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Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.

Chiral induction is an emerging topic of interest in various areas of chemistry because of its relationship to the elusive mechanism of spontaneous symmetry breaking in nature. Buckminsterfullerene (C60 ) with the shape of a highly symmetric truncated icosahedron has rarely been referred for chiral induction due to the difficult symmetry breaking. In this work, we demonstrate that a chiral metal-organic framework (MOF) can provide a key field for chiral induction. C60 could be incorporated into the chiral nanochannels of the MOF using an in situ self-assembly strategy. The circular dichroism spectra of the resulting nanocomposites showed an intense chiral signal in the absorption region of C60 . Experimental and theoretical studies showed that this unprecedented chiral induction of C60 was attributed to hybridization of the molecular orbitals through a close association with the pore surface of the MOF. Our method can endow highly symmetric achiral compounds with chirality, paving the new way toward fabrication of novel chiral nanomaterials.

Signal transduction proteins perceive external stimuli in their sensor module and regulate the biological activities of the effector module, allowing cellular adaptation in response to environmental changes. FixL is a dimeric heme protein kinase that senses the oxygen level in plant root nodules to regulate the transcription of nitrogen fixation genes via the phosphorylation of its cognate transcriptional activator. Dissociation of oxygen from the heme induces conformational changes in the protein, converting it from the inactive form for phosphorylation to the active form. However, how FixL undergoes conformational change to regulate kinase activity upon oxygen dissociation remains poorly understood. Here we report time-resolved ultraviolet resonance Raman spectra showing conformational changes for FixL from Sinorhizobium meliloti. We observed spectral changes with a time constant of about 3 μs, which were oxygen-specific. Furthermore, we found that the conformational changes in the sensor and kinase domains are coupled, enabling allosteric control of kinase activity. Our results demonstrate that concerted structural changes on the microsecond time scale serve as the regulatory switch in FixL.

Ground-level ozone (O3) pollution is a persistent environmental issue that can lead to adverse effects on trees and wood production, thus indicating a need for forestry interventions to mediate O3 effects. We treated hybrid larch (Larix gmelinii var. japonica × L. kaempferi) saplings grown in nutrient-poor soils with 0 or 400 mg L−1 water solutions of the antiozonant ethylenediurea (EDU0, EDU400) and exposed them to ambient O3 (AOZ; 08:00 − 18:00 ≈ 30 nmol mol−1) or elevated O3 (EOZ; 08:00 − 18:00 ≈ 60 nmol mol−1) over three growing seasons. We found that EDU400 protected saplings against most effects of EOZ, which included extensive visible foliar injury, premature senescence, decreased photosynthetic pigment contents and altered balance between pigments, suppressed gas exchange and biomass production, and impaired leaf litter decay. While EOZ had limited effects on plant growth (suppressed stem diameter), it decreased the total number of buds per plant, an effect that was not observed in the first growing season. These results indicate that responses to EOZ might have implications to plant competitiveness, in the long term, as a result of decreased potential for vegetative growth. However, when buds were standardized per unit of branches biomass, EOZ significantly increased the number of buds per unit of biomass, suggesting a potentially increased investment to bud development, in an effort to enhance growth potential and competitiveness in the next growing season. EDU400 minimized most of these effects of EOZ, significantly enhancing plant health under O3-induced stress. The effect of EDU was attributed mainly to a biochemical mode of action. Therefore, hybrid larch, which is superior to its parents, can be significantly improved by EDU under long-term elevated O3 exposure, providing a perspective for enhancing afforestation practices.

Trifluridine/tipiracil (FTD/TPI) is an orally administrated anticancer drug with efficacy validated for patients with metastatic colorectal cancer (mCRC) or gastric cancer. FTD, a key component of FTD/TPI, exerts antitumor effects via its incorporation into DNA. Using specific antibodies against bromodeoxyuridine, FTD incorporation into DNA is detected in tumors and peripheral blood mononuclear cells (PBMC) of patients with mCRC who are administered FTD/TPI. The proportion of FTD‐positive PBMC fluctuates according to the schedule of treatment, although the association between the proportion of FTD‐positive PBMC and the clinical outcomes of patients is unknown. To answer this question, here we monitored the FTD‐positive PBMC of 39 elderly patients with mCRC enrolled in KSCC1602, a single‐arm phase 2 trial of FTD/TPI plus bevacizumab as a first‐line treatment, for 1 month, during the first cycle of treatment. The median values and interquartile ranges of the percentage of FTD‐positive PBMC on days 8, 15, and 29 were 39.3% (30.7%‐52.2%), 66.9% (40.0%‐75.3%), and 13.5% (5.7%‐26.0%), respectively. Receiver operating characteristic analysis revealed that the percentage of FTD‐positive PBMC on day 8 (the end of the first week of treatment) had moderate ability to accurately diagnose the occurrence of severe neutropenia and leukopenia within 1 month (area under the curve = 0.778 [95% confidence interval, 0.554‐0.993]). This result suggests that excess FTD incorporation into PBMC at the initial phase of FTD/TPI plus bevacizumab treatment is a risk factor for early onset of severe hematological adverse events., Severe hematological adverse events were predicted by FTD incorporation into PBMC during the early phase of FTD/TPI plus bevacizumab treatment. However, FTD‐positive PBMC were not associated with prognosis.

Peroxisome proliferator-activated receptor γ (PPARγ) modulators are expected to exert anti-diabetic effects without PPARγ-related adverse effects, such as fluid retention, weight gain, and bone loss. The present study showed that the novel tetrazole derivative KY-903 exerted similar selective PPARγ partial agonist properties to INT-131, a known PPARγ modulator, in transactivation assays, and decreased plasma glucose and triglyceride levels with increases in adiponectin levels in diabetic KK-Ay mice. These effects were similar to those of pioglitazone. Pioglitazone, but not KY-903, increased adipose tissue and heart weights. In pre-adipocytes (3T3-L1), KY-903, in contrast to pioglitazone, increased adiponectin mRNA levels without adipocyte differentiation, indicating anti-diabetic effects via adiponectin without adipogenesis. In ovariectomized rats fed a high-fat diet (OVX/HFD), KY-903 and pioglitazone decreased plasma triglyceride and non-esterified fatty acid levels and increased adiponectin levels, indicating insulin sensitization via adiponectin. KY-903 reduced body weight gain and adipose tissue weight, while pioglitazone increased heart weight and markedly reduced bone mineral density. In mesenchymal stem cell-like ST2 cells, KY-903 slightly reduced osteoblast differentiation without adipocyte differentiation, while pioglitazone markedly reduced it with adipocyte differentiation. In conclusion, KY-903 is a novel PPARγ modulator that exerts anti-diabetic effects without body weight gain or cardiac hypertrophy in diabetic mice and anti-obesity effects with minor bone loss in OVX/HFD, possibly due to increases in adiponectin levels without adipogenesis.

Aims/Introduction We aimed to determine whether glucokinase is required for β‐cell mass expansion induced by high‐starch diet (HSTD)‐feeding, as has been shown in its high‐fat diet‐induced expansion. Materials and Methods Eight‐week‐old male wild‐type (Gck+/+ ) or glucokinase haploinsufficient (Gck+/− ) mice were fed either a normal chow (NC) or an HSTD for 15 weeks. The bodyweight, glucose tolerance, insulin sensitivity, insulin secretion and β‐cell mass were assessed. Results Both HSTD‐fed Gck+/+ and Gck+/− mice had significantly higher bodyweight than NC‐fed mice. Insulin and oral glucose tolerance tests revealed that HSTD feeding did not affect insulin sensitivity nor glucose tolerance in either the Gck+/+ or Gck+/− mice. However, during the oral glucose tolerance test, the 15‐min plasma insulin concentration after glucose loading was significantly higher in the HSTD group than that in the NC group for Gck+/+ , but not for Gck+/− mice. β‐Cell mass was significantly larger in HSTD‐fed Gck+/+ mice than that in NC‐fed Gck+/+ mice. In contrast, the β‐cell mass of the HSTD‐fed Gck+/− mice was not different from that of the NC‐fed Gck+/− mice. Conclusions The results showed that HSTD feeding would increase pancreatic β‐cell mass and insulin secretion in Gck+/+ , but not Gck+/− mice. This observation implies that glucokinase in β‐cells would be required for the increase in β‐cell mass induced by HSTD feeding., Our results indicated that high‐starch diet feeding augmented insulin secretion and increased pancreatic beta‐cell mass in wild‐type mice, but not in the beta cell‐specific glucokinase haploinsufficient mice. These findings demonstrated that glucokinase in beta cells is required for increasing beta cell mass induced by high‐starch diet feeding.

Here we report a bio-adhesive porous organic module (Glue COF) composed of hexagonally packed 1D nanopores based on a covalent organic framework. The nanopores are densely decorated with guanidinium ion (Gu+ ) pendants capable of forming salt bridges with oxyanionic species. Glue COF strongly adheres to biopolymers through multivalent salt-bridging interactions with their ubiquitous oxyanionic species. By taking advantage of its strong bio-adhesive nature, we succeeded in creating a gate that possibly opens the nanopores through a selective interaction with a reporter chemical and releases guest molecules. We chose calmodulin (CaM) as a gating component that can stably entrap a loaded guest, sulforhodamine B (SRB), within the nanopores (CaM COF⊃SRB). CaM is known to change its conformation on binding with Ca2+ ions. We confirmed that mixing CaM COF⊃SRB with Ca2+ resulted in the release of SRB from the nanopores, whereas the use of weakly binding Mg2+ ions resulted in a much slower release of SRB.

It has been over half a century since polyacrylonitrile (PAN)-based carbon fibers were first developed. However, the mechanism of the carbonization reaction remains largely unknown. Structural evolution of PAN during the preoxidation reaction, a stabilization reaction, is one of the most complicated stages because many chemical reactions, including cyclization, dehydration, and cross-linking reactions, simultaneously take place. Here, we report the stabilization reaction of single PAN chains within the one-dimensional nanochannels of metal–organic frameworks (MOFs) to study an effect of interchain interactions on the stabilization process as well as the structure of the resulting ladder polymer (LP). The stabilization reaction of PAN within the MOFs could suppress the rapid generation of heat that initiates the self-catalyzed reaction and inevitably provokes many side-reactions and scission of PAN chains in the bulk state. Consequently, LP prepared within the MOFs had a more extended conjugated backbone than the bulk condition., Accommodation of polyacrylonitrile in MOFs facilitated and regulated the transformation to ladder polymer in the carbonization process.

One hypothesis regarding the cause of diabetic complications is that advanced glycation end products (AGEs) bind to the AGE receptor and induce changes in gene expression. However, what AGEs exist in vivo and how individual AGEs are produced and impact body metabolic process to cause diabetes complications are not understood. We developed a new precise method to measure AGEs using LC-MS/MS with a new column and measured 7 free AGEs, including N(6)-carboxymethyllysine (CML), N(6)-(1-carboxyethyl)- l -lysine (CEL) and N5-(5-hydro-5-methyl-4-imidazolon-2-yl)L-ornithine (MG-H1), in human blood components. Blood was obtained from 9 people, and free AGEs were measured in individual blood components with LC-MS/MS before and after a meal. Free CML and CEL were abundant in erythrocytes, with 92% of free CML and 85% of free CEL localized in erythrocytes. In contrast, 60% of free MG-H1 was distributed in the serum. After the meal, free serum MG-H1 increased, but CML and CEL did not. CML and CEL are mainly distributed in erythrocytes and were not affected by the meal, indicating that they are produced in vivo. However, the main source of MG-H1 is the meal. The effect of genetic polymorphisms on AGEs was also investigated. Low activity type aldehyde dehydrogenase 2 (ALDH2) increased the CML concentration in the blood. This is the first observation that shows that the metabolic process of CML and CEL is different from that of MG-H1 and the effect of ALDH2 SNPs on CML.

Constant mesophyll conductance (gm), and two-resistance gm model (involved in resistances of cell wall and chloroplast), where gm reaches maximum under higher CO2 concentrations, cannot describe the phenomenon that gm decreases with increasing intercellular CO2 concentration (Ci) under relatively higher CO2 concentrations. Yin et al. (2020) proposed a gm model, according to which the ratio of chloroplastic CO2 concentration (Cc) to Ci is constant in the two-resistance gm model, which can describe the decreasing gm with increasing Ci. In the present study, we investigated the relationship between Cc and Ci in leaves of Japanese white birch by using simultaneous measurements of gas exchange and chlorophyll fluorescence under various CO2 concentrations, light intensities, and during progressive drought. Across the range of ambient CO2 from 50 to 1000 μmol mol−1, and light intensities of 50 to 2000 μmol m−2 s−1, measured under well irrigation, the ratio of Cc to Ci kept constant. During the progressive drought, overestimated Ci due to stomatal patchiness and/or cuticular transpiration was empirically corrected (threshold: stomatal conductance

The choice of repair pathways of DNA double-strand breaks (DSBs) is dependent upon the cell cycle phases. While homologous recombination repair (HRR) is active between the S and G2 phases, its involvement in mitotic DSB repair has not been examined in detail. In the present study, we developed a new reporter assay system to detect homology-directed repair (HDR), a major pathway used for HRR, in combination with an inducible DSB-generation system. As expected, the maximal HDR activity was observed in the late S phase, along with minimal activity in the G1 phase and at the G1/S boundary. Surprisingly, significant HDR activity was observed in M phase, and the repair efficiency was similar to that observed in late S phase. HDR was also confirmed in metaphase cells collected with continuous colcemid exposure. ChIP assays revealed the recruitment of RAD51 to the vicinity of DSBs in M phase. In addition, the ChIP assay for gamma-H2AX and phosphorylated DNA-PKcs indicated that a part of M-phase cells with DSBs could proceed into the next G1 phase. These results provide evidence showing that a portion of mitotic cell DSBs are undoubtedly repaired through action of the HDR repair pathway.

Japanese larch (Larix kaempferi (Lamb.) Carr.) and its hybrid are economically important coniferous trees widely grown in the Northern Hemisphere. Ground-level ozone (O3) concentrations have increased since the pre-industrial era, and research projects showed that Japanese larch is susceptible to elevated O3 exposures. Therefore, methodologies are needed to (1) protect Japanese larch against O3 damage and (2) conduct biomonitoring of O3 in Japanese larch forests and, thus, monitor O3 risks to Japanese larch. For the first time, this study evaluates whether the synthetic chemical ethylenediurea (EDU) can protect Japanese larch against O3 damage, in two independent experiments. In the first experiment, seedling communities, simulating natural regeneration, were treated with EDU (0, 100, 200, and 400 mg L−1) and exposed to either ambient or elevated O3 in a growing season. In the second experiment, individually-grown saplings were treated with EDU (0, 200 and 400 mg L−1) and exposed to ambient O3 in two growing seasons and to elevated O3 in the succeeding two growing seasons. The two experiments revealed that EDU concentrations of 200–400 mg L−1 could protect Japanese larch seedling communities and individual saplings against O3-induced inhibition of growth and productivity. However, EDU concentrations ≤ 200 mg L−1 did offer only partial protection when seedling communities were coping with higher level of O3-induced stress, and only 400 mg EDU L−1 fully protected communities under higher stress. Therefore, we conclude that among the concentrations tested the concentration offering maximum protection to Japanese larch plants under high competition and O3-induced stress is that of 400 mg EDU L−1. The results of this study can provide a valuable resource of information for applied forestry in an O3-polluted world.

[Background] Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease related to metabolic syndrome, which can progress to liver cirrhosis. Standard medication has not been established. Pemafibrate is a selective peroxisome proliferatoractivated receptor (PPAR) α modulator. We retrospectively evaluated the efficacy of pemafibrate in patients with NAFLD. [Methods] We retrospectively enrolled 17 patients (ten men, seven women; median age, 63 years; range, 27?81 years). They were all proven to have fatty liver through imaging and had little or no history of drinking (ethanol consumption of < 20 g/day for women and < 30 g/day for men). They were administered pemafibrate from October 2018 to June 2020. [Results] After administration, serum triglyceride (TG) tended to be decreased (300.5 ± 22.5 to 239.5 ± 34.3 mg/dL, P = 0.06). Serum high-density lipoprotein (HDL) cholesterol and low density lipoprotein (LDL) cholesterol levels did not change. ALT was significantly decreased (-47.4%) for six months (57.5 ± 8.8 to 30.3 ± 5.8 U/L, P < 0.01). The values of serum GGT significantly decreased (-48.7%) for sixth months (63.9 ± 10.3 to 32.8 ± 6.6 U/L, P < 0.01). Aspartate aminotransferase (AST) to platelet ratio (APRI), a fibrosis marker, also was significantly decreased in the sixth month (0.7 ± 0.1 to 0.4 ± 0.1, P < 0.05). Body mass index (BMI) and hemoglobin A1c (HbA1c) showed no significant change. [Conclusion] Pemafibrate dramatically ameliorated the values of liver function tests and APRI in patients with NAFLD.

This study evaluated the calcium blooming-reducing effect and the differences of luminal diameter among various-energy virtual monochromatic images (VMIs) using rapid kilovolt-switching dual-energy computed tomography (DECT). Forty-five calcified segments in 31 patients were analyzed. For the analysis, 40- to 140-keV VMIs on both non-contrast CT and coronary CT angiography were generated at 10-keV steps, and calcification size and luminal diameter were measured using CT number profile curve and full-width at half-maximum method. We compared calcification size and luminal diameter on each keV VMIs with those on 70-keV VMI. There was no significant differences among the 40- to 140-keV VMIs regarding calcification size or luminal diameter. The 40- to 140-keV VMIs produced by single-source DECT had no effect on the calcification size or luminal diameter in the coronary artery.

Recent developments in controlling polymer assemblies using metal–organic frameworks (MOFs) are covered in this highlight review. The characteristic features of MOFs are their highly tailorable and...

Indocyanine green (ICG) excretory defect is characterized by an ICG retention rate of more than 50% at 15 min without any other abnormal liver functions. The incidence of ICG excretory defect is 0.007% in the Japanese population. Due to its rarity, the imaging characteristics associated with ICG excretory defect remain unclear. Herein, we present three cases of ICG excretory defect, which showed impaired lesion detectability on gadoxetic acid-enhanced MR imaging (EOB-MRI). In the hepatobiliary phase (HBP) of EOB-MRI, diminished enhancement of the liver parenchyma, prolonged intravascular enhancement, and attenuated gadoxetic acid excretion to the bile duct were observed. Our study also investigated the expression level of organic anion transporting polypeptide (OATP) 1B3 and OATP1B1/1B3, which is related to the uptake of ICG and gadoxetic acid into hepatocytes. All cases showed decreased expression of OATP1B3, which was assumed to be characteristic of ICG excretory defect. The present study indicates that, when patients with ICG excretory defect are evaluated using EOB-MRI, attention should be paid to the impaired lesion detectability in the HBP due to the attenuated gadoxetic acid uptake into the liver parenchyma.

Trifluridine (FTD) is the active component of the nucleoside chemotherapeutic drug trifluridine/tipiracil (FTD/TPI), which is approved worldwide for the treatment of patients with metastatic gastrointestinal cancer. FTD exerts cytotoxic effects via its incorporation into DNA, but FTD has not been detected in the tumor specimens of patients. The purpose of this study was to detect FTD in tumors resected from metastatic colorectal cancer (mCRC) patients who were administered FTD/TPI. Another purpose was to investigate the turnover rate of FTD in tumors and bone marrow in a mouse model. Tumors and normal tissue specimens were obtained from mCRC patients who were administered FTD/TPI or placebo at Kyushu University Hospital. Tumors and bone marrow were resected from mice with peritoneal dissemination treated with FTD/TPI. To detect and quantitate FTD incorporated into DNA, immunohistochemical staining of paraffin-embedded specimens (IHC-p staining) and slot-blot analysis of DNA purified from these tissues were performed using an anti-BrdU antibody. IHC-p staining of proliferation and apoptosis markers was also performed. FTD was detected in metastatic tumors obtained from mCRC patients who were administered FTD/TPI, but who had discontinued the treatment several weeks before surgery. In a peritoneal dissemination mouse model, FTD was still detected in tumors 13 days after the cessation of FTD/TPI treatment, but had disappeared from bone marrow within 6 days. These results indicate that FTD persists longer in tumors than in bone marrow, which may cause a sustained antitumor effect with tolerable hematotoxicity.

Here, we investigate the association and dissociation mechanisms of a typical intrinsically disordered region (IDR), transcriptional activation subdomain of tumor suppressor protein p53 (TAD-p53), with murine double-minute clone 2 protein (MDM2). Using a combination of cycles of association and dissociation parallel cascade molecular dynamics, multiple standard molecular dynamics (MD), and the Markov state model, we were successful in obtaining the lowest free energy structure of the MDM2/TAD-p53 complex as the structure closest to the crystal structure without prior knowledge of the crystal structure. This method also reproduced the experimentally measured standard binding free energy, and the association and dissociation rate constants, requiring only an accumulated MD simulation cost of 11.675 μs even though that actual dissociation occurs on the order of seconds. We identified few complex intermediates with similar free energies; yet TAD-p53 first binds MDM2 as the second lowest free energy intermediate kinetically with >90% of the flux, adopting a conformation similar to that of one of these few intermediates in its monomeric state. Even though the mechanism of the first step has a conformational-selection-type aspect, the second step shows induced-fit-like features and occurs as concomitant dehydration of the interface, side-chain π-π stacking, and main-chain hydrogen-bond formation to complete binding as an α-helix. In addition, dehydration is a key process for the final relaxation process around the complex interface. These results demonstrate that TAD-p53 kinetically selects its initial binding form and then relaxes to complete the binding.

Non-structural protein 15 (Nsp15) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) forms a homo hexamer and functions as an endoribonuclease. Here, we propose that Nsp15 activity may be inhibited by preventing its hexamerization through drug binding. We first explored the stable conformation of the Nsp15 monomer as the global free energy minimum conformation in the free energy landscape using a combination of parallel cascade selection molecular dynamics (PaCS-MD) and the Markov state model (MSM), and found that the Nsp15 monomer forms a more open conformation with larger druggable pockets on the surface. Targeting the pockets with high druggability scores, we conducted ligand docking and identified compounds that tightly bind to the Nsp15 monomer. The top poses with Nsp15 were subjected to binding free energy calculations by dissociation PaCS-MD and MSM (dPaCS-MD/MSM), indicating the stability of the complexes. One of the identified pockets, which is distinctively bound by inosine analogues, may be an alternative binding site to stabilize viral RNA binding and/or an alternative catalytic site. We constructed a stable RNA structure model bound to both UTP and alternative binding sites, providing a reasonable proposed model of the Nsp15/RNA complex.

In this study, we examined the composition of organic constituents of stem woody tissue together with tree growth in Quercus mongolica var. grosseserrata Blume seedlings raised under controlled CO2 and/or O3 concentrations in a Free-Air Concentration Enrichment system. After exposure to ambient air (control), elevated CO2 concentration (550 μmol mol–1 CO2), elevated O3 concentration (double that of the control), and a combination of elevated CO2 and O3 concentrations during a growing season, we measured the diameter and length of stem, and biomass of sampled seedlings and quantified the lignin, extractive, and holocellulose contents of the woody tissue of current-year stems. We confirmed that the growth of seedlings was enhanced under an elevated CO2 concentration condition. In line with this, the extractive content was lower in woody tissue formed under an elevated CO2 concentration than that formed under ambient air, whereas holocellulose content showed an inverse pattern. Elevated O3 concentration itself did not change the organic constituents of the woody tissue, but it reduced the influence of an elevated CO2 concentration. We thus assume that Q. mongolica formed woody tissue with a low extractive content under the high CO2 concentration condition, although this response was possibly mitigated by an elevated O3 concentration. Extractives contains antimicrobial components such as tannins, flavonoids, quinones, and terpenoids. The decrease in extractives within the widely distributed Q. mongolica in East Asia may have a non-negligible impact on C cycling in the future earth with high atmospheric CO2 concentration.

Metal–organic frameworks (MOFs) have recently emerged as a new class of porous materials. Highly ordered and tunable structures of MOFs can serve as a universal platform for controlled polymer synthesis as well as high-precision polymer recognition. In addition, the integration of MOFs and polymers can achieve host–guest synergies, leading to the emergence of intriguing composites with tailored architectures. The integration of MOFs and polymers has provided new aspects for both MOF and polymer chemistry. In this chapter, we highlight recent advances in the hybridization of MOFs and polymers.

Fat mass obesity-associated protein (FTO) is a DNA/RNA demethylase involved in the epigenetic regulation of various genes and is considered a therapeutic target for obesity, cancer, and neurological disorders. Here, we aimed to design novel FTO-selective inhibitors by merging fragments of previously reported FTO inhibitors. Among the synthesized analogues, compound 11b, which merges key fragments of Hz (3) and MA (4), inhibited FTO selectively over alkylation repair homologue 5 (ALKBH5), another DNA/RNA demethylase. Treatment of acute monocytic leukemia NOMO-1 cells with a prodrug of 11b decreased the viability of acute monocytic leukemia cells, increased the level of the FTO substrate N6-methyladenosine in mRNA, and induced upregulation of MYC and downregulation of RARA, which are FTO target genes. Thus, Hz (3)/MA (4) hybrid analogues represent an entry into a new class of FTO-selective inhibitors.

Polyoxometalates (POMs) are oxide cluster anions composed of high-valence early transition metals and are widely used as catalysts. Yet base catalysis of POMs remains an ongoing challenge; group V (V, Nb, and Ta) elements form more negatively charged POMs than group VI (Mo and W) elements, and in particular, polyoxoniobates and polyoxotantalates are known to show strong basicity in solution due to the highly negative surface oxygen atoms. Herein, we report for the first time porous ionic crystals (PICs) comprising Nb or Ta. The PICs are composed of Dawson-type Nb/W or Ta/W mixed-addenda POMs with oxo-centered trinuclear CrIII carboxylates and potassium ions as counter cations to control the crystal structure. Among the PICs, those with Nb or Ta tri-substituted POMs exhibit the highest yield (78–82%) and selectivity (99%) towards the Knoevenagel condensation of benzaldehyde and ethyl cyanoacetate (353 K, 6 h), which is a typical base-catalyzed reaction, as reusable solid catalysts, and they can also catalyze the reaction of other active methylene compounds. A detailed investigation into the crystal structures together with DFT calculations and in situ IR spectroscopy with methanol as a basic probe molecule shows that the exposure of [Nb3O13] or [Ta3O13] units with highly negative surface oxygen atoms to the pore surface of PICs is crucial to the catalytic performance. These findings based on the composition–structure–function relationships show that Nb- and Ta-containing PICs can serve as platforms for rational designing of heterogeneous base catalysts.

Introduction: Sodium-glucose cotransporter 2 inhibitor (SGLT2i) is a medication for type 2 diabetes mellitus (T2DM). Some reports showed SGLT2i improved insulin resistance, however, the effect on insulin resistance is not well established. Hepatic insulin clearance (HIC) is new pathophysiology of T2DM. The effect of SGLT2i on hepatic insulin clearance and insulin resistance is not well known. We investigated the effect of SGLT2i on insulin resistance, insulin secretion, incretins, body composition, and hepatic insulin clearance. Materials and Methods: We conducted a meal tolerance test (MTT), and the hyperinsulinemic-euglycemic clamp in 9 T2DM patients. 50 mg/day ipragliflozin was admitted, MTT and clamp were performed after 4 months. We calculated the postprandial C-peptide AUC to insulin AUC ratio as the HIC. We also measured GLP1, GIP, and glucagon levels during MTT. Results: Body weight, HbA1c, and body composition were not significantly changed after 4 months of treatment. Postprandial glucose, fasting, and postprandial insulin were significantly decreased. The insulin resistance of the glucose clamp was not changed, but HOMA-IR and insulin sensitivity index (ISI) were significantly improved. Incretins and glucagon were not changed. Hepatic insulin clearance was significantly increased, but whole-body insulin clearance was not changed. Fib 4 index and fatty liver index were significantly reduced. HOMA-beta and insulinogenic index was not changed but the C-peptide index was significantly increased. Conclusions: Although patients’ number was small, these results suggest that SGLT2i treatment decreased hepatic insulin resistance, increased hepatic insulin clearance, and decreased hyperinsulinemia, it might protect beta-cell function.

We recently proposed a computational procedure to simulate the dissociation of protein/ligand complexes using the dissociation Parallel Cascade Selection Molecular Dynamics simulation (dPaCS-MD) method and to analyze the generated trajectories using the Markov state model (MSM). This procedure, called dPaCS-MD/MSM, enables calculation of the dissociation free energy profile and the standard binding free energy. To examine whether this method can reproduce experimentally determined binding free energies for a variety of systems, we used it to investigate the dissociation of three protein/ligand complexes: trypsin/benzamine, FKBP/FK506, and adenosine A2A receptor/T4E. First, dPaCS-MD generated multiple dissociation pathways within a reasonable computational time for all the complexes, although the complexes differed significantly in the size of the molecules and in intermolecular interactions. Subsequent MSM analyses produced free energy profiles for the dissociations, which provided insights into how each ligand dissociates from the protein. The standard binding free energies obtained by dPaCS-MD/MSM are in good agreement with experimental values for all the complexes. We conclude that dPaCS-MD/MSM can accurately calculate the binding free energies of these complexes.

To test the effects of elevated CO2 and soil N deficiency on N resorption efficiency (NRE) from senescing leaves in two non-N2-fixing deciduous broadleaved tree species, Japanese oak (Quercus mongolica var. grosseserrata Blume) and Painted maple (Acer mono Maxim. var. glabrum (Lév. Et Van’t.) Hara), potted seedlings were grown in a natural daylight phytotron with either ambient or elevated CO2 conditions (36 Pa and 72 Pa CO2) and with two levels of N (52.5 and 5.25 mg N pot−1 week−1 for high N and low N, respectively). We examined the N content (Nmass) of mature and senescent leaves, as well as photosynthesis and the growth of plants, and calculated both the mass-based NRE (NREmass) and leaf area-based NRE (NREarea). In both species, the Nmass of mature leaves decreased with high CO2 and low N, whereas the leaf mass per area (LMA) increased under elevated CO2, regardless of N treatments. In Q. mongolica, both the maximum rate of carboxylation (Vcmax) and the maximum electron transport rate (Jmax) were reduced by elevated CO2 and low N, but Vcmax exhibited an interactive effect of N and CO2 treatments. However, in A. mono, both the Vcmax and Jmax decreased under elevated CO2, regardless of N treatments. The partitioning of N for the photosynthetic function within leaves was also significantly decreased by elevated CO2 in both species and increased under low N in A. mono. The Nmass of senesced leaves decreased under low N in both species and exhibited an increase (Q. mongolica) or no effect (A. mono) by elevated CO2. The NREarea of Q. mongolica was affected by CO2 and N treatments, with a decrease under elevated CO2 compared to ambient CO2 and under low N compared to high N. The NREarea of A. mono was also affected by CO2 and N treatments and decreased under elevated CO2, however, unlike in the case of Q. mongolica, it increased under low N. We speculate that these interspecific differences in the responses of leaf N allocation, indicated by the photosynthetic (Vcmax and Jmax) and morphological (LMA) responses to elevated CO2, may have affected the NRE during defoliation under high CO2 and soil N-deficient conditions.

Eleven isostructural mesoporous ionic crystals (meso-PICs) are synthesized. The initial activities of the Barbier-Grignard reaction, which is a typical C-C bond formation reaction, catalyzed by the meso-PICs are dependent on the acid dissociation constant of the aqua ions of Mn+ and the types of polyoxometalates, which construct the meso-PICs.

Here, we report an unprecedented chirality transfer from a metal-organic framework (MOF) to a polymer. In this work, unsubstituted polythiophene (PTh) was prepared in the nanochannels of a chiral MOF. Circular dichroism spectroscopy revealed that nanoconfinement of the polymer chains could endow optically inactive PTh with a chiral nature. The thickness of polymer chain assemblies could be controlled by tuning the loading amount of PTh, which resulted in a drastic change in the chiroptical properties. Note that PTh liberated from the host still exhibited chirality even without the chiral support. Remarkably, the recovered PTh presented high thermal stability of chirality up to 250 °C. Our findings show that the encapsulation of the polymer chains in chiral MOFs is a simple and effective methodology not only to express the chirality of polymers but also to elucidate the inter- and intrachain chirality in polymer assemblies.

A novel series of 2,6,7-substituted 3-unsubstituted 1,2,3,4-tetrahydroisoquinoline derivatives were synthesized to find a peroxisome proliferator-activated receptor γ (PPARγ) partial agonist. Among the derivatives, (E)-7-[2-(cyclopent-3-eny)-5-methyloxazol-4-ylmethoxy]-2-[3-(2-furyl)acryloyl]-6-(1H-tetrazol-5-yl)-1,2,3,4-tetrahydroisoquinoline (20g) exhibited potent partial agonist activity (EC50 = 13 nM, maximal response 30%) and very weak protein tyrosine phosphatase 1B (PTP1B) inhibition (IC50 = 1100 nM), indicating a selective PPARγ partial agonist. A computational docking calculation revealed that 20g bound to PPARγ in a similar manner to that of known partial agonists. In male and female KK-Ay mice with insulin resistance and hyperglycemia, 20g at 30 mg/kg for 7 d significantly reduced plasma glucose levels, but not triglyceride levels. The effects of 20g were similar to those of pioglitazone at 10 mg/kg. In conclusion, the 2,6,7-substituted 1,2,3,4-tetrahydroisoquinoline with an acidic group at the 6-position provides a novel scaffold for selective PPARγ partial agonists and 20g exerted anti-diabetic effects via the partial activation of PPARγ.

Objective To explore the beneficial effects of dapagliflozin and/or insulin glargine on the pancreatic beta cell mass and hepatic steatosis in db/db mice. Methods Six-week-old db/db mice were assigned to one of four groups: untreated (Placebo), treated with dapagliflozin (Dapa), treated with insulin glargine (Gla), or treated with dapagliflozin and insulin glargine (Dapa+Gla). After 8 weeks of treatment, we determined glucose tolerance, beta cell mass, hepatic lipid content and gene expression. Results Glucose tolerance was significantly ameliorated in the three treated groups to the same degree compared with the Placebo group. Immunohistochemical analysis revealed that the pancreatic beta cell mass was significantly maintained in the Dapa and Dapa+Gla groups, but not in the Gla group, compared with the Placebo group (Placebo 2.25 ± 1.44 mg, Dapa 5.01 ± 1.63 mg, Gla 3.79 ± 0.96 mg, Dapa+Gla 5.19 ± 1.78 mg). However, the triglyceride content of the liver was markedly elevated in the Gla group compared with that in the other three groups (Placebo 24.1 ± 11.5 mg, Dapa 30.6 ± 12.9 mg, Gla 128 ± 49.7 mg, Dapa+Gla 54.4 ± 14.1 mg per gram liver). The expression levels of genes related to fatty acid synthesis and lipid storage were significantly upregulated in the Gla group. Conclusions Our results showed that beta cell mass was sustained and hepatic steatosis was prevented, after 8 weeks of treatment with either dapagliflozin or dapagliflozin plus insulin glargine, but not with insulin glargine alone, in db/db mice.

The bacterial flagellar motor is a unique supramolecular complex which converts ion flow into rotational force. Many biological devices mainly use two types of ions, proton and sodium ion. This is probably because of the fact that life originated in seawater, which is rich in protons and sodium ions. The polar flagellar motor in Vibrio is coupled with sodium ion and the energy converting unit of the motor is composed of two membrane proteins, PomA and PomB. It has been shown that the ion binding residue essential for ion transduction is the conserved aspartic acid residue (PomB-D24) in the PomB transmembrane region. To reveal the mechanism of ion selectivity, we identified essential residues, PomA-T158 and PomA-T186, other than PomB-D24, in the Na+-driven flagellar motor. It has been shown that the side chain of threonine contacts Na+ in Na+-coupled transporters. We monitored the Na+-binding specific structural changes using ATR-FTIR spectroscopy. The signals were abolished in PomA-T158A and -T186A, as well as in PomB-D24N. Molecular dynamics simulations further confirmed the strong binding of Na+ to D24 and showed that T158A and T186A hindered the Na+ binding and transportation. The data indicate that two threonine residues (PomA-T158 and PomA-T186), together with PomB-D24, are important for Na+ conduction in the Vibrio flagellar motor. The results contribute to clarify the mechanism of ion recognition and conversion of ion flow into mechanical force.

This paper proposes a novel molecular simulation method, called tree search molecular dynamics (TS-MD), to accelerate the sampling of conformational transition pathways, which require considerable computation. In TS-MD, a tree search algorithm, called upper confidence bounds for trees, which is a type of reinforcement learning algorithm, is applied to sample the transition pathway. By learning from the results of the previous simulations, TS-MD efficiently searches conformational space and avoids being trapped in local stable structures. TS-MD exhibits better performance than parallel cascade selection molecular dynamics, which is one of the state-of-the-art methods, for the folding of miniproteins, Chignolin and Trp-cage, in explicit water.

The softness and rigidity of proteins are reflected in the structural dynamics, which are in turn affected by the environment. The characteristic low-frequency vibrational spectrum of a protein, known as boson peak, is an indication of the structural rigidity of the protein at a cryogenic temperature or dehydrated conditions. In this article, the effect of hydration, temperature, and pressure on the boson peak and volumetric properties of a globular protein are evaluated by using inelastic neutron scattering and molecular dynamics simulation. Hydration, pressurization, and cooling shift the boson peak position to higher energy and depress the peak intensity and decreases the protein and cavity volumes. We found the correlation between the boson peak and cavity volume in a protein. A decrease of cavity volume means the increase of rigidity, which is the origin of the boson peak shift. Boson peak is the universal property of a protein, which is rationalized by the correlation.

The NAD+-dependent deacetylase SIRT2 represents an attractive target for drug development. Here, we designed and synthesized drug-like SIRT2-selective inhibitors based on an analysis of the putative binding modes of recently reported SIRT2-selective inhibitors and evaluated their SIRT2-inhibitory activity. This led us to develop a more drug-like diketopiperazine structure as a "hydrogen bond (H-bond) hunter" to target the substrate-binding site of SIRT2. Thioamide 53, a conjugate of diketopiperazine and 2-anilinobenzamide which is expected to occupy the "selectivity pocket" of SIRT2, exhibited potent SIRT2-selective inhibition. Inhibition of SIRT2 by 53 was mediated by the formation of a 53-ADP-ribose conjugate, suggesting that 53 is a mechanism-based inhibitor targeting the "selectivity pocket", substrate-binding site, and NAD+-binding site. Furthermore, 53 showed potent antiproliferative activity toward breast cancer cells and promoted neurite outgrowth of Neuro-2a cells. These findings should pave the way for the discovery of novel therapeutic agents for cancer and neurological disorders.

Trifluridine (FTD), a tri-fluorinated thymidine analogue, is a key component of the oral antitumor drug FTD/TPI (also known as TAS-102), which is used to treat refractory metastatic colorectal cancer. Thymidine kinase 1 (TK1) is thought to be important for the incorporation of FTD into DNA, resulting in DNA dysfunction and cytotoxicity. However, it remains unknown whether TK1 is essential for FTD incorporation into DNA and whether this event is affected by the expression level of TK1 because TK1-specific-deficient human cancer cell lines have not been established. Here, we generated TK1-knock-out human colorectal cancer cells using the CRISPR/Cas9 genome editing system and validated the specificity of TK1 knock-out by measuring expression of AFMID, which is encoded on the same locus as TK1. Using TK1-knock-out cells, we confirmed that TK1 is essential for cellular sensitivity to FTD. Furthermore, we demonstrated a correlation between the TK1 expression level and cytotoxicity of FTD using cells with inducible TK1 expression, which were generated from TK1-knock-out cells. Based on our finding that the TK1 expression level correlates with sensitivity to FTD, we suggest that FTD/TPI might efficiently treat cancers with high TK1 expression.

Although deciduous and evergreen conifers are expected to utilize needle nitrogen differently, their interspecific differences in the ozone sensitivity remain unclear. We compared the growth and physiological responses to elevated O3 concentrations in deciduous Japanese larch (Larix kaempferi) and evergreen Sakhalin fir (Abies sachalinensis) seedlings. Seedlings of both species were exposed to 62.5 ± 1.95 nmol(O3) mol-1 during the day time in open-top chambers. Elevated O3 had no effect on height or diameter growth in either of the species but suppressed photosynthetic parameters. A decline in photosynthetic nitrogen-use efficiency was observed in both species. However, needle N content in larch was decreased by O3, whereas it was not decreased in fir. Needle N responses to O3 were different between larch and fir seedlings, indicating that the O3 sensitivity of photosynthesis could vary depending on needle N dynamics. We also observed a higher correlation between photosynthesis and needle N even under O3 exposure, particularly in the mass-based relationship with higher accuracy. The result indicated that mass-based needle N could explain difference in O3 sensitivity of photosynthesis between the different leaf habits in larch and fir seedlings.

Ammonium sulfate [(NH4)2SO4] deposition and elevated ozone (O3) concentrations may negatively affect plants and trophic interactions. This study aimed to evaluate for the first time the interactive effects of high (NH4)2SO4 load and elevated O3 levels on cauliflower (Brassica oleracea L.) under field conditions. Cauliflower seedlings were treated with 0 (AS0) or 50 (AS50) kg ha−1 (NH4)2SO4 and exposed to ambient (AOZ, ≈20 ppb) or elevated (EOZ, ≈55 ppb) O3 for about one month, in a Free Air O3 Concentration Enrichment (FACE) system. The oligophagous diamondback moth (Plutella xylostella Linnaeus, 1758) showed a clear preference towards the seedlings treated with AS50, which intensively grazed. Plant-herbivore interactions were driven by (NH4)2SO4 availability, rather than O3, via increased nitrogen content in the leaves. Further laboratory bioassays were followed to confirm the validity of these observations using polyphagous Eri silkmoth larvae (Samia ricini) as a biological model in a standardized experimental setup. Choice assays, where larvae could select leaves among leaf samples from the different experimental conditions, and no-choice assays, where larvae could graze leaves from just one experimental condition, were conducted. In the choice assay, the larvae preferred AS50-treated leaves, in agreement with the field observations with diamondback moth. In the no-choice assay, larval body mass growth was inhibited when fed with leaves treated with EOZ and/or AS50. Larvae fed with AS50-treated leaves displayed increased mortality. These observations coincide with higher NO3 and Zn content in AS50-treated leaves. This study shows that plant-herbivore interactions can be driven by (NH4)2SO4 availability, independently of O3, and suggests that high N deposition may have severe health implications in animals consuming such plant tissues. Key message: Plant-herbivore interactions are driven by high (NH4)2SO4 availability, independently of O3.

Objectives The aim of this study was to evaluate the feasibility of myocardial iodine density and extracellular volume fraction (ECV) from delayed iodine density images using dual-energy computed tomography (DECT) for differentiation between non-ischemic dilated cardiomyopathy (NIDCM) patients and normal subjects. Methods Forty-six subjects were imaged, including 35 normal subjects and 11 patients with NIDCM. All subjects underwent myocardial delayed enhancement (MDE) imaging on rapid-kVp switching DECT. Global and segmental iodine density and ECV were calculated from MDE images. Histogram analysis was also performed. Receiver-operator characteristic (ROC) analysis was used to determine the cut-off value and diagnostic performances in differentiating NIDCM patients from normal subjects. Results Global iodine density and ECV were significantly higher in NIDCM compared with normal controls (iodine: 14.19 ± 3.90 vs. 10.69 ± 1.88 in 100 μg/cm3, p = 0.015; ECV: 31.35 ± 2.53% vs. 26.62 ± 2.69%, p Conclusions Iodine density and ECV values from DECT may provide indices offering high diagnostic accuracy for discriminating between NIDCM and normal myocardium.

Matured hop bitter acids (MHBA) are oxidation products from bitter components in hops, which are used widely as food materials to add flavor and bitterness in beer production. Our previous study has shown that MHBA induces thermogenesis in brown adipose tissue (BAT) via sympathetic nerves in rodents and reduces body fat in healthy adults. However, it is unclear how MHBA affects the sympathetic nervous system. In this study, we demonstrate that MHBA treatment of enteroendocrine cells increases Ca2+ levels and induces the secretion of the gastrointestinal hormone, cholecystokinin (CCK), in a dose-dependent manner. These effects were eliminated by Ca2+ depletion from the medium or blockers of L-type voltage-sensitive Ca2+ channels during pretreatment. Induction of CCK secretion by MHBA was also confirmed using isolated rat small intestines. Elevation of the sympathetic nerve activity innervating BAT (BAT-SNA) and BAT temperature by MHBA administration in rats was blocked by pretreatment with a CCK receptor 1 (CCK1R) antagonist. Moreover, the intraperitoneal injection of CCK fragment elevated BAT-SNA, and this increase was blocked by subdiaphragmatic vagotomy. These results demonstrate that MHBA induces CCK secretion in the gastrointestinal tracts and elevates BAT-SNA via CCK1R and vagal afferent nerves. In addition, MHBA increases BAT temperature via CCK1R. Our findings reveal a novel mechanism of the beneficial metabolic effects of food ingredients.

The flagellar type III secretion system (fT3SS) transports flagellar building blocks from the cytoplasm to the distal end of the growing flagellar structure. The C-terminal cytoplasmic domain of FlhA (FlhAC) serves as a docking platform for flagellar chaperones in complex with their cognate substrates and ensures the strict order of protein export for efficient flagellar assembly. FlhAC adopts open and closed conformations, and the chaperones bind to the open form, allowing the fT3SS to transport the substrates to the cell exterior. To clarify the role of the closed form in flagellar protein export, we isolated pseudorevertants from the flhA(G368C/K549C) mutant, in which the closed conformation is stabilized to inhibit the protein transport activity of the fT3SS. Each of M365I, R370S, A446E and P550S substitutions in FlhAC identified in the pseudorevertants affected hydrophobic side-chain interaction networks in the closed FlhAC structure, thereby restoring the protein transport activity to a considerable degree. We propose that a cyclic open-close domain motion of FlhAC is required for rapid and efficient flagellar protein export where a structural transition from the open to the closed form induces the dissociation of empty chaperones from FlhAC.

The latex agglutination test is employed to visualize antigen–antibody reactions through the aggregation of antibody-coated particles in the presence of an antigen. In the present study, we developed an ultrasound scattering technique to detect latex agglutination in an optically turbid media. However, the ultrasonic technique had less sensitivity to the dilute particle suspension than the optical techniques because of its wavelength. Therefore, we applied a time-correlation approach to detect small amounts of these aggregates using a sophisticated noise correction algorithm in the frequency domain. The lowest concentration of avidin used to detect aggregations of the biotin-coated particle using the ultrasound scattering technique was found to be 0.625 μg/ml. Furthermore, since the density differences between the particle and liquid were larger for silica suspensions than for polystyrene (PS) suspensions, a larger signal was proposed to be expected from silica suspensions. Nevertheless, it was found that latex agglutinations with the PS particle were more sensitive than those with the silica particles. The dynamic ultrasound scattering analysis along the sedimentation direction also supported the presence of strongly scattered intensity components of the PS aggregates, which is proposed to be due to the resonance scattering from PS spherical particles. Therefore, this technique can be employed to enhance scattering signals from particles for application in the agglutination test using ultrasound.

Plant growth is not solely determined by the net photosynthetic rate (A), but also influenced by the amount of leaves as a photosynthetic apparatus. To evaluate growth responses to CO2 and O3, we investigated the effects of elevated CO2 (550–560 µmol mol−1) and O3 (52 nmol mol−1, 1.7 × ambient O3) on photosynthesis and biomass allocation in seedlings of Japanese white birch (Betula platyphylla var. japonica) grown in a free-air CO2 and O3 exposure system without any limitation of root growth. Total biomass was enhanced by elevated CO2 but decreased by elevated O3. The ratio of root to shoot (R:S ratio) showed no difference among the treatment combinations, suggesting that neither elevated CO2 nor elevated O3 affected biomass allocation in the leaf. Accordingly, photosynthetic responses to CO2 and O3 might be more important for the growth response of Japanese white birch. Based on A measured under respective growth CO2 conditions, light-saturated A at a light intensity of 1500 µmol m−2 s−1 (A1500) in young leaves (ca. 30 days old) exhibited no enhancement by elevated CO2 in August, suggesting photosynthetic acclimation to elevated CO2. However, lower A1500 was observed in old leaves (ca. 60 days old) of plants grown under elevated O3 (regulated to be twice ambient O3). Conversely, light-limited A measured under a light intensity of 200 µmol m−2 s−1 (A200) was significantly enhanced by elevated CO2 in young leaves, but suppressed by elevated O3 in old leaves. Decreases in total biomass under elevated O3 might be attributed to accelerated leaf senescence by O3, indicated by the reduced A1500 and A200 in old leaves. Increases in total biomass under elevated CO2 might be attributed to enhanced A under high light intensities, which possibly occurred before the photosynthetic acclimation observed in August, and/or enhanced A under limiting light intensities.

Cell-penetrating peptides have important therapeutic applications in drug delivery, but the variety of known cell-penetrating peptides is still limited. With a promise to accelerate peptide development, artificial intelligence (AI) techniques including deep generative models are currently in spotlight. Scientists, however, are often overwhelmed by an excessive number of unannotated sequences generated by AI and find it difficult to obtain insights to prioritize them for experimental validation. To avoid this pitfall, we leverage molecular dynamics (MD) simulations to obtain mechanistic information to prioritize and understand AI-generated peptides. A mechanistic score of permeability is computed from five steered MD simulations starting from different initial structures predicted by homology modelling. To compensate for variability of predicted structures, the score is computed with sample variance penalization so that a peptide with consistent behaviour is highly evaluated. Our computational pipeline involving deep learning, homology modelling, MD simulations and synthesizability assessment generated 24 novel peptide sequences. The top-scoring peptide showed a consistent pattern of conformational change in all simulations regardless of initial structures. As a result of wet-lab-experiments, our peptide showed better permeability and weaker toxicity in comparison to a clinically used peptide, TAT. Our result demonstrates how MD simulations can support de novo peptide design by providing mechanistic information supplementing statistical inference.

The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the Fe(II) active site to form a highly reactive Fe(IV) = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-Fe(IV) = O intermediate and characterized its structure as a Fe(II)-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate–bound ternary Fe(II) active site before the O(2) reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of Fe(IV) = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the Fe(II) site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the Fe(II) site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.

Efficacy of glucokinase activation on glycemic control is limited to a short-term period. One reason might be related with the excess glucose signalling by glucokinase activation towards beta-cells. In this study, we investigated the effect of glucokinase haploinsufficiency on glucose tolerance as well as beta-cell function and mass using a mouse model of type 2 diabetes. Our results showed that db/db mice with glucokinase haploinsufficiency presented amelioration of glucose tolerance by augmented insulin secretion associated with the increase in beta-cell mass when compared with db/db mice. Gene expression profiling, and immunohistochemical and metabolomic analyses revealed that glucokinase haploinsufficiency in the islets of db/db mice was associated with lower expression of stress-related genes, higher expression of transcription factors involved in the maintenance and maturation of beta-cell function, less mitochondrial damage, and a superior metabolic pattern. These effects of glucokinase haploinsufficiency could preserve beta-cell mass under diabetic conditions. These findings verified our hypothesis that optimizing excess glucose signalling in beta-cells by inhibiting glucokinase could prevent beta-cell insufficiency, leading to improving glucose tolerance in diabetes status by preserving beta-cell mass. Therefore, glucokinase inactivation in beta-cells could, paradoxically, be a potential strategy for the treatment of type 2 diabetes.

Synthesis of a metal–organic framework by plasma in liquid was demonstrated with HKUST-1 as an example. HKUST-1 synthesized by this method contains a higher amount of monovalent copper ions than that synthesized by other conventional methods. The enhanced water stability was also confirmed.

Evaluations of ozone effects on vegetation across the globe over the last seven decades have mostly incorporated exposure levels that were multi-fold the preindustrial concentrations. As such, global risk assessments and derivation of critical levels for protecting plants and food supplies were based on extrapolation from high to low exposure levels. These were developed in an era when it was thought that stress biology is framed around a linear dose-response. However, it has recently emerged that stress biology commonly displays non-linear, hormetic processes. The current biological understanding highlights that the strategy of extrapolating from high to low exposure levels may lead to biased estimates. Here, we analyzed a diverse sample of published empirical data of approximately 500 stimulatory, hormetic-like dose-responses induced by ozone in plants. The median value of the maximum stimulatory responses induced by elevated ozone was 124%, and commonly

MicroRNAs (miRNAs) classified as non-coding RNAs regulate various metabolic systems and viral life cycles. To date, numerous DNA viruses, many of which are members of the herpesvirus family, and a relatively small number of RNA viruses, including retroviruses, have been reported to encode and express miRNAs in infected cells. A few retroviruses have been shown to express miRNAs, and foamy viruses (FVs) were initially predicted by computational analyses to possess miRNA-coding regions. Subsequent studies on simian and bovine FVs confirmed the presence of functional and biologically active miRNA expression cassettes. We herein identified feline FV-derived miRNAs using a small RNA deep sequencing ana-lysis. We confirmed their repressive functions on gene expression by dual-luciferase reporter assays. We found that the seed sequences of the miRNAs identified in the present study were conserved among all previously reported FFV isolates. These results suggest that FFV-derived miRNAs play a pivotal role in FFV infection.