Metagenomic characterization of sphingomyelinase C in the microbiome of humans and environments.

Bacterial sphingomyelinases (SMases) hydrolyze sphingomyelin and play an important role in membrane dynamics and the host immune system. While the number of sequenced genomes and metagenomes is increasing, a limited number of experimentally validated SMases have been reported, and the genomic diversity of SMases needs to be elucidated extensively. This study investigated the sequence and structural characteristics of SMases in bacterial genomes and metagenomes. Using previously identified SMases, such as the ß-toxin of Staphylococcus aureus, we identified 276 putative SMases and 15 metagenomic SMases by a sequence homology search. Among the predicted metagenomic SMases, six non-redundant metagenomic SMases (M-SMase1-6) were selected for further analysis. The predicted SMases were confirmed to contain highly conserved residues in the central metal-binding site; however, the edge metal-binding site showed high diversity according to the taxon. In addition, protein structure modeling of metagenomic SMases confirmed structural conservation of the central metal-binding site and variance of the edge metal-binding site. From the activity assay on M-SMase2 and M-SMase5, we found that they displayed sphingomyelinase activity compared to Bacillus cereus SMase. This study elucidates a comprehensive genomic characterization of SMases and provides insight into the sequence-structure-activity relationship.

High-Glucose Diet Attenuates the Dopaminergic Neuronal Function in C. elegans, Leading to the Acceleration of the Aging Process.

Parkinson's disease (PD) is a neurodegenerative disease characterized by the selective degeneration of neurons, primarily in the substantia nigra. Environmental or exogenous factors that cause Parkinson's disease have not been sufficiently elucidated. Our study aims to investigate the causative effect of a high-glucose diet on Parkinson's disease-relevant dopaminergic neuronal system in Caenorhabditis elegans. Aging parameters were first observed by measuring the lifespan, body movement, and body sizes with and without the background of high glucose. The toxic effect of a high-glucose diet was further explored by observing the dopaminergic neurons using transgenic Pdat-1::gfp strains, BZ555, under a Zeiss microscope, and the experiments were extended by assessing dopamine-related behavioral analysis including basal slowing response and alcohol avoidance. The aggregation of the α-synucleins was also assessed by observing the NL5901 mutants. Worms fed with 250 mM glucose showed daf-2-independent regulation of aging, displaying a short lifespan (≤15 days), long body size (max. 140%), and slow movement (min. 30%, 10 bends/min). Anterior dopaminergic neurons were rapidly inactivated (70%) by a glucose-rich diet from 12 h of exposure, suggesting specific degeneration in ADE neurons. The dysregulation of neurons led to deteriorations in dopaminergic behaviors including basal slowing response (BSR). A high-glucose diet decreased dopamine synthesis (40 pg/mg vs 15 pg/mg protein) and induced α-synuclein aggregation in the muscles. Results demonstrate the potential of a high-glucose diet as a trigger of dopaminergic neuronal dysregulation conjugating aging acceleration.

Atomic and Electronic Manipulation of Robust Ferroelectric Polymorphs.

Polymorphism allows the symmetry of the lattice and spatial charge distributions of atomically thin materials to be designed. While various polymorphs for superconducting, magnetic, and topological states have been extensively studied, polymorphic control is a challenge for robust ferroelectricity in atomically thin geometries. Here, the atomic and electric manipulation of ferroelectric polymorphs in Mo1- x Wx Te2 is reported. Atomic manipulation for polymorphic control via chemical pressure (substituting tungsten for molybdenum atoms) and charge density modulation can realize tunable polar lattice structures and robust ferroelectricity up to T = 400 K with a constant coercive field in an atomically thin material. Owing to the effective inversion symmetry breaking, the ferroelectric switching withstands a charge carrier density of up to 1.1 × 1013 cm-2 , developing an original diagram for ferroelectric switching in atomically thin materials.

Highly enhanced ferroelectricity in HfO2-based ferroelectric thin film by light ion bombardment.

Continuous advancement in nonvolatile and morphotropic beyond-Moore electronic devices requires integration of ferroelectric and semiconductor materials. The emergence of hafnium oxide (HfO2)-based ferroelectrics that are compatible with atomic-layer deposition has opened interesting and promising avenues of research. However, the origins of ferroelectricity and pathways to controlling it in HfO2 are still mysterious. We demonstrate that local helium (He) implantation can activate ferroelectricity in these materials. The possible competing mechanisms, including He ion-induced molar volume changes, vacancy redistribution, vacancy generation, and activation of vacancy mobility, are analyzed. These findings both reveal the origins of ferroelectricity in this system and open pathways for nanoengineered binary ferroelectrics.

Quantitative Local Probing of Polarization with Application on HfO2 -Based Thin Films.

Owing to their switchable spontaneous polarization, ferroelectric materials have been applied in various fields, such as information technologies, actuators, and sensors. In the last decade, as the characteristic sizes of both devices and materials have decreased significantly below the nanoscale, the development of appropriate characterization tools became essential. Recently, a technique based on conductive atomic force microscopy (AFM), called AFM-positive-up-negative-down (PUND), is employed for the direct measurement of ferroelectric polarization under the AFM tip. However, the main limitation of AFM-PUND is the low frequency (i.e., on the order of a few hertz) that is used to initiate ferroelectric hysteresis. A significantly higher frequency is required to increase the signal-to-noise ratio and the measurement efficiency. In this study, a novel method based on high-frequency AFM-PUND using continuous waveform and simultaneous signal acquisition of the switching current is presented, in which polarization-voltage hysteresis loops are obtained on a high-polarization BiFeO3 nanocapacitor at frequencies up to 100 kHz. The proposed method is comprehensively evaluated by measuring nanoscale polarization values of the emerging ferroelectric Hf0.5 Zr0.5 O2 under the AFM tip.

Unveiling the Origin of Robust Ferroelectricity in Sub-2 nm Hafnium Zirconium Oxide Films.

HfO2-based ferroelectrics are highly expected to lead the new paradigm of nanoelectronic devices owing to their unexpected ability to enhance ferroelectricity in the ultimate thickness scaling limit (≤2 nm). However, an understanding of its physical origin remains uncertain because its direct microstructural and chemical characterization in such a thickness regime is extremely challenging. Herein, we solve the mystery for the continuous retention of high ferroelectricity in an ultrathin hafnium zirconium oxide (HZO) film (∼2 nm) by unveiling the evolution of microstructures and crystallographic orientations using a combination of state-of-the-art structural analysis techniques beyond analytical limits and theoretical approaches. We demonstrate that the enhancement of ferroelectricity in ultrathin HZO films originates from textured grains with a preferred orientation along an unusual out-of-plane direction of (112). In principle, (112)-oriented grains can exhibit 62% greater net polarization than the randomly oriented grains observed in thicker samples (>4 nm). Our first-principles calculations prove that the hydroxyl adsorption during the deposition process can significantly reduce the surface energy of (112)-oriented films, thereby stabilizing the high-index facet of (112). This work provides new insights into the ultimate scaling of HfO2-based ferroelectrics, which may facilitate the design of future extremely small-scale logic and memory devices.

Enhancement of target specificity of CRISPR-Cas12a by using a chimeric DNA-RNA guide.

The CRISPR-Cas9 system is widely used for target-specific genome engineering. CRISPR-Cas12a (Cpf1) is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cas12a has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cas12a activity is improved for therapeutic purposes. Therefore, we investigated off-target cleavage by Cas12a and modified the Cas12a (cr)RNA to address the off-target cleavage issue. We developed a CRISPR-Cas12a that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR-Cas12a and SpCas9 nickase effectively work in the intracellular genome is suggested. Chimeric guide-based CRISPR- Cas12a genome editing with reduced off-target cleavage, and the resultant, increased safety has potential for therapeutic applications in incurable diseases caused by genetic mutations.

Prediction-based highly sensitive CRISPR off-target validation using target-specific DNA enrichment.

CRISPR effectors, which comprise a CRISPR-Cas protein and a guide (g)RNA derived from the bacterial immune system, are widely used for target-specific genome editing. When the gRNA recognizes genomic loci with sequences that are similar to the target, deleterious mutations can occur. Off-target mutations with a frequency below 0.5% remain mostly undetected by current genome-wide off-target detection techniques. Here we report a method to effectively detect extremely small amounts of mutated DNA based on predicted off-target-specific amplification. In this study, we used various genome editors to induce intracellular genome mutations, and the CRISPR amplification method detected off-target mutations at a significantly higher rate (1.6~984 fold increase) than an existing targeted amplicon sequencing method. In the near future, CRISPR amplification in combination with genome-wide off-target detection methods will allow detection of genome editor-induced off-target mutations with high sensitivity and in a non-biased manner.

Significance of electrostatic interactions due to surface potential in piezoresponse force microscopy.

Piezoresponse force microscopy (PFM) has gradually becomes indispensable tool to investigate local piezoelectric and ferroelectric properties in diverse material systems. However, numerous reports have shown that the PFM signal can originate from several non-piezoelectric origins. Among them, because the electrostatic interaction between the AFM tip/cantilever and sample surface can be readily involved, it can be the most important factor during PFM measurement. In particular, in materials with relatively low piezoelectricity, the situation can be more significant because the PFM signals from weak piezoelectricity can be hidden or buried by the electrostatic interactions. Herein, we examined the significance of the electrostatic interactions induced by the surface potential in PFM. Using piezoelectric and non-piezoelectric materials, we examined how the surface potential-dependent electrostatic interactions can significantly affect the PFM signal. We observed that the electrostatically induced PFM amplitude have a linear relationship with the magnitude of surface potential when the instrumental noise floor is properly considered. Our results demonstrate that electrostatic interactions can be significant and their recognition and minimization are essential during PFM and other AFM-based measurements.

A Room-Temperature Ferroelectric Ferromagnet in a 1D Tetrahedral Chain Network.

Ferroelectricity occurs in crystals with broken spatial inversion symmetry. In conventional perovskite oxides, concerted ionic displacements within a 3D network of transition-metal-oxygen polyhedra (MOx ) manifest spontaneous polarization. Meanwhile, some 2D networks of MOx foster geometric ferroelectricity with magnetism, owing to the distortion of the polyhedra. Because of the fundamentally different mechanism of ferroelectricity in a 2D network, one can further challenge an uncharted mechanism of ferroelectricity in a 1D channel of MOx and estimate its feasibility. Here, ferroelectricity and coupled ferromagnetism in a 1D FeO4 tetrahedral chain network of a brownmillerite SrFeO2.5 epitaxial thin film are presented. The result provides a new paradigm for designing low-dimensional MOx networks, which is expected to benefit the realization of macroscopic ferro-ordering materials including ferroelectric ferromagnets.

Ferroelectric Polarization Rotation in Order-Disorder-Type LiNbO3 Thin Films.

The direction of ferroelectric polarization is prescribed by the symmetry of the crystal structure. Therefore, rotation of the polarization direction is largely limited, despite the opportunity it offers in understanding important dielectric phenomena such as piezoelectric response near the morphotropic phase boundaries and practical applications such as ferroelectric memory. In this study, we report the observation of continuous rotation of ferroelectric polarization in order-disorder-type LiNbO3 thin films. The spontaneous polarization could be tilted from an out-of-plane to an in-plane direction in the thin film by controlling the Li vacancy concentration within the hexagonal lattice framework. Partial inclusion of monoclinic-like phase is attributed to the breaking of macroscopic inversion symmetry along different directions and the emergence of ferroelectric polarization along the in-plane direction.

Tunable Out-of-Plane Piezoelectricity in Thin-Layered MoTe2 by Surface Corrugation-Mediated Flexoelectricity.

Piezoelectricity crystallographically exists only in the in-plane direction in two-dimensional transition metal dichalcogenides. Here, we demonstrated flexoelectricity-tunable out-of-plane piezoelectricity in semiconducting 2H-MoTe2 flakes by creating surface corrugation. In particular, the strong out-of-plane piezoelectricity and its spatial variation depending on local flexoelectricity was observed even though crystallographically there exists only in-plane piezoelectricity. Surface corrugation-mediated flexoelectricity tuning can be applied to other two-dimensional or thin-layered materials and, furthermore, the results could provide useful information on the interweaving nature between mechanical stimulus and electric dipole in low-dimensional materials.

CT findings of small cell lung carcinoma: Can recognizable features be found?

The purpose of this study was to clarify the recognizable computed tomography (CT) features of small cell lung carcinoma (SCLC).Contrast enhanced CT scans were reviewed retrospectively for mass location, mediastinal extension, and other concomitant findings in 142 patients with pathologically proven SCLC. SCLC was classified into hilar mass only (type I), hilar mass with ipsilateral mediastinal extension (type II), hilar mass with bilateral mediastinal extension (type III), and peripheral mass (type IV). When mediastinal lymphadenopathy (m-LAP) was indistinguishable from a hilar mass, we defined it as a mediastinal conglomerate mass (m-CM). Type IIa or IIIa had ipsilateral or bilateral m-LAP and type IIb, IIIb or IIIc had ipsilateral or bilateral m-CM.Type I (n = 8, 5.6%), type II (n = 58, 40.8%), type III (n = 55, 38.8%), and type IV (n = 21, 14.8%) were manifested. The combination of a hilar mass and m-CM was found in 68 patients (47.9%). Type IV masses showed lobulation in 11, microlobulation in 4, both lobulated and irregular margins in 4, and spiculation in 2. A total of 120 patients (84.5%) had a bronchial stenosis/obstruction; single (n = 52) and 2 or more (n = 68). Ninety-five patients (67.0%) had vascular invasion including main/lobar pulmonary artery and superior vena cava, and 55 (38.7%) had pleural effusion and/or pleural nodules. Concomitant parenchymal findings (n = 92, 64.8%) were noted: contiguous consolidation/nodule (n = 45), hematogeneous spread (n = 32), lymphangitic spread (n = 21), obstructive pneumonia (n = 22), and obstructive atelectasis (n = 14).In conclusion, the recognizable CT features of SCLC were a hilar mass with m-CM. Most of the hilar masses showed 2 or more bronchial stenoses/obstructions. Most cases of peripheral SCLC manifested as a lobulated mass rather than a spiculated mass. Vascular invasion and concomitant parenchymal findings were observed commonly.

A case of Mayer-Rokitansky-Küster-Hauser syndrome presenting as Graves disease.

The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is a congenital disorder characterized by aplasia of the uterus and the upper part of the vagina in an XX individual with normal development of secondary sexual characteristics. Individuals with this syndrome may also present with renal and skeletal abnormalities. We report a case of a 16-year-old girl presenting with thyrotoxicosis and primary amenorrhea. After being diagnosed with Graves disease, this patient was placed on antithyroid medication. Although her thyroid function normalized, she did not start to menstruate. Therefore, we assessed her primary amenorrhea and diagnosed the patient with MRKH syndrome through pelvic imaging. To our knowledge, an association between Graves disease and MRKH syndrome has not yet been reported.

Humic acid fractionation upon sequential adsorption onto goethite.

Mineral-humic complexes are commonly distributed in natural environments and are important in regulating the transport and retention of hydrophobic organic contaminants in soils and sediments. This study investigated the structural and conformational changes of humic acid (HA) and mineral-HA complexes after sequential HA adsorption by goethite, using UV-visible spectroscopy, high performance size exclusion chromatography (HPSEC), Fourier transform infrared (FT-IR) spectroscopy, and solid-state 13C nuclear magnetic resonance (NMR) spectroscopy. The HA remaining in the solution after adsorption showed low polarity index values ((N+O)/C), which indicates that polar functional moieties are likely to adsorb on the goethite surface. In addition, we observed decreased E4/E6 and E2/E3 ratios of unbound HA with increasing number of coatings, implying that aliphatic rich HA fractions with polar functional moieties readily adsorb to the goethite surface. According to IR spectra, carbohydrate carbon would be the important fractions associated with goethite. NMR spectra provided evidence for HA fractionation during adsorption onto the mineral surface; that is, aliphatic fractions were preferentially adsorbed by goethite while aromatic fractions were left in solution. Relatively small molecular weight (MW) HA fractions had a greater affinity for the goethite surface based on analyses of the HPSEC chromatograms, which differs from the results reported in the literature. Finally, our results suggest that the polar aliphatic fractions of HA were mainly adsorbed to goethite via electrostatic attraction and/or ligand exchange reactions.

Roles of ERK and NF-kappaB in Interleukin-8 Expression in Response to Heat Shock Protein 22 in Vascular Smooth Muscle Cells.

Heat shock proteins (HSPs) serve as molecular chaperones and play a role in cell protection from damage in response to stress stimuli. The aim of this article is to investigate whether HSP22 affects IL-8 expression in vascular smooth muscle cells (VSMCs), and which cellular factors are involved in the HSP-mediated IL-8 induction in that cell type in terms of mitogen activated protein kinase (MAPK) and transcription element. Exposure of aortic smooth muscle cells (AoSMCs) to HSP22 not only enhanced IL-8 release but also induced IL-8 transcript via promoter activation. HSP22 activated ERK and p38 MAPK in AoSMCs. HSP22-induced IL-8 release was inhibited by U0126, but not by SB202190. A mutation in the IL-8 promoter region at the binding site of NF-kappaB, but not AP-1 or C/EBP, impaired promoter activation in response to HSP22. Delivery of IkappaB, but not dominant negative c-Jun, lowered HSP22-induced IL-8 release from AoSMCs. These results suggest that HSP22 induces IL-8 in VSMCs via ERK1/2, and that transcription factor NF-kB may be required for the HSP22-induced IL-8 up-regulation.

Adsorption of dicarboxylic acids by clay minerals as examined by in situ ATR-FTIR and ex situ DRIFT.

The adsorption of dicarboxylic acids by kaolinite and montmorillonite at different pH conditions was investigated using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) and ex situ diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The sorption capacity of montmorillonite was greater than that of kaolinite. Adsorption of dicarboxylic acids (succinic acid, glutaric acid, adipic acid, and azelaic acid) was the highest at pH 4 as compared with those at pH 7 and 9. These results indicate that sorption is highly pH-dependent and related to the surface characteristics of minerals. The aliphatic chain length of the dicarboxylic acids highly influenced the sorption amount at acidic pH, regardless of the clay mineral species: succinic acid [HOOC(CH2)2COOH] < glutaric acid [HOOC(CH2)3COOH] < adipic acid [HOOC(CH2)4COOH] < azelaic acid [HOOC(CH2)7COOH]. With in situ ATR-FTIR analysis, most samples tend to have outer-sphere adsorption with the mineral surfaces at all tested pHs. However, inner-sphere coordination between the carboxyl groups and mineral surfaces at pH 4 was dominant from DRIFT analysis with freeze-dried complex samples. The complexation types, inner- or outer-sphere, depended on dicarboxylic acid species, pH, mineral surfaces, and solvent conditions. From the experimental data, we suggest that organic acids in an aqueous environment prefer to adsorb onto the test minerals by outer-sphere complexation, but inner-sphere complexation is favored under dry conditions. Thus, organic acid binding onto clay minerals under dry conditions is stronger than that under wet conditions, and we expect different conformations and aggregations of sorbed organic acids as influenced by complexation types. In the environment, natural organic material (NOM) may adsorb predominantly on positively charged mineral surfaces at the aqueous interface, which can convert into inner-sphere coordination during dehydration. The stable NOM/mineral complexes formed by frequent wetting-drying cycles in nature may resist chemical/microbial degradation of the NOM, which will affect carbon storage in the environment and influence the sorption of organic contaminants.

Identification of rat urinary and fecal metabolites of a new herbicide, pyribenzoxim.

Rats were treated with pyribenzoxim (O-[2,6-bis[(4,6-dimethoxy-2-pyrimidinyl)oxy]benzoyl]oxime), a new herbicide, to investigate the related metabolites in urine and feces. Metabolites were identified using LC/MS (electrospray ionization) and GC/MS (electron impact ionization) following the relatively simple and rapid extraction and purification procedures. Three metabolites were identified in urine either from oral gavage or intravenous (iv) injection. They were benzophenone oxime (BO), benzophenone oxime glucuronide (BOG), and 2-hydroxy-6-(4,6-dimethoxypyrimidin-2-yloxy)benzoic acid (HDB). Benzophenone oxime was present in larger quantity than BOG and HDB in urine from oral treatment, while the case was opposite in urine from iv treatment. Glucuronide conjugate was confirmed unambiguously by enzyme hydrolysis. 2,6-Bis(4,6-dimethoxypyrimidin-2-yloxy)benzoic acid (KIH-2023) and benzophenone were identified in feces. Benzophenone was confirmed by GC/MS and HPLC/DAD since LC/MS could not produce an ESI spectrum. On the basis of the results obtained, a metabolic map of pyribenzoxim is proposed.

Phenanthrene sorption to sequentially extracted soil humic acids and humins.

Humic substances strongly influence the environmental fate of hydrophobic organic chemicals in soils and sediments. In this study, the sorption of phenanthrene by humic acids (HAs) and humins was examined. HAs were obtained from progressively extracting a soil, eight times with 0.1 M Na4P207 and two times with 0.1 M NaOH solution, and then the residue was separated into two humin fractions by their organic carbon contents. The chemical and structural heterogeneity of the HAs and humins were characterized by elemental analysis, ultraviolet-visible spectroscopy, diffuse reflectance infrared Fourier transform spectroscopy, and solid-state 13C NMR. There were significant chemical and structural differences among the HA fractions and humins; the later extracted HAs had relatively high aliphatic carbons content. All sorption data were fitted to a Freundlich equation, S = K(F)C(N), where S and C are the sorbed and solution-phase concentrations, respectively, and K(F) and N are constants. All of the phenanthrene sorptions were nonlinear, and the nonlinearity decreased with further extractions from 0.90 (first extracted HA) to 0.96 (ninth HA) and was the lowest (0.88) for the higher organic carbon content humin. Phenanthrene sorption coefficient by HAs significantly increased with progressive extractions, being the highest for the humins. For HAs isotherms, a positive trend was observed between the sorption coefficient and the aliphaticity, but a negative relation was shown between the nonlinearity and the aliphaticity and between the sorption capacity and polarity of HAs. Phenanthrene sorption was greatly affected by chemical structure and composition of humic substances, even from a same soil. In addition, polarity of humic substances seems to mainly regulate the magnitude of phenanthrene sorption rather than structure.