsive electrostatic and attractive van der Waals and depletion forces. A model accounting for these interactions shows that the growth of planar structures is kinetically preferred over similar three-dimensional products, explaining their selective formation. Exploration and mapping of different packing symmetries demonstrates that the hexagonal chiral phase forms exclusively because of geometric constraints imposed by the presence of constituent tetrahedra with sharp tips. A formation mechanism is proposed in which the chiral phase nucleates from within a related 2D achiral phase by clockwise or counterclockwise rotation of tetrahedra about their central axis. These results lay the scientific foundation for the high-throughput assembly of planar chiral metamaterials.
Whether two species will co-crystallize depends on the chemical, physical and structural complementarity of the interacting components. Here, by using DNA as a surface ligand, we selectively ...co-crystallize mixtures of two different anisotropic nanoparticles and systematically investigate the effects of nanoparticle size and shape complementarity on the resultant crystal symmetry, microstrain, and effective 'DNA bond' length and strength. We then use these results to understand a more complicated system where both size and shape complementarity change, and where one nanoparticle can participate in multiple types of directional interactions. Our findings offer improved control of non-spherical nanoparticles as building blocks for the assembly of sophisticated macroscopic materials, and provide a framework to understand complementarity and directional interactions in DNA-mediated nanoparticle crystallization.
The work of the contemporary British sociologist Anthony Giddens, and in particular his structuration theory, has been widely cited by Information Systems researchers. This paper presents a critical ...review of the work of Giddens and its application in the Information Systems field. Following a brief overview of Giddens's work as a whole, some key aspects of structuration theory are described, and their implications for Information Systems research discussed. We then identify 331 Information Systems articles published between 1983 and 2004 that have drawn on Giddens's work and analyze their use of structuration theory. Based on this analysis a number of features of structurational research in the Information Systems field and its relationship to Giddens's ideas are discussed. These findings offer insight on Information Systems researchers' use of social theory in general and suggest that there may be significant opportunities for the Information Systems field in pursuing structurational research that engages sympathetically, yet critically, with Giddens's work.
Current heart failure (HF) treatment is based on targeting symptoms and left ventricle dysfunction severity, relying on a common HF pathway paradigm to justify common treatments for HF patients. This ...common strategy may belie an incomplete understanding of heterogeneous underlying mechanisms and could be a barrier to more precise treatments. We hypothesized we could use RNA-sequencing (RNA-seq) in human heart tissue to delineate HF etiology-specific gene expression signatures.
RNA-seq from 64 human left ventricular samples: 37 dilated (DCM), 13 ischemic (ICM), and 14 non-failing (NF). Using a multi-analytic approach including covariate adjustment for age and sex, differentially expressed genes (DEGs) were identified characterizing HF and disease-specific expression. Pathway analysis investigated enrichment for biologically relevant pathways and functions. DCM vs NF and ICM vs NF had shared HF-DEGs that were enriched for the fetal gene program and mitochondrial dysfunction. DCM-specific DEGs were enriched for cell-cell and cell-matrix adhesion pathways. ICM-specific DEGs were enriched for cytoskeletal and immune pathway activation. Using the ICM and DCM DEG signatures from our data we were able to correctly classify the phenotypes of 24/31 ICM and 32/36 DCM samples from publicly available replication datasets.
Our results demonstrate the commonality of mitochondrial dysfunction in end-stage HF but more importantly reveal key etiology-specific signatures. Dysfunctional cell-cell and cell-matrix adhesion signatures typified DCM whereas signals related to immune and fibrotic responses were seen in ICM. These findings suggest that transcriptome signatures may distinguish end-stage heart failure, shedding light on underlying biological differences between ICM and DCM.
DNA programmable assembly has been combined with top-down lithography to construct superlattices of discrete, reconfigurable nanoparticle architectures on a gold surface over large areas. ...Specifically, the assembly of individual colloidal plasmonic nanoparticles with different shapes and sizes is controlled by oligonucleotides containing "locked" nucleic acids and confined environments provided by polymer pores to yield oriented architectures that feature tunable arrangements and independently controllable distances at both nanometer- and micrometer-length scales. These structures, which would be difficult to construct by other common assembly methods, provide a platform to systematically study and control light-matter interactions in nanoparticle-based optical materials. The generality and potential of this approach are explored by identifying a broadband absorber with a solvent polarity response that allows dynamic tuning of visible light absorption.
One of the key challenges facing liquid-phase transmission electron microscopy (TEM) of biological specimens has been the damaging effects of electron beam irradiation. The strongly ionizing electron ...beam is known to induce radiolysis of surrounding water molecules, leading to the formation of reactive radical species. In this study, we employ DNA-assembled Au nanoparticle superlattices (DNA-AuNP superlattices) as a model system to demonstrate that graphene and its derivatives can be used to mitigate electron beam-induced damage. We can image DNA-AuNP superlattices in their native saline environment when the liquid cell window material is graphene, but not when it is silicon nitride. In the latter case, initial dissociation of assembled AuNPs was followed by their random aggregation and etching. Using graphene-coated silicon nitride windows, we were able to replicate the observation of stable DNA-AuNP superlattices achieved with graphene liquid cells. We then carried out a correlative Raman spectroscopy and TEM study to compare the effect of electron beam irradiation on graphene with and without the presence of water and found that graphene reacts with the products of water radiolysis. We attribute the protective effect of graphene to its ability to efficiently scavenge reactive radical species, especially the hydroxyl radicals which are known to cause DNA strand breaks. We confirmed this by showing that stable DNA-AuNP assemblies can be imaged in silicon nitride liquid cells when graphene oxide and graphene quantum dots, which have also recently been reported as efficient radical scavengers, are added directly to the solution. We anticipate that our study will open up more opportunities for studying biological specimens using liquid-phase TEM with the use of graphene and its derivatives as biocompatible radical scavengers to alleviate the effects of radiation damage.
We develop a Bayesian mixed linear model that simultaneously estimates single-nucleotide polymorphism (SNP)-based heritability, polygenicity (proportion of SNPs with nonzero effects), and the ...relationship between SNP effect size and minor allele frequency for complex traits in conventionally unrelated individuals using genome-wide SNP data. We apply the method to 28 complex traits in the UK Biobank data (N = 126,752) and show that on average, 6% of SNPs have nonzero effects, which in total explain 22% of phenotypic variance. We detect significant (P < 0.05/28) signatures of natural selection in the genetic architecture of 23 traits, including reproductive, cardiovascular, and anthropometric traits, as well as educational attainment. The significant estimates of the relationship between effect size and minor allele frequency in complex traits are consistent with a model of negative (or purifying) selection, as confirmed by forward simulation. We conclude that negative selection acts pervasively on the genetic variants associated with human complex traits.
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