Prediction of cell-type-specific cohesin-mediated chromatin loops based on chromatin state.

Chromatin loop is of crucial importance for the regulation of gene transcription. Cohesin is a type of chromatin-associated protein that mediates the interaction of chromatin through the loop extrusion. Cohesin-mediated chromatin interactions have strong cell-type specificity, posing a challenge for predicting chromatin loops. Existing computational methods perform poorly in predicting cell-type-specific chromatin loops. To address this issue, we propose a random forest model to predict cell-type-specific cohesin-mediated chromatin loops based on chromatin states identified by ChromHMM and the occupancy of related factors. Our results show that chromatin state is responsible for cell-type-specificity of loops. Using only chromatin states as features, the model achieved high accuracy in predicting cell-type-specific loops between two cell types and can be applied to different cell types. Furthermore, when chromatin states are combined with the occurrence frequency of CTCF, RAD21, YY1, and H3K27ac ChIP-seq peaks, more accurate prediction can be achieved. Our feature extraction method provides novel insights into predicting cell-type-specific chromatin loops and reveals the relationship between chromatin state and chromatin loop formation.

ACP_MS: prediction of anticancer peptides based on feature extraction.

Anticancer peptides (ACPs) are bioactive peptides with antitumor activity and have become the most promising drugs in the treatment of cancer. Therefore, the accurate prediction of ACPs is of great significance to the research of cancer diseases. In the paper, we developed a more efficient prediction model called ACP_MS. Firstly, the monoMonoKGap method is used to extract the characteristic of anticancer peptide sequences and form the digital features. Then, the AdaBoost model is used to select the most discriminating features from the digital features. Finally, a stochastic gradient descent algorithm is introduced to identify anticancer peptide sequences. We adopt 7-fold cross-validation and independent test set validation, and the final accuracy of the main dataset reached 92.653% and 91.597%, respectively. The accuracy of the alternate dataset reached 98.678% and 98.317%, respectively. Compared with other advanced prediction models, the ACP_MS model improves the identification ability of anticancer peptide sequences. The data of this model can be downloaded from the public website for free https://github.com/Zhoucaimao1998/Zc.

Analysis of primary metabolites of Morchella fruit bodies and mycelium based on widely targeted metabolomics.

As a medicinal and edible homologous fungi, Morchella is rich in multiple metabolites. The metabolite is a kind of essential substance with active components. In this study, Morchella fruit bodies and mycelium were selected to identify their metabolite components. The primary metabolites of the two experimental groups were analyzed using a method of widely targeted metabolome based on UPLC-ESI-MS/MS. A total of 354 different metabolites were characterized, including 188 upregulated ones and 166 downregulated ones in the fruit bodies. Further, the main 20 metabolic pathways of the metabolites were analyzed. The first 9 ones are tyrosine metabolites, thyroid hormone biosynthetic pathway, phenylalanine metabolites, linoleic metabolites synthetic pathway, glycerophosphate metabolic pathway, choline in tumors, methyl butyl metabolites, arginine synthetic pathway, arginine and proline metabolites. This study provides theoretical basis for the analysis of metabolic pathway of Morchella fruit bodies and mycelium that serve for further research of their medicinal mechanism and effective components.

In Silico Modeling and Simulation to Guide Bioequivalence Testing for Oral Drugs in a Virtual Population.

Model-informed drug discovery and development (MID3) shows great advantages in facilitating drug development. A physiologically based pharmacokinetic model is one of the powerful computational approaches of MID3, and the emerging field of virtual bioequivalence is well recognized to be the future of the physiologically based pharmacokinetic model. Based on the translational link between in vitro, in silico, and in vivo, virtual bioequivalence study can evaluate the similarity and potential difference of pharmacokinetic and clinical performance between test and reference formulations. With the aid of virtual bioequivalence study, the pivotal information of clinical trials can be provided to streamline the development for both new and generic drugs. However, a regulatory framework of virtual bioequivalence study has not reached its full maturity. Therefore, this article aims to present an overview of the current status of bioequivalence study, identify the framework of virtual bioequivalence studies for oral drugs, and also discuss the future opportunities of virtual bioequivalence in supporting the waiver and optimization of in vivo clinical trials.

Accelerating Development of Benziamidazole-Class Proton Pump Inhibitors: A Mechanism-Based PK/PD Model to Optimize Study Design with Ilaprazole as a Case Drug.

Proton pump inhibitors (PPIs) are the mainstay for treatment of acid-related diseases. This study developed a mechanism-based pharmacokinetic (PK) and pharmacodynamics (PD) model with ilaprazole as case drug, so as to support and accelerate the development of novel PPIs. The model was established and verified using the PK and PD data from 26 subjects receiving 5 to 30 mg of ilaprazole and 22 subjects receiving the loading dose of ilaprazole 20 mg followed by 10 mg once daily for 2 days. The nonlinear mixed-effects modeling approach was performed for the PK/PD model. A two-compartment model with linear elimination and covariates (body weight and gender) described the observed data well. The relationship between plasma concentrations of ilaprazole and gastric acid pH was well quantified with individual variability, in which the synthesis and degradation of H+/K+-ATPase, the food effect, the circular rhythms of gastric acid secretion, and the irreversible inhibition of H+/K+-ATPase by ilaprazole were integrated. This PK/PD model well predicted the PK and PD profile of ilaprazole in healthy subjects and patients with duodenal ulcers receiving wide range dose regimens. The mechanism-based PK/PD model provided a potential strategy to accelerate the development of novel PPIs by waiving the unnecessary clinical trials.

Development of a rapid and sensitive UPLC-MS/MS assay for simultaneous quantitation of Vorolanib and its metabolite in human plasma and application to a pharmacokinetics study.

Vorolanib is an oral tyrosine kinase inhibitor that targets vascular endothelial growth factor receptor (VEGFR) and platelet-derived growth factor receptor (PDGFR). A sensitive and specific LC-MS/MS assay was developed and fully validated for simultaneous quantification of vorolanib and its main metabolite X297 in human plasma. The two analytes were extracted from K2-EDTA plasma samples by protein precipitation (PP) with acetonitrile, and chromatographically separated on a C18 reverse-phase column using a gradient elution. A SCIEX 5500 QTRAP® mass spectrometer system was operated in multiple-reaction monitoring mode (MRM) and all components were detected using positive electrospray ionization (ESI). The results successfully demonstrated that the method had satisfactory linearity, sensitivity, and selectivity in the concentration ranges of vorolanib (1.00-1000 ng/mL) and X297 (0.500-500 ng/mL). In this study, two concentration related peaks in the vorolanib and X297 detection channels were observed, which were speculated to be isomers of vorolanib and X297. In order to standardize the sample pretreatment process, the effect of lamp light and pH on the isomer reconversion was evaluated. The results indicated, that the exposure of samples to lamp light during the handling procedures, did not cause the conversion of the isomers. For the first time a robust and specific ultra-performance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) assay for the high-throughput quantification of vorolanib and X297 in human plasma was established and validated following bioanalytical validation guidelines. The proposed method was successfully applied to clinical trials evaluating the pharmacokinetics of vorolanib tablets in Chinese advanced solid tumor patients.

In silico prediction of bioequivalence of Isosorbide Mononitrate tablets with different dissolution profiles using PBPK modeling and simulation.

AIM: The waiver of bioequivalence (BE) studies is well accepted for Biopharmaceutics Classification System (BCS) class I drugs in form of immediate-release solid oral products. This study aimed to assess whether the rapid dissolution profiles (≥85% in 30 min) was crucial to guarantee bioequivalence of isosorbide mononitrate (ISMN) and then established a clinically relevant dissolution specification (CRDS) for screening BE or non-BE batches. METHOD: A physiologically based pharmacokinetic (PBPK) model was constructed by integrating clinical and non-clinical data by B2O simulator. The model was verified by an actual clinical study (NMPA registration number: CTR20191360) with 28 healthy Chinese subjects. Then a virtual BE study was simulated to evaluate the bioequivalence of 7 virtual batches of ISMN tablets with different dissolution profiles, and the CRDS was established by integrating the results. RESULT: The simulated PK behavior of ISMN was comparable to the observed. Even though the batches with slower dissolution were not equivalent to a rapid dissolution profile (≥85% in 30 min), it was demonstrated these batches would exhibit the similar in vivo performance. Meanwhile, the in vitro dissolution specification time point and the percentage of drug release (75% in 45 min) proved to have clinical relevance. CONCLUSION: The virtual BE simulation by integrating in vitro dissolution profiles into the PBPK model provided a powerful tool for screening formulations, contributing to gaining time and reducing costs in BE evaluations.

Three new Scheffersomyces species associated with insects and rotting wood in China.

Three species of Scheffersomyces were identified during a diversity study of yeasts. All three are associated with insects and rotting wood in China. Phylogenetic analyses of a genomic dataset combining ITS and nrLSU revealed that these new collections are distinct from known species, thus three new species are introduced i.e. S. jinghongensis, S. paraergatensis, and S. anoplophorae. In our phylogenetic analyses, Scheffersomyces jinghongensis possesses a strong independent lineage and is closely related to S. titanus. S. paraergatensis is closely related to S. ergatensis, while S. anoplophorae is related to S. stambukii. Several differences in physiological traits and molecular data indicate that S. jinghongensis, S. paraergatensis, and S. anoplophorae are three newly identified species.

Determination of Isosorbide-5-Mononitrate in Human Plasma by High-Performance Liquid Chromatography-Tandem Mass Spectrometry and Its Application to a Bioequivalence Study.

Isosorbide-5-mononitrate (5-ISMN), an organic nitrate vasodilator, has been widely used worldwide to prevent angina pectoris for more than two decades. A simple and sensitive high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method was developed and validated for the determination of 5-ISMN in human plasma. 13C6-5-ISMN is an internal standard, and 5-ISMN was extracted from human plasma (50 µL) with ethyl acetate (200 µL) by a simple liquid-liquid extraction method. The chromatographic separation was carried out on LC-20A (Shimadzu, Japan) using an analytical column ZORBAX XDB-C18 (4.6 × 50 mm, 5 µm), coupled with API 4000 tandem mass spectrometers in a multiple reaction monitoring (MRM) mode. The mobile phase was composed of acetonitrile (organic phase A) and 2 mM ammonium acetate in water (aqueous phase B) with an isocratic elution of A/B = 90 : 10 (v/v). The total run time was 3.5 min with a small injection volume (5 µL). This method was fully validated in every aspect of selectivity, linearity, accuracy, precision, matrix effect, extraction recovery, and different stabilities. It was proved that the calibration standards within the 5.00-1000 ng/mL concentration range were linear. The lower limit of quantification was 5.00 ng/mL for 5-ISMN. The intrabatch and interbatch accuracy (RE) ranged from -8.8% to 7.1% with precision between 2.4% and 6.6%. The mean values of 5-ISMN extraction recovery and matrix effect were 87.0% and 102.0%, respectively. The fully validated method was successfully applied for a bioequivalence clinical trial of oral 20 mg 5-ISMN tablets in healthy Chinese subjects.

Blastobotrys baotianmanensis sp. nov. and Blastobotrys xishuangbannaensis f.a., sp. nov., two novel yeast species associated with insects and rotting wood.

Five yeast strains were isolated from the gut of the groundbeetle Pterostichus gebleri and rotting wood, which were collected from two different localities in China. These strains were identified as representing two novel species of the genus Blastobotrys through comparison of sequences in the D1/D2 domains of the LSU rRNA gene and other taxonomic characteristics. Blastobotrys baotianmanensis sp. nov. produces two to three spherical ascospores per ascus, and is most closely related to the type strains of B. elegans, B. capitulata, B. arbuscula, and an undescribed species represented by strain BG02-7-20-006A-3-1. Blastobotrys baotianmanensis sp. nov. differed from these strains by 3.6-8.4 % divergence (21-46 substitutions and 0-4 gaps) in the D1/D2 sequences. Blastobotrys xishuangbannaensis f.a., sp. nov. is closely related to B. nivea, B. elegans and B. aristata but the formation of ascospores was not observed on various sporulation media, and it differed from its relatives by 6.2-8.5 % divergence (34-43 substitutions and 2-6 gaps) in the D1/D2 sequences. The holotype of Blastobotrys baotianmanensis sp. nov. is NYNU 1581 and the holotype of Blastobotrys xishuangbannaensis f.a., sp. nov. is NYNU 181030.

Development and validation of a UPLC-MS/MS method for simultaneous determination of LBPT and its metabolites in human plasma.

Aim: A UPLC-MS/MS method was developed to determine LBPT as well as its four metabolites in human plasma to support the clinical study aiming to evaluate the efficacy of LBPT tablet in patients undergoing hip/knee replacement. Methodology: Plasma samples were prepared by protein precipitation and then separated on a C18 analytical column using (A) acetonitrile (B) 0.1% formic acid and 10 mM ammonium formate in water. The detection was performed on a triple quadrupole tandem mass spectrometer in positive electrospray ionization using multiple reactions monitoring mode. Results & conclusion: The method has been validated in accordance with the US FDA guidelines and was applied to the measurement of five analytes in human plasma samples from a Phase II clinical trial.

Unveiling the Activity Origin of a Copper-based Electrocatalyst for Selective Nitrate Reduction to Ammonia.

Unveiling the active phase of catalytic materials under reaction conditions is important for the construction of efficient electrocatalysts for selective nitrate reduction to ammonia. The origin of the prominent activity enhancement for CuO (Faradaic efficiency: 95.8 %, Selectivity: 81.2 %) toward selective nitrate electroreduction to ammonia was probed. 15 N isotope labeling experiments showed that ammonia originated from nitrate reduction. 1 H NMR spectroscopy and colorimetric methods were performed to quantify ammonia. In situ Raman and ex situ experiments revealed that CuO was electrochemically converted into Cu/Cu2 O, which serves as an active phase. The combined results of online differential electrochemical mass spectrometry (DEMS) and DFT calculations demonstrated that the electron transfer from Cu2 O to Cu at the interface could facilitate the formation of *NOH intermediate and suppress the hydrogen evolution reaction, leading to high selectivity and Faradaic efficiency.

Gold nanoclusters as a near-infrared fluorometric nanothermometer for living cells.

The authors describe the syntheses and application of glutathione-capped gold nanoclusters (AuNCs) with thermoresponsive properties. The AuNCs have excitation/emission maxima at 430/610 nm and the bright redfluorescence changes along with the temperature in the range from 0 to 90 °C which covers the normal temperature range of living cells. In the range of physiological temperatures (35-42 °C), the temperature resolution is 0.73 °C. The AuNCs display excellent colloidal stability and biocompatibility. They were used for fluorometric temperature detection and imaging of hepatic stellate cells. With such attractive features, the AuNCs are quite promising luminescence nanothermometers. Graphical abstract Schematic presentation of the fluorescence of glutathione-capped gold nanoclusters (AuNCs) as nanothermometers in living cells. The AuNCs have excitation/emission maxima at 430/610 nm and the red fluorescence changes with temperature in a wide range of 0 to 90 °C which covers the normal temperature of living cells.

Electrochemical synthesis of nitric acid from air and ammonia through waste utilization.

Commercial nitric acid (HNO3) and ammonia (NH3) are mostly produced through the Ostwald process and the Haber-Bosch process, respectively. However, high energy demand and enormous greenhouse gas accompy these processes. The development of economical and green ways to synthesize HNO3 and NH3 is highly desirable for solving the global energy and environmental crisis. Here, we present two energy-efficient and environmentally friendly strategies to synthesize HNO3 and NH3 at distributed sources, including the electrocatalytic oxidation of N2 in air to HNO3 and the electrocatalytic reduction of residual [Formula: see text] contamination in water to NH3. The isotope-labeling studies combined with theoretical calculation reveal the reaction path of the two proposed strategies, confirming the origin of the electrochemical products. Importantly, the electrooxidation-generated [Formula: see text] ions may also serve as reactants for the electroreduction synthesis of NH3 in the future. Our work may open avenues for energy-efficient and green production of HNO3 and NH3 at distributed sources.

In Vivo Antioxidant and Anti-Skin-Aging Activities of Ethyl Acetate Extraction from Idesia polycarpa Defatted Fruit Residue in Aging Mice Induced by D-Galactose.

Two different concentrations of D-galactose (D-gal) induced organism and skin aging in Kunming mice were used to examine comprehensively the antioxidant and antiaging activities of ethyl acetate extraction (EAE) from Idesia polycarpa defatted fruit residue for the first time. The oxygen radical absorbance capacity (ORAC) of EAE was 13.09 ± 0.11 µ mol Trolox equivalents (TE)/mg, which showed EAE had great in vitro free radical scavenging and antioxidant activity. Biochemical indexes and morphological analysis of all tested tissues showed that EAE could effectively improve the total antioxidant capacity (T-AOC) of the antioxidant defense system of the aging mice, enhance the activities of superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px) of tissues and serum, increase glutathione (GSH) content and decrease the malondialdehyde (MDA) content, and maintain the skin collagen, elastin, and moisture content. Meanwhile, EAE could effectively attenuate the morphological damage in brain, liver, kidney, and skin induced by D-gal and its effect was not less than that of the well-known L-ascorbic acid (VC) and α -tocopherol (VE). Overall, EAE is a potent natural antiaging agent with great antioxidant activity, which can be developed as a new medicine and cosmetic for the treatment of age-related conditions.