Orthogonal protein decoration of DNA nanostructures based on SpyCatcher–SpyTag interaction

We present an efficient and readily applicable strategy for the covalent ligation of proteins to DNA origami by using the SpyCatcher–SpyTag (SC–ST) connector system. This approach showed orthogonality with other covalent connectors and has been used exemplarily for the immobilization and study of stereoselective ketoreductases to gain insight into the spatial arrangement of enzymes on DNA nanostructures

Accurate quantification of DNA content in DNA hydrogels prepared by rolling circle amplification

Accurate quantification of polymerized DNA in rolling circle amplification (RCA)-based hydrogels is challenging due to the high viscosity of these materials, however, it can be achieved with a photometric nucleotide depletion assay or qPCR. We show that the DNA content strongly depends on the template sequence and correlates with the mechanical properties of the hydrogels

Multiscale Microstructure for Investigation of Cell–Cell Communication

A multiscale polydimethylsiloxane (PDMS) chip is presented, which provides an array of mesoscale open wells for cell culturing and, as unique feature, an array of microscale 1 µm deep channels to fluidically connect neighboring wells. As demonstrated with SH‐SY5Y cells, the small dimensions of the channels prevent migration of the cell soma but allow physical contacts established by the outgrowth of protoplasmic protrusions between cells in adjacent wells. Another important feature is the chip\u27s mountability on solid substrates, such as glass. This enables the use of substrates previously patterned with biomolecules, as demonstrated by DNA‐directed immobilization of proteins inside the reactor wells. Given the versatile addressability of cells, whether through surface‐bound or inkjet‐based administration of bioactive substances, it is believed that the reactor could be used for research in cell–cell communication networks, for example, in neurodegenerative diseases such as Alzheimer\u27s disease

Single-Atom Resolved Fluorescence Imaging of an Atomic Mott Insulator

The reliable detection of single quantum particles has revolutionized the field of quantum optics and quantum information processing. For several years, researchers have aspired to extend such detection possibilities to larger scale strongly correlated quantum systems, in order to record in-situ images of a quantum fluid in which each underlying quantum particle is detected. Here we report on fluorescence imaging of strongly interacting bosonic Mott insulators in an optical lattice with single-atom and single-site resolution. From our images, we fully reconstruct the atom distribution on the lattice and identify individual excitations with high fidelity. A comparison of the radial density and variance distributions with theory provides a precise in-situ temperature and entropy measurement from single images. We observe Mott-insulating plateaus with near zero entropy and clearly resolve the high entropy rings separating them although their width is of the order of only a single lattice site. Furthermore, we show how a Mott insulator melts for increasing temperatures due to a proliferation of local defects. Our experiments open a new avenue for the manipulation and analysis of strongly interacting quantum gases on a lattice, as well as for quantum information processing with ultracold atoms. Using the high spatial resolution, it is now possible to directly address individual lattice sites. One could, e.g., introduce local perturbations or access regions of high entropy, a crucial requirement for the implementation of novel cooling schemes for atoms on a lattice

Histone Deacetylase 9 Activates IKK to Regulate Atherosclerotic Plaque Vulnerability

Rationale: Arterial inflammation manifested as atherosclerosis is the leading cause of mortality worldwide. Genome-wide association studies have identified a prominent role of histone deacetylase 9 (HDAC9) in atherosclerosis and its clinical complications including stroke and myocardial infarction. Objective: To determine the mechanisms linking HDAC9 to these vascular pathologies and explore its therapeutic potential for atheroprotection. Methods and Results: We studied the effects of Hdac9 on features of plaque vulnerability using bone marrow reconstitution experiments and pharmacological targeting with a small molecule inhibitor in hyperlipidemic mice. We further employed two-photon and intravital microscopy to study endothelial activation and leukocyte-endothelial interactions. We show that hematopoietic Hdac9 deficiency reduces lesional macrophage content whilst increasing fibrous cap thickness thus conferring plaque stability. We demonstrate that HDAC9 binds to IKKα and β resulting in their deacetylation and subsequent activation, which drives inflammatory responses in both macrophages and endothelial cells. Pharmacological inhibition of HDAC9 with the class IIa HDAC inhibitor TMP195 attenuates lesion formation by reducing endothelial activation and leukocyte recruitment along with limiting pro-inflammatory responses in macrophages. Transcriptional profiling using RNA-Seq revealed that TMP195 downregulates key inflammatory pathways consistent with inhibitory effects on IKKβ. TMP195 mitigates the progression of established lesions and inhibits the infiltration of inflammatory cells. Moreover, TMP195 diminishes features of plaque vulnerability and thereby enhances plaque stability in advanced lesions. Ex vivo treatment of monocytes from patients with established atherosclerosis reduced the production of inflammatory cytokines including IL-1β and IL-6. Conclusions: Our findings identify HDAC9 as a regulator of atherosclerotic plaque stability and IKK activation thus providing a mechanistic explanation for the prominence of HDAC9 as a vascular risk locus in genome-wide association studies. Its therapeutic inhibition may provide a potent lever to alleviate vascular inflammation

Simultaneous retrieval of atmospheric CO_2 and light path modification from space-based spectroscopic observations of greenhouse gases: methodology and application to GOSAT measurements over TCCON sites

This paper presents an improved photon path length probability density function method that permits simultaneous retrievals of column-average greenhouse gas mole fractions and light path modifications through the atmosphere when processing high-resolution radiance spectra acquired from space. We primarily describe the methodology and retrieval setup and then apply them to the processing of spectra measured by the Greenhouse gases Observing SATellite (GOSAT). We have demonstrated substantial improvements of the data processing with simultaneous carbon dioxide and light path retrievals and reasonable agreement of the satellite-based retrievals against ground-based Fourier transform spectrometer measurements provided by the Total Carbon Column Observing Network (TCCON)

Characterizing model errors in chemical transport modeling of methane: impact of model resolution in versions v9-02 of GEOS-Chem and v35j of its adjoint model

The GEOS-Chem simulation of atmospheric CH$_{4}$ was evaluated against observations from the Thermal and Near Infrared Sensor for Carbon Observations Fourier Transform Spectrometer (TANSO-FTS) on the Greenhouse Gases Observing Satellite (GOSAT), the Atmospheric Chemistry Experiment Fourier Transform Spectrometer (ACE-FTS), and the Total Carbon Column Observing Network (TCCON). We focused on the model simulations at the 4°×5° and 2°×2.5° horizontal resolutions for the period of February–May 2010. Compared to the GOSAT, TCCON, and ACE-FTS data, we found that the 2°×2.5° model produced a better simulation of CH$_{4}$, with smaller biases and a higher correlation to the independent data. We found large resolution-dependent differences such as a latitude-dependent XCH$_{4}$ bias, with higher column abundances of CH$_{4}$ at high latitudes and lower abundances at low latitudes at the 4°×5° resolution than at 2°×2.5°. We also found large differences in CH$_{4}$ column abundances between the two resolutions over major source regions such as China. These differences resulted in up to 30 % differences in inferred regional CH$_{4}$ emission estimates from the two model resolutions. We performed several experiments using 222Rn, 7Be, and CH$_{4}$ to determine the origins of the resolution-dependent errors. The results suggested that the major source of the latitude-dependent errors is excessive mixing in the upper troposphere and lower stratosphere, including mixing at the edge of the polar vortex, which is pronounced at the 4°×5° resolution. At the coarser resolution, there is weakened vertical transport in the troposphere at midlatitudes to high latitudes due to the loss of sub-grid tracer eddy mass flux in the storm track regions. The vertical air mass fluxes are calculated in the model from the degraded coarse-resolution wind fields and the model does not conserve the air mass flux between model resolutions; as a result, the low resolution does not fully capture the vertical transport. This produces significant localized discrepancies, such as much greater CH$_{4}$ abundances in the lower troposphere over China at 4°×5° than at 2°×2.5°. Although we found that the CH$_{4}$ simulation is significantly better at 2°×2.5° than at 4°×5°, biases may still be present at 2°×2.5° resolution. Their importance, particularly in regards to inverse modeling of CH$_{4}$ emissions, should be evaluated in future studies using online transport in the native general circulation model as a benchmark simulation

Strain-engineering of the charge and spin-orbital interactions in Sr2IrO4

In the high spin-orbit coupled Sr2IrO4, the high sensitivity of the ground state to the details of the local lattice structure shows a large potential for the manipulation of the functional properties by inducing local lattice distortions. We use epitaxial strain to modify the Ir-O bond geometry in Sr2IrO4 and perform momentum-dependent Resonant Inelastic X-ray Scattering (RIXS) at the metal and at the ligand sites to unveil the response of the low energy elementary excitations. We observe that the pseudospin-wave dispersion for tensile-strained Sr2IrO4 films displays large softening along the [h,0] direction, while along the [h,h] direction it shows hardening. This evolution reveals a renormalization of the magnetic interactions caused by a strain-driven crossover from anisotropic to isotropic interactions between the magnetic moments. Moreover, we detect dispersive electron-hole pair excitations which shift to lower (higher) energies upon compressive (tensile) strain, manifesting a reduction (increase) in the size of the charge gap. This behavior shows an intimate coupling between charge excitations and lattice distortions in Sr2IrO4, originating from the modified hopping elements between the t2g orbitals. Our work highlights the central role played by the lattice degrees of freedom in determining both the pseudospin and charge excitations of Sr2IrO4 and provides valuable information towards the control of the ground state of complex oxides in the presence of high spin-orbit coupling.Comment: Published in Proceedings of the National Academy of Sciences, September 202