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Dorney RD, Johnston EB, Karnaneedi S, Ruethers T, Kamath SD, Gopi K, Mazumder D, Sammut J, Jerry D, Williamson NA, Nie S, Lopata AL. Variation in Shrimp Allergens: Place of Origin Effects on Food Safety Assessment. Int J Mol Sci 2024; 25:4531. [PMID: 38674116 PMCID: PMC11050280 DOI: 10.3390/ijms25084531] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/13/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
Due to the widespread use of shellfish ingredients in food products, accurate food labelling is urgently needed for consumers with shellfish allergies. Most crustacean allergen detection systems target the immunorecognition of the allergenic protein tropomyosin. However, this mode of detection may be affected by an origin-dependent protein composition. This study determined if the geographic location of capture, or aquaculture, influenced the allergenic protein profiles of Black Tiger Shrimp (Penaeus monodon), one of the most farmed and consumed shrimp species worldwide. Protein composition was analysed in shrimp from nine different locations in the Asia-Pacific by SDS-PAGE, immunoblotting, and mass spectrometry. Ten of the twelve known shrimp allergens were detected, but with considerable differences between locations. Sarcoplasmic calcium-binding protein, myosin light chain, and tropomyosin were the most abundant allergens in all locations. Hemocyanin-specific antibodies could identify up to six different isoforms, depending on the location of origin. Similarly, tropomyosin abundance varied by up to 13 times between locations. These findings suggest that allergen abundance may be related to shrimp origin and, thus, shrimp origin might directly impact the readout of commercial crustacean allergen detection kits, most of which target tropomyosin, and this should be considered in food safety assessments.
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Affiliation(s)
- Ryley D. Dorney
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
| | - Elecia B. Johnston
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Thimo Ruethers
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Tropical Futures Institute, James Cook University Singapore, Singapore 387380, Singapore
| | - Sandip D. Kamath
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Karthik Gopi
- School of Public Health, University Centre for Rural Health, The University of Sydney, Sydney, NSW 2006, Australia
| | - Debashish Mazumder
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jesmond Sammut
- Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
- Centre for Ecosystem Science, The School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Dean Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Tropical Futures Institute, James Cook University Singapore, Singapore 387380, Singapore
| | - Nicholas A. Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Andreas L. Lopata
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary Sciences, Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, QLD 4811, Australia (S.K.)
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
- Centre for Food and Allergy Research, Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
- Tropical Futures Institute, James Cook University Singapore, Singapore 387380, Singapore
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Wang J, Hu H, Jiang X, Zhang S, Yang W, Dong J, Yang T, Ma Y, Zhou L, Chen J, Nie S, Liu C, Ning Y, Zhu X, Liu B, Yang J, Zhao J. Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice. Rice (N Y) 2024; 17:27. [PMID: 38607544 PMCID: PMC11014823 DOI: 10.1186/s12284-024-00707-x] [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: 12/22/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the qPBR1 locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The qPBR1, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.
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Affiliation(s)
- Jian Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Xianya Jiang
- Yangjiang Institute of Agricultural Sciences, Yangjiang, 529500, China
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Wu Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yuese Ning
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoyuan Zhu
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China
| | - Bin Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Jianyuan Yang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, 510640, China.
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
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Wang X, Nie S, Wen Y, Zhao Z, Li J, Wang N, Zhang J. Age-related differences in auditory spatial processing revealed by acoustic change complex. Front Hum Neurosci 2024; 18:1342931. [PMID: 38681742 PMCID: PMC11045960 DOI: 10.3389/fnhum.2024.1342931] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/01/2024] [Indexed: 05/01/2024] Open
Abstract
Objectives The auditory spatial processing abilities mature throughout childhood and degenerate in older adults. This study aimed to compare the differences in onset cortical auditory evoked potentials (CAEPs) and location-evoked acoustic change complex (ACC) responses among children, adults, and the elderly and to investigate the impact of aging and development on ACC responses. Design One hundred and seventeen people were recruited in the study, including 57 typically-developed children, 30 adults, and 30 elderlies. The onset-CAEP evoked by white noise and ACC by sequential changes in azimuths were recorded. Latencies and amplitudes as a function of azimuths were analyzed using the analysis of variance, Pearson correlation analysis, and multiple linear regression model. Results The ACC N1'-P2' amplitudes and latencies in adults, P1'-N1' amplitudes in children, and N1' amplitudes and latencies in the elderly were correlated with angles of shifts. The N1'-P2' and P2' amplitudes decreased in the elderly compared to adults. In Children, the ACC P1'-N1' responses gradually differentiated into the P1'-N1'-P2' complex. Multiple regression analysis showed that N1'-P2' amplitudes (R2 = 0.33) and P2' latencies (R2 = 0.18) were the two most variable predictors in adults, while in the elderly, N1' latencies (R2 = 0.26) explained most variances. Although the amplitudes of onset-CAEP differed at some angles, it could not predict angle changes as effectively as ACC responses. Conclusion The location-evoked ACC responses varied among children, adults, and the elderly. The N1'-P2' amplitudes and P2' latencies in adults and N1' latencies in the elderly explained most variances of changes in spatial position. The differentiation of the N1' waveform was observed in children. Further research should be conducted across all age groups, along with behavioral assessments, to confirm the relationship between aging and immaturity in objective ACC responses and poorer subjective spatial performance. Significance ACCs evoked by location changes were assessed in adults, children, and the elderly to explore the impact of aging and development on these differences.
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Affiliation(s)
| | | | | | | | | | - Ningyu Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Juan Zhang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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4
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Stott EK, Nie S, Williamson NA, Skerratt LF. Free drug percentage of moxidectin declines with increasing concentrations in the serum of marsupials. Int J Parasitol Parasites Wildl 2024; 23:100899. [PMID: 38274349 PMCID: PMC10808906 DOI: 10.1016/j.ijppaw.2023.100899] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024]
Abstract
Moxidectin (MOX) is a macrocyclic lactone used to eliminate endo and ectoparasites in many mammalian species. It is notably the active ingredient of the anti-parasitic drug Cydectin®, manufactured by Virbac, and is frequently used to treat sarcoptic mange in Australian wildlife. Protein binding plays a significant role in the efficacy of a drug, as the unbound/free drug in plasma ultimately reflects the pharmacologically relevant concentration. This study aimed to investigate the free drug percentage of Moxidectin after in vitro spiking into the sera of four sarcoptic mange-susceptible Australian wildlife species; the koala (Phascolarctos cinereus), the bare-nosed wombat (Vombatus ursinus), the eastern grey kangaroo (Macropus giganteus), and the mountain brushtail possum (Trichosurus cunninghami). Three concentration points of MOX were tested for each individual: 20 pg/μL, 100 pg/μL and 500 pg/μL. Serum from five individuals of each species underwent an equilibrium dialysis followed by liquid chromatography tandem mass spectrometry (LC-MS/MS). The results showed an atypical concentration dependent binding across all species, where free drug percentage decreased as MOX concentration increased. In addition, wombats showed significantly lower free drug levels. These findings call for further research into the mechanisms of moxidectin protein binding to help understand MOX pharmacokinetics in marsupials.
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Affiliation(s)
- Eliza K. Stott
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, Werribee, The University of Melbourne, Victoria, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Victoria, Australia
| | - Nicholas A. Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Victoria, Australia
| | - Lee F. Skerratt
- One Health Research Group, Melbourne Veterinary School, Faculty of Science, Werribee, The University of Melbourne, Victoria, Australia
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5
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Shanley HT, Taki AC, Nguyen N, Wang T, Byrne JJ, Ang CS, Leeming MG, Nie S, Williamson N, Zheng Y, Young ND, Korhonen PK, Hofmann A, Chang BCH, Wells TNC, Häberli C, Keiser J, Jabbar A, Sleebs BE, Gasser RB. Structure-activity relationship and target investigation of 2-aryl quinolines with nematocidal activity. Int J Parasitol Drugs Drug Resist 2024; 24:100522. [PMID: 38295619 PMCID: PMC10845918 DOI: 10.1016/j.ijpddr.2024.100522] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX464 or obefazimod, as a nematocidal candidate; synthesised a series of analogues which were assessed for activity against the free-living nematode Caenorhabditis elegans; and predicted compound-target relationships by thermal proteome profiling (TPP) and in silico docking. Here, we logically extended this work and critically evaluated the anthelmintic activity of ABX464 analogues on Haemonchus contortus (barber's pole worm) - a highly pathogenic nematode of ruminant livestock. First, we tested a series of 44 analogues on H. contortus (larvae and adults) to investigate the nematocidal pharmacophore of ABX464, and identified one compound with greater potency than the parent compound and showed moderate activity against a select number of other parasitic nematodes (including Ancylostoma, Heligmosomoides and Strongyloides species). Using TPP and in silico modelling studies, we predicted protein HCON_00074590 (a predicted aldo-keto reductase) as a target candidate for ABX464 in H. contortus. Future work aims to optimise this compound as a nematocidal candidate and investigate its pharmacokinetic properties. Overall, this study presents a first step toward the development of a new nematocide.
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Affiliation(s)
- Harrison T Shanley
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Aya C Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Nghi Nguyen
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Joseph J Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; National Reference Centre for Authentic Food, Max Rubner-Institut, 95326, Kulmbach, Germany
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Tim N C Wells
- Medicines for Malaria Venture (MMV), 1215, Geneva, Switzerland
| | - Cécile Häberli
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland; University of Basel, 4001, Basel, Switzerland
| | - Jennifer Keiser
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, 4123, Allschwil, Switzerland; University of Basel, 4001, Basel, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brad E Sleebs
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria, 3010, Australia.
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Tian XC, Chen ZY, Nie S, Shi TL, Yan XM, Bao YT, Li ZC, Ma HY, Jia KH, Zhao W, Mao JF. Plant-LncPipe: a computational pipeline providing significant improvement in plant lncRNA identification. Hortic Res 2024; 11:uhae041. [PMID: 38638682 PMCID: PMC11024640 DOI: 10.1093/hr/uhae041] [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] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/02/2024] [Indexed: 04/20/2024]
Abstract
Long non-coding RNAs (lncRNAs) play essential roles in various biological processes, such as chromatin remodeling, post-transcriptional regulation, and epigenetic modifications. Despite their critical functions in regulating plant growth, root development, and seed dormancy, the identification of plant lncRNAs remains a challenge due to the scarcity of specific and extensively tested identification methods. Most mainstream machine learning-based methods used for plant lncRNA identification were initially developed using human or other animal datasets, and their accuracy and effectiveness in predicting plant lncRNAs have not been fully evaluated or exploited. To overcome this limitation, we retrained several models, including CPAT, PLEK, and LncFinder, using plant datasets and compared their performance with mainstream lncRNA prediction tools such as CPC2, CNCI, RNAplonc, and LncADeep. Retraining these models significantly improved their performance, and two of the retrained models, LncFinder-plant and CPAT-plant, alongside their ensemble, emerged as the most suitable tools for plant lncRNA identification. This underscores the importance of model retraining in tackling the challenges associated with plant lncRNA identification. Finally, we developed a pipeline (Plant-LncPipe) that incorporates an ensemble of the two best-performing models and covers the entire data analysis process, including reads mapping, transcript assembly, lncRNA identification, classification, and origin, for the efficient identification of lncRNAs in plants. The pipeline, Plant-LncPipe, is available at: https://github.com/xuechantian/Plant-LncRNA-pipline.
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Affiliation(s)
- Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kai-Hua Jia
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Wei Zhao
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå 90187, Sweden
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå 90187, Sweden
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7
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Wang M, Zhu X, Huang Z, Chen M, Xu P, Liao S, Zhao Y, Gao Y, He J, Luo Y, Chen H, Wei X, Nie S, Dong J, Zhu L, Zhuang C, Zhao J, Liu Z, Zhou H. Controlling diurnal flower-opening time by manipulating the jasmonate pathway accelerates development of indica-japonica hybrid rice breeding. Plant Biotechnol J 2024. [PMID: 38526838 DOI: 10.1111/pbi.14343] [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: 10/03/2023] [Revised: 02/21/2024] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Inter-subspecific indica-japonica hybrid rice (Oryza sativa) has the potential for increased yields over traditional indica intra-subspecies hybrid rice, but limited yield of F1 hybrid seed production (FHSP) hinders the development of indica-japonica hybrid rice breeding. Diurnal flower-opening time (DFOT) divergence between indica and japonica rice has been a major contributing factor to this issue, but few DFOT genes have been cloned. Here, we found that manipulating the expression of jasmonate (JA) pathway genes can effectively modulate DFOT to improve the yield of FHSP in rice. Treating japonica cultivar Zhonghua 11 (ZH11) with methyl jasmonate (MeJA) substantially advanced DFOT. Furthermore, overexpressing the JA biosynthesis gene OPDA REDUCTASE 7 (OsOPR7) and knocking out the JA inactivation gene CHILLING TOLERANCE 1 (OsHAN1) in ZH11 advanced DFOT by 1- and 2-h respectively; and knockout of the JA signal suppressor genes JASMONATE ZIM-DOMAIN PROTEIN 7 (OsJAZ7) and OsJAZ9 resulted in 50-min and 1.5-h earlier DFOT respectively. The yields of FHSP using japonica male-sterile lines GAZS with manipulated JA pathway genes were significantly higher than that of GAZS wildtype. Transcriptome analysis, cytological observations, measurements of elastic modulus and determination of cell wall components indicated that the JA pathway could affect the loosening of the lodicule cell walls by regulating their composition through controlling sugar metabolism, which in turn influences DFOT. This research has vital implications for breeding japonica rice cultivars with early DFOT to facilitate indica-japonica hybrid rice breeding.
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Affiliation(s)
- Mumei Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, China
| | - Xiaopei Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Zhen Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Minghao Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Peng Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Shitang Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yongzhen Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yannan Gao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jiahui He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yutong Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Huixuan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Xiaoying Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Liya Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuxiong Zhuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Guangdong Key Laboratory of New Technology in Rice Breeding & Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhenlan Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Hai Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory for Enhancing Resource Use Efficiency of Crops in South China, Ministry of Agriculture and Rural Affairs, College of Life Sciences, South China Agricultural University, Guangzhou, China
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8
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Dong J, Ma Y, Hu H, Wang J, Yang W, Fu H, Zhang L, Chen J, Zhou L, Li W, Nie S, Liu Z, Zhao J, Liu B, Yang T, Zhang S. The Function of SD1 on Shoot Length and its Pyramiding Effect on Shoot Length and Plant Height in Rice (Oryza sativa L.). Rice (N Y) 2024; 17:21. [PMID: 38526756 DOI: 10.1186/s12284-024-00699-8] [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: 11/22/2023] [Accepted: 03/08/2024] [Indexed: 03/27/2024]
Abstract
Strong seedling vigor is imperative to achieve stable seedling establishment and enhance the competitiveness against weeds in rice direct seeding. Shoot length (SL) is one of the important traits associated with seedling vigor in rice, but few genes for SL have been cloned so far. In the previous study, we identified two tightly linked and stably expressed QTLs for SL, qSL-1f and qSL-1d by genome-wide association study, and cloned the causal gene (LOC_Os01g68500) underlying qSL-1f. In the present study, we identify LOC_Os01g66100 (i.e. the semidwarf gene SD1), a well-known gene controlling plant height (PH) at the adult-plant stage, as the causal gene underlying qSL-1d through gene-based haplotype analysis and knockout transgenic verification. By measuring the phenotypes (SL and PH) of various haplotypes of the two genes and their knockout lines, we found SD1 and LOC_ Os01g68500 controlled both SL and PH, and worked in the same direction, which provided the directly genetic evidence for a positive correlation between SL and PH combined with the analysis of SL and PH in the diverse natural population. Moreover, the knockout transgenic experiments suggested that SD1 had a greater effect on PH compared with LOC_ Os01g68500, but no significant difference in the effect on SL. Further investigation of the pyramiding effects of SD1 and LOC_Os01g68500 based on their haplotype combinations suggested that SD1 may play a dominant role in controlling SL and PH when the two genes coexist. In this study, the effect of SD1 on SL at the seedling stage is validated. In total, two causal genes, SD1 and LOC_ Os01g68500, for SL are cloned in our studies, which controlled both SL and PH, and the suitable haplotypes of SD1 and LOC_ Os01g68500 are beneficial to achieve the desired SL and PH in different rice breeding objectives. These results provide a new clue to develop rice varieties for direct seeding and provide new genetic resources for molecular breeding of rice with suitable PH and strong seedling vigor.
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Affiliation(s)
- Jingfang Dong
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Yamei Ma
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Haifei Hu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Jian Wang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wu Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Hua Fu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Longting Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Jiansong Chen
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Lian Zhou
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Wenhui Li
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Ziqiang Liu
- College of Agriculture, South China Agricultural University, 510642, Guangzhou, China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Bin Liu
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China
| | - Tifeng Yang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
| | - Shaohong Zhang
- Rice Research Institute, Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Engineering Laboratory, Key Laboratory of Genetics and Breeding of High -Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Academy of Agricultural Sciences, 510640, Guangzhou, Guangdong, China.
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9
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Wu J, Nie S, Li C, Wang X, Peng Y, Shang J, Diao L, Ding H, Si Q, Wang S, Tong R, Li Y, Sun L, Zhang J. Sound-localization-related activation and functional connectivity of dorsal auditory pathway in relation to demographic, cognitive, and behavioral characteristics in age-related hearing loss. Front Neurosci 2024; 18:1353413. [PMID: 38562303 PMCID: PMC10982313 DOI: 10.3389/fnins.2024.1353413] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/26/2024] [Indexed: 04/04/2024] Open
Abstract
Background Patients with age-related hearing loss (ARHL) often struggle with tracking and locating sound sources, but the neural signature associated with these impairments remains unclear. Materials and methods Using a passive listening task with stimuli from five different horizontal directions in functional magnetic resonance imaging, we defined functional regions of interest (ROIs) of the auditory "where" pathway based on the data of previous literatures and young normal hearing listeners (n = 20). Then, we investigated associations of the demographic, cognitive, and behavioral features of sound localization with task-based activation and connectivity of the ROIs in ARHL patients (n = 22). Results We found that the increased high-level region activation, such as the premotor cortex and inferior parietal lobule, was associated with increased localization accuracy and cognitive function. Moreover, increased connectivity between the left planum temporale and left superior frontal gyrus was associated with increased localization accuracy in ARHL. Increased connectivity between right primary auditory cortex and right middle temporal gyrus, right premotor cortex and left anterior cingulate cortex, and right planum temporale and left lingual gyrus in ARHL was associated with decreased localization accuracy. Among the ARHL patients, the task-dependent brain activation and connectivity of certain ROIs were associated with education, hearing loss duration, and cognitive function. Conclusion Consistent with the sensory deprivation hypothesis, in ARHL, sound source identification, which requires advanced processing in the high-level cortex, is impaired, whereas the right-left discrimination, which relies on the primary sensory cortex, is compensated with a tendency to recruit more resources concerning cognition and attention to the auditory sensory cortex. Overall, this study expanded our understanding of the neural mechanisms contributing to sound localization deficits associated with ARHL and may serve as a potential imaging biomarker for investigating and predicting anomalous sound localization.
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Affiliation(s)
- Junzhi Wu
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Shuai Nie
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Chunlin Li
- School of Biomedical Engineering, Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Xing Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ye Peng
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jiaqi Shang
- Center of Clinical Hearing, Shandong Second Provincial General Hospital, Jinan, Shandong, China
| | - Linan Diao
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Hongping Ding
- College of Special Education, Binzhou Medical University, Yantai, Shandong, China
| | - Qian Si
- School of Cyber Science and Technology, Beihang University, Beijing, China
| | - Songjian Wang
- Key Laboratory of Otolaryngology, Head and Neck Surgery, Ministry of Education, Beijing Institute of Otolaryngology, Beijing, China
- Department of Otolaryngology, Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Renjie Tong
- School of Biomedical Engineering, Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Yutang Li
- School of Biomedical Engineering, Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Liwei Sun
- School of Biomedical Engineering, Beijing Key Laboratory of Fundamental Research on Biomechanics in Clinical Application, Capital Medical University, Beijing, China
| | - Juan Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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10
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Li JY, Wang NY, Wang X, Li BN, Nie S, Li H, Zhang J. [Horizontal sound localization in presence of noise in normal-hearing young adults]. Zhonghua Er Bi Yan Hou Tou Jing Wai Ke Za Zhi 2024; 59:204-211. [PMID: 38561257 DOI: 10.3760/cma.j.cn115330-20231010-00132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Objective: This study investigates the effect of signal-to-noise ratio (SNR), frequency, and bandwidth on horizontal sound localization accuracy in normal-hearing young adults. Methods: From August 2022 to December 2022, a total of 20 normal-hearing young adults, including 7 males and 13 females, with an age range of 20 to 35 years and a mean age of 25.4 years, were selected to participate in horizontal azimuth recognition tests under both quiet and noisy conditions. Six narrowband filtered noise stimuli were used with central frequencies (CF) of 250, 2 000, and 4 000 Hz and bandwidths of 1/6 and 1 octave. Continuous broadband white noise was used as the background masker, and the signal-to-noise ratio (SNR) was 0, -3, and -12 dB. The root-mean-square error (RMS error) was used to measure sound localization accuracy, with smaller values indicating higher accuracy. Friedman test was used to compare the effects of SNR and CF on sound localization accuracy, and Wilcoxon signed-rank test was used to compare the impact of the two bandwidths on sound localization accuracy in noise. Results: In a quiet environment, the RMS error in horizontal azimuth in normal-hearing young adults ranged from 4.3 to 8.1 degrees. Sound localization accuracy decreased with decreasing SNR: at 0 dB SNR (range: 5.3-12.9 degrees), the difference from the quiet condition was not significant (P>0.05); however, at -3 dB (range: 7.3-16.8 degrees) and -12 dB SNR (range: 9.4-41.2 degrees), sound localization accuracy significantly decreased compared to the quiet condition (all P<0.01). Under noisy conditions, there were differences in sound localization accuracy among stimuli with different frequencies and bandwidths, with higher frequencies performing the worst, followed by middle frequencies, and lower frequencies performing the best, with significant differences (all P<0.01). Sound localization accuracy for 1/6 octave stimuli was more susceptible to noise interference than 1 octave stimuli (all P<0.01). Conclusions: The ability of normal-hearing young adults to localize sound in the horizontal plane in the presence of noise is influenced by SNR, CF, and bandwidth. Noise with SNRs of ≥-3 dB can lead to decreased accuracy in narrowband sound localization. Higher CF signals and narrower bandwidths are more susceptible to noise interference.
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Affiliation(s)
- J Y Li
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - N Y Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - X Wang
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - B N Li
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - S Nie
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - H Li
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
| | - J Zhang
- Department of Otolaryngology Head and Neck Surgery, Beijing Chaoyang Hospital of Capital Medical University, Beijing 100020, China
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11
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Shi TL, Jia KH, Bao YT, Nie S, Tian XC, Yan XM, Chen ZY, Li ZC, Zhao SW, Ma HY, Zhao Y, Li X, Zhang RG, Guo J, Zhao W, El-Kassaby YA, Müller N, Van de Peer Y, Wang XR, Street NR, Porth I, An X, Mao JF. High-quality genome assembly enables prediction of allele-specific gene expression in hybrid poplar. Plant Physiol 2024:kiae078. [PMID: 38412470 DOI: 10.1093/plphys/kiae078] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 02/29/2024]
Abstract
Poplar (Populus) is a well-established model system for tree genomics and molecular breeding, and hybrid poplar is widely used in forest plantations. However, distinguishing its diploid homologous chromosomes is difficult, complicating advanced functional studies on specific alleles. In this study, we applied a trio-binning design and PacBio High-Fidelity long-read sequencing to obtain haplotype-phased telomere-to-telomere genome assemblies for the two parents of the well-studied F1 hybrid "84K" (Populus alba × P. tremula var. glandulosa). Almost all chromosomes, including the telomeres and centromeres, were completely assembled for each haplotype subgenome apart from two small gaps on one chromosome. By incorporating information from these haplotype assemblies and extensive RNA-seq data, we analyzed gene expression patterns between the two subgenomes and alleles. Transcription bias at the subgenome level was not uncovered, but extensive expression differences were detected between alleles. We developed machine-learning (ML) models to predict allele-specific expression (ASE) with high accuracy and identified underlying genome features most highly influencing ASE. One of our models with 15 predictor variables achieved 77% accuracy on the training set and 74% accuracy on the testing set. ML models identified gene body CHG methylation, sequence divergence, and transposon occupancy both upstream and downstream of alleles as important factors for ASE. Our haplotype-phased genome assemblies and ML strategy highlight an avenue for functional studies in Populus and provide additional tools for studying ASE and heterosis in hybrids.
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Affiliation(s)
- Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Kai-Hua Jia
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji'nan 250100, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
| | - Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Ye Zhao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xiang Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, China
| | - Jing Guo
- College of Forestry, Shandong Agricultural University, Tai'an 271000, China
| | - Wei Zhao
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Yousry Aly El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Niels Müller
- Thünen-Institute of Forest Genetics, Sieker Landstrasse 2, 22927 Grosshansdorf, Germany
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University and, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiao-Ru Wang
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, SE-901 87 Umeå, Sweden
| | - Nathaniel Robert Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Xinmin An
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden
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12
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MCS, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Nat Commun 2024; 15:937. [PMID: 38297033 PMCID: PMC10831071 DOI: 10.1038/s41467-024-45224-z] [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: 07/24/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024] Open
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl-tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure-activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Craig J Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, VIC, Australia
| | - Riley D Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Charisse Flerida A Pasaje
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Calibr, Division of the Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Kate J Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | | | - Dana M Klug
- School of Pharmacy, University College London, London, WC1N 1AX, UK
| | - Peter J Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW, 2006, Australia
| | - Luiz C Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jair L Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Gouranga P Jana
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Bikash C Maity
- TCG Lifesciences Private Limited, Salt-Lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh, EH9 3JJ, UK
| | - Derek S Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences and Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul, 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - David A Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY, 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY, 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA
| | - Marcus C S Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee, DD1 4HN, UK
| | - Elizabeth A Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Matthew H Todd
- School of Pharmacy, University College London, London, WC1N 1AX, UK.
- Structural Genomics Consortium, University College London, London, WC1N 1AX, UK.
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, 3010, Australia.
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13
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Nie S, Yan Y, Wang Y, Liu S, Guo W, Yang L, Shen H. Proper doses of brassinolide enhance somatic embryogenesis in different competent Korean pine cell lines during embryogenic callus differentiation. Front Plant Sci 2024; 15:1330103. [PMID: 38322821 PMCID: PMC10845146 DOI: 10.3389/fpls.2024.1330103] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/05/2024] [Indexed: 02/08/2024]
Abstract
Somatic embryogenesis of Korean pine (Pinus koraiensis Sieb. Et Zucc.), an ecologically and econimically very important conifer species, was hindered by the gradually weakens and fast runaway of the embryogenicity and embryo competence of the embryogenic callus. Brassinolide (BL) has shown the enhancing capability of somatic embryo regeneration. For checking the function of BL in this issue, we applied different concentrations of BL to Korean pine callus materials exhibiting different embryogenic capacities and subsequently monitored the physiological alterations and hormone dynamics of the embryogenic callus. Our study revealed that calli with different embryogenic strengths responded differently to different concentrations of BL, but the effect after the addition of BL was very uniform. The addition of BL during the proliferation phase of embryogenic callus may help to stimulate the biological activity of callus during the proliferation process and improve the level of cell metabolism, which is accompanied by a reduction in storage substances. BL could reduce the level of endogenous auxin IAA in embryogenic callus and increase the level of abscisic acid to regulate cell division and differentiation. In addition, the MDA content in the callus was significantly decreased and the activity of antioxidant enzymes was significantly increased after the addition of BL. During the proliferation of embryogenic callus, BL was added to participate in the metabolism of phenylpropane in the cells and to increase the activity of phenylalanine ammonia-lyase and the content of lignin in the cells. We deduced that the proper doses of BL for Korean pine embryogenic callus culture were as follow: calli with low, high and decreasing embryogenicity were subcultured after the addition of 0.75 mg/L, 0.35 mg/L, 2.00 mg/L BL, respectively, during proliferation culture stage.
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Affiliation(s)
- Shuai Nie
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Yong Yan
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Yue Wang
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Shanshan Liu
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Wenhui Guo
- College of Forestry, Northeast Forestry University, Harbin, China
| | - Ling Yang
- College of Forestry, Northeast Forestry University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), Harbin, China
| | - Hailong Shen
- College of Forestry, Northeast Forestry University, Harbin, China
- State Forestry and Grassland Administration Engineering Technology Research Center of Korean Pine, Harbin, China
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14
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Shi TL, Ma HY, Wang X, Liu H, Yan XM, Tian XC, Li ZC, Bao YT, Chen ZY, Zhao SW, Xiang Q, Jia KH, Nie S, Guan W, Mao JF. Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn ( Xanthoceras sorbifolium), an oil-producing tree with significant deployment values. Front Plant Sci 2024; 14:1297817. [PMID: 38312356 PMCID: PMC10834690 DOI: 10.3389/fpls.2023.1297817] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/22/2023] [Indexed: 02/06/2024]
Abstract
Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.
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Affiliation(s)
- Tian-Le Shi
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hai-Yao Ma
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xinrui Wang
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hui Liu
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Mei Yan
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao-Yang Chen
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qiuhong Xiang
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan, China
| | - Shuai Nie
- Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Rice Research Institute, Guangzhou, China
- Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangzhou, China
| | - Wenbin Guan
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jian-Feng Mao
- State Key Laboratory of Tree Genetics and Breeding, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, School of Ecology and Nature Conservation, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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15
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Stuart SF, Curpen P, Gomes AJ, Lan MC, Nie S, Williamson NA, Kannourakis G, Morokoff AP, Achuthan AA, Luwor RB. Interleukin-11/IL-11 Receptor Promotes Glioblastoma Cell Proliferation, Epithelial-Mesenchymal Transition, and Invasion. Brain Sci 2024; 14:89. [PMID: 38248304 PMCID: PMC10813507 DOI: 10.3390/brainsci14010089] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/22/2023] [Accepted: 12/29/2023] [Indexed: 01/23/2024] Open
Abstract
Glioblastoma is highly proliferative and invasive. However, the regulatory cytokine networks that promote glioblastoma cell proliferation and invasion into other areas of the brain are not fully defined. In the present study, we define a critical role for the IL-11/IL-11Rα signalling axis in glioblastoma proliferation, epithelial to mesenchymal transition, and invasion. We identified enhanced IL-11/IL-11Rα expression correlated with reduced overall survival in glioblastoma patients using TCGA datasets. Proteomic analysis of glioblastoma cell lines overexpressing IL-11Rα displayed a proteome that favoured enhanced proliferation and invasion. These cells also displayed greater proliferation and migration, while the knockdown of IL-11Rα reversed these tumourigenic characteristics. In addition, these IL-11Rα overexpressing cells displayed enhanced invasion in transwell invasion assays and in 3D spheroid invasion assays, while knockdown of IL-11Rα resulted in reduced invasion. Furthermore, IL-11Rα-overexpressing cells displayed a more mesenchymal-like phenotype compared to parental cells and expressed greater levels of the mesenchymal marker Vimentin. Overall, our study identified that the IL-11/IL-11Rα pathway promotes glioblastoma cell proliferation, EMT, and invasion.
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Affiliation(s)
- Sarah F. Stuart
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia; (S.F.S.); (A.J.G.); (A.P.M.)
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia;
| | - Peter Curpen
- Townsville Hospital and Health Service, James Cook University, Townsville, QLD 4814, Australia;
| | - Adele J. Gomes
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia; (S.F.S.); (A.J.G.); (A.P.M.)
| | - Michelle C. Lan
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia; (S.F.S.); (A.J.G.); (A.P.M.)
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia; (S.N.); (N.A.W.)
| | - Nicholas A. Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3052, Australia; (S.N.); (N.A.W.)
| | - George Kannourakis
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia;
- Federation University, Ballarat, VIC 3350, Australia
| | - Andrew P. Morokoff
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia; (S.F.S.); (A.J.G.); (A.P.M.)
- Department of Neurosurgery, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia
| | - Adrian A. Achuthan
- Department of Medicine, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia;
| | - Rodney B. Luwor
- Department of Surgery, The University of Melbourne, The Royal Melbourne Hospital, Parkville, VIC 3050, Australia; (S.F.S.); (A.J.G.); (A.P.M.)
- Fiona Elsey Cancer Research Institute, Ballarat, VIC 3350, Australia;
- Federation University, Ballarat, VIC 3350, Australia
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16
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Shanley HT, Taki AC, Nguyen N, Wang T, Byrne JJ, Ang CS, Leeming MG, Nie S, Williamson N, Zheng Y, Young ND, Korhonen PK, Hofmann A, Wells TNC, Jabbar A, Sleebs BE, Gasser RB. Structure activity relationship and target prediction for ABX464 analogues in Caenorhabditis elegans. Bioorg Med Chem 2024; 98:117540. [PMID: 38134663 DOI: 10.1016/j.bmc.2023.117540] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/20/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023]
Abstract
Global challenges with treatment failures and/or widespread resistance in parasitic worms against commercially available anthelmintics lend impetus to the development of new anthelmintics with novel mechanism(s) of action. The free-living nematode Caenorhabditis elegans is an important model organism used for drug discovery, including the screening and structure-activity investigation of new compounds, and target deconvolution. Previously, we conducted a whole-organism phenotypic screen of the 'Pandemic Response Box' (from Medicines for Malaria Venture, MMV) and identified a hit compound, called ABX464, with activity against C. elegans and a related, parasitic nematode, Haemonchus contortus. Here, we tested a series of 44 synthesized analogues to explore the pharmacophore of activity on C. elegans and revealed five compounds whose potency was similar or greater than that of ABX464, but which were not toxic to human hepatoma (HepG2) cells. Subsequently, we employed thermal proteome profiling (TPP), protein structure prediction and an in silico-docking algorithm to predict ABX464-target candidates. Taken together, the findings from this study contribute significantly to the early-stage drug discovery of a new nematocide based on ABX464. Future work is aimed at validating the ABX464-protein interactions identified here, and at assessing ABX464 and associated analogues against a panel of parasitic nematodes, towards developing a new anthelmintic with a mechanism of action that is distinct from any of the compounds currently-available commercially.
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Affiliation(s)
- Harrison T Shanley
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Aya C Taki
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nghi Nguyen
- Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joseph J Byrne
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael G Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; National Reference Centre for Authentic Food, Max Rubner-Institut, 95326 Kulmbach, Germany
| | - Tim N C Wells
- Medicines for Malaria Venture (MMV), 1215 Geneva, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Brad E Sleebs
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia; Chemical Biology Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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17
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Li Y, Li X, Nie S, Zhang M, Yang Q, Xu W, Duan Y, Wang X. Reticulate evolution of the tertiary relict Osmanthus. Plant J 2024; 117:145-160. [PMID: 37837261 DOI: 10.1111/tpj.16480] [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] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 10/15/2023]
Abstract
When interspecific gene flow is common, species relationships are more accurately represented by a phylogenetic network than by a bifurcating tree. This study aimed to uncover the role of introgression in the evolution of Osmanthus, the only genus of the subtribe Oleinae (Oleaceae) with its distribution center in East Asia. We built species trees, detected introgression, and constructed networks using multiple kinds of sequencing data (whole genome resequencing, transcriptome sequencing, and Sanger sequencing of nrDNA) combined with concatenation and coalescence approaches. Then, based on well-understood species relationships, historical biogeographic analyses and diversification rate estimates were employed to reveal the history of Osmanthus. Osmanthus originated in mid-Miocene Europe and dispersed to the eastern Tibetan Plateau in the late Miocene. Thereafter, it continued to spread eastwards. Phylogenetic conflict is common within the 'Core Osmanthus' clade and is seen at both early and late stages of diversification, leading to hypotheses of net-like species relationships. Incomplete lineage sorting proved ineffective in explaining phylogenetic conflicts and thus supported introgression as the main cause of conflicts. This study elucidates the diversification history of a relict genus in the subtropical regions of eastern Asia and reveals that introgression had profound effects on its evolutionary history.
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Affiliation(s)
- Yongfu Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xuan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Shuai Nie
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, China
| | - Min Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Qinghua Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Wenbin Xu
- Wuhan Botanical Garden, the Chinese Academy of Sciences, Wuhan, 430074, Hubei, China
| | - Yifan Duan
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
| | - Xianrong Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Sciences, International Cultivar Registration Center for Osmanthus, Nanjing Forestry University, Nanjing, 210037, Jiangsu, China
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18
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Asadollahi K, Rajput S, de Zhang LA, Ang CS, Nie S, Williamson NA, Griffin MDW, Bathgate RAD, Scott DJ, Weikl TR, Jameson GNL, Gooley PR. Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1. Nat Commun 2023; 14:8155. [PMID: 38071229 PMCID: PMC10710507 DOI: 10.1038/s41467-023-44010-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/26/2023] [Indexed: 12/18/2023] Open
Abstract
The conformational ensembles of G protein-coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced-fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.
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Affiliation(s)
- Kazem Asadollahi
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sunnia Rajput
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Lazarus Andrew de Zhang
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
- Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC, 3052, Australia
| | - Ching-Seng Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Nicholas A Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ross A D Bathgate
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Daniel J Scott
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia
- The Florey, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thomas R Weikl
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Guy N L Jameson
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia
- School of Chemistry, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul R Gooley
- Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, 3010, Australia.
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19
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Ruethers T, Johnston EB, Karnaneedi S, Nie S, Nugraha R, Taki AC, Kamath SD, Williamson NA, Mehr SS, Campbell DE, Lopata AL. Commercial shellfish skin prick test extracts show critical variability in allergen repertoire. Allergy 2023; 78:3261-3265. [PMID: 37602511 PMCID: PMC10952831 DOI: 10.1111/all.15853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 08/22/2023]
Affiliation(s)
- Thimo Ruethers
- Tropical Futures Institute, James Cook UniversitySingaporeSingapore
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
| | - Elecia B. Johnston
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneParkvilleVictoriaAustralia
| | - Roni Nugraha
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
- Department of Aquatic Product Technology, Faculty of Fisheries and Marine ScienceIPB UniversityBogorIndonesia
| | - Aya C. Taki
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Melbourne Veterinary School, Faculty of ScienceThe University of MelbourneParkvilleVictoriaAustralia
| | - Sandip D. Kamath
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
- Division of Medical BiotechnologyInstitute of Pathophysiology and Allergy Research, Center of Pathophysiology, Infectiology and Immunology, Medical University of ViennaViennaAustria
| | - Nicholas A. Williamson
- Bio21 Molecular Science and Biotechnology Institute, University of MelbourneParkvilleVictoriaAustralia
| | - Sam S. Mehr
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of Allergy and ImmunologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Epworth Allergy Specialists, Epworth HospitalRichmondVictoriaAustralia
- Paediatric Allergy and Immunology Unit, The Royal Children's HospitalMelbourneVictoriaAustralia
| | - Dianne E. Campbell
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Department of Allergy and ImmunologyThe Children's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Child and Adolescent Health, Faculty of Medicine and HealthThe University of SydneySydneyNew South WalesAustralia
| | - Andreas L. Lopata
- Tropical Futures Institute, James Cook UniversitySingaporeSingapore
- Molecular Allergy Research Laboratory, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy Research, Murdoch Children's Research InstituteMelbourneVictoriaAustralia
- Australian Institute of Tropical Health and Medicine, James Cook UniversityTownsvilleQueenslandAustralia
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20
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Agarwala PK, Nie S, Reid GE, Kapoor S. Global lipid remodelling by hypoxia aggravates migratory potential in pancreatic cancer while maintaining plasma membrane homeostasis. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159398. [PMID: 37748704 DOI: 10.1016/j.bbalip.2023.159398] [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: 06/14/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Hypoxia plays an important role in pancreatic cancer progression. It drives various metabolic reprogramming in cells including that of lipids, which in turn, can modify the structure and function of cell membranes. Homeostatic adaptation of membranes is well-recognized, but how and if it is regulated in hypoxic pancreatic cancer and its relation to aggressive phenotype and metastasis remains elusive. Here we show hypoxia-induced extensive global lipid remodelling spanning changes in lipid classes, unsaturation levels, glyceryl backbone and acyl chain lengths. No major modulation of plasma membrane biophysical properties revealed a decoupling of lipidome modulation from membrane properties under hypoxia. This was supported by observing minor changes in the lipidome of plasma membranes under hypoxia. Further, hypoxia increased migration and invasion underpinned by reduced actin volume, cell cortical stiffness and facile tether dynamics. In conclusion, we demonstrate buffering of the lipidome alterations leading to a homeostatic membrane response. These findings will help to understand the hypoxic regulation of pancreatic membrane homeostasis and identify tangible theranostic avenues.
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Affiliation(s)
- Prema Kumari Agarwala
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Gavin E Reid
- School of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia; Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, Victoria 3010, Australia; Bio21 Institute of Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India; Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima 739-8528, Japan.
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21
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Taki AC, Ruethers T, Nugraha R, Karnaneedi S, Williamson NA, Nie S, Leeming MG, Mehr SS, Campbell DE, Lopata AL. Thermostable allergens in canned fish: Evaluating risks for fish allergy. Allergy 2023; 78:3221-3234. [PMID: 37650248 PMCID: PMC10952748 DOI: 10.1111/all.15864] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 12/30/2022] [Revised: 07/30/2023] [Accepted: 08/08/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Major fish allergens, including parvalbumin (PV), are heat stable and can withstand extensive cooking processes. Thus, the management of fish allergy generally relies on complete avoidance. Fish-allergic patients may be advised to consume canned fish, as some fish-allergic individuals have reported tolerance to canned fish. However, the safety of consuming canned fish has not been evaluated with comprehensive immunological and molecular analysis of canned fish products. METHODS We characterized the in vitro immunoreactivity of serum obtained from fish-allergic subjects to canned fish. Seventeen canned fish products (salmon n = 8; tuna n = 7; sardine n = 2) were assessed for the content and integrity of PV using allergen-specific antibodies. Subsequently, the sIgE binding of five selected products was evaluated for individual fish-allergic patients (n = 53). Finally, sIgE-binding proteins were identified by mass spectrometry. RESULTS The canned fish showed a markedly reduced PV content and binding to PV-specific antibodies compared with conventionally cooked fish. However, PV and other heat-stable fish allergens, including tropomyosin and collagen, still maintained their sIgE-binding capacity. Of 53 patients, 66% showed sIgE binding to canned fish proteins. The canned sardine contained proteins bound to sIgE from 51% of patients, followed by canned salmon (43%-45%) and tuna (8%-17%). PV was the major allergen in canned salmon and sardine. Tropomyosin and/or collagen also showed sIgE binding. CONCLUSION We showed that canned fish products may not be safe for all fish-allergic patients. Canned fish products should only be considered into the diet of individuals with fish allergy, after detailed evaluation which may include in vitro diagnostics to various heat-stable fish allergens and food challenge conducted in suitable environments.
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Affiliation(s)
- Aya C. Taki
- Molecular Allergy Research Laboratory, Discipline of Molecular and Cell Biology, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of ScienceThe University of MelbourneParkvilleVictoriaAustralia
| | - Thimo Ruethers
- Molecular Allergy Research Laboratory, Discipline of Molecular and Cell Biology, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Tropical Futures InstituteJames Cook UniversitySingapore CitySingapore
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Roni Nugraha
- Molecular Allergy Research Laboratory, Discipline of Molecular and Cell Biology, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Department of Aquatic Product Technology, Faculty of Fisheries and Marine ScienceIPB UniversityBogorIndonesia
| | - Shaymaviswanathan Karnaneedi
- Molecular Allergy Research Laboratory, Discipline of Molecular and Cell Biology, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Nicholas A. Williamson
- Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Shuai Nie
- Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Michael G. Leeming
- Bio21 Molecular Science and Biotechnology InstituteThe University of MelbourneParkvilleVictoriaAustralia
| | - Sam S. Mehr
- Centre for Food and Allergy ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of Allergy and ImmunologyThe Royal Children's HospitalParkvilleVictoriaAustralia
| | - Dianne E. Campbell
- Centre for Food and Allergy ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
- Department of Allergy and ImmunologyThe Children's Hospital at WestmeadWestmeadNew South WalesAustralia
- Discipline of Paediatrics and Child HealthThe University of SydneyWestmeadNew South WalesAustralia
| | - Andreas L. Lopata
- Molecular Allergy Research Laboratory, Discipline of Molecular and Cell Biology, College of Public Health, Medical and Veterinary SciencesJames Cook UniversityTownsvilleQueenslandAustralia
- Tropical Futures InstituteJames Cook UniversitySingapore CitySingapore
- Australian Institute of Tropical Health and MedicineJames Cook UniversityTownsvilleQueenslandAustralia
- Centre for Food and Allergy ResearchMurdoch Children's Research InstituteParkvilleVictoriaAustralia
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22
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Abstract
The construction of p-n heterojunctions has become a widely adopted strategy for achieving the selective detection of reducing gases, including H2 and CO. Nevertheless, the elucidation of the gas selectivity mechanism at the nanoscale remains elusive. First-principle calculations provide an attractive avenue for comprehending the influence of coordination structures on gas-sensitive selectivity, thereby unveiling the structure-activity relationship of p-n heterojunction sites. In this study, we investigate the selective adsorption behavior of H2 and CO on a NiO-TiO2 heterojunction using density functional theory. The results of d-band center analysis confirm that the NiO-TiO2 heterojunction with adsorbed oxygen significantly enhances the adsorption stability of reducing gases. Intriguingly, our calculations reveal that H2 has a higher affinity for adsorbed oxygen on the heterojunction surface compared to that of CO, corresponding to a lower H2 adsorption energy. Density of states (DOS) results indicate that the NiO-TiO2 heterojunction, with preadsorbed oxygen, exhibits ultrahigh selectivity with an n-type gas-sensitive response to H2, effectively eliminating the cross-sensitivity observed with CO, as confirmed by gas-sensitive characterization research. The sensing mechanism of the NiO-TiO2 heterojunction's selective detection of H2 without interference from CO can be visually explained by electron transfer and potential barrier changes, paving the way for future developments in novel, selective gas-sensitive materials.
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Affiliation(s)
- Shuai Nie
- School of Materials and Metallurgy, University of Science and Technology Liaoning, Anshan 114051, China
| | - Jing Li
- School of Materials and Metallurgy, University of Science and Technology Liaoning, Anshan 114051, China
| | - Lin Tao
- School of Chemical Engineering, University of Science and Technology Liaoning, Anshan 114051, China
| | - Yunxia He
- School of Materials and Metallurgy, University of Science and Technology Liaoning, Anshan 114051, China
| | - Davoud Dastan
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Xianze Meng
- School of Materials, Sun Yat-sen University, Guangzhou 510006, China
| | - Preeyaporn Poldorn
- Center for Organic Electronic and Alternative Energy, Faculty of Science, Ubon Ratchathani University, Ubon Ratchathani 34190, Thailand
| | - Xitao Yin
- School of Physics and Optoelectronic Engineering, Ludong University, Yantai 264000, China
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23
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Yao W, Wang A, Nie Y, Lv Z, Nie S, Huang C, Liu Z. Study on the Recognition of Coal Miners' Unsafe Behavior and Status in the Hoist Cage Based on Machine Vision. Sensors (Basel) 2023; 23:8794. [PMID: 37960492 PMCID: PMC10647559 DOI: 10.3390/s23218794] [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: 09/21/2023] [Revised: 10/21/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]
Abstract
The hoist cage is used to lift miners in a coal mine's auxiliary shaft. Monitoring miners' unsafe behaviors and their status in the hoist cage is crucial to production safety in coal mines. In this study, a visual detection model is proposed to estimate the number and categories of miners, and to identify whether the miners are wearing helmets and whether they have fallen in the hoist cage. A dataset with eight categories of miners' statuses in hoist cages was developed for training and validating the model. Using the dataset, the classical models were trained for comparison, from which the YOLOv5s model was selected to be the basic model. Due to small-sized targets, poor lighting conditions, and coal dust and shelter, the detection accuracy of the Yolov5s model was only 89.2%. To obtain better detection accuracy, k-means++ clustering algorithm, a BiFPN-based feature fusion network, the convolutional block attention module (CBAM), and a CIoU loss function were proposed to improve the YOLOv5s model, and an attentional multi-scale cascaded feature fusion-based YOLOv5s model (AMCFF-YOLOv5s) was subsequently developed. The training results on the self-built dataset indicate that its detection accuracy increased to 97.6%. Moreover, the AMCFF-YOLOv5s model was proven to be robust to noise and light.
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Affiliation(s)
- Wei Yao
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
- Digital Inteltech, CHN Energy, Beijing 100011, China
| | - Aiming Wang
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
| | - Yifan Nie
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
| | - Zhengyan Lv
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
| | - Shuai Nie
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
| | - Congwei Huang
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
| | - Zhenyu Liu
- School of Mechanical and Electrical Engineering, China University of Mining & Technology, Beijing 100083, China; (W.Y.); (Y.N.); (Z.L.); (S.N.); (C.H.); (Z.L.)
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24
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Yan XM, Zhou SS, Liu H, Zhao SW, Tian XC, Shi TL, Bao YT, Li ZC, Jia KH, Nie S, Guo JF, Kong L, Porth IM, Mao JF. Unraveling the evolutionary dynamics of the TPS gene family in land plants. Front Plant Sci 2023; 14:1273648. [PMID: 37900760 PMCID: PMC10600500 DOI: 10.3389/fpls.2023.1273648] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/15/2023] [Indexed: 10/31/2023]
Abstract
Terpenes and terpenoids are key natural compounds for plant defense, development, and composition of plant oil. The synthesis and accumulation of a myriad of volatile terpenoid compounds in these plants may dramatically alter the quality and flavor of the oils, which provide great commercial utilization value for oil-producing plants. Terpene synthases (TPSs) are important enzymes responsible for terpenic diversity. Investigating the differentiation of the TPS gene family could provide valuable theoretical support for the genetic improvement of oil-producing plants. While the origin and function of TPS genes have been extensively studied, the exact origin of the initial gene fusion event - it occurred in plants or microbes - remains uncertain. Furthermore, a comprehensive exploration of the TPS gene differentiation is still pending. Here, phylogenetic analysis revealed that the fusion of the TPS gene likely occurred in the ancestor of land plants, following the acquisition of individual C- and N- terminal domains. Potential mutual transfer of TPS genes was observed among microbes and plants. Gene synteny analysis disclosed a differential divergence pattern between TPS-c and TPS-e/f subfamilies involved in primary metabolism and those (TPS-a/b/d/g/h subfamilies) crucial for secondary metabolites. Biosynthetic gene clusters (BGCs) analysis suggested a correlation between lineage divergence and potential natural selection in structuring terpene diversities. This study provides fresh perspectives on the origin and evolution of the TPS gene family.
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Affiliation(s)
- Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shan-Shan Zhou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Shuangyushu No.1 Primary School, Beijing, China
| | - Hui Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kai-Hua Jia
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Crop Genetic Improvement & Ecology and Physiology, Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences & Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs & Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Horticulture and Food, Guangdong Eco-Engineering Polytechnic, Guangzhou, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Personnel Section, Qufu Nishan National Forest Park Management Service Center, Qufu, China
| | - Ilga M. Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, Québec, QC, Canada
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
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25
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Peng X, Han J, Li X, Liu G, Xu Y, Peng Y, Nie S, Li W, Li X, Chen Z, Peng H, Cao R, Fang Y. Electrocatalytic hydrogen evolution with a copper porphyrin bearing meso-( o-carborane) substituents. Chem Commun (Camb) 2023; 59:10777-10780. [PMID: 37593777 DOI: 10.1039/d3cc03104g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
A newly designed copper complex of 5,15-bis(pentafluorophenyl)-10,20-bis(o-carborane)porphyrin (1) was synthesized and tested for the electrocatalytic hydrogen evolution reaction (HER). In acetonitrile, 1 was much more efficient than Cu 5,15-bis(pentafluorophenyl)-10,20-diphenylporphyrin (2) for electrocatalytic HER by shifting the catalytic wave to the anodic direction by 190 mV. In aqueous media, 1 also outperformed 2 by achieving higher current densities under smaller overpotentials. This enhancement was attributed to the aromatic and the strong electron-withdrawing properties of o-carborane groups. This work is significant to address the crucial effects of meso-(o-carborane) substituents of metal porphyrins on boosting the electrocatalytic HER.
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Affiliation(s)
- Xinyang Peng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Jinxiu Han
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Xialiang Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Guijun Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Yuhan Xu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Yuxin Peng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Shuai Nie
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Wenzi Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Xinrui Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Zhuo Chen
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Haonan Peng
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
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26
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Suwanchaikasem P, Nie S, Selby‐Pham J, Walker R, Boughton BA, Idnurm A. Hormonal and proteomic analyses of southern blight disease caused by Athelia rolfsii and root chitosan priming on Cannabis sativa in an in vitro hydroponic system. Plant Direct 2023; 7:e528. [PMID: 37692128 PMCID: PMC10485662 DOI: 10.1002/pld3.528] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/05/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023]
Abstract
Southern blight disease, caused by the fungal pathogen Athelia rolfsii, suppresses plant growth and reduces product yield in Cannabis sativa agriculture. Mechanisms of pathology of this soil-borne disease remain poorly understood, with disease management strategies reliant upon broad-spectrum antifungal use. Exposure to chitosan, a natural elicitor, has been proposed as an alternative method to control diverse fungal diseases in an eco-friendly manner. In this study, C. sativa plants were grown in the Root-TRAPR system, a transparent hydroponic growth device, where plant roots were primed with .2% colloidal chitosan prior to A. rolfsii inoculation. Both chitosan-primed and unprimed inoculated plants displayed classical symptoms of wilting and yellowish leaves, indicating successful infection. Non-primed infected plants showed increased shoot defense responses with doubling of peroxidase and chitinase activities. The levels of growth and defense hormones including auxin, cytokinin, and jasmonic acid were increased 2-5-fold. In chitosan-primed infected plants, shoot peroxidase activity and phytohormone levels were decreased 1.5-4-fold relative to the unprimed infected plants. When compared with shoots, roots were less impacted by A. rolfsii infection, but the pathogen secreted cell wall-degrading enzymes into the root-growth solution. Chitosan priming inhibited root growth, with root lengths of chitosan-primed plants approximately 65% shorter than the control, but activated root defense responses, with root peroxidase activity increased 2.7-fold along with increased secretion of defense proteins. The results suggest that chitosan could be an alternative platform to manage southern blight disease in C. sativa cultivation; however, further optimization is required to maximize effectiveness of chitosan.
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Affiliation(s)
| | - Shuai Nie
- Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneMelbourneVictoriaAustralia
| | - Jamie Selby‐Pham
- School of BioSciencesUniversity of MelbourneMelbourneVictoriaAustralia
- Cannabis and Biostimulants Research Group Pty LtdMelbourneVictoriaAustralia
| | - Robert Walker
- School of BioSciencesUniversity of MelbourneMelbourneVictoriaAustralia
| | - Berin A. Boughton
- School of BioSciencesUniversity of MelbourneMelbourneVictoriaAustralia
- Australian National Phenome CentreMurdoch UniversityPerthWestern AustraliaAustralia
| | - Alexander Idnurm
- School of BioSciencesUniversity of MelbourneMelbourneVictoriaAustralia
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27
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Xie SC, Wang Y, Morton CJ, Metcalfe RD, Dogovski C, Pasaje CFA, Dunn E, Luth MR, Kumpornsin K, Istvan ES, Park JS, Fairhurst KJ, Ketprasit N, Yeo T, Yildirim O, Bhebhe MN, Klug DM, Rutledge PJ, Godoy LC, Dey S, De Souza ML, Siqueira-Neto JL, Du Y, Puhalovich T, Amini M, Shami G, Loesbanluechai D, Nie S, Williamson N, Jana GP, Maity BC, Thomson P, Foley T, Tan DS, Niles JC, Han BW, Goldberg DE, Burrows J, Fidock DA, Lee MC, Winzeler EA, Griffin MDW, Todd MH, Tilley L. Reaction hijacking inhibition of Plasmodium falciparum asparagine tRNA synthetase. Res Sq 2023:rs.3.rs-3198291. [PMID: 37546892 PMCID: PMC10402266 DOI: 10.21203/rs.3.rs-3198291/v1] [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] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Malaria poses an enormous threat to human health. With ever increasing resistance to currently deployed drugs, breakthrough compounds with novel mechanisms of action are urgently needed. Here, we explore pyrimidine-based sulfonamides as a new low molecular weight inhibitor class with drug-like physical parameters and a synthetically accessible scaffold. We show that the exemplar, OSM-S-106, has potent activity against parasite cultures, low mammalian cell toxicity and low propensity for resistance development. In vitro evolution of resistance using a slow ramp-up approach pointed to the Plasmodium falciparum cytoplasmic asparaginyl tRNA synthetase (PfAsnRS) as the target, consistent with our finding that OSM-S-106 inhibits protein translation and activates the amino acid starvation response. Targeted mass spectrometry confirms that OSM-S-106 is a pro-inhibitor and that inhibition of PfAsnRS occurs via enzyme-mediated production of an Asn-OSM-S-106 adduct. Human AsnRS is much less susceptible to this reaction hijacking mechanism. X-ray crystallographic studies of human AsnRS in complex with inhibitor adducts and docking of pro-inhibitors into a model of Asn-tRNA-bound PfAsnRS provide insights into the structure activity relationship and the selectivity mechanism.
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Affiliation(s)
- Stanley C. Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yinuo Wang
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Craig J. Morton
- Biomedical Manufacturing Program, CSIRO, Clayton South, Australia
| | - Riley D. Metcalfe
- Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Con Dogovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeline R Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Calibr, Division of the Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eva S Istvan
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, USA
| | - Joon Sung Park
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Kate J. Fairhurst
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Nutpakal Ketprasit
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tomas Yeo
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Okan Yildirim
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | | | - Dana M. Klug
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Camperdown, NSW 2006, Australia
| | - Luiz C. Godoy
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mariana Laureano De Souza
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Jair L. Siqueira-Neto
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Mona Amini
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gerry Shami
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | | | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Gouranga P. Jana
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Bikash C. Maity
- TCG Lifesciences Private Limited, Salt-lake Electronics Complex, Kolkata, India
| | - Patrick Thomson
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Thomas Foley
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3JJ, United Kingdom
| | - Derek S. Tan
- Chemical Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jacquin C Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Byung Woo Han
- Research Institute of Pharmaceutical Sciences & Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea
| | - Daniel E Goldberg
- Division of Infectious Diseases, Department of Medicine, Washington University in St. Louis, USA
| | - Jeremy Burrows
- Medicines for Malaria Venture, 20, Route de Pré-Bois 1215, Geneva 15, Switzerland
| | - David A. Fidock
- Center for Malaria Therapeutics and Antimicrobial Resistance, Columbia University Medical Center, New York, NY 10032, USA
- Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
- Division of Infectious Diseases, Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Marcus C.S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
- Wellcome Centre for Anti-Infectives Research, Biological Chemistry and Drug Discovery, University of Dundee, Dundee DD1 4HN, United Kingdom
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Michael D. W. Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Matthew H. Todd
- School of Pharmacy, University College London, London WC1N 1AX, United Kingdom
- Structural Genomics Consortium, University College London, London WC1N 1AX, United Kingdom
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
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28
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Wang T, Koukoulis TF, Vella LJ, Su H, Purnianto A, Nie S, Ang CS, Ma G, Korhonen PK, Taki AC, Williamson NA, Reid GE, Gasser RB. The Proteome and Lipidome of Extracellular Vesicles from Haemonchus contortus to Underpin Explorations of Host-Parasite Cross-Talk. Int J Mol Sci 2023; 24:10955. [PMID: 37446130 DOI: 10.3390/ijms241310955] [Citation(s) in RCA: 1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 06/29/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023] Open
Abstract
Many parasitic worms have a major adverse impact on human and animal populations worldwide due to the chronicity of their infections. There is a growing body of evidence indicating that extracellular vesicles (EVs) are intimately involved in modulating (suppressing) inflammatory/immune host responses and parasitism. As one of the most pathogenic nematodes of livestock animals, Haemonchus contortus is an ideal model system for EV exploration. Here, employing a multi-step enrichment process (in vitro culture, followed by ultracentrifugation, size exclusion and filtration), we enriched EVs from H. contortus and undertook the first comprehensive (qualitative and quantitative) multi-omic investigation of EV proteins and lipids using advanced liquid chromatography-mass spectrometry and informatics methods. We identified and quantified 561 proteins and 446 lipids in EVs and compared these molecules with those of adult worms. We identified unique molecules in EVs, such as proteins linked to lipid transportation and lipid species (i.e., sphingolipids) associated with signalling, indicating the involvement of these molecules in parasite-host cross-talk. This work provides a solid starting point to explore the functional roles of EV-specific proteins and lipids in modulating parasite-host cross-talk, and the prospect of finding ways of disrupting or interrupting this relationship to suppress or eliminate parasite infection.
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Affiliation(s)
- Tao Wang
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Tiana F Koukoulis
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Laura J Vella
- Department of Surgery, The Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Huaqi Su
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Adityas Purnianto
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Shuai Nie
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Ching-Seng Ang
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Guangxu Ma
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Pasi K Korhonen
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Aya C Taki
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Nicholas A Williamson
- Bio21 Mass Spectrometry and Proteomics Facility, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Gavin E Reid
- Department of Biochemistry and Pharmacology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bio21 Molecular Science and Biotechnology Institute, School of Chemistry, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Robin B Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia
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29
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Suwanchaikasem P, Nie S, Idnurm A, Selby‐Pham J, Walker R, Boughton BA. Effects of chitin and chitosan on root growth, biochemical defense response and exudate proteome of Cannabis sativa. Plant Environ Interact 2023; 4:115-133. [PMID: 37362423 PMCID: PMC10290428 DOI: 10.1002/pei3.10106] [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] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/09/2023] [Accepted: 03/19/2023] [Indexed: 06/28/2023]
Abstract
Fungal pathogens pose a major threat to Cannabis sativa production, requiring safe and effective management procedures to control disease. Chitin and chitosan are natural molecules that elicit plant defense responses. Investigation of their effects on C. sativa will advance understanding of plant responses towards elicitors and provide a potential pathway to enhance plant resistance against diseases. Plants were grown in the in vitro Root-TRAPR system and treated with colloidal chitin and chitosan. Plant morphology was monitored, then plant tissues and exudates were collected for enzymatic activity assays, phytohormone quantification, qPCR analysis and proteomics profiling. Chitosan treatments showed increased total chitinase activity and expression of pathogenesis-related (PR) genes by 3-5 times in the root tissues. In the exudates, total peroxidase and chitinase activities and levels of defense proteins such as PR protein 1 and endochitinase 2 were increased. Shoot development was unaffected, but root development was inhibited after chitosan exposure. In contrast, chitin treatments had no significant impact on any defense parameters, including enzymatic activities, hormone quantities, gene expression levels and root secreted proteins. These results indicate that colloidal chitosan, significantly enhancing defense responses in C. sativa root system, could be used as a potential elicitor, particularly in hydroponic scenarios to manage crop diseases.
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Affiliation(s)
| | - Shuai Nie
- Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology InstituteUniversity of MelbourneMelbourneVictoria3052Australia
| | - Alexander Idnurm
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
| | - Jamie Selby‐Pham
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
- Cannabis and Biostimulants Research Group Pty LtdMelbourneVictoria3020Australia
| | - Robert Walker
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
| | - Berin A. Boughton
- School of BioSciencesUniversity of MelbourneMelbourneVictoria3010Australia
- Australian National Phenome CentreMurdoch UniversityPerthWestern Australia6150Australia
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30
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Zhao SW, Guo JF, Kong L, Nie S, Yan XM, Shi TL, Tian XC, Ma HY, Bao YT, Li ZC, Chen ZY, Zhang RG, Ma YP, El-Kassaby YA, Porth I, Zhao W, Mao JF. Haplotype-resolved genome assembly of Coriaria nepalensis a non-legume nitrogen-fixing shrub. Sci Data 2023; 10:259. [PMID: 37156769 PMCID: PMC10167230 DOI: 10.1038/s41597-023-02171-6] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/20/2023] [Indexed: 05/10/2023] Open
Abstract
Coriaria nepalensis Wall. (Coriariaceae) is a nitrogen-fixing shrub which forms root nodules with the actinomycete Frankia. Oils and extracts of C. nepalensis have been reported to be bacteriostatic and insecticidal, and C. nepalensis bark provides a valuable tannin resource. Here, by combining PacBio HiFi sequencing and Hi-C scaffolding techniques, we generated a haplotype-resolved chromosome-scale genome assembly for C. nepalensis. This genome assembly is approximately 620 Mb in size with a contig N50 of 11 Mb, with 99.9% of the total assembled sequences anchored to 40 pseudochromosomes. We predicted 60,862 protein-coding genes of which 99.5% were annotated from databases. We further identified 939 tRNAs, 7,297 rRNAs, and 982 ncRNAs. The chromosome-scale genome of C. nepalensis is expected to be a significant resource for understanding the genetic basis of root nodulation with Frankia, toxicity, and tannin biosynthesis.
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Affiliation(s)
- Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Hai-Yao Ma
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Zhao-Yang Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Ren-Gang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yong-Peng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden.
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, SE-901 87, Sweden.
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Li N, Chen Y, Li W, Ding Z, Zhao D, Nie S. BViT: Broad Attention-Based Vision Transformer. IEEE Trans Neural Netw Learn Syst 2023; PP. [PMID: 37126636 DOI: 10.1109/tnnls.2023.3264730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Recent works have demonstrated that transformer can achieve promising performance in computer vision, by exploiting the relationship among image patches with self-attention. They only consider the attention in a single feature layer, but ignore the complementarity of attention in different layers. In this article, we propose broad attention to improve the performance by incorporating the attention relationship of different layers for vision transformer (ViT), which is called BViT. The broad attention is implemented by broad connection and parameter-free attention. Broad connection of each transformer layer promotes the transmission and integration of information for BViT. Without introducing additional trainable parameters, parameter-free attention jointly focuses on the already available attention information in different layers for extracting useful information and building their relationship. Experiments on image classification tasks demonstrate that BViT delivers superior accuracy of 75.0%/81.6% top-1 accuracy on ImageNet with 5M/22M parameters. Moreover, we transfer BViT to downstream object recognition benchmarks to achieve 98.9% and 89.9% on CIFAR10 and CIFAR100, respectively, that exceed ViT with fewer parameters. For the generalization test, the broad attention in Swin Transformer, T2T-ViT and LVT also brings an improvement of more than 1%. To sum up, broad attention is promising to promote the performance of attention-based models. Code and pretrained models are available at https://github.com/DRL/BViT.
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Qiu F, Nie S. Liquid chromatography coupled with tandem mass spectrometry for simultaneous quantification of valproate, valproate-glucuronide and lamotrigine in various biological matrices of rat. Biomed Chromatogr 2023:e5652. [PMID: 37056037 DOI: 10.1002/bmc.5652] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/06/2023] [Accepted: 04/11/2023] [Indexed: 04/15/2023]
Abstract
Valproate and lamotrigine are commonly used as antiepileptic drugs even in pregnant and breastfeeding women. The extent and effects of drug exposure on the developing brain of the offspring are not well understood. Animal models can be utilised to investigate the transfer of substances into fetal brain with the ultimate aim of providing insights to aid clinical decisions. In the present study, a LC-MS/MS method was developed and validated for quantification of valproate (VPA), valproate-glucuronide (VPA-Gluc, a major metabolite of valproate) and lamotrigine (LTG) in rat blood plasma, cerebrospinal fluid, and brain tissue. 10 μl of sample was spiked with stable isotope-labelled internal standards and extracted by methanol. An Agilent RRHD Eclipse Plus C18 column (2.1×100 mm, 1.8 μm) was used. The MS/MS transitions were 143.1016 to 143.1016 (VPA), 319.1392 to 143.0978 (VPA-Gluc), and 256.0157 to 210.9826 (LTG). The linear ranges of VPA, VPA-Gluc and LTG were 30-250 μg/ml, 10-140 μg/ml and 0.3-1 μg/ml, respectively. The intra- and inter-day accuracy and precision, carryover, sensitivity, and recovery were evaluated according to the FDA guidance for Bioanalytical method validation. Finally, the validated method was applied to a set of experimental animal samples and produced results highly comparable to an orthogonal analytical method.
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Affiliation(s)
- Fiona Qiu
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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Karimkhanloo H, Keenan SN, Bayliss J, De Nardo W, Miotto PM, Devereux CJ, Nie S, Williamson NA, Ryan A, Watt MJ, Montgomery MK. Mouse strain-dependent variation in metabolic associated fatty liver disease (MAFLD): a comprehensive resource tool for pre-clinical studies. Sci Rep 2023; 13:4711. [PMID: 36949095 PMCID: PMC10033881 DOI: 10.1038/s41598-023-32037-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/21/2023] [Indexed: 03/24/2023] Open
Abstract
Non-alcoholic steatohepatitis (NASH), characterized as the joint presence of steatosis, hepatocellular ballooning and lobular inflammation, and liver fibrosis are strong contributors to liver-related and overall mortality. Despite the high global prevalence of NASH and the substantial healthcare burden, there are currently no FDA-approved therapies for preventing or reversing NASH and/or liver fibrosis. Importantly, despite nearly 200 pharmacotherapies in different phases of pre-clinical and clinical assessment, most therapeutic approaches that succeed from pre-clinical rodent models to the clinical stage fail in subsequent Phase I-III trials. In this respect, one major weakness is the lack of adequate mouse models of NASH that also show metabolic comorbidities commonly observed in NASH patients, including obesity, type 2 diabetes and dyslipidaemia. This study provides an in-depth comparison of NASH pathology and deep metabolic profiling in eight common inbred mouse strains (A/J, BALB/c, C3H/HeJ, C57BL/6J, CBA/CaH, DBA/2J, FVB/N and NOD/ShiLtJ) fed a western-style diet enriched in fat, sucrose, fructose and cholesterol for eight months. Combined analysis of histopathology and hepatic lipid metabolism, as well as measures of obesity, glycaemic control and insulin sensitivity, dyslipidaemia, adipose tissue lipolysis, systemic inflammation and whole-body energy metabolism points to the FVB/N mouse strain as the most adequate diet-induced mouse model for the recapitulation of metabolic (dysfunction) associated fatty liver disease (MAFLD) and NASH. With efforts in the pharmaceutical industry now focussed on developing multi-faceted therapies; that is, therapies that improve NASH and/or liver fibrosis, and concomitantly treat other metabolic comorbidities, this mouse model is ideally suited for such pre-clinical use.
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Affiliation(s)
- Hamzeh Karimkhanloo
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
- Metabolism, Diabetes and Obesity Program, Monash Biomedicine Discovery Institute, and Department of Physiology, Monash University, Clayton, VIC, Australia
| | - Stacey N Keenan
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - William De Nardo
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Paula M Miotto
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Camille J Devereux
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Nicholas A Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Andrew Ryan
- TissuPath, Mount Waverley, VIC, 3149, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Magdalene K Montgomery
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, University of Melbourne, Melbourne, VIC, 3010, Australia.
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34
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Tian XC, Guo JF, Yan XM, Shi TL, Nie S, Zhao SW, Bao YT, Li ZC, Kong L, Su GJ, Mao JF, Lin J. Unique gene duplications and conserved microsynteny potentially associated with resistance to wood decay in the Lauraceae. Front Plant Sci 2023; 14:1122549. [PMID: 36968354 PMCID: PMC10030967 DOI: 10.3389/fpls.2023.1122549] [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] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Wood decay resistance (WDR) is marking the value of wood utilization. Many trees of the Lauraceae have exceptional WDR, as evidenced by their use in ancient royal palace buildings in China. However, the genetics of WDR remain elusive. Here, through comparative genomics, we revealed the unique characteristics related to the high WDR in Lauraceae trees. We present a 1.27-Gb chromosome-level assembly for Lindera megaphylla (Lauraceae). Comparative genomics integrating major groups of angiosperm revealed Lauraceae species have extensively shared gene microsynteny associated with the biosynthesis of specialized metabolites such as isoquinoline alkaloids, flavonoid, lignins and terpenoid, which play significant roles in WDR. In Lauraceae genomes, tandem and proximal duplications (TD/PD) significantly expanded the coding space of key enzymes of biosynthesis pathways related to WDR, which may enhance the decay resistance of wood by increasing the accumulation of these compounds. Among Lauraceae species, genes of WDR-related biosynthesis pathways showed remarkable expansion by TD/PD and conveyed unique and conserved motifs in their promoter and protein sequences, suggesting conserved gene collinearity, gene expansion and gene regulation supporting the high WDR. Our study thus reveals genomic profiles related to biochemical transitions among major plant groups and the genomic basis of WDR in the Lauraceae.
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Affiliation(s)
- Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Guang-Ju Su
- National Tree Breeding Station for Nanmu in Zhuxi, Forest Farm of Zhuxi County, Hubei, China
| | - Jian-Feng Mao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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35
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Nie S, Zhao SW, Shi TL, Zhao W, Zhang RG, Tian XC, Guo JF, Yan XM, Bao YT, Li ZC, Kong L, Ma HY, Chen ZY, Liu H, El-Kassaby YA, Porth I, Yang FS, Mao JF. Gapless genome assembly of azalea and multi-omics investigation into divergence between two species with distinct flower color. Hortic Res 2023; 10:uhac241. [PMID: 36643737 PMCID: PMC9832866 DOI: 10.1093/hr/uhac241] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/17/2022] [Indexed: 05/09/2023]
Abstract
The genus Rhododendron (Ericaceae), with more than 1000 species highly diverse in flower color, is providing distinct ornamental values and a model system for flower color studies. Here, we investigated the divergence between two parental species with different flower color widely used for azalea breeding. Gapless genome assembly was generated for the yellow-flowered azalea, Rhododendron molle. Comparative genomics found recent proliferation of long terminal repeat retrotransposons (LTR-RTs), especially Gypsy, has resulted in a 125 Mb (19%) genome size increase in species-specific regions, and a significant amount of dispersed gene duplicates (13 402) and pseudogenes (17 437). Metabolomic assessment revealed that yellow flower coloration is attributed to the dynamic changes of carotenoids/flavonols biosynthesis and chlorophyll degradation. Time-ordered gene co-expression networks (TO-GCNs) and the comparison confirmed the metabolome and uncovered the specific gene regulatory changes underpinning the distinct flower pigmentation. B3 and ERF TFs were found dominating the gene regulation of carotenoids/flavonols characterized pigmentation in R. molle, while WRKY, ERF, WD40, C2H2, and NAC TFs collectively regulated the anthocyanins characterized pigmentation in the red-flowered R simsii. This study employed a multi-omics strategy in disentangling the complex divergence between two important azaleas and provided references for further functional genetics and molecular breeding.
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Affiliation(s)
- Shuai Nie
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Shi-Wei Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Tian-Le Shi
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-901 87 Umeå, Sweden
| | - Ren-Gang Zhang
- Department of Bioinformatics, Ori (Shandong) Gene Science and Technology Co., Ltd., Weifang 261322, China
| | - Xue-Chan Tian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Jing-Fang Guo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xue-Mei Yan
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yu-Tao Bao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhi-Chao Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Lei Kong
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hai-Yao Ma
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Zhao-Yang Chen
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Hui Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
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Farzana F, McConville MJ, Renoir T, Li S, Nie S, Tran H, Hannan AJ, Hatters DM, Boughton BA. Longitudinal spatial mapping of lipid metabolites reveals pre-symptomatic changes in the hippocampi of Huntington's disease transgenic mice. Neurobiol Dis 2023; 176:105933. [PMID: 36436748 DOI: 10.1016/j.nbd.2022.105933] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 11/23/2022] [Indexed: 11/26/2022] Open
Abstract
In Huntington's disease (HD), a key pathological feature includes the development of inclusion-bodies of fragments of the mutant huntingtin protein in the neurons of the striatum and hippocampus. To examine the molecular changes associated with inclusion-body formation, we applied MALDI-mass spectrometry imaging and deuterium pulse labelling to determine lipid levels and synthesis rates in the hippocampus of a transgenic mouse model of HD (R6/1 line). The R6/1 HD mice lacked inclusions in the hippocampus at 6 weeks of age (pre-symptomatic), whereas inclusions were pervasive by 16 weeks of age (symptomatic). Hippocampal subfields (CA1, CA3 and DG), which formed the highest density of inclusion formation in the mouse brain showed a reduction in the relative abundance of neuron-enriched lipids that have roles in neurotransmission, synaptic plasticity, neurogenesis, and ER-stress protection. Lipids involved in the adaptive response to ER stress (phosphatidylinositol, phosphatidic acid, and ganglioside classes) displayed increased rates of synthesis in HD mice relative to WT mice at all the ages examined, including prior to the formation of the inclusion bodies. Our findings, therefore, support a role for ER stress occurring pre-symptomatically and potentially contributing to pathological mechanisms underlying HD.
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Affiliation(s)
- Farheen Farzana
- Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Victoria 3010, Australia; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Malcolm J McConville
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia; Metabolomics Australia, The University of Melbourne, Victoria 3010, Australia
| | - Thibault Renoir
- Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Shanshan Li
- Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Harvey Tran
- Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Victoria 3010, Australia
| | - Anthony J Hannan
- Florey Institute of Neuroscience & Mental Health, The University of Melbourne, Victoria 3010, Australia.
| | - Danny M Hatters
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia.
| | - Berin A Boughton
- School of Biosciences, The University of Melbourne, Victoria 3010, Australia; Australian National Phenome Centre, Murdoch University, Murdoch 6150, Western Australia, Australia.
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37
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Burgin H, Sharpe AJ, Nie S, Ziemann M, Crameri JJ, Stojanovski D, Pitt J, Ohtake A, Murayama K, McKenzie M. Loss of mitochondrial fatty acid β-oxidation protein short-chain Enoyl-CoA hydratase disrupts oxidative phosphorylation protein complex stability and function. FEBS J 2023; 290:225-246. [PMID: 35962613 PMCID: PMC10087869 DOI: 10.1111/febs.16595] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/24/2022] [Accepted: 08/11/2022] [Indexed: 01/14/2023]
Abstract
Short-chain enoyl-CoA hydratase 1 (ECHS1) is involved in the second step of mitochondrial fatty acid β-oxidation (FAO), catalysing the hydration of short-chain enoyl-CoA esters to short-chain 3-hyroxyl-CoA esters. Genetic deficiency in ECHS1 (ECHS1D) is associated with a specific subset of Leigh Syndrome, a disease typically caused by defects in oxidative phosphorylation (OXPHOS). Here, we examined the molecular pathogenesis of ECHS1D using a CRISPR/Cas9 edited human cell 'knockout' model and fibroblasts from ECHS1D patients. Transcriptome analysis of ECHS1 'knockout' cells showed reductions in key mitochondrial pathways, including the tricarboxylic acid cycle, receptor-mediated mitophagy and nucleotide biosynthesis. Subsequent proteomic analyses confirmed these reductions and revealed additional defects in mitochondrial oxidoreductase activity and fatty acid β-oxidation. Functional analysis of ECHS1 'knockout' cells showed reduced mitochondrial oxygen consumption rates when metabolising glucose or OXPHOS complex I-linked substrates, as well as decreased complex I and complex IV enzyme activities. ECHS1 'knockout' cells also exhibited decreased OXPHOS protein complex steady-state levels (complex I, complex III2 , complex IV, complex V and supercomplexes CIII2 /CIV and CI/CIII2 /CIV), which were associated with a defect in complex I assembly. Patient fibroblasts exhibit varied reduction of mature OXPHOS complex steady-state levels, with defects detected in CIII2 , CIV, CV and the CI/CIII2 /CIV supercomplex. Overall, these findings highlight the contribution of defective OXPHOS function, in particular complex I deficiency, to the molecular pathogenesis of ECHS1D.
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Affiliation(s)
- Harrison Burgin
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Alice J Sharpe
- Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia
| | - Jordan J Crameri
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - Diana Stojanovski
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Australia
| | - James Pitt
- Department of Paediatrics, Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, The University of Melbourne, Australia
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Japan.,Centre for Intractable Diseases, Saitama Medical University Hospital, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Japan
| | - Matthew McKenzie
- School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Geelong, Australia.,Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, Australia.,Department of Molecular and Translational Science, Monash University, Melbourne, Australia
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38
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Montgomery MK, Bayliss J, Nie S, de Nardo W, Keenan SN, Anari M, Taddese AZ, Williamson NA, Ooi GJ, Brown WA, Burton PR, Gregorevic P, Goodman CA, Watt KI, Watt MJ. Liver-Secreted Hexosaminidase A Regulates Insulin-Like Growth Factor Signalling and Glucose Transport in Skeletal Muscle. Diabetes 2022; 72:715-727. [PMID: 36580496 DOI: 10.2337/db22-0590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/24/2022] [Indexed: 12/30/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) and impaired glycaemic control are closely linked, however, the pathophysiological mechanisms underpinning this bidirectional relationship remain unresolved. The high secretory capacity of the liver and impairments in protein secretion in NAFLD suggest that endocrine changes in the liver are likely to contribute to glycaemic defects. We identify hexosaminidase A (HEXA) as a NAFLD-induced hepatokine in both mice and humans. HEXA regulates sphingolipid metabolism, converting GM2 to GM3 gangliosides; sphingolipids that are primarily localized to cell surface lipid rafts. Using recombinant murine HEXA protein, an enzymatically inactive HEXA(R178H) mutant, or adeno-associated viral vectors to induce hepatocyte-specific overexpression of HEXA, we show that HEXA improves blood glucose control by increasing skeletal muscle glucose uptake in mouse models of insulin resistance and type 2 diabetes, with these effects being dependent on HEXA's enzymatic action. Mechanistically, HEXA remodels muscle lipid raft ganglioside composition, thereby increasing insulin-like growth factor 1 signalling and glucose transporter 4 localization to the cell surface. Disrupting lipid rafts reverses these HEXA-mediated effects. Together, this study identifies a novel pathway for inter-tissue communication between liver and skeletal muscle in the regulation of systemic glycaemic control.
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Affiliation(s)
- Magdalene K Montgomery
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jacqueline Bayliss
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - William de Nardo
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stacey N Keenan
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Marziyeh Anari
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Amanuiel Z Taddese
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Nicholas A Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science & Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Geraldine J Ooi
- Centre for Obesity Research and Education, Department of Surgery, Monash University, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Wendy A Brown
- Centre for Obesity Research and Education, Department of Surgery, Monash University, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Paul R Burton
- Centre for Obesity Research and Education, Department of Surgery, Monash University, The Alfred Hospital, Melbourne, VIC 3004, Australia
| | - Paul Gregorevic
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Craig A Goodman
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Kevin I Watt
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
- Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew J Watt
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, VIC 3010, Australia
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Leeming MG, Ang CS, Nie S, Varshney S, Williamson NA. Simulation of mass spectrometry-based proteomics data with Synthedia. Bioinform Adv 2022; 3:vbac096. [PMID: 36698761 PMCID: PMC9825309 DOI: 10.1093/bioadv/vbac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Motivation A large number of experimental and bioinformatic parameters must be set to identify and quantify peptides in mass spectrometry experiments and each of these will impact the results. An ability to simulate raw data with known contents would allow researchers to rapidly explore the effects of varying experimental parameters and systematically investigate downstream processing software. A range of data simulators are available for established data-dependent acquisition methodologies, but these do not extend to the rapidly developing field of data-independent acquisition (DIA) strategies. Results Here, we present Synthedia-a software package to simulate DIA liquid chromatography-mass spectrometry for bottom-up proteomics experiments. Synthedia can generate datasets with known peptide precursor ions and fragments and allows for the customization of a wide variety of chromatographic and mass spectrometry parameters. Availability and implementation Synthedia is freely available via the internet and can be used through a graphical website (https://synthedia.org/) or locally via the command line (https://github.com/mgleeming/synthedia/). Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
| | - Ching-Seng Ang
- Bio21 Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Shuai Nie
- Bio21 Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, VIC 3052, Australia
| | - Swati Varshney
- Bio21 Molecular Science & Biotechnology Institute, Melbourne Mass Spectrometry and Proteomics Facility, The University of Melbourne, Melbourne, VIC 3052, Australia
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Song XC, Nie S, Xiao JL, Shen X, Hong L, Chen SY, Zhang C, Mu XW. Risk factors and long-term prognosis for postoperative hypoxemia in patients with acute type A aortic dissection: A retrospective observational study. Medicine (Baltimore) 2022; 101:e32337. [PMID: 36550865 PMCID: PMC9771246 DOI: 10.1097/md.0000000000032337] [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] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Hypoxemia is 1 of the most common complications in the patients with acute Type A aortic dissection (ATAAD). This study aimed to summarize the risk factors, management strategies and long-term prognosis for postoperative hypoxemia in ATAAD patients. Baseline characteristics and clinical data of all the patients were collected. Patients were divided into 2 groups according to the PaO2/FiO2 after surgery: Hypoxemia group (n = 142) and Non-hypoxemia group (n = 68). The differences in gender, age, body mass index, operation time, cardiopulmonary bypass (CPB) time, aortic cross-clamping time, deep hypothermic circulatory arrest time, preoperative PaO2/FiO2, postoperative PaO2/FiO2, PaO2/FiO2 before extubating, time of mechanical ventilation, length of intensive care unit stay, length of hospital stay, in-hospital mortality, and overall mortality were compared between the 2 groups. The incidence of postoperative hypoxemia in this study was 67.6% (142/210). body mass index (26.4 ± 3.8 vs 24.4 ± 3.3kg/m2, P < .001) in the hypoxemia group were markedly higher and CPB time (196.3 ± 41.0 vs 181.0 ± 37.3 minutes, P = .010) in the hypoxemia group were significantly longer than those in the non-hypoxemia group. While preoperative PaO2/FiO2 (229.7 ± 91.4 vs 299.7 ± 101.2mmHg, P < .001) was significantly lower than those in the non-hypoxemia group. In the hypoxemia group, PaO2/FiO2 before extubating was significantly higher than that after operation, and the difference was significant. Logistic regression analysis showed that overweight (odds ratio [OR]: 1.113, P = .030), CPB time (OR: 1.009, P = .043) and preoperative PaO2/FiO2 (OR: 0.994, P = .001) were independent risk factors for postoperative hypoxemia. Further follow-up results showed no significant difference in long-term mortality between the 2 groups. Logistic regression analysis revealed that PaO2/FiO2 before extubating (OR: 0.985, P < .001), paraplegia (OR: 10.994, P = .019), acute renal failure (OR: 12.590, P < .001), re-operation (OR: 4.721, P = .014) and re-admission to intensive care unit (OR: 13.727, P = .001) were independent risk factors for long-term mortality. Our results showed that overweight and prolonged CPB time were risk factors for postoperative hypoxemia in ATAAD patients. While PaO2/FiO2 before extubating were independent risk factors for long-term mortality, indicating that active correction of hypoxemia and maintain a higher PaO2/FiO2 before extubating may help to improve the prognosis of the ATAAD patients.
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Affiliation(s)
- Xiao-Chun Song
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Shuai Nie
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Ji-Lai Xiao
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Xiao Shen
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- * Correspondence: Xiao Shen, Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Nanjing 210006, People’s Republic of China (e-mail: ); Cui Zhang, Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Nanjing 210006, People's Republic of China (e-mail: )
| | - Liang Hong
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Shang-Yu Chen
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
| | - Cui Zhang
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
- * Correspondence: Xiao Shen, Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Nanjing 210006, People’s Republic of China (e-mail: ); Cui Zhang, Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, No. 68 Changle Road, Nanjing 210006, People's Republic of China (e-mail: )
| | - Xin-Wei Mu
- Cardiovascular Intensive Care Unit (CVICU), Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing, People’s Republic of China
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Pereira-Fantini PM, Ferguson K, McCall K, Oakley R, Perkins E, Byars S, Williamson N, Nie S, Tingay DG. Respiratory strategy at birth initiates distinct lung injury phenotypes in the preterm lamb lung. Respir Res 2022; 23:346. [DOI: 10.1186/s12931-022-02244-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/07/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
A lack of clear trial evidence often hampers clinical decision-making during support of the preterm lung at birth. Protein biomarkers have been used to define acute lung injury phenotypes and improve patient selection for specific interventions in adult respiratory distress syndrome. The objective of the study was to use proteomics to provide a deeper biological understanding of acute lung injury phenotypes resulting from different aeration strategies at birth in the preterm lung.
Methods
Changes in protein abundance against an unventilated group (n = 7) were identified via mass spectrometry in a biobank of gravity dependent and non-dependent lung tissue from preterm lambs managed with either a Sustained Inflation (SI, n = 20), Dynamic PEEP (DynPEEP, n = 19) or static PEEP (StatPEEP, n = 11). Ventilation strategy-specific pathways and functions were identified (PANTHER and WebGestalt Tool) and phenotypes defined using integrated analysis of proteome, physiological and clinical datasets (MixOmics package).
Results
2372 proteins were identified. More altered proteins were identified in the non-dependent lung, and in SI group than StatPEEP and DynPEEP. Different inflammation, immune system, apoptosis and cytokine pathway enrichment were identified for each strategy and lung region. Specific integration maps of clinical and physiological outcomes to specific proteins could be generated for each strategy.
Conclusions
Proteomics mapped the molecular events initiating acute lung injury and identified detailed strategy-specific phenotypes. This study demonstrates the potential to characterise preterm lung injury by the direct aetiology and response to lung injury; the first step towards true precision medicine in neonatology.
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Nie S, Tian XC, Kong L, Zhao SW, Chen ZY, Jiao SQ, El-Kassaby YA, Porth I, Yang FS, Zhao W, Mao JF. Potential allopolyploid origin of Ericales revealed with gene-tree reconciliation. Front Plant Sci 2022; 13:1006904. [PMID: 36457535 PMCID: PMC9706204 DOI: 10.3389/fpls.2022.1006904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 10/27/2022] [Indexed: 05/31/2023]
Abstract
Few incidents of ancient allopolyploidization (polyploidization by hybridization or merging diverged genomes) were previously revealed, although there is significant evidence for the accumulation of whole genome duplications (WGD) in plants. Here, we focused on Ericales, one of the largest and most diverse angiosperm orders with significant ornamental and economic value. Through integrating 24 high-quality whole genome data selected from ~ 200 Superasterids genomes/species and an algorithm of topology-based gene-tree reconciliation, we explored the evolutionary history of in Ericales with ancient complex. We unraveled the allopolyploid origin of Ericales and detected extensive lineage-specific gene loss following the polyploidization. Our study provided a new hypothesis regarding the origin of Ericales and revealed an instructive perspective of gene loss as a pervasive source of genetic variation and adaptive phenotypic diversity in Ericales.
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Affiliation(s)
- Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xue-Chan Tian
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Lei Kong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shi-Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Zhao-Yang Chen
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, China
| | - Yousry A. El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, Canada
| | - Fu-Sheng Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- China National Botanical Garden, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Wei Zhao
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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Taki AC, Wang T, Nguyen NN, Ang CS, Leeming MG, Nie S, Byrne JJ, Young ND, Zheng Y, Ma G, Korhonen PK, Koehler AV, Williamson NA, Hofmann A, Chang BCH, Häberli C, Keiser J, Jabbar A, Sleebs BE, Gasser RB. Thermal proteome profiling reveals Haemonchus orphan protein HCO_011565 as a target of the nematocidal small molecule UMW-868. Front Pharmacol 2022; 13:1014804. [PMID: 36313370 PMCID: PMC9616048 DOI: 10.3389/fphar.2022.1014804] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 08/11/2022] [Accepted: 09/20/2022] [Indexed: 11/25/2022] Open
Abstract
Parasitic roundworms (nematodes) cause destructive diseases, and immense suffering in humans and other animals around the world. The control of these parasites relies heavily on anthelmintic therapy, but treatment failures and resistance to these drugs are widespread. As efforts to develop vaccines against parasitic nematodes have been largely unsuccessful, there is an increased focus on discovering new anthelmintic entities to combat drug resistant worms. Here, we employed thermal proteome profiling (TPP) to explore hit pharmacology and to support optimisation of a hit compound (UMW-868), identified in a high-throughput whole-worm, phenotypic screen. Using advanced structural prediction and docking tools, we inferred an entirely novel, parasite-specific target (HCO_011565) of this anthelmintic small molecule in the highly pathogenic, blood-feeding barber’s pole worm, and in other socioeconomically important parasitic nematodes. The “hit-to-target” workflow constructed here provides a unique prospect of accelerating the simultaneous discovery of novel anthelmintics and associated parasite-specific targets.
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Affiliation(s)
- Aya C. Taki
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Nghi N. Nguyen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ching-Seng Ang
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Michael G. Leeming
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Joseph J. Byrne
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Neil D. Young
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Yuanting Zheng
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Guangxu Ma
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Institute of Preventive Veterinary Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Pasi K. Korhonen
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Anson V. Koehler
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Nicholas A. Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, The Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Bill C. H. Chang
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Cécile Häberli
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Jennifer Keiser
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Abdul Jabbar
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
| | - Brad E. Sleebs
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Brad E. Sleebs, ; Robin B. Gasser,
| | - Robin B. Gasser
- Department of Veterinary Biosciences, Faculty of Veterinary and Agricultural Sciences, Melbourne Veterinary School, The University of Melbourne, Parkville, VIC, Australia
- *Correspondence: Brad E. Sleebs, ; Robin B. Gasser,
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Ju B, Yun P, Hao Q, Nie S, Liu G. A low phase and amplitude noise microwave source for vapor cell atomic clocks. Rev Sci Instrum 2022; 93:104709. [PMID: 36319356 DOI: 10.1063/5.0096589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
A low-noise microwave source plays a key role in high-performance passive atomic clocks. Here, we propose and implement a microwave frequency synthesizer featuring a low phase and amplitude noise. With the help of a high-Q factor surface acoustic wave band-pass filter, we generate a microwave with targeted frequency by frequency multiplication of a low noise local oscillator at a radio frequency with the closest integer. At the frequency offset of 1 Hz, 10 Hz, 100 Hz, 1 kHz, and 10 kHz, the absolute phase noise of the output 3.417 GHz signal is -53.0, -83.3, -107.7, -119.2, and -124.0 dBc/Hz, respectively. After the microwave-to-optical conversion, the expected intermodulation effect contribution to the frequency stability of the coherent population trapping (CPT) atomic clock is 5.95 × 10-14 at an averaging time of 1 s. Meanwhile, with a feature of low fluctuation of this chain's output microwave power at the level of 1.19 × 10-5 W at 1 s, its contribution to the frequency stability of the CPT atomic clock is 7.85 × 10-14 at the 1 s integration time. Our simple and low noise microwave chain is an ideal microwave source for high-performance, compact CPT clocks and could also be applied to cold atom or ion based microwave clocks.
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Affiliation(s)
- Bowen Ju
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
| | - Peter Yun
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
| | - Qiang Hao
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
| | - Shuai Nie
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
| | - Guobin Liu
- National Time Service Center, Chinese Academy of Sciences, Xi'an 710600, China
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Leonard W, Zhang P, Ying D, Nie S, Liu S, Fang Z. Post-extrusion physical properties, techno-functionality and microbiota-modulating potential of hempseed (Cannabis sativa L.) hull fiber. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Xu J, Luo H, Zhou SS, Jiao SQ, Jia KH, Nie S, Liu H, Zhao W, Wang XR, El-Kassaby YA, Porth I, Mao JF. UV-B and UV-C radiation trigger both common and distinctive signal perceptions and transmissions in Pinus tabuliformis Carr. Tree Physiol 2022; 42:1587-1600. [PMID: 35234958 DOI: 10.1093/treephys/tpac021] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 02/17/2022] [Indexed: 06/14/2023]
Abstract
In plants, ultraviolet (UV)-light is an important driver for growth and natural distribution, and is also a valuable tool for manipulating productivity as well as biotic interactions. Understanding of plant responses to different UV radiation is sparse, especially from a systems biology perspective and particularly for conifers. Here, we evaluated the physiological and transcriptomic responses to the short-term application of high-irradiance UV-B and UV-C waves on Pinus tabuliformis Carr., a major conifer in Northern China. By undertaking time-ordered gene coexpression network analyses and network comparisons incorporating physiological traits and gene expression variation, we uncovered communalities but also differences in P. tabuliformis responses to UV-B and UV-C. Both types of spectral bands caused a significant inhibition of photosynthesis, and conversely, the improvement of antioxidant capacity, flavonoid production and signaling pathways related to stress resistance, indicating a clear switch from predominantly primary metabolism to enhanced defensive metabolism in pine. We isolated distinct subnetworks for photoreceptor-mediated signal transduction, maximum quantum efficiency of photosystem II (Fv/Fm) regulation and flavonoid biosynthesis in response to UV-B and UV-C radiation. From these subnetworks, we further identified phototropins as potentially important elements in both UV-B and UV-C signaling and, for the first time, suggesting peptide hormones to be involved in promoting flavonoid biosynthesis against UV-B, while these hormones seem not to be implicated in the defense against UV-C exposure. The present study employed an effective strategy for disentangling the complex physiological and genetic regulatory mechanisms in a nonmodel plant species, and thus, provides a suitable reference for future functional evaluations and artificial UV-light mediated growing strategies in plant production.
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Affiliation(s)
- Jie Xu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Hang Luo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Shan-Shan Zhou
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Kai-Hua Jia
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Shuai Nie
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
| | - Wei Zhao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, Umeå SE-901 87, Sweden
| | - Xiao-Ru Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
- Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, Linnaeus väg 6, Umeå SE-901 87, Sweden
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, The University of British Columbia, 2424 Main Mall, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval Québec, 1030 Avenue de la Médecine, Québec, Québec City G1V 0A6, Canada
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Qinghua East Road No35, Beijing 100083, China
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Leonard W, Zhang P, Ying D, Nie S, Tindal E, Fang Z. Transformation of hempseed (Cannabis sativa L.) oil cake proteome, structure and functionality after extrusion. Food Chem 2022; 384:132499. [DOI: 10.1016/j.foodchem.2022.132499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/22/2021] [Accepted: 02/15/2022] [Indexed: 11/15/2022]
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Xie SC, Metcalfe RD, Dunn E, Morton CJ, Huang SC, Puhalovich T, Du Y, Wittlin S, Nie S, Luth MR, Ma L, Kim MS, Pasaje CFA, Kumpornsin K, Giannangelo C, Houghton FJ, Churchyard A, Famodimu MT, Barry DC, Gillett DL, Dey S, Kosasih CC, Newman W, Niles JC, Lee MC, Baum J, Ottilie S, Winzeler EA, Creek DJ, Williamson N, Parker MW, Brand SL, Langston SP, Dick LR, Griffin MD, Gould AE, Tilley L. Reaction hijacking of tyrosine tRNA synthetase as a new whole-of-life-cycle antimalarial strategy. Science 2022; 376:1074-1079. [PMID: 35653481 PMCID: PMC7613620 DOI: 10.1126/science.abn0611] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Aminoacyl transfer RNA (tRNA) synthetases (aaRSs) are attractive drug targets, and we present class I and II aaRSs as previously unrecognized targets for adenosine 5'-monophosphate-mimicking nucleoside sulfamates. The target enzyme catalyzes the formation of an inhibitory amino acid-sulfamate conjugate through a reaction-hijacking mechanism. We identified adenosine 5'-sulfamate as a broad-specificity compound that hijacks a range of aaRSs and ML901 as a specific reagent a specific reagent that hijacks a single aaRS in the malaria parasite Plasmodium falciparum, namely tyrosine RS (PfYRS). ML901 exerts whole-life-cycle-killing activity with low nanomolar potency and single-dose efficacy in a mouse model of malaria. X-ray crystallographic studies of plasmodium and human YRSs reveal differential flexibility of a loop over the catalytic site that underpins differential susceptibility to reaction hijacking by ML901.
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Affiliation(s)
- Stanley C. Xie
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Riley D. Metcalfe
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Elyse Dunn
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Craig J. Morton
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shih-Chung Huang
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Tanya Puhalovich
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Yawei Du
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sergio Wittlin
- Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland,University of Basel, 4003 Basel, Switzerland
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Madeline R. Luth
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Liting Ma
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Mi-Sook Kim
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | | | - Krittikorn Kumpornsin
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Carlo Giannangelo
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Fiona J. Houghton
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alisje Churchyard
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Daniel C. Barry
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - David L. Gillett
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Sumanta Dey
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Clara C. Kosasih
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - William Newman
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jacquin C. Niles
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Marcus C.S. Lee
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, United Kingdom
| | - Jake Baum
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sabine Ottilie
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Elizabeth A. Winzeler
- Department of Pediatrics, School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Nicholas Williamson
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael W. Parker
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,St. Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
| | - Stephen L. Brand
- Medicines for Malaria Venture, PO Box 1826, 20, Route de Pré-Bois, 1215, Geneva 15, Switzerland
| | - Steven P. Langston
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA
| | - Lawrence R. Dick
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,Seofon Consulting, 30 Tucker Street, Natick, Massachusetts 01760, USA
| | - Michael D.W. Griffin
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alexandra E. Gould
- Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA,For correspondence. Alexandra E. Gould, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA, (Chemistry) and Leann Tilley, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. (Biology)
| | - Leann Tilley
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia,For correspondence. Alexandra E. Gould, Takeda Development Center Americas, Inc., Cambridge, Massachusetts 02139, USA, (Chemistry) and Leann Tilley, Department of Biochemistry and Pharmacology, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia. (Biology)
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Song XC, Zhou XH, Cheng JH, Zhang WH, Shen X, Xu H, Nie S, Xiao JL, Sun F, Shu C, Chen JD, Tang Y, Wang X, Sun XP, Sun JK, Feng P, Shi QK. The roles of inactivated vaccines in older patients with infection of Delta variant in Nanjing, China. Aging (Albany NY) 2022; 14:4211-4219. [PMID: 35585022 PMCID: PMC9186756 DOI: 10.18632/aging.204085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/07/2022] [Indexed: 11/29/2022]
Abstract
Background: The coronavirus disease 2019 (COVID-19) is spreading around the world. The COVID-19 vaccines may improve concerns about the pandemic. However, the roles of inactivated vaccines in older patients (aged ≥60 years) with infection of Delta variant were less studied. Methods: We classified the older patients with infection of Delta variant into three groups based on the vaccination status: no vaccination (group A, n = 113), one dose of vaccination (group B, n = 46), and two doses of vaccination (group C, n = 22). Two inactivated COVID-19 vaccines (BBIBP-CorV or CoronaVac) were evaluated in this study. The demographic data, laboratory parameters, and clinical severity were recorded. Results: A total of 181 older patients with infection of Delta variant were enrolled. 111 (61.3%) patients had one or more co-morbidities. The days of "turn negative" and hospital stay in Group C were lower than those in the other groups (P < 0.05). The incidences of multiple organ dysfunction syndrome (MODS), septic shock, acute respiratory distress syndrome (ARDS), acute kidney injury, and cardiac injury in Group A were higher than those in the other groups (P < 0.05). The MV-free days and ICU-free days during 28 days in Group A were also lower than those in the other groups (P < 0.05). In patients with co-morbidities, vaccinated cases had lower incidences of MODS (P = 0.015), septic shock (P = 0.015), and ARDS (P = 0.008). Conclusions: The inactivated COVID-19 vaccines were effective in improving the clinical severity of older patients with infection of Delta variant.
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Affiliation(s)
- Xiao-Chun Song
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Xue-Hui Zhou
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Jing-Hui Cheng
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Wen-Hao Zhang
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Xiao Shen
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Huan Xu
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Shuai Nie
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Ji-Lai Xiao
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Fang Sun
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Chang Shu
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Jiu-Dong Chen
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Yan Tang
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Xiang Wang
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Xin-Pei Sun
- Department of General Office, Productivity Center of Jiangsu Province, Nanjing 210042, Jiangsu Province, China
| | - Jia-Kui Sun
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Ping Feng
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
| | - Qian-Kun Shi
- Department of Critical Care Medicine, Nanjing First Hospital, Nanjing Medical University, Nanjing 210006, Jiangsu Province, China
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50
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Sui X, Cox D, Nie S, Reid GE, Hatters DM. A Census of Hsp70-Mediated Proteome Solubility Changes upon Recovery from Heat Stress. J Proteome Res 2022; 21:1251-1261. [PMID: 35388693 DOI: 10.1021/acs.jproteome.1c00920] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eukaryotic cells respond to heat shock through several regulatory processes including upregulation of stress responsive chaperones and reversible shutdown of cellular activities through formation of protein assemblies. However, the underlying regulatory mechanisms of the recovery of these heat-induced protein assemblies remain largely elusive. Here, we measured the proteome abundance and solubility changes during recovery from heat shock in the mouse Neuro2a cell line. We found that prefoldins and translation machinery are rapidly down-regulated as the first step in the heat shock response. Analysis of proteome solubility reveals that a rapid mobilization of protein quality control machineries, along with changes in cellular energy metabolism, translational activity, and actin cytoskeleton are fundamental to the early stress responses. In contrast, longer term adaptation to stress involves renewal of core cellular components. Inhibition of the Hsp70 family, pivotal for the heat shock response, selectively and negatively affects the ribosomal machinery and delays the solubility recovery of many nuclear proteins. ProteomeXchange: PXD030069.
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Affiliation(s)
- Xiaojing Sui
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois 60208, United States
| | - Dezerae Cox
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Shuai Nie
- Melbourne Mass Spectrometry and Proteomics Facility, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Gavin E Reid
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia.,School of Chemistry, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Danny M Hatters
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
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