Search

In this paper, the minimal observability of switching Boolean networks (SBNs) is investigated. Firstly, applying the semi‐tensor product (STP) method of matrices, a parallel extension system is constructed, based on which a necessary and sufficient condition to detect the observability of the SBNs is given. Secondly, when an SBN is unobservable, the specific steps to obtain the required measurements to make the system observable are given using the set reachable method; however, the measurements given in this part are not necessarily the fewest. Then, a criterion for determining the minimum number of measurements is further proposed through a constructed indicator matrix. Lastly, the effectiveness of the new results is verified by an example. [ABSTRACT FROM AUTHOR]

Growing evidences have proved that tumors evade recognition and attack by the immune system through immune escape mechanisms, and PDL1/Pbrm1 genes have a strong correlation with poor response or resistance to immune checkpoint blockade (ICB) therapy. Herein, a multifunctional biomimetic nanocarrier (siRNA‐CaP@PD1‐NVs) is developed, which can not only enhance the cytotoxic activity of immune cells by blocking PD1/PDL1 axis, but also reduce tumor immune escape via Pbrm1/PDL1 gene silencing, leading to a significant improvement in tumor immunosuppressive microenvironment. Consequently, the nanocarrier promotes DC cell maturation, enhances the infiltration and activity of CD8+ T cells, and forms long‐term immune memory, which can effectively inhibit tumor growth or even eliminate tumors, and prevent tumor recurrence and metastasis. Overall, this study presents a powerful strategy for co‐delivery of siRNA drugs, immune adjuvant, and immune checkpoint inhibitors, and holds great promise for improving the effectiveness and safety of current immunotherapy regimens. [ABSTRACT FROM AUTHOR]

The immune status of tumor‐infiltrating lymphocytes (TILs) is essential for the effectiveness of cancer immunotherapies. However, due to the diversity of immune status in TILs, cellular heterogeneity, and the applicability to the clinic, it is still lacking effective strategies to meet clinical needs. We developed a novel immuno‐recognition‐induced method based on rolling circle amplification (RCA), namely immunoRCA, to in situ visualize the immune status of TILs in actual clinical samples. This developed immunoRCA method, in which, feature mRNAs were used as the biomarkers for the immune status of TILs, has a low fluorescence background, high sensitivity, and specificity. The immunoRCA was able to efficiently evaluate the immune status of CD8+ T cells regulated by activating or inhibiting factors, track the T cell type and immune status during in vitro expansion, and in situ visualize the number, location, and immune status of TILs in clinical specimens. [ABSTRACT FROM AUTHOR]

Currently, malaria is still one of the major public health problems commonly caused by the four Plasmodium species. The similar symptoms of malaria and the COVID‐19 epidemic of fever or fatigue lead to frequent misdiagnosis. The disadvantages of existing detection methods, such as time‐consuming, costly, complicated operation, need for experienced technicians, and indistinguishable typing, lead to difficulties in meeting the clinical requirements of rapid, easy, and accurate typing of common Plasmodium species. In this study, we developed and optimized a universal two‐dimensional labelled probe‐mediated melting curve analysis (UP‐MCA) assay based on multiplex and asymmetric PCR for rapid and accurate typing of five Plasmodium species, including novel human Plasmodium, Plasmodium knowlesi (Pk), in a single closed tube following genome extraction. The assay showed a limit of detection (LOD) of 10 copies per reaction and could accurately distinguish Plasmodium species from intra‐plasmodium and other pathogens. Additionally, we proposed and validated different methods of fluorescence quenching and tag design for probes that are suitable for UP‐MCA assays. Moreover, the clinical performance of the Plasmodium UP‐MCA assay using a base‐quenched universal probe was evaluated using 226 samples and showed a sensitivity of 100% (164/164) and specificity of 100% (62/62) at a 99% confidence interval, with the microscopy method as the gold standard. In summary, the UP‐MCA assay showed excellent sensitivity, specificity, and accuracy for genotyping Plasmodium species spp. Additionally, it facilitates convenient and rapid Plasmodium detection in routine clinical practice and has great potential for clinical translation. [ABSTRACT FROM AUTHOR]

N6‐methyladenosine (m6A) modification—the most prevalent mammalian RNA internal modification—plays key regulatory roles in mRNA metabolism. Current approaches for m6A modified RNA analysis limit at bulk‐population level, resulting in a loss of spatiotemporal and cell‐to‐cell variability information. Here we proposed a m6A‐specific in situ hybridization mediated proximity ligation assay (m6AISH‐PLA) for cellular imaging of m6A RNA, allowing to identify m6A modification at specific location in RNAs and image m6A RNA with single‐cell and single‐molecule resolution. Using m6AISH‐PLA, we investigated the m6A level and subcellular location of HSP70 RNA103‐m6A in response to heat shock stress, and found an increased m6A modified ratio and an increased distribution ratio in cytoplasm under heat shock. m6AISH‐PLA can serve in the study of m6A RNA in single cells for deciphering epitranscriptomic mechanisms and assisting clinical diagnosis. [ABSTRACT FROM AUTHOR]

The long reads of Nanopore sequencing permit accurate transcript assembly and ease in discovering novel transcripts with potentially important functions in cancers. The wide adoption of Nanopore sequencing for transcript quantification, however, is largely limited by high costs. To address this issue, we developed a bioinformatics software, NovelQuant, that can specifically quantify long‐read‐assembled novel transcripts with short‐read sequencing data. Nanopore Direct RNA Sequencing was carried out on three hepatocellular carcinoma (HCC) patients' tumor, matched portal vein tumor thrombus, and peritumor to reconstruct the HCC transcriptome. Then, based on the reconstructed transcriptome, NovelQuant was applied on Illumina RNA sequencing data of 59 HCC patients' tumor and paired peritumor to quantify novel transcripts. Our further analysis revealed 361 novel transcripts dysregulated in HCC and that 101 of them were significantly associated with prognosis. There were 19 novel prognostic transcripts predicted to be long noncoding RNAs (lncRNAs), and some of them had regulatory targets that were reported to be associated with HCC. Additionally, 42 novel prognostic transcripts were predicted to be protein‐coding mRNAs, and many of them could be involved in xenobiotic metabolism. Moreover, the tumor‐suppressive roles of two representative novel prognostic transcripts, CDO1‐novel (lncRNA) and CYP2A6‐novel (protein‐coding mRNA), were further functionally validated during HCC progression. Overall, the current study shows a possibility of combining long‐ and short‐read sequencing to explore functionally important novel transcripts in HCC with accuracy and cost‐efficiency, which expands the pool of molecular biomarkers that could enhance our understanding of the molecular mechanisms of HCC. [ABSTRACT FROM AUTHOR]

Flexible pressure sensors are widely demanded in human care systems. A simple and effective strategy for sensor fabrication can markedly promote its application. Herein, a facile strategy is employed to prepare a flexible capacitive pressure sensor with a polydimethylsiloxane microbeads‐modified dielectric layer. Owing to the microbeads structure, the proposed sensor achieves a sensitivity of 0.048 kPa−1 in the range of 0–10 kPa with a wide dynamic range (up to 100 kPa). The sensitivity is nine times higher than that of the planar structure. Moreover, the microbeads structured sensor obtains a low limit of detection (0.2 kPa), fast response time (120 ms), and good stability (variation lower than 3.30% after 1000 loading/unloading cycles at 20 kPa). The finite‐elemental analysis reveals that the microbeads structure is critical to enhance the performance of sensors. Finally, the pressure sensor is successfully applied to detect touch signal, joints movement, and breathing, exhibiting its promising prospects as smart wearable devices. Furthermore, the strategy may provide a new idea for the microstructural design of capacitive pressure sensors. [ABSTRACT FROM AUTHOR]

Abstract: Helicid is an active natural aromatic phenolic glycoside ingredient originating from a well‐known traditional Chinese herbal medicine and has the significant effects of sedative hypnosis, anti‐inflammatory analgesia and antidepressant. In this study, we analyzed the potential metabolites of Helicid in rats by multiple mass defect filter and dynamic background subtraction in ultra‐high‐performance liquid chromatography–quadrupole time‐of‐flight mass spectrometry (UHPLC‐Q‐TOF‐MS). Moreover, we used a novel data processing method, ‘key product ions’, to rapidly detect and identify metabolites as an assistant tool. MetabolitePilot™ 2.0 software and PeakView™ 2.2 software were used for analyzing metabolites. Twenty metabolites of Helicid (including 15 phase I metabolites and five phase II metabolites) were detected by comparison with the blank samples. The biotransformation route of Helicid was identified as demethylation, oxidation, dehydroxylation, hydrogenation, decarbonylation, glucuronide conjugation and methylation. This is the first study simultaneously detecting and identifying Helicid metabolism in rats employing UHPLC‐Q‐TOF‐MS technology. This experiment not only proposed a method for rapidly detecting and identifying metabolites, but also provided useful information for further study of the pharmacology and mechanism of Helicid in vivo. Furthermore, it provided an effective method for the analysis of other aromatic phenolic glycosides metabolic components in vivo. [ABSTRACT FROM AUTHOR]

Abstract: Farfarae Flos, the dried flower buds of Tussilago farfara L., is usually used to treat coughs, bronchitic and asthmatic conditions as an important traditional Chinese medicine. Tussilagone and methl butyric acid tussilagin ester are seen as representatives of two kinds of active substances. In addition, the pyrrolizidine alkaloids, mainly senkirkine and senecionine, present in the herb can be hepatoxic. In this study, a rapid and sensitive ultra‐high‐performance liquid chromatography coupled with hybrid triple quadrupole time‐of‐flight mass spectrometry method was successfully applied to identify the metabolites of tussilagone, methl butyric acid tussilagin ester, senkirkine and senecionine. A total of 35, 37, 18 and nine metabolites of tussilagone, methl butyric acid tussilagin ester, senkirkine and senecionine in rats were tentatively identified. Hydrolysis, oxidation, reduction and demethylation were the major metabolic reactions for tussilagone and methl butyric acid tussilagin ester. The main biotransformation routes of senkirkine and senecionine were identified as demethylation, N‐methylation, oxidation and reduction. This study is the first reported analysis and characterization of the metabolites and the proposed metabolic pathways might provide further understanding of the metabolic fate of the chemical constituents after oral administration of Farfarae Flos extract in vivo. [ABSTRACT FROM AUTHOR]

Prim -O-glucosylcimifugin (PGCN) and cimifugin (CN) are major constituents of Radix Saposhnikoviae that have antipyretic, analgesic and anti-inflammatory pharmacological activities. However, there were few reports with respect to the metabolism of PGCN and CN in vitro. In this paper, we describe a strategy using ultra-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) for fast analysis of the metabolic profile of PGCN and CN in human liver microsomes. In total, five phase I metabolites of PGCN, seven phase I metabolites and two phase II metabolites of CN were identified in the incubation of human liver microsomes. The results revealed that the main phase I metabolic pathways of PGCN were hydroxylation and hydrolysis reactions. The phase I metabolic pathways of CN were found to be hydroxylation, demethylation and dehydrogenation. Meanwhile, the results indicated that O-glucuronidation was the major metabolic pathway of CN in phase II metabolism. The specific UDP-glucuronosyltransferase (UGT) enzymes responsible for CN glucuronidation metabolites were identified using recombinant UGT enzymes. The results indicated that UGT1A1, UGT1A9, UGT2B4 and UGT2B7 might play major roles in the glucuronidation of CN. Overall, this study may be useful for the investigation of metabolic mechanism of PGCN and CN, and it can provide reference and evidence for further pharmacodynamic experiments. Copyright © 2016 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

m-Nisoldipine, as a novel 1,4-dihydropyridine calcium ion antagonist, was presented as a couple of enantiomers [(−), (+)- m-nisoldipine]. In this report, the in vitro metabolism of m-nisoldipine enantiomers was investigated in rat liver microsomes (RLM) by the combination of two liquid chromatography mass spectrometric techniques for the first time. The metabolites were separated and assayed by ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry and further identified by comparison of their mass and chromatographic behaviors with reference substances. A total of 18 metabolites of (−)- m-nisoldipine and 16 metabolites of (+)- m-nisoldipine were detected, respectively, which demonstrated that (+)- m-nisoldipine is more metabolically stable than (−)- m-nisoldipine. In addition, the identified metabolic pathways of m-nisoldipine enantiomers were involved in dehydrogenation, oxidation and ester hydrolysis . Afterwards, based on high-performance liquid chromatography coupled to triple quadrupole linear ion trap mass spectrometry, various selective cytochrome P450 (CYP) enzyme inhibitors were employed to evaluate CYP isoforms. The results indicated that the inhibitors of CYP1A1/2, CYP2B1/2, 2D and 2C11 had no obvious inhibitory effects, yet the inhibitor of CYP 3A had a significant inhibitory effect on metabolism of m-nisoldipine enantiomers. This showed that CYP 3A might primarily metabolize m-nisoldipine in RLM. Copyright © 2015 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Titelbild: Single-Cell Imaging of m6A Modified RNA Using m6A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m6AISH-PLA) (Angew. In ihrer Zuschrift auf S. 22828 postulieren Jinghong Li et al. eine leistungsstarke In-situ-Imaging-Methode, die als "m SP 6 sp A-specific in situ hybridization mediated proximity ligation assay" (m SP 6 sp AISH-PLA) bezeichnet wird und die Identifizierung von m SP 6 sp A-Modifikationen an spezifischen Stellen in RNA und die Bildgebung von m SP 6 sp A-RNA mit Einzelzell- und Einzelmolekül-Auflösung ermöglicht. In ihrer Zuschrift auf S. 22828 postulieren Jinghong Li et al. eine leistungsstarke In-situ-Imaging-Methode, die als "m SP 6 sp A-specific in situ hybridization mediated proximity ligation assay" (m SP 6 sp AISH-PLA) bezeichnet wird und die Identifizierung von m SP 6 sp A-Modifikationen an spezifischen Stellen in RNA und die Bildgebung von m SP 6 sp A-RNA mit Einzelzell- und Einzelmolekül-Auflösung ermöglicht. [Extracted from the article]

In their Communication on page 22646, Jinghong Li et al. propose a powerful in situ imaging method, termed m SP 6 sp A-specific in situ hybridization mediated proximity ligation assay (m SP 6 sp AISH-PLA), that enables the identification of m SP 6 sp A modifications at a specific location in RNAs and the imaging of m SP 6 sp A RNA with single-cell and single-molecule resolution. Keywords: in situ imaging; m6A; proximity ligation; single-molecule; spatiotemporal information EN in situ imaging m6A proximity ligation single-molecule spatiotemporal information 22589 22589 1 10/06/21 20211011 NES 211011 B N b SP B 6 b sp B -methyladenosine b (m SP 6 sp A)-modified RNA analysis is limited at the bulk-population level, thus not giving access to spatiotemporal and cell-to-cell variability information. Cover Picture: Single-Cell Imaging of m6A Modified RNA Using m6A-Specific In Situ Hybridization Mediated Proximity Ligation Assay (m6AISH-PLA) (Angew. [Extracted from the article]