Assessing the Resolution of Methyltransferase-Mediated DNA Optical Mapping

[Image: see text] Interest in the human microbiome is growing and has been, for the past decade, leading to new insights into disease etiology and general human biology. Stimulated by these advances and in a parallel trend, new DNA sequencing platforms have been developed, radically expanding the possibilities in microbiome research. While DNA sequencing plays a pivotal role in this field, there are some technological hurdles that are yet to be overcome. Targeting of the 16S rRNA gene with amplicon sequencing, for instance, is frequently used for sample composition profiling due to its short sample-to-result time and low cost, which counterbalance its low resolution (genus to species level). On the other hand, more comprehensive methods, namely, whole-genome sequencing (WGS) and shallow shotgun sequencing, are capable of yielding single-gene- and functional-level resolution at a higher cost and much higher sample processing time. It goes without saying that the existing gap between these two types of approaches still calls for the development of a fast, robust, and low-cost analytical platform. In search of the latter, we investigated the taxonomic resolution of methyltransferase-mediated DNA optical mapping and found that strain-level identification can be achieved with both global and whole-genome analyses as well as using a unique identifier (UI) database. In addition, we demonstrated that UI selection in DNA optical mapping, unlike variable region selection in 16S amplicon sequencing, is not limited to any genomic location, explaining the increase in resolution. This latter aspect was highlighted by SCCmec typing in methicillin-resistant Staphylococcus aureus (MRSA) using a simulated data set. In conclusion, we propose DNA optical mapping as a method that has the potential to be highly complementary to current sequencing platforms

Cumulative Experience of Educational Assets from Preschool through First Grade and the Social-emotional Well-being of English- and Spanish-Speaking Children

Children’s social and emotional experiences influence brain development and are therefore central to outcomes of behavior, learning, and health. The current study examined associations between children’s cumulative educational assets in the early grades and end of first grade social-emotional outcomes for children from English- and Spanish-speaking families. Data were drawn from a sample of preschool-aged children (N = 1,132) from low-income families in a large, culturally, and linguistically diverse sample followed annually from pre-kindergarten through first grade. A multi-method, multi-informant approach was used to assess predictor and outcome variables. Results indicate overall that cumulative experiences of educational assets (teacher-student interaction and relationships, parent-teacher communication) were associated with indicators of children’s social-emotional well-being and matter in similar ways for children from English- and Spanish-speaking families. However, we did find some evidence of significant interactions of Spanish as a home language with cumulative educational assets on children’s conduct problems and feelings about peers

Microstructured soft devices for the growth and analysis of populations of homogenous multicellular tumor spheroids

: Multicellular tumor spheroids are rapidly emerging as an improved in vitro model with respect to more traditional 2D culturing. Microwell culturing is a simple and accessible method for generating a large number of uniformly sized spheroids, but commercially available systems often do not enable researchers to perform complete culturing and analysis pipelines and the mechanical properties of their culture environment are not commonly matching those of the target tissue. We herein report a simple method to obtain custom-designed self-built microwell arrays made of polydimethylsiloxane or agarose for uniform 3D cell structure generation. Such materials can provide an environment of tunable mechanical flexibility. We developed protocols to culture a variety of cancer and non-cancer cell lines in such devices and to perform molecular and imaging characterizations of the spheroid growth, viability, and response to pharmacological treatments. Hundreds of tumor spheroids grow (in scaffolded or scaffold-free conditions) at homogeneous rates and can be harvested at will. Microscopy imaging can be performed in situ during or at the end of the culture. Fluorescence (confocal) microscopy can be performed after in situ staining while retaining the geographic arrangement of spheroids in the plate wells. This platform can enable statistically robust investigations on cancer biology and screening of drug treatments

Correctly validating results from single molecule data: the case of stretched exponential decay in the catalytic activity of single lipase B molecules

The question of how to validate and interpret correctly the waiting time probability density functions (WT-PDFs) from single molecule data is addressed. It is shown by simulation that when a stretched exponential WT-PDF, with a stretched exponent alfa and a time scale parameter tau, generates the off periods of a two-state trajectory, a reliable recovery of the input WT-PDF from the trajectory is obtained even when the bin size used to define the trajectory, dt, is much larger than the parameter tau. This holds true as long as the first moment of the WT-PDF is much larger than dt. Our results validate the results in an earlier study of the activity of single Lipase B molecules and disprove recent related critique

An embedded interfacial network stabilizes inorganic CsPbI₃ perovskite thin films

The black perovskite phase of CsPbI(3) is promising for optoelectronic applications; however, it is unstable under ambient conditions, transforming within minutes into an optically inactive yellow phase, a fact that has so far prevented its widespread adoption. Here we use coarse photolithography to embed a PbI(2)-based interfacial microstructure into otherwise-unstable CsPbI(3) perovskite thin films and devices. Films fitted with a tessellating microgrid are rendered resistant to moisture-triggered decay and exhibit enhanced long-term stability of the black phase (beyond 2.5 years in a dry environment), due to increasing the phase transition energy barrier and limiting the spread of potential yellow phase formation to structurally isolated domains of the grid. This stabilizing effect is readily achieved at the device level, where unencapsulated CsPbI(3) perovskite photodetectors display ambient-stable operation. These findings provide insights into the nature of phase destabilization in emerging CsPbI(3) perovskite devices and demonstrate an effective stabilization procedure which is entirely orthogonal to existing approaches

A critical assessment on calculating vibrational spectra in nanostructured materials

Vibrational spectroscopy is an omnipresent spectroscopic technique to characterize functional nanostructured materials such as zeolites, metal–organic frameworks (MOFs), and metal–halide perovskites (MHPs). The resulting experimental spectra are usually complex, with both low-frequency framework modes and high-frequency functional group vibrations. Therefore, theoretically calculated spectra are often an essential element to elucidate the vibrational fingerprint. In principle, there are two possible approaches to calculate vibrational spectra: (i) a static approach that approximates the potential energy surface (PES) as a set of independent harmonic oscillators and (ii) a dynamic approach that explicitly samples the PES around equilibrium by integrating Newton’s equations of motions. The dynamic approach considers anharmonic and temperature effects and provides a more genuine representation of materials at true operating conditions; however, such simulations come at a substantially increased computational cost. This is certainly true when forces and energy evaluations are performed at the quantum mechanical level. Molecular dynamics (MD) techniques have become more established within the field of computational chemistry. Yet, for the prediction of infrared (IR) and Raman spectra of nanostructured materials, their usage has been less explored and remain restricted to some isolated successes. Therefore, it is currently not a priori clear which methodology should be used to accurately predict vibrational spectra for a given system. A comprehensive comparative study between various theoretical methods and experimental spectra for a broad set of nanostructured materials is so far lacking. To fill this gap, we herein present a concise overview on which methodology is suited to accurately predict vibrational spectra for a broad range of nanostructured materials and formulate a series of theoretical guidelines to this purpose. To this end, four different case studies are considered, each treating a particular material aspect, namely breathing in flexible MOFs, characterization of defects in the rigid MOF UiO-66, anharmonic vibrations in the metal–halide perovskite CsPbBr3, and guest adsorption on the pores of the zeolite H-SSZ-13. For all four materials, in their guest- and defect-free state and at sufficiently low temperatures, both the static and dynamic approach yield qualitatively similar spectra in agreement with experimental results. When the temperature is increased, the harmonic approximation starts to fail for CsPbBr3 due to the presence of anharmonic phonon modes. Also, the spectroscopic fingerprints of defects and guest species are insufficiently well predicted by a simple harmonic model. Both phenomena flatten the potential energy surface (PES), which facilitates the transitions between metastable states, necessitating dynamic sampling. On the basis of the four case studies treated in this Review, we can propose the following theoretical guidelines to simulate accurate vibrational spectra of functional solid-state materials: (i) For nanostructured crystalline framework materials at low temperature, insights into the lattice dynamics can be obtained using a static approach relying on a few points on the PES and an independent set of harmonic oscillators. (ii) When the material is evaluated at higher temperatures or when additional complexity enters the system, e.g., strong anharmonicity, defects, or guest species, the harmonic regime breaks down and dynamic sampling is required for a correct prediction of the phonon spectrum. These guidelines and their illustrations for prototype material classes can help experimental and theoretical researchers to enhance the knowledge obtained from a lattice dynamics study

Edge stabilization in reduced-dimensional perovskites

Reduced-dimensional perovskites are attractive light-emitting materials due to their efficient luminescence, color purity, tunable bandgap, and structural diversity. A major limitation in perovskite light-emitting diodes is their limited operational stability. Here we demonstrate that rapid photodegradation arises from edge-initiated photooxidation, wherein oxidative attack is powered by photogenerated and electrically-injected carriers that diffuse to the nanoplatelet edges and produce superoxide. We report an edge-stabilization strategy wherein phosphine oxides passivate unsaturated lead sites during perovskite crystallization. With this approach, we synthesize reduced-dimensional perovskites that exhibit 97 ± 3% photoluminescence quantum yields and stabilities that exceed 300 h upon continuous illumination in an air ambient. We achieve green-emitting devices with a peak external quantum efficiency (EQE) of 14% at 1000 cd m-2; their maximum luminance is 4.5 × 104 cd m-2 (corresponding to an EQE of 5%); and, at 4000 cd m-2, they achieve an operational half-lifetime of 3.5 h.This publication is based in part on work supported by an award (KUS-11-009-21) from the King Abdullah University of Science and Technology (KAUST), by the Ontario Research Fund Research Excellence Program, by the Ontario Research Fund (ORF), by the Natural Sciences and Engineering Research Council (NSERC) of Canada, and by the US Department of Navy, Office of Naval Research (Grant Award No. N00014-17-1-2524). H.Y. acknowledges the Research Foundation-Flanders (FWO Vlaanderen) for a postdoctoral fellowship. E.B. gratefully acknowledges financial support by the Research Foundation-Flanders (FWO Vlaanderen). S.B. acknowledges financial support from European Research Council (ERC Starting Grant #815128-REALNANO). M.B.J.R. and J.H. acknowledge the Research Foundation-Flanders (FWO, Grants G.0962.13, G.0B39.15, AKUL/11/14 and G0H6316N), KU Leuven Research Fund (C14/15/053) and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement No. [307523], ERC-Stg LIGHT to M.B.J.R. DFT calculations were performed on the IBM BlueGene Q supercomputer with support from the Southern Ontario Smart Computing Innovation Platform (SOSCIP). M.I.S. acknowledges the Banting Postdoctoral Fellowship program from the Natural Sciences and Engineering Research Council of Canada (NSERC). H.T. acknowledges the Netherlands Organisation for Scientific Research (NWO) for a Rubicon grant (680-50-1511)