Cold suppresses virus accumulation and alters the host transcriptomic response in the turnip mosaic virus ̶ Arabidopsis halleri system.

Since plant viruses cause lifelong infections, virus-plant interactions are exposed to large temperature fluctuations in evergreen perennials. In such circumstances, virus-plant interactions are expected to change significantly between the warm and cold seasons. However, few studies have investigated the effects of cold temperatures on virus-plant interactions.

Discovery of TP0628103: A Highly Potent and Selective MMP-7 Inhibitor with Reduced OATP-Mediated Clearance Designed by Shifting Isoelectric Points.

Matrix metalloproteinase-7 (MMP-7) has been shown to play an important role in pathophysiological processes such as cancer and fibrosis. We previously discovered selective MMP-7 inhibitors by molecular hybridization and structure-based drug design. However, the systemic clearance (CL) of the biologically active lead compound was very high.

Discovery of novel indole derivatives as potent and selective inhibitors of proMMP-9 activation.

Matrix metalloproteinase-9 (MMP-9) is a secreted zinc-dependent endopeptidase that degrades the extracellular matrix and basement membrane of neurons, and then contributes to synaptic plasticity by remodeling the extracellular matrix. Inhibition of MMP-9 activity has therapeutic potential for neurodegenerative diseases such as fragile X syndrome. This paper reports the molecular design, synthesis, and in vitro studies of novel indole derivatives as inhibitors of proMMP-9 activation.

Structure-Based Optimization and Biological Evaluation of Potent and Selective MMP-7 Inhibitors for Kidney Fibrosis.

Matrix metalloproteinase-7 (MMP-7) has been shown to play important roles in pathophysiological processes involved in the development/progression of diseases such as cancer and fibrosis. We discovered selective MMP-7 inhibitors composed of arylsulfonamide, carboxylate, and short peptides by a molecular hybridization approach. These compounds interacted with MMP-7 via multiple hydrogen bonds in the cocrystal structures.

Single-carbon atom transfer to α,β-unsaturated amides from N-heterocyclic carbenes.

Single-carbon atom transfer reactions are lacking in organic synthesis, partly because of the absence of atomic carbon sources under standard solution-phase conditions. We report here that N-heterocyclic carbenes can serve as atomic carbon donors through the loss of a 1,2-diimine moiety. This strategy is applicable to single-carbon atom transfer to α,β-unsaturated amides, which can be converted into homologated γ-lactams through the formation of four single bonds to one carbon center in one operation.

Feasibility study of direct CT lymphangiography in mice: comparison with interstitial CT/MR lymphangiography.

Objectives: To establish a CT lymphangiography method in mice via direct lymph node puncture.

Methods: We injected healthy mice (n = 8) with 50 µl of water-soluble iodine contrast agent (iomeprol; iodine concentration, 350 mg/mL) subcutaneously into the left-rear foot pad (interstitial injection) and 20 µl of the same contrast agent directly into the popliteal lymph node (direct puncture) 2 days later. Additionally, we performed interstitial MR lymphangiography on eight mice as a control group.

Acceleration of knee magnetic resonance imaging using a combination of compressed sensing and commercially available deep learning reconstruction: a preliminary study.

Purpose: To evaluate whether deep learning reconstruction (DLR) accelerates the acquisition of 1.5-T magnetic resonance imaging (MRI) knee data without image deterioration.

Materials And Methods: Twenty-one healthy volunteers underwent MRI of the right knee on a 1.

Discovery of TP0597850: A Selective, Chemically Stable, and Slow Tight-Binding Matrix Metalloproteinase-2 Inhibitor with a Phenylbenzamide-Pentapeptide Hybrid Scaffold.

Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase and a promising target for various diseases, including cancer and fibrosis. Herein, we report the discovery of a novel MMP2-selective inhibitor with high chemical stability and slow tight-binding features. Based on the degradation mechanism of our small-molecule-peptide hybrid , the tripeptide linker {5-aminopentanoic acid [Ape(5)]-Glu-Asp} of was replaced by a shorter linker (γ-D-Glu).

Discovery of Highly Potent and Selective Matrix Metalloproteinase-7 Inhibitors by Hybridizing the S1' Subsite Binder with Short Peptides.

Matrix metalloproteinase-7 (MMP-7) has emerged as a protein playing important roles in both physiological and pathophysiological processes. Despite the growing interest in MMP-7 as a potential therapeutic target for diseases including cancer and fibrosis, potent and selective MMP-7 inhibitors have yet to be identified. Compound , previously reported by Edman and co-workers, binds to the S1' subsite of MMP-7, exhibiting moderate inhibitory activity and selectivity.

DeLTa-Seq: direct-lysate targeted RNA-Seq from crude tissue lysate.

Background: Quantification of gene expression such as RNA-Seq is a popular approach to study various biological phenomena. Despite the development of RNA-Seq library preparation methods and sequencing platforms in the last decade, RNA extraction remains the most laborious and costly step in RNA-Seq of tissue samples of various organisms. Thus, it is still difficult to examine gene expression in thousands of samples.

Discovery of Aryloxyphenyl-Heptapeptide Hybrids as Potent and Selective Matrix Metalloproteinase-2 Inhibitors for the Treatment of Idiopathic Pulmonary Fibrosis.

Matrix metalloproteinase-2 (MMP2) is a zinc-dependent endopeptidase that plays important roles in the degradation of extracellular matrix proteins. MMP2 is considered to be an attractive target for the treatment of various diseases such as cancer, arthritis, and fibrosis. In this study, we have developed a novel class of MMP2-selective inhibitors by hybridizing the peptide that binds to a zinc ion and S2-S5 pockets with small molecules that bind to the S1' pocket.

Fillable and unfillable gaps in plant transcriptome under field and controlled environments.

The differences between plants grown in field and in controlled environments have long been recognized. However, few studies have addressed the underlying molecular mechanisms. To evaluate plant responses to fluctuating environments using laboratory equipment, we developed SmartGC, a high-performance growth chamber that reproduces the fluctuating irradiance, temperature and humidity of field environments.

Chemically robust and readily available quinoline-based PNN iron complexes: application in C-H borylation of arenes.

Iron catalysts have been used for over a century to produce ammonia industrially. However, the use of iron catalysts generally remained quite limited until relatively recently, when the abundance and low toxicity of iron spurred the development of a variety of iron catalysts. Despite the fact that iron catalysts are being developed as alternatives to precious metal catalysts, their reactivities and stabilities are quite different because of their unique electronic structures.

Real-Space Observation of Emergent Complexity of Phase Evolution in Micrometer-Sized IrTe_{2} Crystals.

We report complex behaviors in the phase evolution of transition-metal dichalcogenide IrTe_{2} thin flakes, captured with real-space observations using scanning Raman microscopy. The phase transition progresses via growth of a small number of domains, which is unlikely in statistical models that assume a macroscopic number of nucleation events. Consequently, the degree of phase evolution in the thin flakes is quite variable for the selected specimen and for a repeated measurement sequence, representing the emergence of complexity in the phase evolution.

H3K27me3 demethylases alter HSP22 and HSP17.6C expression in response to recurring heat in Arabidopsis.

Acclimation to high temperature increases plants' tolerance of subsequent lethal high temperatures. Although epigenetic regulation of plant gene expression is well studied, how plants maintain a memory of environmental changes over time remains unclear. Here, we show that JUMONJI (JMJ) proteins, demethylases involved in histone H3 lysine 27 trimethylation (H3K27me3), are necessary for Arabidopsis thaliana heat acclimation.

N-Heterocyclic Carbene-Catalyzed Truce-Smiles Rearrangement of -Arylacrylamides via the Cleavage of Unactivated C(aryl)-N Bonds.

We report on the N-heterocyclic carbene (NHC)-catalyzed Truce-Smiles rearrangement of aniline derivatives, in which an unactivated C(aryl)-N bond is cleaved, leading to the formation of a new C(aryl)-C bond. The key to the success of this reaction is the utilization of a highly nucleophilic NHC, which enables the formation of a highly nucleophilic ylide intermediate that is generated from an α,β-unsaturated amide.

Pepper vein yellows virus 9: a novel polerovirus isolated from chili pepper in Indonesia.

In 2017, a leaf sample from a single chili pepper (Capsicum annuum) plant exhibiting yellowing was collected from Aceh province, Indonesia. Total RNA was extracted from this sample, and RNA-Seq analysis was conducted. Putative infecting viruses were detected by mapping the obtained reads to the full-length viral genome sequences available in the GenBank database (7457 sequences) and the de novo-assembled contigs.

Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors.

The global increase in multidrug-resistant pathogens has caused severe problems in the treatment of infections. To overcome these difficulties, the advent of a new chemical class of antibacterial drug is eagerly desired. We aimed at creating novel antibacterial agents against bacterial type II topoisomerases, which are well-validated targets.

Complete genome sequence of a novel partitivirus from a wild brassicaceous plant, Arabidopsis halleri.

Two contigs with high similarity to partitivirus sequences were identified by de novo assembly of sequences obtained by RNA-Seq from a wild brassicaceous plant, Arabidopsis halleri subsp. gemmifera. Here, we report the complete genome sequence of a putative novel partitivirus.

Nanoscale Imaging of Unusual Photoacoustic Waves in Thin Flake VTe.

The control of acoustic phonons, which are the carriers of sound and heat, has become the focus of increasing attention because of a demand for manipulating the sonic and thermal properties of nanometric devices. In particular, the photoacoustic effect using ultrafast optical pulses has a promising potential for the optical manipulation of phonons in the picosecond time regime. So far, its mechanism has been mostly based on the commonplace thermoelastic expansion in isotropic media, which has limited applicability.

Switching of band inversion and topological surface states by charge density wave.

Topologically nontrivial materials host protected edge states associated with the bulk band inversion through the bulk-edge correspondence. Manipulating such edge states is highly desired for developing new functions and devices practically using their dissipation-less nature and spin-momentum locking. Here we introduce a transition-metal dichalcogenide VTe, that hosts a charge density wave (CDW) coupled with the band inversion involving V3d and Te5p orbitals.

Evolution of Electronic States and Emergence of Superconductivity in the Polar Semiconductor GeTe by Doping Valence-Skipping Indium.

GeTe is a chemically simple IV-VI semiconductor which bears a rich plethora of different physical properties induced by doping and external stimuli. Here, we report a superconductor-semiconductor-superconductor transition controlled by finely-tuned In doping. Our results reveal the existence of a critical doping concentration x_{c}=0.

Seasonality of interactions between a plant virus and its host during persistent infection in a natural environment.

Persistent infection, wherein a pathogen is continually present in a host individual, is widespread in virus-host systems. However, little is known regarding how seasonal environments alter virus-host interaction during such metastability. We observed a lineage-to-lineage infection of the host plant Arabidopsis halleri with Turnip mosaic virus for 3 years without severe damage.

N-Heterocyclic Carbene Catalyzed Concerted Nucleophilic Aromatic Substitution of Aryl Fluorides Bearing α,β-Unsaturated Amides.

Concerted nucleophilic aromatic substitution (CS Ar) has emerged as a powerful mechanistic manifold, in which nucleophilic aromatic substitution can proceed in one step without the need to form a Meisenheimer intermediate. However, all of the CS Ar reactions reported thus far require a stoichiometric strong base or activating reagent, and no catalytic variants have yet been reported. Herein, we report an N-heterocyclic carbene (NHC)-catalyzed intramolecular cyclization of acrylamides that contain a 2-fluorophenyl group on the nitrogen through a CS Ar reaction.

Lasy-Seq: a high-throughput library preparation method for RNA-Seq and its application in the analysis of plant responses to fluctuating temperatures.

RNA-Seq is a whole-transcriptome analysis method used to research biological mechanisms and functions but its use in large-scale experiments is limited by its high cost and labour requirements. In this study, we have established a high-throughput and cost-effective RNA-Seq library preparation method that does not require mRNA enrichment. The method adds unique index sequences to samples during reverse transcription (RT) that is conducted at a higher temperature (≥62 °C) to suppress RT of A-rich sequences in rRNA, and then pools all samples into a single tube.