We report time- and angle-resolved photoemission spectroscopy (trARPES) measurements on the Sb(111) surface. We observe band- and momentum-dependent binding-energy oscillations in the bulk and ...surface bands driven by $A_{1g}$ and $E_{g}$ coherent phonons. While the bulk band shows simultaneous $A_{1g}$ and $E_{g}$ oscillations, the surface bands show either $A_{1g}$ or $E_{g}$ oscillations. The observed behavior is reproduced by frozen-phonon calculations based on density-functional theory. Furthermore, this evidences the connection between electron-phonon coupling and coherent binding energy dynamics tied to lattice vibration and confirms that band-, momentum-, and mode-dependent electron-phonon coupling can indeed be probed by trARPES in the low fluence limit.
Research in topological matter has expanded to include the Dirac and Weyl semimetals1–10, which feature three-dimensional Dirac states protected by symmetry. Zirconium pentatelluride has been of ...recent interest as a potential Dirac or Weyl semimetal material. Here, we report the results of experiments performed by in situ three-dimensional double-axis rotation to extract the full 4π solid angular dependence of the transport properties. A clear anomalous Hall effect is detected in every sample studied, with no magnetic ordering observed in the system to the experimental sensitivity of torque magnetometry. Large anomalous Hall signals develop when the magnetic field is rotated in the plane of the stacked quasi-two-dimensional layers, with the values vanishing above about 60 K, where the negative longitudinal magnetoresistance also disappears. This suggests a close relation in their origins, which we attribute to the Berry curvature generated by the Weyl nodes.
We report time- and angle-resolved photoemission spectroscopy (trARPES) measurements on the Sb(111) surface. We observe band- and momentum-dependent binding-energy oscillations in the bulk and ...surface bands driven by $A_{1g}$ and $E_{g}$ coherent phonons. While the bulk band shows simultaneous $A_{1g}$ and $E_{g}$ oscillations, the surface bands show either $A_{1g}$ or $E_{g}$ oscillations. The observed behavior is reproduced by frozen-phonon calculations based on density-functional theory. Furthermore, this evidences the connection between electron-phonon coupling and coherent binding energy dynamics tied to lattice vibration and confirms that band-, momentum-, and mode-dependent electron-phonon coupling can indeed be probed by trARPES in the low fluence limit.
Human activities have greatly increased the transport of biologically available nitrogen (N) through watersheds to potentially sensitive coastal ecosystems. Lentie water bodies (lakes and reservoirs) ...have the potential to act as important sinks for this reactive N as it is transported across the landscape because they offer ideal conditions for N burial in sediments or permanent loss via denitrification. However, the patterns and controls on lentie N removal have not been explored in great detail at large regional to global scales. In this paper we describe, evaluate, and apply a new, spatially explicit, annual-scale, global model of lentie N removal called NiRReLa (Nitrogen Retention in Reservoirs and Lakes). The NiRReLa model incorporates small lakes and reservoirs than have been included in previous global analyses, and also allows for separate treatment and analysis of reservoirs and natural lakes. Model runs for the mid-1990s indicate that lentie systems are indeed important sinks for N and are conservatively estimated to remove 19.7 Tg N year⁻¹ from watersheds globally. Small lakes (<50 km²) were critical in the analysis, retaining almost half (9.3 Tg N year⁻¹) of the global total. In model runs, capacity of lakes and reservoirs to remove watershed N varied substantially at the half-degree scale (0-100%) both as a function of climate and the density of lentie systems. Although reservoirs occupy just 6% of the global lentie surface area, we estimate they retain ~33% of the total N removed by lentie systems, due to a combination of higher drainage ratios (catchment surface areailake or reservoir surface area), higher apparent settling velocities for N, and greater average N loading rates in reservoirs than in lakes. Finally, a sensitivity analysis of NiRReLa suggests that, on-average, N removal within lentie systems will respond more strongly to changes in land use and N loading than to changes in climate at the global scale.
Small RNA-guided protein complexes play an essential role in CRISPR-mediated immunity in prokaryotes. While these complexes initiate interference by flagging cognate invader DNA for destruction, ...recent evidence has implicated their involvement in new CRISPR memory formation, called priming, against mutated invader sequences. The mechanism by which the target recognition complex mediates these disparate responses—interference and priming—remains poorly understood. Using single-molecule FRET, we visualize how bona fide and mutated targets are differentially probed by E. coli Cascade. We observe that the recognition of bona fide targets is an ordered process that is tightly controlled for high fidelity. Mutated targets are recognized with low fidelity, which is featured by short-lived and PAM- and seed-independent binding by any segment of the crRNA. These dual roles of Cascade in immunity with distinct fidelities underpin CRISPR-Cas robustness, allowing for efficient degradation of bona fide targets and priming of mutated DNA targets.
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•Cascade exhibits two distinct binding modes that guide interference and priming•Target recognition for interference initiates from the PAM and seed sequence•Stepwise target recognition promotes high fidelity in the interference pathway•Priming is promoted by low-fidelity binding that is independent from PAM and seed
It has remained unknown how the CRISPR effector complex recognizes a mutated viral genome. Using single-molecule fluorescence, Blosser et al. show that E. coli Cascade uses a distinct DNA binding mode to flag mutated targets for updating CRISPR memory.
Abstract
Studying emerging or neglected pathogens is often challenging due to insufficient information and absence of genetic tools. Dual RNA-seq provides insights into host-pathogen interactions, ...and is particularly informative for intracellular organisms. Here we apply dual RNA-seq to
Orientia tsutsugamushi
(Ot), an obligate intracellular bacterium that causes the vector-borne human disease scrub typhus. Half the Ot genome is composed of repetitive DNA, and there is minimal collinearity in gene order between strains. Integrating RNA-seq, comparative genomics, proteomics, and machine learning to study the transcriptional architecture of Ot, we find evidence for wide-spread post-transcriptional antisense regulation. Comparing the host response to two clinical isolates, we identify distinct immune response networks for each strain, leading to predictions of relative virulence that are validated in a mouse infection model. Thus, dual RNA-seq can provide insight into the biology and host-pathogen interactions of a poorly characterized and genetically intractable organism such as Ot.
Bat cells and tissue have elevated basal expression levels of antiviral genes commonly associated with interferon alpha (IFNα) signaling. Here, we show Interferon Regulatory Factor 1 (IRF1), 3, and 7 ...levels are elevated in most bat tissues and that, basally, IRFs contribute to the expression of type I IFN ligands and high expression of interferon regulated genes (IRGs). CRISPR knockout (KO) of IRF 1/3/7 in cells reveals distinct subsets of genes affected by each IRF in an IFN-ligand signaling-dependent and largely independent manner. As the master regulators of innate immunity, the IRFs control the kinetics and maintenance of the IRG response and play essential roles in response to influenza A virus (IAV), herpes simplex virus 1 (HSV-1), Melaka virus/Pteropine orthoreovirus 3 Melaka (PRV3M), and Middle East respiratory syndrome-related coronavirus (MERS-CoV) infection. With its differential expression in bats compared to that in humans, this highlights a critical role for basal IRF expression in viral responses and potentially immune cell development in bats with relevance for IRF function in human biology.
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•IRF1, 3, and 7 are highly expressed in multiple bat tissues and control gene expression•Antiviral IRG expression in bat cells is largely IFN independent•IRF1 and 7 regulate distinct subsets and alter the kinetics/maintenance of IRGs•IRF1, 3, and 7 regulate antiviral responses to IAV/MERS/HSV-1/PRV3M in bat cells
Bats express high levels of antiviral genes in response to synthetic dsRNA, IFN, or virus by the transcription factors IRF1/3/7. Irving et al. show that this induction largely bypasses IFNα/β production and that this may be a method for limiting the inflammation induced by IFN signaling while still restricting virus infection.
Engineered T cells transiently expressing tumor-targeting receptors are an attractive form of engineered T cell therapy as they carry no risk of insertional mutagenesis or long-term adverse ...side-effects. However, multiple rounds of treatment are often required, increasing patient discomfort and cost. To mitigate this, we sought to improve the antitumor activity of transient engineered T cells by screening a panel of small molecules targeting epigenetic regulators for their effect on T cell cytotoxicity. Using a model for engineered T cells targetting hepatocellular carcinoma, we find that short-term inhibition of G9a/GLP increases T cell antitumor activity in in vitro models and an orthotopic mouse model. G9a/GLP inhibition increases granzyme expression without terminal T cell differentiation or exhaustion and results in specific changes in expression of genes and proteins involved in pro-inflammatory pathways, T cell activation and cytotoxicity.
Silicon crystalline samples were exposed to intense single pulses of XUV radiation (λ=13.5nm) what lead to melting and ablation of the surface material. The deformation field around craters along the ...whole thickness of silicon wafers was observed by means of the synchrotron transmission section topography using the beam perpendicular to the surface of the sample. The geometrical shape and depth extension around craters was evaluated based on numerous, dense series of section topographs spaced by 10µm. In the topographs we observed the direct image connected with the boundary of the crater associated with some deformation of the Kato fringes. The evaluated depth extension, different for individual craters, was in the range of 30–100µm. The depth values were confirmed also by evaluations based on the Bragg case section topographs.
It was possible to reproduce the contrast of the craters in transmission section topographs by numerical simulation based on integration of the Takagi–Taupin equations. The damage of the crystal defects connected with craters was approximated as droplet-like inclusions.
•The vicinity of ablation craters induced by XUV FEL radiation was studied.•Disturbed crystal lattice was found below the ablation craters.•The evaluated depth extension was in the range of 30–100µm.•Approximation of droplet-like inclusion was used for numerical simulations.•Melting and recrystallization may be responsible for observed defects.
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