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Xu S, Mi R, Zheng G, Li X. Cobalt- or rhodium-catalyzed synthesis of 1,2-dihydrophosphete oxides via C-H activation and formal phosphoryl migration. Chem Sci 2024; 15:6012-6021. [PMID: 38665527 PMCID: PMC11040647 DOI: 10.1039/d4sc00649f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 03/11/2024] [Indexed: 04/28/2024] Open
Abstract
A highly stereo- and chemoselective intermolecular coupling of diverse heterocycles with dialkynylphosphine oxides has been realized via cobalt/rhodium-catalyzed C-H bond activation. This protocol provides an efficient synthetic entry to functionalized 1,2-dihydrophosphete oxides in excellent yields via the merger of C-H bond activation and formal 1,2-migration of the phosphoryl group. Compared with traditional methods of synthesis of 1,2-dihydrophosphetes that predominantly relied on stoichiometric metal reagents, this catalytic system features high efficiency, a relatively short reaction time, atom-economy, and operational simplicity. Photophysical properties of selected 1,2-dihydrophosphete oxides are also disclosed.
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Affiliation(s)
- Shengbo Xu
- School of Chemistry and Chemical Engineering, Shaanxi Normal University (SNNU) Xi'an 710062 P. R. China
| | - Ruijie Mi
- Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Sciences, Shandong University Qingdao 266237 P. R. China
| | - Guangfan Zheng
- Department of Chemistry, Northeast Normal University Changchun 130024 P. R. China
| | - Xingwei Li
- School of Chemistry and Chemical Engineering, Shaanxi Normal University (SNNU) Xi'an 710062 P. R. China
- Institute of Molecular Science and Engineering, Institute of Frontier and Interdisciplinary Sciences, Shandong University Qingdao 266237 P. R. China
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Xu X, Wang Y, Huang W, Li D, Deng Z, Long F. Structural insights into the Clp protein degradation machinery. mBio 2024; 15:e0003124. [PMID: 38501868 PMCID: PMC11005422 DOI: 10.1128/mbio.00031-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 02/27/2024] [Indexed: 03/20/2024] Open
Abstract
The Clp protease system is important for maintaining proteostasis in bacteria. It consists of ClpP serine proteases and an AAA+ Clp-ATPase such as ClpC1. The hexameric ATPase ClpC1 utilizes the energy of ATP binding and hydrolysis to engage, unfold, and translocate substrates into the proteolytic chamber of homo- or hetero-tetradecameric ClpP for degradation. The assembly between the hetero-tetradecameric ClpP1P2 chamber and the Clp-ATPases containing tandem ATPase domains from the same species has not been studied in depth. Here, we present cryo-EM structures of the substrate-bound ClpC1:shClpP1P2 from Streptomyces hawaiiensis, and shClpP1P2 in complex with ADEP1, a natural compound produced by S. hawaiiensis and known to cause over-activation and dysregulation of the ClpP proteolytic core chamber. Our structures provide detailed information on the shClpP1-shClpP2, shClpP2-ClpC1, and ADEP1-shClpP1/P2 interactions, reveal conformational transition of ClpC1 during the substrate translocation, and capture a rotational ATP hydrolysis mechanism likely dominated by the D1 ATPase activity of chaperones.IMPORTANCEThe Clp-dependent proteolysis plays an important role in bacterial homeostasis and pathogenesis. The ClpP protease system is an effective drug target for antibacterial therapy. Streptomyces hawaiiensis can produce a class of potent acyldepsipeptide antibiotics such as ADEP1, which could affect the ClpP protease activity. Although S. hawaiiensis hosts one of the most intricate ClpP systems in nature, very little was known about its Clp protease mechanism and the impact of ADEP molecules on ClpP. The significance of our research is in dissecting the functional mechanism of the assembled Clp degradation machinery, as well as the interaction between ADEP1 and the ClpP proteolytic chamber, by solving high-resolution structures of the substrate-bound Clp system in S. hawaiiensis. The findings shed light on our understanding of the Clp-dependent proteolysis in bacteria, which will enhance the development of antimicrobial drugs targeting the Clp protease system, and help fighting against bacterial multidrug resistance.
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Affiliation(s)
- Xiaolong Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Yanhui Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Wei Huang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Danyang Li
- Cryo-EM Center and the Core Facility of Wuhan University, Wuhan, China
| | - Zixin Deng
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Feng Long
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
- Ministry of Education Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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Fan W, Yang S, Chen J, Guo LX, Zhang M. A Biomechanical Comparison of 2 Different Topping-off Devices and Their Influence on the Sacroiliac Joint Following Lumbosacral Fusion Surgery. Neurospine 2024; 21:244-252. [PMID: 38317555 PMCID: PMC10992661 DOI: 10.14245/ns.2347108.554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Interspinous spacer (ISS)-based and pedicle screw-rod dynamic fixator (PDF)-based topping-off devices have been applied in lumbar/lumbosacral fusion surgeries for preventing the development of proximal adjacent segment degeneration. However, little attention has been paid to sacroiliac joint (SIJ), which belongs to the adjacent joints. Accordingly, the objective of this study was to compare how these 2 topping-off devices affect the SIJ biomechanics. METHODS A validated, normal finite-element lumbopelvic model (L3-pelvis) was initially adjusted to simulate interbody fusion with rigid fixation at the L5-S1 level, and then the DIAM or BioFlex system was instrumented at the L4-5 level to establish the ISS-based or PDF-based topping-off model, respectively. All the developed models were loaded with moments of 4 physiological motions using hybrid loading protocol. RESULTS Compared with the rigid fusion model (without topping-off devices), range of motion and von-Mises stress at the SIJs were increased by 23.1%-64.1% and 23.6%-62.8%, respectively, for the ISS-based model and by 51.2%-126.7% and 50.4%-108.7%, respectively, for the PDF-based model. CONCLUSION The obtained results suggest that the PDF-based topping-off device leads to higher increments in SIJ motion and stress than ISS-based topping-off device following lumbosacral fusion, implying topping-off technique could be linked to an increased risk of SIJ degeneration, especially when using PDF-based device.
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Affiliation(s)
- Wei Fan
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Song Yang
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Jie Chen
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Li-Xin Guo
- School of Mechanical Engineering and Automation, Northeastern University, Shenyang, China
| | - Ming Zhang
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Hong Kong, China
- Research Institute for Sports Science and Technology, The Hong Kong Polytechnic University, Hong Kong, China
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Zhang H, Zhao H, Cao L, Yu B, Wei J, Pan G, Bao J, Zhou Z. Harnessing multiplex crRNA enables an amplification-free/CRISPR-Cas12a-based diagnostic methodology for Nosema bombycis. Microbiol Spectr 2024; 12:e0301423. [PMID: 38014967 PMCID: PMC10783057 DOI: 10.1128/spectrum.03014-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/17/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE The multiplex-crRNA CRISPR/Cas12a detection method saves hands-on time, reduces the risk of aerosol pollution, and can be directly applied to detecting silkworms infected with Nosema bombycis. This study provides a new approach for the inspection and quarantine of silkworm pébrine disease in sericulture and provides a new method for the detection of other pathogens.
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Affiliation(s)
- Huarui Zhang
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Huijuan Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Lu Cao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Bin Yu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Junhong Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Guoqing Pan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Jialing Bao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
| | - Zeyang Zhou
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Chongqing Key Laboratory of Microsporidia Infection and Control, Southwest University, Chongqing, China
- College of Life Science, Chongqing Normal University, Chongqing, China
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Huang H, Xiao D, Zhu Z, Zhang C, Yang L, He H, You J, Jiang Q, Xu X, Yamauchi Y. A 2D/2D heterojunction of ultrathin Pd nanosheet/MXene towards highly efficient methanol oxidation reaction: the significance of 2D material nanoarchitectonics. Chem Sci 2023; 14:9854-9862. [PMID: 37736638 PMCID: PMC10510762 DOI: 10.1039/d3sc03735e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/29/2023] [Indexed: 09/23/2023] Open
Abstract
Two-dimensional (2D) Pd nanosheet-based catalysts have recently garnered widespread attention due to their high atom utilization efficiency. However, their catalytic ability and structural stability still require significant enhancement before they can be widely applied. In this study, we presented the rational design and controllable fabrication of a novel 2D/2D heterojunction, which consists of ultrathin Pd nanosheets (NSs) grown on the Ti3C2Tx MXene surface (Pd NSs/MXene). This heterostructure was achieved through a robust and convenient stereo-assembly strategy. The newly developed Pd NSs/MXene heterojunction not only provides numerous exposed active Pd atoms with an optimized electronic structure but also enables an intimate Pd/MXene interfacial interaction, ensuring a stable hybrid configuration. Consequently, the resulting Pd NSs/MXene heterojunction exhibits exceptional methanol oxidation properties. It possesses a large electrochemically active surface area, high mass and specific activities, and a long operating life, which are significantly superior to those of traditional Pd nanoparticle/carbon and Pd nanosheet/carbon catalysts. Theoretical simulations further reveal strong electronic interactions between the Pd nanosheet and MXene, which dramatically enhance the adsorption energy of the Pd component and simultaneously lower its d-band center. As a result, the Pd NSs/MXene heterojunction is less susceptible to CO poisoning. This work introduces a new 2D/2D heterojunction based on MXene and noble metallic materials and holds significance for the development of other novel heterojunctions, particularly within the realm of 2D material nanoarchitectonics.
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Affiliation(s)
- Huajie Huang
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Di Xiao
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Zihan Zhu
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Chi Zhang
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Lu Yang
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Haiyan He
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Jungmok You
- Department of Plant & Environmental New Resources, College of Life Sciences, Kyung Hee University 1732 Deogyeong-daero, Giheung-gu Yongin-si Gyeonggi-do 17104 South Korea
| | - Quanguo Jiang
- College of Mechanics and Materials, Hohai University Nanjing 210098 China
| | - Xingtao Xu
- Marine Science and Technology College, Zhejiang Ocean University Zhoushan 316022 China
| | - Yusuke Yamauchi
- Department of Plant & Environmental New Resources, College of Life Sciences, Kyung Hee University 1732 Deogyeong-daero, Giheung-gu Yongin-si Gyeonggi-do 17104 South Korea
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland Brisbane QLD 4072 Australia
- Department of Materials Process Engineering, Graduate School of Engineering, Nagoya University, Nagoya University Nagoya 464-8601 Japan
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Ali A, Ma L, Shahzad M, Musonda J, Hussain S. How various stakeholder pressure influences mega-project sustainable performance through corporate social responsibility and green competitive advantage. Environ Sci Pollut Res Int 2023:10.1007/s11356-023-29717-w. [PMID: 37702865 DOI: 10.1007/s11356-023-29717-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 08/31/2023] [Indexed: 09/14/2023]
Abstract
Although numerous research studies have revealed that mega-projects are closely linked to globalization and civilization, few researchers have performed logical assessments of mega-projects using stakeholder theory. As stakeholders demand greater sustainability in the construction industry, sustainable development (SD) has become a priority. However, corporate social responsibility (CSR) and green competitive advantage (GCA) have often been overlooked. This study aims to fill this knowledge gap by creating a comprehensive model to predict mega-project sustainable performance (MSP). Data was collected from 289 respondents in Pakistan's construction industry, and hypotheses were tested using partial least squares structural equation modeling and fuzzy set qualitative comparative analysis. The results indicate that both secondary and primary stakeholders' pressure positively impacts CSR and MSP. Moreover, CSR significantly affects GCA and MSP, with CSR and GCA partially mediating these relationships. Thus, the proposed model could offer innovative insights for decision-makers and engineering managers, recommend adopting social and green practices to enhance MSP with the support of concerned stakeholders' pressure, and help achieve SD objectives.
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Affiliation(s)
- Azhar Ali
- Department of Construction Management, Dalian University of Technology, Dalian, 116024, China
| | - Li Ma
- Department of Construction Management, Dalian University of Technology, Dalian, 116024, China.
| | - Mohsin Shahzad
- LNU-MSU College of International Business, Liaoning Normal University, Dalian, 116024, China
| | - Jonathan Musonda
- Department of Construction Management, Dalian University of Technology, Dalian, 116024, China
| | - Shahid Hussain
- Department of Business Management, Karakoram International University, Gilgit, 15100, Pakistan
- Department of Management, University of Religious and Denomination, Qom, 37491-13357, Iran
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Yan C, Meng Y, Yang J, Chen J, Jiang W. Translational landscape in human early neural fate determination. Development 2023; 150:297188. [PMID: 36846898 DOI: 10.1242/dev.201177] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 02/19/2023] [Indexed: 03/01/2023]
Abstract
Gene expression regulation in eukaryotes is a multi-level process, including transcription, mRNA translation and protein turnover. Many studies have reported sophisticated transcriptional regulation during neural development, but the global translational dynamics are still ambiguous. Here, we differentiate human embryonic stem cells (ESCs) into neural progenitor cells (NPCs) with high efficiency and perform ribosome sequencing and RNA sequencing on both ESCs and NPCs. Data analysis reveals that translational controls engage in many crucial pathways and contribute significantly to regulation of neural fate determination. Furthermore, we show that the sequence characteristics of the untranslated region (UTR) might regulate translation efficiency. Specifically, genes with short 5'UTR and intense Kozak sequence are associated with high translation efficiency in human ESCs, whereas genes with long 3'UTR are related to high translation efficiency in NPCs. In addition, we have identified four biasedly used codons (GAC, GAT, AGA and AGG) and dozens of short open reading frames during neural progenitor differentiation. Thus, our study reveals the translational landscape during early human neural differentiation and provides insights into the regulation of cell fate determination at the translational level.
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Affiliation(s)
- Chenchao Yan
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Yajing Meng
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jie Yang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| | - Jian Chen
- Chinese Institute for Brain Research (Beijing), Research Unit of Medical Neurobiology, Chinese Academy of Medical Sciences, Beijing 102206, China
| | - Wei Jiang
- Department of Biological Repositories, Frontier Science Center for Immunology and Metabolism, Medical Research Institute, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
- Human Genetics Resource Preservation Center of Wuhan University, Wuhan 430071, China
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Su Y, Peng Q, Yin L, Li C. Evaluation of Exercise Tolerance in Non-obstructive Hypertrophic Cardiomyopathy With Myocardial Work and Peak Strain Dispersion by Speckle-Tracking Echocardiography. Front Cardiovasc Med 2022; 9:927671. [PMID: 35958415 PMCID: PMC9361015 DOI: 10.3389/fcvm.2022.927671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe aim of this study was to evaluate exercise tolerance in non-obstructive hypertrophic cardiomyopathy (HCM) by investigating the value of myocardial work (MW) combined with strain peak dispersion.MethodsA total of 65 patients with non-obstructive HCM and normal left ventricular ejection fraction were enrolled and 60 healthy subjects were selected as controls. The automated function imaging (AFI)-two-dimensional ultrasonic speckle-tracking technology was used to obtain the values for peak global longitudinal strain (GLS), longitudinal strain peak time dispersion (PSD), 18-segment systolic longitudinal peak strain (LPS), 18-segment longitudinal strain peak time (TTPLS), global waste work (GWW), global constructive work (GCW), global work index (GWI), global work efficiency (GWE), and exercise metabolic equivalents (METS).Results(1) Values for LV-GLS (−17.77 ± 0.20 vs. −21.66 ± 0.42%) were lower and PSD (95.10 ± 8.15 vs. 28.97 ± 1.50 ms) was prolonged in patients with HCM (p < 0.01). (2) An increasing trend was shown in the basal segment < intermediate segment < apical segment for both patients with HCM and controls, although each segment had lower values in the HCM group. (3) TTPLS was prolonged in the HCM group (p < 0.01). (4) GWE, GWI, and GCW were all lower (p < 0.01) and GWW was higher in patients with HCM (p < 0.01). (5) Values of GWE were less than 92.5%, GWI less than 1,200 mmHg, GCW less than 1,399 mmHg, these abnormal values are helpful for the diagnosis of impaired exercise tolerance and poor prognosis (6) The METS and LV-GLS of HCM in the asymmetric group were significantly lower than that in AHCM group, but the PSD was significantly greater than that in the AHCM group. Values of LPS-BL (−13.13% ± 2.51% vs −10.17% ± 2.20%) in the apical HCM group were better than in the asymmetric HCM group (p < 0.05).ConclusionGCW, GWI, and GWE can be safely measured by resting echocardiography to evaluate exercise tolerance in patients with HCM who cannot perform an exercise-based examination. Such measurements provide a basis for clinical decisions regarding exercise and drug prescription.
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Affiliation(s)
- Ye Su
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Cardiovascular Ultrasound, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Qionghui Peng
- Department of Cardiovascular Ultrasound, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
| | - Lixue Yin
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Cardiovascular Ultrasound, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- *Correspondence: Lixue Yin, ;
| | - Chunmei Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
- Department of Cardiovascular Ultrasound, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, China
- Chunmei Li,
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Wang J, Tang X, Mo Z, Mao Y. Metagenome-Assembled Genomes From Pyropia haitanensis Microbiome Provide Insights Into the Potential Metabolic Functions to the Seaweed. Front Microbiol 2022; 13:857901. [PMID: 35401438 PMCID: PMC8984609 DOI: 10.3389/fmicb.2022.857901] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 12/24/2022] Open
Abstract
Pyropia is an economically important edible red alga worldwide. The aquaculture industry and Pyropia production have grown considerably in recent decades. Microbial communities inhabit the algal surface and produce a variety of compounds that can influence host adaptation. Previous studies on the Pyropia microbiome were focused on the microbial components or the function of specific microbial lineages, which frequently exclude metabolic information and contained only a small fraction of the overall community. Here, we performed a genome-centric analysis to study the metabolic potential of the Pyropia haitanensis phycosphere bacteria. We reconstructed 202 unique metagenome-assembled genomes (MAGs) comprising all major taxa present within the P. haitanensis microbiome. The addition of MAGs to the genome tree containing all publicly available Pyropia-associated microorganisms increased the phylogenetic diversity by 50% within the bacteria. Metabolic reconstruction of the MAGs showed functional redundancy across taxa for pathways including nitrate reduction, taurine metabolism, organophosphorus, and 1-aminocyclopropane-1-carboxylate degradation, auxin, and vitamin B12 synthesis. Some microbial functions, such as auxin and vitamin B12 synthesis, that were previously assigned to a few Pyropia-associated microorganisms were distributed across the diverse epiphytic taxa. Other metabolic pathways, such as ammonia oxidation, denitrification, and sulfide oxidation, were confined to specific keystone taxa.
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Affiliation(s)
- Junhao Wang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xianghai Tang
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Zhaolan Mo
- Key Laboratory of Marine Genetics and Breeding (Ministry of Education), College of Marine Life Sciences, Ocean University of China, Qingdao, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya, China
| | - Yunxiang Mao
- Key Laboratory of Utilization and Conservation of Tropical Marine Bioresource (Ministry of Education), College of Fisheries and Life Sciences, Hainan Tropical Ocean University, Sanya, China
- Yazhou Bay Innovation Research Institute, Hainan Tropical Ocean University, Sanya, China
- Key Laboratory for Conservation and Utilization of Tropical Marine Fishery Resources of Hainan Province, Hainan Tropical Ocean University, Sanya, China
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Liang XY, Battini N, Sui YF, Ansari MF, Gan LL, Zhou CH. Aloe-emodin derived azoles as a new structural type of potential antibacterial agents: design, synthesis, and evaluation of the action on membrane, DNA, and MRSA DNA isomerase. RSC Med Chem 2021; 12:602-608. [PMID: 34046631 PMCID: PMC8128066 DOI: 10.1039/d0md00429d] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 01/25/2021] [Indexed: 12/30/2022] Open
Abstract
As serious global drug resistance motivated the exploration of new structural drugs, we developed a type of novel structural aloe-emodin azoles as potential antibacterial agents in this work. Some target aloe-emodin azoles displayed effective activity against the tested strains, especially tetrazolyl aloe-emodin 4b showed a low MIC value of 2 μg mL-1 towards MRSA, being more efficient than the reference drug norfloxacin (MIC = 8 μg mL-1). Also, the active molecule 4b exhibited low cytotoxicity against LO2 cells with no distinct tendency to induce the concerned resistance towards MRSA. The tetrazolyl derivative 4b was preliminarily investigated for the possible mechanism; it was revealed that tetrazolyl derivative 4b could both disrupt the integrity of MRSA membrane and form 4b-DNA supramolecular complex by intercalating into DNA. Moreover, tetrazolyl aloe-emodin 4b could bind with MRSA DNA isomerase at multiple sites through hydrogen bonds in molecular simulation.
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Affiliation(s)
- Xin-Yuan Liang
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Narsaiah Battini
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Yan-Fei Sui
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Mohammad Fawad Ansari
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
| | - Lin-Ling Gan
- Chongqing Engineering Research Center of Pharmaceutical Sciences, School of Pharmacy, Chongqing Medical and Pharmaceutical College Chongqing 401331 PR China
| | - Cheng-He Zhou
- Institute of Bioorganic & Medicinal Chemistry, Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University Chongqing 400715 PR China +86 23 68254967 +86 23 68254967
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11
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Wang H, Tao S. Fabrication of a porous NiFeP/Ni electrode for highly efficient hydrazine oxidation boosted H 2 evolution. Nanoscale Adv 2021; 3:2280-2286. [PMID: 36133764 PMCID: PMC9417549 DOI: 10.1039/d1na00043h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 03/02/2021] [Indexed: 05/16/2023]
Abstract
Rational optimization of the surface electronic states and physical structures of non-noble metal nanomaterials is essential to improve their electrocatalytic performance. Herein, we report a facile dual-regulation strategy to fabricate NiFeP/Ni (P-NiFeP/Ni) porous nanoflowers, which involves Fe-doping and creating pores on nanosheets. The as-prepared P-NiFeP/Ni has a hierarchically porous surface, which exposes more electrochemically active sites and dramatically enhances the electron transfer rate. Thus, it exhibits excellent catalytic activity in both anodic hydrazine oxidation reaction (HzOR) and cathodic hydrogen evolution reaction (HER). Interestingly, the coupled electrolysis cell only offers a potential of 0.162 V at 10 mA cm-2 to enable HzOR boosted H2 evolution, highlighting an energy-saving hydrogen evolution strategy.
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Affiliation(s)
- Honglei Wang
- Department of Chemistry, School of Chemical Engineering, Dalian University of Technology Dalian 116024 China
| | - Shengyang Tao
- Department of Chemistry, School of Chemical Engineering, Dalian University of Technology Dalian 116024 China
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12
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Xu J, Zhou L, He G, Ji X, Dai Y, Dang Y. Comprehensive Machine Learning-Based Model for Predicting Compressive Strength of Ready-Mix Concrete. Materials (Basel) 2021; 14:1068. [PMID: 33668806 PMCID: PMC7956418 DOI: 10.3390/ma14051068] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/13/2021] [Accepted: 02/17/2021] [Indexed: 11/18/2022]
Abstract
Considering that compressive strength (CS) is an important mechanical property parameter in many design codes, in order to ensure structural safety, concrete CS needs to be tested before application. However, conducting CS tests with multiple influencing variables is costly and time-consuming. To address this issue, a machine learning-based modeling framework is put forward in this work to evaluate the concrete CS under complex conditions. The influential factors of this process are systematically categorized into five aspects: man, machine, material, method and environment (4M1E). A genetic algorithm (GA) was applied to identify the most important influential factors for CS modeling, after which, random forest (RF) was adopted as the modeling algorithm to predict the CS from the selected influential factors. The effectiveness of the proposed model was tested on a case study, and the high Pearson correlation coefficient (0.9821) and the low mean absolute percentage error and delta (0.0394 and 0.395, respectively) indicate that the proposed model can deliver accurate and reliable results.
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Affiliation(s)
| | | | | | - Xu Ji
- Department of Chemical Engineering, Sichuan University, Chengdu 610065, China; (J.X.); (L.Z.); (G.H.); (Y.D.); (Y.D.)
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Wang JX, Zhuang JY, Fu L, Lei Q. Social Orientation in the Luteal Phase: Increased Social Feedback Sensitivity, Inhibitory Response, Interpersonal Anxiety and Cooperation Preference. Evol Psychol 2021; 19:1474704920986866. [PMID: 33487056 PMCID: PMC10355302 DOI: 10.1177/1474704920986866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 12/16/2020] [Indexed: 12/20/2022] Open
Abstract
Cyclical fluctuations of the ovarian hormones estrogen (E2) and progesterone (PROG) have multiple effects on reproduction and development. However, little is known about the roles of E2 and PROG in women's social behaviors. Here, based on evolutionary theory suggesting social sensitivity and inhibition ability are conductive to maintaining social relationships, we provide evidence for the association between menstrual phases and social orientation. In Study 1, 78 women provided saliva samples and reported their intensity of behavioral activation/inhibition system (BAS/BIS) and interpersonal sensitivity at either of two phases of the menstrual cycle: late follicular phase (FP), and mid-luteal phase (LP). A significant between-subject association emerged, revealing that women with higher PROG levels reported higher levels of social feedback sensitivity, and women with relatively high PROG levels showed a positive association between their E2 levels and inhibitory response. In Study 2, 30 women reported their interpersonal anxiety and finished the social value orientation (SVO) measures at both late FP and mid-LP. A significant within-person effect emerged: women in the mid-LP, which is characterized by higher PROG levels, reported higher levels of interpersonal anxiety and SVO. In sum, these findings revealed that women's social orientation could fluctuate naturally with ovarian hormones across the menstrual cycle.
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Affiliation(s)
- Jia-Xi Wang
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Jin-Ying Zhuang
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
| | - Lulu Fu
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
| | - Qin Lei
- School of Psychology and Cognitive Science, East China Normal University, Shanghai, China
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14
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Beaudry G, Zhong S, Whiting D, Javid B, Frater J, Fazel S. Managing outbreaks of highly contagious diseases in prisons: a systematic review. BMJ Glob Health 2020; 5:e003201. [PMID: 33199278 PMCID: PMC7670855 DOI: 10.1136/bmjgh-2020-003201] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 09/28/2020] [Accepted: 10/06/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND There are reports of outbreaks of COVID-19 in prisons in many countries. Responses to date have been highly variable and it is not clear whether public health guidance has been informed by the best available evidence. We conducted a systematic review to synthesise the evidence on outbreaks of highly contagious diseases in prison. METHODS We searched seven electronic databases for peer-reviewed articles and official reports published between 1 January 2000 and 28 July 2020. We included quantitative primary research that reported an outbreak of a given contagious disease in a correctional facility and examined the effects of interventions. We excluded studies that did not provide detail on interventions. We synthesised common themes using the Synthesis Without Meta-analysis (SWiM) guideline, identified gaps in the literature and critically appraised the effectiveness of various containment approaches. RESULTS We identified 28 relevant studies. Investigations were all based in high-income countries and documented outbreaks of tuberculosis, influenza (types A and B), varicella, measles, mumps, adenovirus and COVID-19. Several themes were common to these reports, including the public health implications of infectious disease outbreaks in prison, and the role of interagency collaboration, health communication, screening for contagious diseases, restriction, isolation and quarantine, contact tracing, immunisation programmes, epidemiological surveillance and prison-specific guidelines in addressing any outbreaks. DISCUSSION Prisons are high-risk settings for the transmission of contagious diseases and there are considerable challenges in managing outbreaks in them. A public health approach to managing COVID-19 in prisons is required. PROSPERO REGISTRATION NUMBER CRD42020178827.
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Affiliation(s)
- Gabrielle Beaudry
- Department of Psychiatry, University of Oxford, Oxford, Oxfordshire, UK
| | - Shaoling Zhong
- Department of Psychiatry, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daniel Whiting
- Department of Psychiatry, University of Oxford, Oxford, Oxfordshire, UK
| | - Babak Javid
- Division of Experimental Medicine, University of California San Francisco, San Francisco, California, USA
| | - John Frater
- Peter Medawar Building for Pathogen Research, Nuffield Department of Medicine, University of Oxford, Oxford, Oxfordshire, UK
| | - Seena Fazel
- Department of Psychiatry, University of Oxford, Oxford, Oxfordshire, UK
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15
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Min S, Niu C, Shan W, Sun W, Liu C, Zheng F, Wang J, Li Q. Composition, source, and influencing factors of white spots formation in soybean paste. J Food Sci 2020; 85:3113-3123. [PMID: 32954501 DOI: 10.1111/1750-3841.15457] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Revised: 07/29/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022]
Abstract
White spots are commonly found in bean-based fermented food, which will significantly lower the product quality. This study aimed to analyze the composition of white spots and further reveal the source and influencing factors of white spots in bean-based fermented food using soybean paste as study model. The results showed that white spots were mainly composed of 40.96% free tyrosine and 37.94% tyrosine in combination form. During soybean paste fermentation, tyrosine was found to be produced by the actions of proteolytic enzymes secreted by Aspergillus oryzae 3.042 instead of the microbial metabolism and the excessive accumulation of tyrosine in soybean paste led to the formation of white spots. Among all influencing factors, high temperature treatment favored the formation of white spots. The existence of soy peptone and phenylalanine would postpone the precipitation of tyrosine while promoting the aggregation of the tyrosine precipitation. Field emission scanning electron microscope analysis showed that tyrosine would accumulate around the soybean protein particles and treatment at 120 °C would disrupt the structure of tyrosine-protein complex. Based on the above results, we proposed that treatment of soybean paste at temperature lower than 80 °C was the current practically applicable method to control the formation of white spots in soybean paste. PRACTICAL APPLICATION: This study developed a new idea to understand the composition and formation of white spots in soybean paste, which would provide guidance for prevention and control of white spots during the production of soybean paste for manufacturers and researchers.
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Affiliation(s)
- Shihao Min
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chengtuo Niu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Wanxiang Shan
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Weikang Sun
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Chunfeng Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Feiyun Zheng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Jinjing Wang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
| | - Qi Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
- Lab of Brewing Science and Technology, School of Biotechnology, Jiangnan University, Wuxi, 214122, China
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Abstract
Vibration analysis of the classical elastic structures is not only essential for the study of vibration reduction by predicting the dynamic behavior, but also important to ensure a reliable, safe, and lasting structural performance through the proper design procedure. In this paper, the influence of boundary conditions on the free and forced three-dimensional vibration analysis of thick rectangular plates has been performed using the improved Fourier series method. For the elastically restrained thick rectangular plate, the three-dimensional improved Fourier series displacement forms are used to model the vibration field. The energy formula is employed to describe the three-dimensional dynamics of the plate. All the unknown Fourier series coefficients are then solved by the Rayleigh-Ritz method. In order to validate the proposed model, several numerical examples are provided and compared against the results from the literature and Finite Element Analysis (FEA). In addition, the effects of the boundary restraining spring stiffness and the thickness ratios of thick rectangular plates are analyzed under elastically restrained boundary conditions to develop an in-depth understanding of the three-dimensional vibration characteristics of thick rectangular plates.
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Affiliation(s)
- Yufei Zhang
- College of Marine Engineering, Dalian Maritime University, Dalian, China
| | - Jingtao Du
- College of Power and Energy Engineering, Harbin Engineering University, Harbin, China
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17
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Abstract
Green and low cost production of strategic materials such as steel and graphene at large scale is a critical step towards sustainable industrial developments. Hydrogen is a green fuel for the future, and a key element for the clean production of steel. However, the sustainable and economic production of hydrogen is a barrier towards its large scale utilisation in iron and steelmaking, and other possible applications. As a key challenge, the water electrolysis, which is commonly used for the carbon-free production of hydrogen, is uneconomic and involves various problems including the corrosion of equipment, the use of expensive catalysts and high over-potentials, limiting its viability. Moreover, the hydrogen transportation from the electrolyser to the utilisation unit is problematic in terms of cost and safety. From a thermodynamic point of view, the potential and efficiency of the water splitting process can greatly be improved at high temperatures. Therefore, a practical approach to resolve the above-mentioned shortcomings can be based on the electro-generation of hydrogen in high temperature molten salts, and the utilisation of the generated hydrogen in situ to produce metals, alloys or other commercially valuable materials. Clean production of alloy powders is particularly interesting due to the rising of advanced manufacturing methods like additive manufacturing. The hydrogen produced in molten salts can also be used for the large scale preparation of high value advanced carbon nanostructures such as single and multi-layer high quality graphene and nanodiamonds. The combination of these findings can lead to the fabrication of hybrid structures with interesting energy and environmental applications. Surprisingly, the production of a large variety of materials such as Fe, Mo, W, Ni and Co-based alloys should be achievable by the electrolytic hydrogen produced in molten salts at a potential of around 1 V, which can easily be powered by advanced photovoltaic cells. This review discusses the recent advancements on these topics.
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Affiliation(s)
- Ali Reza Kamali
- Energy and Environmental Materials Research Centre (E2MC), School of Metallurgy, Northeastern University Shenyang 110819 People's Republic of China
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Shohag MJI, Wei Y, Zhang J, Feng Y, Rychlik M, He Z, Yang X. Genetic and physiological regulation of folate in pak choi (Brassica rapa subsp. Chinensis) germplasm. J Exp Bot 2020; 71:4914-4929. [PMID: 32639001 PMCID: PMC7410185 DOI: 10.1093/jxb/eraa218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/07/2020] [Indexed: 05/21/2023]
Abstract
Folates are one of the essential micronutrients for all living organisms. Due to inadequate dietary intake, folate deficiency remains prevalent in humans. Genetically diverse germplasms can potentially be used as parents in breeding programs and also for understanding the folate regulatory network. Therefore, we investigated the natural genetic diversity of folates and their physiological regulation in pak choi (Brassica rapa subsp. Chinensis) germplasm. The total folate concentration ranged from 52.7 μg 100 gFW-1 to 166.9 μg 100 gFW-1, with 3.2-fold variation. The main folate vitamer was represented by 5-CH3-H4folate, with 4.5-fold variation. The activities of GTP cyclohydrolase I and aminodeoxy chorismate synthase, the first step of folate synthesis, were high in high folate accessions and low in low folate accessions. Analysis of the transcription levels of 11 genes associated with folate metabolism demonstrated that the difference in folate concentrations may be primarily controlled at the post-transcriptional level. A general correlation between total folate and their precursors was observed. Folate diversity and chlorophyll content were tightly regulated through the methyl cycle. The diverse genetic variation in pak choi germplasm indicated the great genetic potential to integrate breeding programs for folate biofortification and unravel the physiological basis of folate homeostasis in planta.
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Affiliation(s)
- M J I Shohag
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Department of Agriculture, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
| | - Yanyan Wei
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Cultivation Base of Guangxi Key Laboratory for Agro-Environment and Agro-Products Safety, College of Agriculture, Guangxi University, Nanning, China
| | - Jie Zhang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- International Research Center for Environmental Membrane Biology, Department of Horticulture, Foshan University, Guangdong, China
| | - Ying Feng
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
| | - Michael Rychlik
- Chair of Analytical Food Chemistry, Technische Universitat Munchen, Lise-Meitner-Str. 34, Freising, Germany
| | - Zhenli He
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
| | - Xiaoe Yang
- Ministry of Education (MOE) Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, China
- Indian River Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Fort Pierce, FL, USA
- Correspondence:
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Cao B, Wu X, Zhou J, Wu H, Liu L, Zhang Q, DeMott MS, Gu C, Wang L, You D, Dedon PC. Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. Nucleic Acids Res 2020; 48:6715-6725. [PMID: 32484547 PMCID: PMC7337925 DOI: 10.1093/nar/gkaa473] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/16/2020] [Accepted: 05/22/2020] [Indexed: 12/12/2022] Open
Abstract
DNA damage and epigenetic marks are well established to have profound influences on genome stability and cell phenotype, yet there are few technologies to obtain high-resolution genomic maps of the many types of chemical modifications of DNA. Here we present Nick-seq for quantitative, sensitive, and accurate mapping of DNA modifications at single-nucleotide resolution across genomes. Pre-existing breaks are first blocked and DNA modifications are then converted enzymatically or chemically to strand-breaks for both 3'-extension by nick-translation to produce nuclease-resistant oligonucleotides and 3'-terminal transferase tailing. Following library preparation and next generation sequencing, the complementary datasets are mined with a custom workflow to increase sensitivity, specificity and accuracy of the map. The utility of Nick-seq is demonstrated with genomic maps of site-specific endonuclease strand-breaks in purified DNA from Eschericia coli, phosphorothioate epigenetics in Salmonella enterica Cerro 87, and oxidation-induced abasic sites in DNA from E. coli treated with a sublethal dose of hydrogen peroxide. Nick-seq applicability is demonstrated with strategies for >25 types of DNA modification and damage.
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Affiliation(s)
- Bo Cao
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xiaolin Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Jieliang Zhou
- KK Research Center, KK Women's and Children's Hospital, 229899, Singapore
| | - Hang Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Lili Liu
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Qinghua Zhang
- College of Life Sciences, Qufu Normal University, Qufu, Shandong 273165, China
| | - Michael S DeMott
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chen Gu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei 430071, China
| | - Delin You
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore 138602, Singapore
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Zhu Z, Meng G. ASFVdb: an integrative resource for genomic and proteomic analyses of African swine fever virus. Database (Oxford) 2020; 2020:baaa023. [PMID: 32294195 PMCID: PMC7159030 DOI: 10.1093/database/baaa023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/23/2020] [Accepted: 03/03/2020] [Indexed: 11/17/2022]
Abstract
The recent outbreaks of African swine fever (ASF) in China and Europe have threatened the swine industry globally. To control the transmission of ASF virus (ASFV), we developed the African swine fever virus database (ASFVdb), an online data visualization and analysis platform for comparative genomics and proteomics. On the basis of known ASFV genes, ASFVdb reannotates the genomes of every strain and newly annotates 5352 possible open reading frames (ORFs) of 45 strains. Moreover, ASFVdb performs a thorough analysis of the population genetics of all the published genomes of ASFV strains and performs functional and structural predictions for all genes. Users can obtain not only basic information for each gene but also its distribution in strains and conserved or high mutation regions, possible subcellular location and topology. In the genome browser, ASFVdb provides a sliding window for results of population genetic analysis, which facilitates genetic and evolutionary analyses at the genomic level. The web interface was constructed based on SWAV 1.0. ASFVdb is freely accessible at http://asfvdb.popgenetics.net.
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Affiliation(s)
- Zhenglin Zhu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Geng Meng
- Laboratory of Biomedical Research and College of Veterinary Medicine, China Agricultural University, Beijing, China
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