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Wu HYL, Ai Q, Teixeira RT, Nguyen PHT, Song G, Montes C, Elmore JM, Walley JW, Hsu PY. Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis. Plant Cell 2024; 36:510-539. [PMID: 38000896 PMCID: PMC10896292 DOI: 10.1093/plcell/koad290] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/26/2023]
Abstract
A crucial step in functional genomics is identifying actively translated ORFs and linking them to biological functions. The challenge lies in identifying short ORFs, as their identification is greatly influenced by data quality and depth. Here, we improved the coverage of super-resolution Ribo-seq in Arabidopsis (Arabidopsis thaliana), revealing uncharacterized translation events for nuclear, chloroplastic, and mitochondrial genes. Assisted by a transcriptome assembly, we identified 7,751 unconventional translation events, comprising 6,996 upstream ORFs (uORFs) and 209 downstream ORFs on annotated protein-coding genes, as well as 546 ORFs in presumed noncoding RNAs. Proteomic data confirmed the production of stable proteins from some of these unannotated translation events. We present evidence of active translation from primary transcripts of trans-acting small interfering RNAs (TAS1-4) and microRNAs (pri-MIR163 and pri-MIR169) and periodic ribosome stalling supporting cotranslational decay. Additionally, we developed a method for identifying extremely short uORFs, including 370 minimum uORFs (AUG-stop), and 2,921 tiny uORFs (2 to 10 amino acids) and 681 uORFs that overlap with each other. Remarkably, these short uORFs exhibit strong translational repression as do longer uORFs. We also systematically discovered 594 uORFs regulated by alternative splicing, suggesting widespread isoform-specific translational control. Finally, these prevalent uORFs are associated with numerous important pathways. In summary, our improved Arabidopsis translational landscape provides valuable resources to study gene expression regulation.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Qiaoyun Ai
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Rita Teresa Teixeira
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Phong H T Nguyen
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gaoyuan Song
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Christian Montes
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - J Mitch Elmore
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Justin W Walley
- Department of Plant Pathology, Entomology, and Microbiology, Iowa State University, Ames, IA 50011, USA
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
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2
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Watkins JM, Montes C, Clark NM, Song G, Oliveira CC, Mishra B, Brachova L, Seifert CM, Mitchell MS, Yang J, Braga Dos Reis PA, Urano D, Muktar MS, Walley JW, Jones AM. Phosphorylation Dynamics in a flg22-Induced, G Protein-Dependent Network Reveals the AtRGS1 Phosphatase. Mol Cell Proteomics 2024; 23:100705. [PMID: 38135118 PMCID: PMC10837098 DOI: 10.1016/j.mcpro.2023.100705] [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: 04/03/2023] [Revised: 11/22/2023] [Accepted: 12/19/2023] [Indexed: 12/24/2023] Open
Abstract
The microbe-associated molecular pattern flg22 is recognized in a flagellin-sensitive 2-dependent manner in root tip cells. Here, we show a rapid and massive change in protein abundance and phosphorylation state of the Arabidopsis root cell proteome in WT and a mutant deficient in heterotrimeric G-protein-coupled signaling. flg22-induced changes fall on proteins comprising a subset of this proteome, the heterotrimeric G protein interactome, and on highly-populated hubs of the immunity network. Approximately 95% of the phosphorylation changes in the heterotrimeric G-protein interactome depend, at least partially, on a functional G protein complex. One member of this interactome is ATBα, a substrate-recognition subunit of a protein phosphatase 2A complex and an interactor to Arabidopsis thaliana Regulator of G Signaling 1 protein (AtRGS1), a flg22-phosphorylated, 7-transmembrane spanning modulator of the nucleotide-binding state of the core G-protein complex. A null mutation of ATBα strongly increases basal endocytosis of AtRGS1. AtRGS1 steady-state protein level is lower in the atbα mutant in a proteasome-dependent manner. We propose that phosphorylation-dependent endocytosis of AtRGS1 is part of the mechanism to degrade AtRGS1, thus sustaining activation of the heterotrimeric G protein complex required for the regulation of system dynamics in innate immunity. The PP2A(ATBα) complex is a critical regulator of this signaling pathway.
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Affiliation(s)
- Justin M Watkins
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Celio Cabral Oliveira
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Biochemistry and Molecular Biology/BIOAGRO, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Bharat Mishra
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Clara M Seifert
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Malek S Mitchell
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jing Yang
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Daisuke Urano
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - M Shahid Muktar
- Department of Biology, University of Alabama-Birmingham, Birmingham, Alabama, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA.
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
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3
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Suen A, Pham HT, Suen K, Narayanan S, Song G, Post AB, Mitsuyama P, Wechter D, Le Q, Grumley J, Robinson N, O'Malley M, Lavigne J, Stevens L, Youn V, Yao MS. Intra-Operative Radiotherapy (IORT) in Breast Conserving Therapy in Early-Stage Breast Cancer and DCIS. Int J Radiat Oncol Biol Phys 2023; 117:e209. [PMID: 37784871 DOI: 10.1016/j.ijrobp.2023.06.1096] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Initial breast intra-operative radiotherapy (IORT) results in clinical trials were encouraging though with longer follow up, increased local recurrences have been reported compared with whole breast radiation or other partial breast radiation including accelerated partial breast irradiation (APBI) methods. The goal of the study is to report our prospective single institution IORT breast study outcomes of local recurrence (LR) including true recurrence and breast elsewhere failures, breast cancer specific survival (BCSS), and overall survival (OS) with low energy x-ray IORT in early-stage breast cancer or ductal carcinoma in situ. MATERIALS/METHODS A total of 480 patients with early-stage breast cancer or DCIS were prospectively enrolled in an IRB approved single institution trial and treated with low energy X-ray IORT 20 Gy at time of breast-conserving surgery. Eligibility criteria included ≥ 45 years of age with unifocal tumors < 3 cm deemed candidates for partial mastectomy. Supplemental external beam radiation was recommended for patients with high-risk surgical pathology including multifocal disease, positive nodes, close margins < 2 mm, or lymphovascular invasion. Ipsilateral breast tumor recurrences were classified as true recurrence versus elsewhere failure by location and histology: same/different quadrant and similar/different histology. Kaplan-Meier methods were used to estimate survival probabilities across time. RESULTS Median age of enrolled patients was 64 years with the majority of patients having favorable phenotype with 94% ER+ and 93% Her-2 - disease. 110 patients (23%) had supplemental EBRT delivered; 103 to the whole breast and 7 to the breast and regional nodes. At a median follow up of 73 months (range 17 - 131 months), there were 23 (4.8%) ipsilateral breast tumor recurrences, of which 9 were true recurrences (1.9%) and 14 elsewhere failures (2.9%). One patient with true recurrence and 3 patients with elsewhere breast failures synchronously presented with clinical or radiographic regional node involvement. Seven patient developed contralateral breast cancer and 8 patients developed distant metastases during the follow-up period. There were 2 breast cancer related deaths. At 6-years, overall survival rate was 96.8% and breast cancer specific survival was 98.7%. CONCLUSION Our study outcomes reflect similar outcomes as other reported IORT studies with electron or low energy X-ray in breast cancer, with higher risk of local failure than historical whole breast and other partial breast radiation techniques. This supports current radiation society guidelines for IORT monotherapy for breast cancer to be optimally considered in the context of prospective clinical trials.
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Affiliation(s)
- A Suen
- Virginia Mason Medical Center, Seattle, WA
| | - H T Pham
- Virginia Mason Medical Center, Seattle, WA
| | - K Suen
- Virginia Mason Medical Center, Seattle, WA
| | | | - G Song
- Virginia Mason Medical Center, Seattle, WA, United States
| | - A B Post
- Virginia Mason Medical Center, Seattle, WA, United States
| | | | - D Wechter
- Virginia Mason Medical Center, Seattle, WA
| | - Q Le
- Virginia Mason Medical Center, Seattle, WA
| | - J Grumley
- St. John's Cancer Institute, Santa Monica, CA
| | - N Robinson
- Virginia Mason Medical Center, Seattle, WA
| | - M O'Malley
- Virginia Mason Medical Center, Seattle, WA, United States
| | - J Lavigne
- Virginia Mason Medical Center, Seattle, WA
| | - L Stevens
- Virginia Mason Medical Center, Seattle, WA
| | - V Youn
- Virginia Mason Medical Center, Seattle, WA
| | - M S Yao
- Virginia Mason Medical Center, Seattle, WA, United States
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Li J, Sun L, Hu N, Li L, Song G, Xu H, Xu T, Cheng Y, Xiao L, Wang L, Gong R, Li C. A Novel MR Imaging Sequence of 3D-ZOOMit Real Inversion-Recovery Imaging Improves Endolymphatic Hydrops Detection in Patients with Ménière Disease. AJNR Am J Neuroradiol 2023; 44:595-601. [PMID: 37105675 PMCID: PMC10171393 DOI: 10.3174/ajnr.a7842] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/08/2023] [Indexed: 04/29/2023]
Abstract
BACKGROUND AND PURPOSE The detection rate of premortem MR imaging endolymphatic hydrops is lower than that of postmortem endolymphatic hydrops in Ménière disease, indicating that current MR imaging techniques may underestimate endolymphatic hydrops. Therefore, we prospectively investigated whether a novel high-resolution MR imaging technique, the 3D zoomed imaging technique with parallel transmission real inversion-recovery (3D-ZOOMit real IR), would improve the detection of endolymphatic hydrops compared with conventional 3D TSE inversion-recovery with real reconstruction. MATERIALS AND METHODS Fifty patients with definite unilateral Ménière disease were enrolled and underwent 3D-ZOOMit real IR and 3D TSE inversion-recovery with real reconstruction 6 hours after IV gadolinium injection. The endo- and perilymph spaces were scored separately. The contrast-to-noise ratio, SNR, and signal intensity ratio of the 2 sequences were respectively calculated and compared. The presence of endolymphatic hydrops was evaluated. RESULTS The endolymphatic space in the cochlea and vestibule was better visualized with 3D-ZOOMit real IR than with conventional 3D TSE inversion-recovery with real reconstruction (P < .001). There were differences between the 2 sequences in the evaluation of no cochlear hydrops and cochlear hydrops (both, P < .017). All contrast-to-noise ratio, SNR, and signal intensity ratio values of 3D-ZOOMit real IR images were statistically higher than those of conventional 3D TSE inversion-recovery with real reconstruction (all, P < .001). CONCLUSIONS The 3D-ZOOMit real IR sequences are superior to conventional 3D TSE inversion-recovery with real reconstruction sequences in visualizing the endolymphatic space, detecting endolymphatic hydrops, and discovering contrast permeability.
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Affiliation(s)
- J Li
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
| | - L Sun
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
| | - N Hu
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
| | - L Li
- Medical Service (L.L.), Shandong Provincial ENT Hospital, Shandong University, Jinan, China
| | - G Song
- Department of Radiology (G.S.), Shandong Province Qianfoshan Hospital, Jinan, China
| | - H Xu
- Department of Radiology (H.X., R.G., C.L.)
| | - T Xu
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
| | - Y Cheng
- Siemens Healthineers Digital Technology (Shanghai) Co. Ltd (Y.C.), Shanghai, China
| | - L Xiao
- MR Scientific Marketing (L.X.), Diagnostic Imaging, Siemens Healthineers Ltd, Shanghai, China
| | - L Wang
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
| | - R Gong
- From the Departments of Radiology (J.L., L.S., N.H., T.X., L.W., R.G.)
- Department of Radiology (H.X., R.G., C.L.)
- Gong Ruozhen Innovation Studio (R.G.), Shandong Provincial Hospital, Shandong University, Jinan, China
| | - C Li
- Department of Radiology (H.X., R.G., C.L.)
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Liu C, Yu J, Liu B, Liu M, Song G, Zhu L, Peng B. BACH1 regulates the proliferation and odontoblastic differentiation of human dental pulp stem cells. BMC Oral Health 2022; 22:536. [DOI: 10.1186/s12903-022-02588-2] [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: 08/31/2022] [Accepted: 11/14/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
The preservation of biological and physiological vitality as well as the formation of dentin are among the main tasks of human dental pulp for a life time. Odontoblastic differentiation of human dental pulp stem cells (hDPSCs) exhibits the capacity of dental pulp regeneration and dentin complex rebuilding. Exploration of the mechanisms regulating differentiation and proliferation of hDPSCs may help to investigate potential clinical applications. BTB and CNC homology 1 (BACH1) is a transcription repressor engaged in the regulation of multiple cellular functions. This study aimed to investigate the effects of BACH1 on the proliferation and odontoblastic differentiation of hDPSCs in vitro.
Methods
hDPSCs and pulpal tissues were obtained from extracted human premolars or third molars. The distribution of BACH1 was detected by immunohistochemistry. The mRNA and protein expression of BACH1 were examined by qRT-PCR and Western blot analysis. BACH1 expression was regulated by stable lentivirus-mediated transfection. Cell proliferation and cell cycle were assessed by cell counting kit-8 assay, 5-Ethynyl-2'-deoxyuridine assay and flow cytometry. The expression of mineralization markers, alkaline phosphatase (ALP) activity and alizarin red S staining were conducted to assess the odontoblastic differentiation ability.
Results
BACH1 expression was stronger in the odontoblast layer than in the cell rich zone. The total and nuclear protein level of BACH1 during odontoblastic differentiation was downregulated initially and then upregulated gradually. Knockdown of BACH1 greatly inhibited cell proliferation, arrested cell cycle, upregulated the heme oxygenase-1 (HO-1) expression and attenuated ALP activity, decreased calcium deposits and downregulated the expression of mineralization markers. Treatment of Tin-protoporphyrin IX, an HO-1 inhibitor, failed to rescue the impaired odonto/osteogenic differentiation capacity. Overexpression of BACH1 increased cell proliferation, ALP activity and the expression of mineralization markers.
Conclusions
Our findings suggest that BACH1 is an important regulator of the proliferation and odontoblastic differentiation of hDPSCs in vitro. Manipulation of BACH1 expression may provide an opportunity to promote the regenerative capacity of hDPSCs.
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Montes C, Wang P, Liao C, Nolan TM, Song G, Clark NM, Elmore JM, Guo H, Bassham DC, Yin Y, Walley JW. Integration of multi-omics data reveals interplay between brassinosteroid and Target of Rapamycin Complex signaling in Arabidopsis. New Phytol 2022; 236:893-910. [PMID: 35892179 PMCID: PMC9804314 DOI: 10.1111/nph.18404] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 04/06/2022] [Accepted: 07/16/2022] [Indexed: 06/01/2023]
Abstract
Brassinosteroids (BRs) and Target of Rapamycin Complex (TORC) are two major actors coordinating plant growth and stress responses. Brassinosteroids function through a signaling pathway to extensively regulate gene expression and TORC is known to regulate translation and autophagy. Recent studies have revealed connections between these two pathways, but a system-wide view of their interplay is still missing. We quantified the level of 23 975 transcripts, 11 183 proteins, and 27 887 phosphorylation sites in wild-type Arabidopsis thaliana and in mutants with altered levels of either BRASSINOSTEROID INSENSITIVE 2 (BIN2) or REGULATORY ASSOCIATED PROTEIN OF TOR 1B (RAPTOR1B), two key players in BR and TORC signaling, respectively. We found that perturbation of BIN2 or RAPTOR1B levels affects a common set of gene-products involved in growth and stress responses. Furthermore, we used the multi-omic data to reconstruct an integrated signaling network. We screened 41 candidate genes identified from the reconstructed network and found that loss of function mutants of many of these proteins led to an altered BR response and/or modulated autophagy activity. Altogether, these results establish a predictive network that defines different layers of molecular interactions between BR- or TORC-regulated growth and autophagy.
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Affiliation(s)
- Christian Montes
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Ping Wang
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Ching‐Yi Liao
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Trevor M. Nolan
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Department of BiologyDuke UniversityDurhamNC27708USA
| | - Gaoyuan Song
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - Natalie M. Clark
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
| | - J. Mitch Elmore
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- USDA‐ARS Cereal Disease LaboratoryUniversity of MinnesotaSt PaulMN55108USA
| | - Hongqing Guo
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Diane C. Bassham
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
| | - Yanhai Yin
- Department of Genetics, Development and Cell BiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
| | - Justin W. Walley
- Department of Plant Pathology and MicrobiologyIowa State UniversityAmesIA50011USA
- Plant Sciences InstituteIowa State UniversityAmesIA50011USA
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7
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Crawford T, Darras B, Day J, Barrett D, Song G, O'Neil J, Kertesz N, Bilic S, Patel J, Nomikos G, Chyung Y. P.102 Apitegromab in SMA: An analysis of multiple efficacy endpoints in the TOPAZ extension study. Neuromuscul Disord 2022. [DOI: 10.1016/j.nmd.2022.07.187] [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: 11/07/2022]
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8
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Song G, Ip K, Liu Y, Banov D, Bassani A, Carvalho M. 595 In vitro evaluation of skin distribution and human dermal papilla cells proliferation for minoxidil 5% topical lotion hydrogel. J Invest Dermatol 2022. [DOI: 10.1016/j.jid.2022.05.604] [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: 11/16/2022]
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9
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Wang P, Clark NM, Nolan TM, Song G, Bartz PM, Liao CY, Montes-Serey C, Katz E, Polko JK, Kieber JJ, Kliebenstein DJ, Bassham DC, Walley JW, Yin Y, Guo H. Integrated omics reveal novel functions and underlying mechanisms of the receptor kinase FERONIA in Arabidopsis thaliana. Plant Cell 2022; 34:2594-2614. [PMID: 35435236 PMCID: PMC9252503 DOI: 10.1093/plcell/koac111] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 04/09/2022] [Indexed: 05/20/2023]
Abstract
The receptor kinase FERONIA (FER) is a versatile regulator of plant growth and development, biotic and abiotic stress responses, and reproduction. To gain new insights into the molecular interplay of these processes and to identify new FER functions, we carried out quantitative transcriptome, proteome, and phosphoproteome profiling of Arabidopsis (Arabidopsis thaliana) wild-type and fer-4 loss-of-function mutant plants. Gene ontology terms for phytohormone signaling, abiotic stress, and biotic stress were significantly enriched among differentially expressed transcripts, differentially abundant proteins, and/or misphosphorylated proteins, in agreement with the known roles for FER in these processes. Analysis of multiomics data and subsequent experimental evidence revealed previously unknown functions for FER in endoplasmic reticulum (ER) body formation and glucosinolate biosynthesis. FER functions through the transcription factor NAI1 to mediate ER body formation. FER also negatively regulates indole glucosinolate biosynthesis, partially through NAI1. Furthermore, we found that a group of abscisic acid (ABA)-induced transcription factors is hypophosphorylated in the fer-4 mutant and demonstrated that FER acts through the transcription factor ABA INSENSITIVE5 (ABI5) to negatively regulate the ABA response during cotyledon greening. Our integrated omics study, therefore, reveals novel functions for FER and provides new insights into the underlying mechanisms of FER function.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | | | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Parker M Bartz
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Christian Montes-Serey
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
| | - Ella Katz
- Department of Plant Science, University of California, Davis, California 95616, USA
| | - Joanna K Polko
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Joseph J Kieber
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | | | - Diane C Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011, USA
- Plant Sciences Institutes, Iowa State University, Ames, Iowa 50011, USA
| | - Yanhai Yin
- Author for correspondence: (H.G.); (Y.Y)
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Park S, Song G, Seo H, Lee S, Kim D, Jang A. PD-4 Genetic aberration from normal tissues adjacent to biliary tract cancers. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.082] [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: 11/29/2022] Open
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11
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Kim D, Cho J, Han S, Park S, Song G, Seo H. P-67 Comparison of the malignant predictors in intrahepatic and extrahepatic intraductal papillary neoplasm of bile duct. Ann Oncol 2022. [DOI: 10.1016/j.annonc.2022.04.157] [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: 11/28/2022] Open
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12
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Wang J, Song J, Song G, Hu P, Sun T, Liu K, Xu W, Liu J, Ruan Y. Lycium barbarum polysaccharides improves erectile function through suppression of inflammation and apoptosis in rats with bilateral cavernous nerve injury. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.426] [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: 10/18/2022]
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13
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Wang J, Song J, Song G, Hu P, Sun T, Liu K, Xu W, Liu J, Ruan Y. Acetyl-L-carnitine improves erectile function in bilateral cavernous nerve injury rats via promoting cavernous nerve regeneration. J Sex Med 2022. [DOI: 10.1016/j.jsxm.2022.03.364] [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: 10/18/2022]
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14
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Song G, Wu X. CdS/BiOBr Nanocomposite with Enhanced Activity under Visible Light for Photocatalytic Reduction of CO2 in Cyclohexanol. Kinet Catal 2022. [DOI: 10.1134/s0023158422020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Song G, Ruan M. Novel biopsy scheme in men with multiple multiparametric MRI visible lesions undergoing transperineal prostate biopsy. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00543-7] [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: 11/25/2022]
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16
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Hu W, Wang B, Song G, Wang X, Wang X. Gene therapy in the fight against pediatric blood disorders: sickle cell disease and beta-thalassemia. DRUG FUTURE 2022. [DOI: 10.1358/dof.2022.47.6.3389004] [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: 10/18/2022]
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Wang P, Clark NM, Nolan TM, Song G, Whitham OG, Liao CY, Montes-Serey C, Bassham DC, Walley JW, Yin Y, Guo H. FERONIA functions through Target of Rapamycin (TOR) to negatively regulate autophagy. Front Plant Sci 2022; 13:961096. [PMID: 36082288 PMCID: PMC9446147 DOI: 10.3389/fpls.2022.961096] [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: 06/03/2022] [Accepted: 07/29/2022] [Indexed: 05/20/2023]
Abstract
FERONIA (FER) receptor kinase plays versatile roles in plant growth and development, biotic and abiotic stress responses, and reproduction. Autophagy is a conserved cellular recycling process that is critical for balancing plant growth and stress responses. Target of Rapamycin (TOR) has been shown to be a master regulator of autophagy. Our previous multi-omics analysis with loss-of-function fer-4 mutant implicated that FER functions in the autophagy pathway. We further demonstrated here that the fer-4 mutant displayed constitutive autophagy, and FER is required for TOR kinase activity measured by S6K1 phosphorylation and by root growth inhibition assay to TOR kinase inhibitor AZD8055. Taken together, our study provides a previously unknown mechanism by which FER functions through TOR to negatively regulate autophagy.
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Affiliation(s)
- Ping Wang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Natalie M. Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Trevor M. Nolan
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Olivia G. Whitham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Ching-Yi Liao
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Christian Montes-Serey
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, United States
- Plant Sciences Institute, Iowa State University, Ames, IA, United States
| | - Yanhai Yin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
- Plant Sciences Institute, Iowa State University, Ames, IA, United States
| | - Hongqing Guo
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, United States
- *Correspondence: Hongqing Guo,
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Clark NM, Nolan TM, Wang P, Song G, Montes C, Valentine CT, Guo H, Sozzani R, Yin Y, Walley JW. Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis. Nat Commun 2021; 12:5858. [PMID: 34615886 PMCID: PMC8494934 DOI: 10.1038/s41467-021-26165-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 09/22/2021] [Indexed: 11/14/2022] Open
Abstract
Brassinosteroids (BRs) are plant steroid hormones that regulate cell division and stress response. Here we use a systems biology approach to integrate multi-omic datasets and unravel the molecular signaling events of BR response in Arabidopsis. We profile the levels of 26,669 transcripts, 9,533 protein groups, and 26,617 phosphorylation sites from Arabidopsis seedlings treated with brassinolide (BL) for six different lengths of time. We then construct a network inference pipeline called Spatiotemporal Clustering and Inference of Omics Networks (SC-ION) to integrate these data. We use our network predictions to identify putative phosphorylation sites on BES1 and experimentally validate their importance. Additionally, we identify BRONTOSAURUS (BRON) as a transcription factor that regulates cell division, and we show that BRON expression is modulated by BR-responsive kinases and transcription factors. This work demonstrates the power of integrative network analysis applied to multi-omic data and provides fundamental insights into the molecular signaling events occurring during BR response.
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Affiliation(s)
- Natalie M Clark
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Trevor M Nolan
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Ping Wang
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Conner T Valentine
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Hongqing Guo
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Rosangela Sozzani
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Yanhai Yin
- Department of Genetics, Developmental, and Cell Biology, Iowa State University, Ames, IA, 50011, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
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Place A, Barrett D, Cote S, Nomikos G, Song G, Bilic S, Kalra A, Sadanowicz M, O'Neil J, Iarrobino R, Kertesz N, Chyung Y. SMA - TREATMENT. Neuromuscul Disord 2021. [DOI: 10.1016/j.nmd.2021.07.302] [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: 10/20/2022]
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20
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Xiong XL, Song G. [The Mongolian physicians in the Chuo Ban Chu of the Shang Si Yuan in the Qing Dynasty]. Zhonghua Yi Shi Za Zhi 2021; 51:269-275. [PMID: 34794265 DOI: 10.3760/cma.j.cn112155-20210628-00082] [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] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Chuo Ban Chu of Shang Si Yuan in the Qing Dynasty was an institution for Mongolian physicians who provided bone injury diagnosis and treatment for the royal family. This paper reports on an examination of the archives at the First Historical Archives of China, where 171 relevant archives were obtained. Based on this data, the paper summarises and verifies the directories of 112 Mongolian physicians, the authenticity and inheritance of 26 of these physicians, and a brief biography of 16 of them in each period of the Qing Dynasty.
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Affiliation(s)
- X L Xiong
- China Institute for History of Medicine and Medical Literature, China Academy of Chinese Medical Sciences,Beijing 100700, China
| | - G Song
- China Institute for History of Medicine and Medical Literature, China Academy of Chinese Medical Sciences,Beijing 100700, China
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21
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Zhang Y, Liu JY, Shao JW, Luo QQ, Zhang YQ, Song G, Wang CY, Zhao SY, Wan C, Du XH, Xu LZ. Effective Model of Food Allergy in Mice Sensitized with Ovalbumin and Freud's Adjuvant. Bull Exp Biol Med 2021; 171:352-356. [PMID: 34297293 DOI: 10.1007/s10517-021-05226-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 11/27/2020] [Indexed: 12/29/2022]
Abstract
To better explore the pathophysiology of FA and its therapy, we aimed to establish a simple and practicable FA model with Freund's adjuvant and introduce an easy and reliable laboratory evaluation method for assessment of inflammation in intestinal segments at different anatomical locations. BALB/c mice were sensitized with ovalbumin combined with Freund's adjuvant. Complete Freund's adjuvant was chosen for the first sensitization and two weeks later incomplete Freund's adjuvant was used for a second sensitization. Two weeks later, the sensitized mice were challenged with 50 mg ovalbumin every other day. After the 6 challenge, all mice were assessed for systemic anaphylaxis, and then sacrificed for sample collection. All sensitized mice showed anaphylactic symptoms and markedly increased levels of serum ovalbumin-specific IgE and IgG1. The activity of mast cell protease-1 (mMCPT-1) was significantly increased in the serum and interstitial fluid of the duodenum, jejunum, ileum, and colon. A successful FA model was established, of which inflammation occurred in the duodenum, jejunum, ileum, and colon. This model provides a reliable and simple tool for analysis of the mechanism of FA and methods of immunotherapy. Moreover, combined detection of ovalbumin-specific antibody and local mMCPT-1 levels could potentially be used as the major indicator for assessment of food allergy.
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Affiliation(s)
- Y Zhang
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - J Y Liu
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - J W Shao
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Q Q Luo
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - Y Q Zhang
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - G Song
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - C Y Wang
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - S Y Zhao
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - C Wan
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - X H Du
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China
| | - L Z Xu
- Key Lab for Immunology, Universities of Shandong Province, School of Basic Medical Sciences, Weifang Medical University, Weifang, China.
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Zeyu W, Liang T, Song G, Lin J, Xiao Y, Wang F, Zhang J, Xu Y, Fu Q. The effects of primary realignment or suprapubic cystostomy on prostatic displacement in patients with pelvic fracture urethral injury: A clinical study based on MR urethrography. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01508-6] [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: 11/28/2022]
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23
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Song G. Circular rna zfp644 enahances the therapeutic efficacy of mesenchymal stem cells in rats with severe acute pancreatitis by sponging MIR-21-3P. Cytotherapy 2021. [DOI: 10.1016/s1465324921004977] [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: 11/16/2022]
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24
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Song G, Ip K, Shan A, Banov D, Song H, Bassani A, Carvalho M, Day A. 476 Evaluation of the in vitro percutaneous absorption of progesterone, testosterone, estriol and estradiol topical compounded formulations. J Invest Dermatol 2021. [DOI: 10.1016/j.jid.2021.02.500] [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: 11/27/2022]
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Juan J, Yang HX, Wei YM, Song G, Su RN, Chen X, Yang QH, Yan JY, Xiao M, Li Y, Cui SH, Hu YL, Zhao XL, Fan SR, Feng L, Zhang MH, Ma YY, You ZS, Meng HX, Liu HW, Zhu Y, Wu CF, Cai Y, Hu KJ, Ding HJ. [Effects of interpregnancy interval on pregnancy outcomes of subsequent pregnancy: a multicenter retrospective study]. Zhonghua Fu Chan Ke Za Zhi 2021; 56:161-170. [PMID: 33874710 DOI: 10.3760/cma.j.cn112141-20201010-00767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the effects of interpregnancy interval (IPI) on pregnancy outcomes of subsequent pregnancy. Methods: A multicenter retrospective study was conducted in 21 hospitals in China. Information of age, height, pre-pregnancy weight, IPI, history of diseases, complications of pregnancy, gestational age of delivery, delivery mode, and pregnancy outcomes of the participants were collected by consulting medical records of pregnant women who had two consecutive deliveries in the same hospital during 2011 to 2018. The participants were divided into 4 groups according to IPI:<18 months, 18-23 months, 24-59 months and ≥60 months. According to the WHO's recommendation, with the IPI of 24-59 months group as a reference, to the effects of IPI on pregnancy outcomes of subsequent pregnancy were analyzed. Stratified analysis was further carried out based on age, history of gestational diabetes mellitus (GDM), macrosomia, and premature delivery, to explore the differences in the effects of IPI on pregnancy outcomes among women with different characteristics. Results: A total of 8 026 women were included in this study. There were 423, 623, 5 512 and 1 468 participants in <18 months group, 18-23 months group, 24-59 months group and ≥60 months group, respectively. (1) The age, pre-pregnancy body mass index (BMI), history of cesarean section, GDM, gestational hypertension and cesarean section delivery rate of <18 months group, 18-23 months group, 24-59 months group and ≥60 months group were gradually increased, and the differences were statistically significant (P<0.05). (2) After adjusting for potential confounding factors, compared with women in the IPI of 24-59 months group, the risk of premature delivery, premature rupture of membranes, and oligohydramnios were increased by 42% (OR=1.42, 95%CI: 1.07-1.88, P=0.015), 46% (OR=1.46, 95%CI: 1.13-1.88, P=0.004), and 64% (OR=1.64, 95%CI: 1.13-2.38, P=0.009) respectively for women in the IPI≥60 months group. No effects of IPI on other pregnancy outcomes were found in this study (P>0.05). (3) After stratified by age and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would significantly increase the risk of oligohydramnios for women with advanced age (OR=2.87, 95%CI: 1.41-5.83, P=0.004); and <18 months could increase the risk of premature rupture of membranes for women under the age of 35 (OR=1.59, 95%CI: 1.04-2.43, P=0.032). Both the risk of premature rupture of membranes (OR=1.58, 95%CI: 1.18-2.13, P=0.002) and premature delivery (OR=1.52, 95%CI: 1.07-2.17, P=0.020) were significantly increased in the IPI≥60 months group. After stratified by history of GDM and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would lead to an increased risk of postpartum hemorrhage for women with a history of GDM (OR=5.34, 95%CI: 1.45-19.70, P=0.012) and an increased risk of premature rupture of membranes for women without a history of GDM (OR=1.44, 95%CI: 1.10-1.90, P=0.009). After stratified by history of macrosomia and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months could increase the proportion of cesarean section for women with a history of macrosomia (OR=4.11, 95%CI: 1.18-14.27, P=0.026) and the risk of premature rupture of membranes for women without a history of macrosomia (OR=1.46, 95%CI: 1.12-1.89, P=0.005). After stratified by history of premature delivery and adjusted for confounding factors, compared with women in the IPI of 24-59 months group, IPI≥60 months would significantly increase the risk of premature rupture of membranes for women without a history of premature delivery (OR=1.47, 95%CI: 1.13-1.92, P=0.004). Conclusions: Both IPI≥60 months and <18 months would increase the risk of adverse pregnancy outcomes in the subsequent pregnancy. Healthcare education and consultation should be conducted for women of reproductive age to maintain an appropriate IPI when they plan to pregnant again, to reduce the risk of adverse pregnancy outcomes in the subsequent pregnancy.
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Affiliation(s)
- J Juan
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - H X Yang
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - Y M Wei
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - G Song
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - R N Su
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - X Chen
- Department of Obstetrics, Tianjin Central Obstetrics and Gynecology Hospital, Tianjin 300052, China
| | - Q H Yang
- Department of Obstetrics, Jinan Maternal and Child Health Hospital, Jinan 250000, China
| | - J Y Yan
- Department of Obstetrics, Fujian Maternal and Child Health Hospital, Fuzhou 350001, China
| | - M Xiao
- Department of Obstetrics, Maternal and Child Hospital of Hubei Province, Wuhan 430070, China
| | - Y Li
- Department of Obstetrics, Dalian Maternity Hospital, Dalian 116033, China
| | - S H Cui
- Department of Obstetrics and Gynecology, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Y L Hu
- Department of Obstetrics and Gynecology, Nanjing Drum Tower Hospital, the Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - X L Zhao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - S R Fan
- Department of Obstetrics, Peking University Shenzhen Hospital, Shenzhen 518036, China
| | - L Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - M H Zhang
- Department of Obstetrics, Taiyuan Maternal and Child Health Hospital, Taiyuan 030012, China
| | - Y Y Ma
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Z S You
- Department of Obstetrics and Gynecology, Suzhou Jiulong Hospital Affiliated to Shanghai Jiaotong University, Suzhou 320571, China
| | - H X Meng
- Department of Obstetrics, Affiliated Hospital of Inner Mongolia Medical University, Huhhot 010050, China
| | - H W Liu
- Department of Endocrinology, Hainan General Hospital, Haikou 570311, China
| | - Y Zhu
- Department of Obstetrics and Gynecology, Harbin Red Cross Central Hospital, Harbin 150070, China
| | - C F Wu
- Department of Obstetrics, the First Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - Y Cai
- Department of Obstetrics and Gynecology, the Fourth Affiliated Hospital of Harbin Medical University, Harbin 150001, China
| | - K J Hu
- Department of Obstetrics, the Hospital of Shunyi District Beijing, Beijing 101300, China
| | - H J Ding
- Department of Obstetrics, Nanjing Maternal and Child Health Hospital, Nanjing 210000, China
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Hao R, Ma K, Ru Y, Li D, Song G, Lu B, Liu H, Li Y, Zhang J, Wu C, Zhang G, Hu H, Luo J, Zheng H. Amber codon is genetically unstable in generation of premature termination codon (PTC)-harbouring Foot-and-mouth disease virus (FMDV) via genetic code expansion. RNA Biol 2021; 18:2330-2341. [PMID: 33849391 DOI: 10.1080/15476286.2021.1907055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The foot-and-mouth disease virus (FMDV) is the causative agent of FMD, a highly infectious and devastating viral disease of domestic and wild cloven-hoofed animals. FMD affects livestock and animal products' national and international trade, causing severe economic losses and social consequences. Currently, inactivated vaccines play a vital role in FMD control, but they have several limitations. The genetic code expansion technology provides powerful strategies for generating premature termination codon (PTC)-harbouring virus as a live but replication-incompetent viral vaccine. However, this technology has not been explored for the design and development of new FMD vaccines. In this study, we first expanded the genetic code of the FMDV genome via a transgenic cell line containing an orthogonal translation machinery. We demonstrated that the transgenic cells stably integrated the orthogonal pyltRNA/pylRS pair into the genome and enabled efficient, homogeneous incorporation of unnatural amino acids into target proteins in mammalian cells. Next, we constructed 129 single-PTC FMDV mutants and four dual-PTC FMDV mutants after considering the tolerance, location, and potential functions of those mutated sites. Amber stop codons individually substituted the selected amino acid codons in four viral proteins (3D, L, VP1, and VP4) of FMDV. We successfully rescued PTC-FMDV mutants, but the amber codon unexpectedly showed a highly degree of mutation rate during PTC-FMDV packaging and replication. Our findings highlight that the genetic code expansion technology for the generation of PTC-FMD vaccines needs to be further improved and that the genetic stability of amber codons during the packaging and replication of FMDV is a concern.
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Affiliation(s)
- Rongzeng Hao
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Kun Ma
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yi Ru
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Dan Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Gaoyuan Song
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingzhou Lu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huanan Liu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Yajun Li
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jiaoyan Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunping Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Guicai Zhang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haitao Hu
- Department of Microbiology and Immunology, Sealy Center for Vaccine Development and Institute for Human Infections and Immunity, University of Texas Medical Branch (UTMB), Galveston, TX, USA
| | - Jianxun Luo
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Haixue Zheng
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, OIE/National Foot and Mouth Diseases Reference Laboratory, Chinese Academy of Agricultural Sciences, Lanzhou, China
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Song G, Ruan M. How many targeted biopsy cores are needed for prostate cancer detection during magnetic resonance imaging ultrasound fusion biopsy? EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)32668-9] [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: 10/23/2022] Open
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28
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Zhang Y, Zhang H, Wang B, Song G, Hayden JC, Amirthalingam P, Rahmani J, Bhagavathula AS, Li Z. Pregnancy outcomes after a mass vaccination campaign with an oral cholera vaccine: a systematic review and meta-analysis. BJOG 2020; 127:1066-1073. [PMID: 32289871 DOI: 10.1111/1471-0528.16260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2020] [Indexed: 02/03/2023]
Abstract
BACKGROUND Cholera has harmful effects on the fetus but safety data on the oral cholera vaccine in pregnant women are controversial. OBJECTIVES We conducted the first meta-analysis of studies in pregnant women comparing the effect of oral cholera vaccination on pregnancy outcomes with unvaccinated women. Outcomes of interest were adverse pregnancy outcome, miscarriage, stillbirth, preterm delivery, low birthweight, abortion and malformation. SEARCH STRATEGY The search was run in MEDLINE/PubMed, SCOPUS and Embase databases from inception up to December 2019. SELECTION CRITERIA Inclusion criteria were: (1) studies that investigated the association between oral cholera vaccines and adverse pregnancy outcomes; (2) studies that reported outcomes with appropriate estimates; and (3) studies that contained an unvaccinated control group. DATA COLLECTION AND ANALYSIS A random-effects model (DerSimonian and Laird) was run to evaluate the overall treatment effect (relative risk, RR). The PRISMA statement was followed in reporting this meta-analysis. MAIN RESULTS Five studies included in meta-analysis with 5584 women (2920 exposed and 2664 not exposed). No significant increase in adverse pregnancy outcome (RR 1.03, 95% CI 0.79-1.34), miscarriage (RR 1.15, 95% CI 0.84-1.57) or stillbirth (RR 1.11, 95% CI 0.69-1.80) following cholera vaccine administration was found compared with control group. There was also no association with an increased risk of preterm delivery (RR 0.61, 95% CI 0.35-1.06) low birthweight (RR 0.84, 95% CI 0.56- 1.26), accidental abortion (RR 1.02, 95% CI 0.77-1.35) or malformation (RR 0.70, 95% CI 0.22-2.25). CONCLUSIONS This study shows no evidence of an association between oral cholera vaccination and adverse pregnancy outcomes. The findings do not rigorously exclude the possibility that the vaccine protocol may result in some degree of harm. TWEETABLE ABSTRACT There is no evidence of an association between oral cholera vaccination and adverse pregnancy outcomes. The findings do not rigorously exclude the possibility that the vaccine protocol may result in some degree of harm.
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Affiliation(s)
- Y Zhang
- Department of Obstetrics, The Fourth People's Hospital of Jinan City, Jinan, Shandong Province, China
| | - H Zhang
- Department of Integrated Treatment Area 1, Affiliated Jinan Third Hospital of Jining Medical University, Jining Medical University, Jinan, Shandong Province, China
| | - B Wang
- Department of Paediatrics, Jinan Maternity and Child Hospital, Jinan, Shandong Province, China
| | - G Song
- Department of Obstetrics, Jinan Maternity and Child Hospital, Jinan, Shandong Province, China
| | - J C Hayden
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - P Amirthalingam
- Department of Pharmacy Practice, Faculty of Pharmacy, University of Tabuk, Tabuk, Kingdom of Saudi Arabia
| | - J Rahmani
- Department of Community Nutrition, Student Research Committee, Faculty of Nutrition and Food Technology, National Nutrition and Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - A S Bhagavathula
- Department of Internal Medicine, College of Medicine and Health Sciences, UAE University, Al Ain, UAE
| | - Z Li
- Department of Endocrinology, The Fourth People's Hospital of Jinan City, Jinan, Shandong Province, China
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Rosenthal VD, Bat-Erdene I, Gupta D, Belkebir S, Rajhans P, Zand F, Myatra SN, Afeef M, Tanzi VL, Muralidharan S, Gurskis V, Al-Abdely HM, El-Kholy A, AlKhawaja SAA, Sen S, Mehta Y, Rai V, Hung NV, Sayed AF, Guerrero-Toapanta FM, Elahi N, Morfin-Otero MDR, Somabutr S, De-Carvalho BM, Magdarao MS, Velinova VA, Quesada-Mora AM, Anguseva T, Ikram A, Aguilar-de-Moros D, Duszynska W, Mejia N, Horhat FG, Belskiy V, Mioljevic V, Di-Silvestre G, Furova K, Gamar-Elanbya MO, Gupta U, Abidi K, Raka L, Guo X, Luque-Torres MT, Jayatilleke K, Ben-Jaballah N, Gikas A, Sandoval-Castillo HR, Trotter A, Valderrama-Beltrán SL, Leblebicioglu H, Riera F, López M, Maurizi D, Desse J, Pérez I, Silva G, Chaparro G, Golschmid D, Cabrera R, Montanini A, Bianchi A, Vimercati J, Rodríguez-del-Valle M, Domínguez C, Saul P, Chediack V, Piastrelini M, Cardena L, Ramasco L, Olivieri M, Gallardo P, Juarez P, Brito M, Botta P, Alvarez G, Benchetrit G, Caridi M, Stagnaro J, Bourlot I, García M, Arregui N, Saeed N, Abdul-Aziz S, ALSayegh S, Humood M, Mohamed-Ali K, Swar S, Magray T, Aguiar-Portela T, Sugette-de-Aguiar T, Serpa-Maia F, Fernandes-Alves-de-Lima L, Teixeira-Josino L, Sampaio-Bezerra M, Furtado-Maia R, Romário-Mendes A, Alves-De-Oliveira A, Vasconcelos-Carneiro A, Anjos-Lima JD, Pinto-Coelho K, Maciel-Canuto M, Rocha-Batista M, Moreira T, Rodrigues-Amarilo N, Lima-de-Barros T, Guimarães KA, Batista C, Santos C, de-Lima-Silva F, Santos-Mota E, Karla L, Ferreira-de-Souza M, Luzia N, de-Oliveira S, Takeda C, Azevedo-Ferreira-Lima D, Faheina J, Coelho-Oliveira L, do-Nascimento S, Machado-Silva V, Bento-Ferreira, Olszewski J, Tenorio M, Silva-Lemos A, Ramos-Feijó C, Cardoso D, Correa-Barbosa M, Assunção-Ponte G, Faheina J, da-Silva-Escudero D, Servolo-Medeiros E, Andrade-Oliveira-Reis M, Kostadinov E, Dicheva V, Petrov M, Guo C, Yu H, Liu T, Song G, Wang C, Cañas-Giraldo L, Marin-Tobar D, Trujillo-Ramirez E, Andrea-Rios P, Álvarez-Moreno C, Linares C, González-Rubio P, Ariza-Ayala B, Gamba-Moreno L, Gualtero-Trujill S, Segura-Sarmiento S, Rodriguez-Pena J, Ortega R, Olarte N, Pardo-Lopez Y, Luis Marino Otela-Baicue A, Vargas-Garcia A, Roncancio E, Gomez-Nieto K, Espinosa-Valencia M, Barahona-Guzman N, Avila-Acosta C, Raigoza-Martinez W, Villamil-Gomez W, Chapeta-Parada E, Mindiola-Rochel A, Corchuelo-Martinez A, Martinez A, Lagares-Guzman A, Rodriguez-Ferrer M, Yepes-Gomez D, Muñoz-Gutierrez G, Arguello-Ruiz A, Zuniga-Chavarria M, Maroto-Vargas L, Valverde-Hernández M, Solano-Chinchilla A, Calvo-Hernandez I, Chavarria-Ugalde O, Tolari G, Rojas-Fermin R, Diaz-Rodriguez C, Huascar S, Ortiz M, Bovera M, Alquinga N, Santacruz G, Jara E, Delgado V, Salgado-Yepez E, Valencia F, Pelaez C, Gonzalez-Flores H, Coello-Gordon E, Picoita F, Arboleda M, Garcia M, Velez J, Valle M, Unigarro L, Figueroa V, Marin K, Caballero-Narvaez H, Bayani V, Ahmed S, Alansary A, Hassan A, Abdel-Halim M, El-Fattah M, Abdelaziz-Yousef R, Hala A, Abdelhady K, Ahmed-Fouad H, Mounir-Agha H, Hamza H, Salah Z, Abdel-Aziz D, Ibrahim S, Helal A, AbdelMassih A, Mahmoud AR, Elawady B, El-sherif R, Fattah-Radwan Y, Abdel-Mawla T, Kamal-Elden N, Kartsonaki M, Rivera D, Mandal S, Mukherjee S, Navaneet P, Padmini B, Sorabjee J, Sakle A, Potdar M, Mane D, Sale H, Abdul-Gaffar M, Kazi M, Chabukswar S, Anju M, Gaikwad D, Harshe A, Blessymole S, Nair P, Khanna D, Chacko F, Rajalakshmi A, Mubarak A, Kharbanda M, Kumar S, Mathur P, Saranya S, Abubakar F, Sampat S, Raut V, Biswas S, Kelkar R, Divatia J, Chakravarthy M, Gokul B, Sukanya R, Pushparaj L, Thejasvini A, Rangaswamy S, Saini N, Bhattacharya C, Das S, Sanyal S, Chaudhury B, Rodrigues C, Khanna G, Dwivedy A, Binu S, Shetty S, Eappen J, Valsa T, Sriram A, Todi S, Bhattacharyya M, Bhakta A, Ramachandran B, Krupanandan R, Sahoo P, Mohanty N, Sahu S, Misra S, Ray B, Pattnaik S, Pillai H, Warrier A, Ranganathan L, Mani A, Rajagopal S, Abraham B, Venkatraman R, Ramakrishnan N, Devaprasad D, Siva K, Divekar D, Satish Kavathekar M, Suryawanshi M, Poojary A, Sheeba J, Patil P, Kukreja S, Varma K, Narayanan S, Sohanlal T, Agarwal A, Agarwal M, Nadimpalli G, Bhamare S, Thorat S, Sarda O, Nadimpalli P, Nirkhiwale S, Gehlot G, Bhattacharya S, Pandya N, Raphel A, Zala D, Mishra S, Patel M, Aggarwal D, Jawadwal B, Pawar N, Kardekar S, Manked A, Tamboli A, Manked A, Khety Z, Singhal T, Shah S, Kothari V, Naik R, Narain R, Sengupta S, Karmakar A, Mishra S, Pati B, Kantroo V, Kansal S, Modi N, Chawla R, Chawla A, Roy I, Mukherjee S, Bej M, Mukherjee P, Baidya S, Durell A, Vadi S, Saseedharan S, Anant P, Edwin J, Sen N, Sandhu K, Pandya N, Sharma S, Sengupta S, Palaniswamy V, Sharma P, Selvaraj M, Saurabh L, Agarwal M, Punia D, Soni D, Misra R, Harsvardhan R, Azim A, Kambam C, Garg A, Ekta S, Lakhe M, Sharma C, Singh G, Kaur A, Singhal S, Chhabra K, Ramakrishnan G, Kamboj H, Pillai S, Rani P, Singla D, Sanaei A, Maghsudi B, Sabetian G, Masjedi M, Shafiee E, Nikandish R, Paydar S, Khalili H, Moradi A, Sadeghi P, Bolandparvaz S, Mubarak S, Makhlouf M, Awwad M, Ayyad O, Shaweesh A, Khader M, Alghazawi A, Hussien N, Alruzzieh M, Mohamed Y, ALazhary M, Abdul Aziz O, Alazmi M, Mendoza J, De Vera P, Rillorta A, de Guzman M, Girvan M, Torres M, Alzahrani N, Alfaraj S, Gopal U, Manuel M, Alshehri R, Lessing L, Alzoman H, Abdrahiem J, Adballah H, Thankachan J, Gomaa H, Asad T, AL-Alawi M, Al-Abdullah N, Demaisip N, Laungayan-Cortez E, Cabato A, Gonzales J, Al Raey M, Al-Darani S, Aziz M, Al-Manea B, Samy E, AlDalaton M, Alaliany M, Alabdely H, Helali N, Sindayen G, Malificio A, Al-Dossari H, Kelany A, Algethami A, Mohamed D, Yanne L, Tan A, Babu S, Abduljabbar S, Al-Zaydani M, Ahmed H, Al Jarie A, Al-Qathani A, Al-Alkami H, AlDalaton M, Alih S, Alaliany M, Gasmin-Aromin R, Balon-Ubalde E, Diab H, Kader N, Hassan-Assiry I, Kelany A, Albeladi E, Aboushoushah S, Qushmaq N, Fernandez J, Hussain W, Rajavel R, Bukhari S, Rushdi H, Turkistani A, Mushtaq J, Bohlega E, Simon S, Damlig E, Elsherbini S, Abraham S, Kaid E, Al-Attas A, Hawsawi G, Hussein B, Esam B, Caminade Y, Santos A, Abdulwahab M, Aldossary A, Al-Suliman S, AlTalib A, Albaghly N, HaqlreMia M, Kaid E, Altowerqi R, Ghalilah K, Alradady M, Al-Qatri A, Chaouali M, Shyrine E, Philipose J, Raees M, AbdulKhalik N, Madco M, Acostan C, Safwat R, Halwani M, Abdul-Aal N, Thomas A, Abdulatif S, Ali-Karrar M, Al-Gosn N, Al-Hindi A, Jaha R, AlQahtani S, Ayugat E, Al-Hussain M, Aldossary A, Al-Suliman S, Al-Talib A, Albaghly N, Haqlre-Mia M, Briones S, Krishnan R, Tabassum K, Alharbi L, Madani A, Al-Hindi A, Al-Gethamy M, Alamri D, Spahija G, Gashi A, Kurian A, George S, Mohamed A, Ramapurath R, Varghese S, Abdo N, Foda-Salama M, Al-Mousa H, Omar A, Salama M, Toleb M, Khamis S, Kanj S, Zahreddine N, Kanafani Z, Kardas T, Ahmadieh R, Hammoud Z, Zeid I, Al-Souheil A, Ayash H, Mahfouz T, Kondratas T, Grinkeviciute D, Kevalas R, Dagys A, Mitrev Z, Bogoevska-Miteva Z, Jankovska K, Guroska S, Petrovska M, Popovska K, Ng C, Hoon Y, Hasan YM, Othman-Jailani M, Hadi-Jamaluddin M, Othman A, Zainol H, Wan-Yusoff W, Gan C, Lum L, Ling C, Aziz F, Zhazali R, Abud-Wahab M, Cheng T, Elghuwael I, Wan-Mat W, Abd-Rahman R, Perez-Gomez H, Kasten-Monges M, Esparza-Ahumada S, Rodriguez-Noriega E, Gonzalez-Diaz E, Mayoral-Pardo D, Cerero-Gudino A, Altuzar-Figueroa M, Perez-Cruz J, Escobar-Vazquez M, Aragon D, Coronado-Magana H, Mijangos-Mendez J, Corona-Jimenez F, Aguirre-Avalos G, Lopez-Mateos A, Martinez-Marroquin M, Montell-Garcia M, Martinez-Martinez A, Leon-Sanchez E, Gomez-Flores G, Ramirez M, Gomez M, Lozano M, Mercado V, Zamudio-Lugo I, Gomez-Gonzalez C, Miranda-Novales M, Villegas-Mota I, Reyes-Garcia C, Ramirez-Morales M, Sanchez-Rivas M, Cureno-Diaz M, Matias-Tellez B, Gonzalez-Martinez J, Juarez-Vargas R, Pastor-Salinas O, Gutierrez-Munoz V, Conde-Mercado J, Bruno-Carrasco G, Manrique M, Monroy-Colin V, Cruz-Rivera Z, Rodriguez-Pacheco J, Cruz N, Hernandez-Chena B, Guido-Ramirez O, Arteaga-Troncoso G, Guerra-Infante F, Lopez-Hurtado M, Caleco JD, Leyva-Medellin E, Salamanca-Meneses A, Cosio-Moran C, Ruiz-Rendon R, Aguilar-Angel L, Sanchez-Vargas M, Mares-Morales R, Fernandez-Alvarez L, Castillo-Cruz B, Gonzalez-Ma M, Zavala-Ramír M, Rivera-Reyna L, del-Moral-Rossete L, Lopez-Rubio C, Valadez-de-Alba M, Bat-Erdene A, Chuluunchimeg K, Baatar O, Batkhuu B, Ariyasuren Z, Bayasgalan G, Baigalmaa S, Uyanga T, Suvderdene P, Enkhtsetseg D, Suvd-Erdene D, Chimedtseye E, Bilguun G, Tuvshinbayar M, Dorj M, Khajidmaa T, Batjargal G, Naranpurev M, Bat-Erdene A, Bolormaa T, Battsetseg T, Batsuren C, Batsaikhan N, Tsolmon B, Saranbaatar A, Natsagnyam P, Nyamdawa O, Madani N, Abouqal R, Zeggwagh A, Berechid K, Dendane T, Koirala A, Giri R, Sainju S, Acharya S, Paul N, Parveen A, Raza A, Nizamuddin S, Sultan F, Imran X, Sajjad R, Khan M, Sana F, Tayyab N, Ahmed A, Zaman G, Khan I, Khurram F, Hussain A, Zahra F, Imtiaz A, Daud N, Sarwar M, Roop Z, Yusuf S, Hanif F, Shumaila X, Zeb J, Ali S, Demas S, Ariff S, Riaz A, Hussain A, Kanaan A, Jeetawi R, Castaño E, Moreno-Castillo L, García-Mayorca E, Prudencio-Leon W, Vivas-Pardo A, Changano-Rodriguez M, Castillo-Bravo L, Aibar-Yaranga K, Marquez-Mondalgo V, Mueras-Quevedo J, Meza-Borja C, Flor J, Fernandez-Camacho Y, Banda-Flores C, Pichilingue-Chagray J, Castaneda-Sabogal A, Caoili J, Mariano M, Maglente R, Santos S, de-Guzman G, Mendoza M, Javellana O, Tajanlangit A, Tapang A, Sg-Buenaflor M, Labro E, Carma R, Dy A, Fortin J, Navoa-Ng J, Cesar J, Bonifacio B, Llames M, Gata H, Tamayo A, Calupit H, Catcho V, Bergosa L, Abuy M, Barteczko-Grajek B, Rojek S, Szczesny A, Domanska M, Lipinska G, Jaroslaw J, Wieczoreka A, Szczykutowicza A, Gawor M, Piwoda M, Rydz-Lutrzykowska J, Grudzinska M, Kolat-Brodecka P, Smiechowicz K, Tamowicz B, Mikstacki A, Grams A, Sobczynski P, Nowicka M, Kretov V, Shalapuda V, Molkov A, Puzanov S, Utkin I, Tchekulaev A, Tulupova V, Vasiljevic S, Nikolic L, Ristic G, Eremija J, Kojovic J, Lekic D, Simic A, Hlinkova S, Lesnakova A, Kadankunnel S, Abdo-Ali M, Pimathai R, Wanitanukool S, Supa N, Prasan P, Luxsuwong M, Khuenkaew Y, Lamngamsupha J, Siriyakorn N, Prasanthai V, Apisarnthanarak A, Borgi A, Bouziri A, Cabadak H, Tuncer G, Bulut C, Hatipoglu C, Sebnem F, Demiroz A, Kaya A, Ersoz G, Kuyucu N, Karacorlu S, Oncul O, Gorenek L, Erdem H, Yildizdas D, Horoz O, Guclu E, Kaya G, Karabay O, Altindis M, Oztoprak N, Sahip Y, Uzun C, Erben N, Usluer G, Ozgunes I, Ozcelik M, Ceyda B, Oral M, Unal N, Cigdem Y, Bayar M, Bermede O, Saygili S, Yesiler I, Memikoglu O, Tekin R, Oncul A, Gunduz A, Ozdemir D, Geyik M, Erdogan S, Aygun C, Dilek A, Esen S, Turgut H, Sungurtekin H, Ugurcan D, Yarar V, Bilir Y, Bayram N, Devrim I, Agin H, Ceylan G, Yasar N, Oruc Y, Ramazanoglu A, Turhan O, Cengiz M, Yalcin A, Dursun O, Gunasan P, Kaya S, Senol G, Kocagoz A, Al-Rahma H, Annamma P, El-Houfi A, Vidal H, Perez F, D-Empaire G, Ruiz Y, Hernandez D, Aponte D, Salinas E, Vidal H, Navarrete N, Vargas R, Sanchez E, Ngo Quy C, Thu T, Nguyet L, Hang P, Hang T, Hanh T, Anh D. International Nosocomial Infection Control Consortium (INICC) report, data summary of 45 countries for 2012-2017: Device-associated module. Am J Infect Control 2020; 48:423-432. [PMID: 31676155 DOI: 10.1016/j.ajic.2019.08.023] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/20/2019] [Accepted: 08/21/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND We report the results of International Nosocomial Infection Control Consortium (INICC) surveillance study from January 2012 to December 2017 in 523 intensive care units (ICUs) in 45 countries from Latin America, Europe, Eastern Mediterranean, Southeast Asia, and Western Pacific. METHODS During the 6-year study period, prospective data from 532,483 ICU patients hospitalized in 242 hospitals, for an aggregate of 2,197,304 patient days, were collected through the INICC Surveillance Online System (ISOS). The Centers for Disease Control and Prevention-National Healthcare Safety Network (CDC-NHSN) definitions for device-associated health care-associated infection (DA-HAI) were applied. RESULTS Although device use in INICC ICUs was similar to that reported from CDC-NHSN ICUs, DA-HAI rates were higher in the INICC ICUs: in the medical-surgical ICUs, the pooled central line-associated bloodstream infection rate was higher (5.05 vs 0.8 per 1,000 central line-days); the ventilator-associated pneumonia rate was also higher (14.1 vs 0.9 per 1,000 ventilator-days,), as well as the rate of catheter-associated urinary tract infection (5.1 vs 1.7 per 1,000 catheter-days). From blood cultures samples, frequencies of resistance, such as of Pseudomonas aeruginosa to piperacillin-tazobactam (33.0% vs 18.3%), were also higher. CONCLUSIONS Despite a significant trend toward the reduction in INICC ICUs, DA-HAI rates are still much higher compared with CDC-NHSN's ICUs representing the developed world. It is INICC's main goal to provide basic and cost-effective resources, through the INICC Surveillance Online System to tackle the burden of DA-HAIs effectively.
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Zhang Z, Li A, Song G, Geng S, Gill BS, Faris JD, Mao L. Comprehensive analysis of Q gene near-isogenic lines reveals key molecular pathways for wheat domestication and improvement. Plant J 2020; 102:299-310. [PMID: 31778224 DOI: 10.1111/tpj.14624] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 07/13/2019] [Revised: 10/14/2019] [Accepted: 11/12/2019] [Indexed: 06/10/2023]
Abstract
The wheat AP2-like transcription factor gene Q has played a major role in domestication by conferring the free-threshing character and pleiotropically affecting numerous other traits. However, little information is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3000 differentially expressed genes (DEGs) involved in a number of pathways. Using phenotypic, microscopic, transcriptomic, and tissue-specific gene expression analyses, we demonstrated that Q governs threshability through extensive modification of wheat glumes including their structure, cell wall thickness, and chemical composition. Critical DEGs and pathways involved in secondary cell wall synthesis and regulation of the chemical composition of glumes were identified. We also showed that the mutation giving rise to the Q allele synchronized the expression of genes for micro-sporogenesis that affected pollen fertility, and may determine the final grain number for wheat spikes. Transcriptome dissection of genes and genetic pathways regulated by Q should further our understanding of wheat domestication and improvement.
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Affiliation(s)
- Zengcui Zhang
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Aili Li
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Gaoyuan Song
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Shuaifeng Geng
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, 66506, KS, USA
| | - Justin D Faris
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, USDA-ARS, Fargo, ND, 58102, USA
| | - Long Mao
- Institute of Crop Science (ICS), Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
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Abstract
Proteins produce or regulate nearly every component of cells. Thus, the ability to quantitatively determine the protein abundance and posttranslational modification (PTM) state is a critical aspect toward our understanding of biological processes. In this chapter, we describe methods to globally quantify protein abundance and phosphorylation state using isobaric labeling with tandem mass tags followed by phosphopeptide enrichment.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Christian Montes
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, USA.
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Jia H, Song G, Werth EG, Walley JW, Hicks LM, Jones AM. Front Cover: Receptor‐Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G‐Protein Gα ‐Subunit AtGPA1. Proteomics 2019. [DOI: 10.1002/pmic.201970211] [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: 11/12/2022]
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Jia H, Song G, Werth EG, Walley JW, Hicks LM, Jones AM. Receptor-Like Kinase Phosphorylation of Arabidopsis Heterotrimeric G-Protein Gα -Subunit AtGPA1. Proteomics 2019; 19:e1900265. [PMID: 31693794 PMCID: PMC7014827 DOI: 10.1002/pmic.201900265] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/04/2019] [Indexed: 01/07/2023]
Abstract
As molecular on-off switches, heterotrimeric G protein complexes, comprised of a Gα subunit and an obligate Gβγ dimer, transmit extracellular signals received by G protein-coupled receptors (GPCRs) to cytoplasmic targets that respond to biotic and abiotic stimuli. Signal transduction is modulated by phosphorylation of GPCRs and G protein complexes. In Arabidopsis thaliana, the Gα subunit AtGPA1 is phosphorylated by the receptor-like kinase (RLK) BRI1-associated Kinase 1 (BAK1), but the extent that other RLKs phosphorylates AtGPA1 is unknown. Twenty-two trans-phosphorylation sites on AtGPA1 are mapped by 12 RLKs hypothesized to act in the Arabidopsis G protein signaling pathway. Cis-phosphorylation sites are also identified on these RLKs, some newly shown to be dual specific kinases. Multiple sites are present in the core AtGPA1 functional units, including pSer52 and/or pThr53 of the conserved P-loop that directly binds nucleotide/phosphate, pThr164, and pSer175 from αE helix in the intramolecular domain interface for nucleotide exchange and GTP hydrolysis, and pThr193 and/or pThr194 in Switch I (SwI) that coordinates nucleotide exchange and protein partner binding. Several AtGPA1 S/T phosphorylation sites are potentially nucleotide-dependent phosphorylation patterns, such as Ser52/Thr53 in the P-loop and Thr193 and/or Thr194 in SwI.
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Affiliation(s)
- Haiyan Jia
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alan M Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
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Xu EY, Zhang YF, Song G, Jiang R, Liu GQ, Liu JT. Rapid Identification of Four New Synthetic Cannabinoids in Whole Blood. Fa Yi Xue Za Zhi 2019; 35:677-681. [PMID: 31970953 DOI: 10.12116/j.issn.1004-5619.2019.06.006] [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] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Indexed: 06/10/2023]
Abstract
Objective To establish accurate and rapid methods to identify four new synthetic cannabinoids (JWH-203, JWH-122, 5F-APINACA and AB-CHMINACA) in blood samples. Methods The whole blood samples were extracted by acetonitrile and methanol, screened by gas chromatography-mass spectrometry (GC-MS) then confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) method, and multiple reaction monitoring (MRM) mode was used for quantitative analysis. Results The GC-MS method needed 21 min to complete the analysis, while the LC-MS/MS method needed 5 min. The AB-CHMINACA, JWH-203, 5F-APINACA and JWH-122 all used quasi molecular ion peak as a parent ion. The precursor-product ion combinations were m/z 357.4→312.2, m/z 340.2→125.0, m/z 384.1→135.1 and m/z 356.4→169.2. The four synthetic cannabinoids in blood samples had good linearity in the 1-250 ng/mL mass concentration range (r>0.99). The limits of detection (LODs) were in the range of 0.1-0.5 ng/mL, the recovery rate was 85.4%-95.2%, the RSD less than 10.0%, and the matrix effect was 80.3%-92.8%. Conclusion The GC-MS and LC-MS/MS chromatographic behaviors and mass spectrometry analysis information of four synthetic cannabinoids were obtained in this study, and the possible causes of differences in chromatographic behaviors were discussed preliminarily. Therefore this study has a suggestive effect on judging the development trend of synthetic cannabinoids. This method can be used for rapid identification of four synthetic cannabinoids in blood, which can provide reference for identification of new synthetic cannabinoids when they are proliferating at present.
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Affiliation(s)
- E Y Xu
- Department of Forensic Analytical Toxicology, China Medical University, Shenyang 110122, China
| | - Y F Zhang
- Institute of Forensic Science, Ministry of Public Security, PRC, Beijing 100038, China
| | - G Song
- Institute of Forensic Science, Ministry of Public Security, PRC, Beijing 100038, China
| | - R Jiang
- Department of Forensic Analytical Toxicology, China Medical University, Shenyang 110122, China
| | - G Q Liu
- Department of Forensic Analytical Toxicology, China Medical University, Shenyang 110122, China
| | - J T Liu
- Department of Forensic Analytical Toxicology, China Medical University, Shenyang 110122, China
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Jia J, Zheng H, Cheng M, Zhao J, Song J, Song G, He T, Wu Y. PV-113: Development and Validation of the Intensity-modulated Accurate Radiotherapy System KylinRay-IMRT. Radiother Oncol 2019. [DOI: 10.1016/s0167-8140(20)30550-8] [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: 11/24/2022]
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36
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Liu XR, Song G, Jiang H, Di LJ, Yu J, Jia S, Li H, Liang X. Peripheral cytotoxic T cell correlates with tumor mutational burden and is predictive for progression free survival in advanced breast cancer. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.060] [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: 11/13/2022] Open
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37
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Popat S, Liu G, Lu S, Song G, Samnotra V, Yang JCH. Phase III ALTA-3 study of brigatinib (BRG) vs alectinib (ALC) in patients (pts) with advanced anaplastic lymphoma kinase (ALK)−positive non–small cell lung cancer (NSCLC) that progressed on crizotinib (CRZ). Ann Oncol 2019. [DOI: 10.1093/annonc/mdz260.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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38
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Li H, Xu J, shao B, Liu R, ran R, Song G, Jiang H, Wang K, Shi Y, Liu J, Hu W, Chen F, Zhang G, Wang Y, Zhao C, Ru J, wang Q, Rugo H, Li G. Phase I dose-escalation and expansion study of the PARP inhibitor, fluzoparib (SHR3162), in patients with advanced solid tumours. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz242.040] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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39
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Wu HYL, Song G, Walley JW, Hsu PY. The Tomato Translational Landscape Revealed by Transcriptome Assembly and Ribosome Profiling. Plant Physiol 2019; 181:367-380. [PMID: 31248964 PMCID: PMC6716236 DOI: 10.1104/pp.19.00541] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 06/10/2019] [Indexed: 05/14/2023]
Abstract
Recent applications of translational control in Arabidopsis (Arabidopsis thaliana) highlight the potential power of manipulating mRNA translation for crop improvement. However, to what extent translational regulation is conserved between Arabidopsis and other species is largely unknown, and the translatome of most crops remains poorly studied. Here, we combined de novo transcriptome assembly and ribosome profiling to study global mRNA translation in tomato (Solanum lycopersicum) roots. Exploiting features corresponding to active translation, we discovered widespread unannotated translation events, including 1,329 upstream open reading frames (uORFs) within the 5' untranslated regions of annotated coding genes and 354 small ORFs (sORFs) among unannotated transcripts. uORFs may repress translation of their downstream main ORFs, whereas sORFs may encode signaling peptides. Besides evolutionarily conserved sORFs, we uncovered 96 Solanaceae-specific sORFs, revealing the importance of studying translatomes directly in crops. Proteomic analysis confirmed that some of the unannotated ORFs generate stable proteins in planta. In addition to defining the translatome, our results reveal the global regulation by uORFs and microRNAs. Despite diverging over 100 million years ago, many translational features are well conserved between Arabidopsis and tomato. Thus, our approach provides a high-throughput method to discover unannotated ORFs, elucidates evolutionarily conserved and unique translational features, and identifies regulatory mechanisms hidden in a crop genome.
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Affiliation(s)
- Hsin-Yen Larry Wu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa 50011
| | - Polly Yingshan Hsu
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
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40
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Yoon M, Ring C, Van Landingham CB, Suh M, Song G, Antonijevic T, Gentry PR, Taylor MD, Keene AM, Andersen ME, Clewell HJ. Assessing children's exposure to manganese in drinking water using a PBPK model. Toxicol Appl Pharmacol 2019; 380:114695. [PMID: 31394159 DOI: 10.1016/j.taap.2019.114695] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 05/10/2019] [Revised: 07/20/2019] [Accepted: 07/30/2019] [Indexed: 12/27/2022]
Abstract
A previously published human PBPK model for manganese (Mn) in infants and children has been updated with Mn in drinking water as an additional exposure source. Built upon the ability to capture differences in Mn source-specific regulation of intestinal uptake in nursing infants who are breast-fed and formula-fed, the updated model now describes the bioavailability of Mn from drinking water in children of ages 0-18. The age-related features, including the recommended age-specific Mn dietary intake, age-specific water consumption rates, and age-specific homeostasis of Mn, are based on the available human data and knowledge of the biology of essential-metal homeostasis. Model simulations suggest that the impact of adding drinking-water exposure to daily Mn exposure via dietary intake and ambient air inhalation in children is not greater than the impacts in adults, even at a drinking-water concentration that is 2 times higher than the USEPA's lifetime health advisory value. This conclusion was also valid for formula-fed infants who are considered at the highest potential exposure to Mn from drinking water compared to all other age groups. Our multi-route, multi-source Mn PBPK model for infants and children provides insights about the potential for Mn-related health effects on growing children and will thereby improve the level of confidence in properly interpreting Mn exposure-health effects relationships in children in human epidemiological studies.
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Affiliation(s)
- M Yoon
- ToxStrategies, Inc., RTP, NC, USA.
| | - C Ring
- ToxStrategies, Inc., Austin, TX, USA
| | | | - M Suh
- ToxStrategies, Inc., Orange County, CA, USA
| | - G Song
- ToxStrategies, Inc., Orange County, CA, USA
| | | | | | | | - A M Keene
- Afton Chemical Corporation, Richmond, VA, USA
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41
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Zhang Y, Song G, Lal NK, Nagalakshmi U, Li Y, Zheng W, Huang PJ, Branon TC, Ting AY, Walley JW, Dinesh-Kumar SP. TurboID-based proximity labeling reveals that UBR7 is a regulator of N NLR immune receptor-mediated immunity. Nat Commun 2019; 10:3252. [PMID: 31324801 PMCID: PMC6642208 DOI: 10.1038/s41467-019-11202-z] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 07/01/2019] [Indexed: 11/25/2022] Open
Abstract
Nucleotide-binding leucine-rich repeat (NLR) immune receptors play a critical role in defence against pathogens in plants and animals. However, we know very little about NLR-interacting proteins and the mechanisms that regulate NLR levels. Here, we used proximity labeling (PL) to identify the proteome proximal to N, which is an NLR that confers resistance to Tobacco mosaic virus (TMV). Evaluation of different PL methods indicated that TurboID-based PL provides more efficient levels of biotinylation than BioID and BioID2 in plants. TurboID-based PL of N followed by quantitative proteomic analysis and genetic screening revealed multiple regulators of N-mediated immunity. Interestingly, a putative E3 ubiquitin ligase, UBR7, directly interacts with the TIR domain of N. UBR7 downregulation leads to an increased amount of N protein and enhanced TMV resistance. TMV-p50 effector disrupts the N-UBR7 interaction and relieves negative regulation of N. These findings demonstrate the utility of TurboID-based PL in plants and the N-interacting proteins we identified enhance our understanding of the mechanisms underlying NLR regulation.
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Affiliation(s)
- Yongliang Zhang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
- State Key Laboratory of Agro-Biotechnology and Ministry of Agriculture Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Neeraj K Lal
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Yuanyuan Li
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Wenjie Zheng
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA
| | - Tess C Branon
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alice Y Ting
- Departments of Genetics, Stanford University, Stanford, CA, 94305, USA
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Justin W Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA.
| | - Savithramma P Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, 95616, USA.
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42
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Zhang J, Wu S, Boehlein SK, McCarty DR, Song G, Walley JW, Myers A, Settles AM. Maize defective kernel5 is a bacterial TamB homologue required for chloroplast envelope biogenesis. J Cell Biol 2019; 218:2638-2658. [PMID: 31235479 PMCID: PMC6683743 DOI: 10.1083/jcb.201807166] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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] [Received: 07/23/2018] [Revised: 05/07/2019] [Accepted: 06/04/2019] [Indexed: 01/10/2023] Open
Abstract
Zhang et al. show that the maize dek5 locus is required for chloroplast envelope biogenesis and encodes a TamB-like protein. Bacterial TamB proteins facilitate insertion of β-barrel outer membrane proteins, indicating plastids have a conserved mechanism for envelope membrane biogenesis. Chloroplasts are of prokaryotic origin with a double-membrane envelope separating plastid metabolism from the cytosol. Envelope membrane proteins integrate chloroplasts with the cell, but envelope biogenesis mechanisms remain elusive. We show that maize defective kernel5 (dek5) is critical for envelope biogenesis. Amyloplasts and chloroplasts are larger and reduced in number in dek5 with multiple ultrastructural defects. The DEK5 protein is homologous to rice SSG4, Arabidopsis thaliana EMB2410/TIC236, and Escherichia coli tamB. TamB functions in bacterial outer membrane biogenesis. DEK5 is localized to the envelope with a topology analogous to TamB. Increased levels of soluble sugars in dek5 developing endosperm and elevated osmotic pressure in mutant leaf cells suggest defective intracellular solute transport. Proteomics and antibody-based analyses show dek5 reduces levels of Toc75 and chloroplast envelope transporters. Moreover, dek5 chloroplasts reduce inorganic phosphate uptake with at least an 80% reduction relative to normal chloroplasts. These data suggest that DEK5 functions in plastid envelope biogenesis to enable transport of metabolites and proteins.
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Affiliation(s)
- Junya Zhang
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL
| | - Shan Wu
- Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Susan K Boehlein
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL.,Horticultural Sciences Department, University of Florida, Gainesville, FL
| | - Gaoyuan Song
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Justin W Walley
- Plant Pathology and Microbiology, Iowa State University, Ames, IA
| | - Alan Myers
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA
| | - A Mark Settles
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL .,Horticultural Sciences Department, University of Florida, Gainesville, FL
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43
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Suri A, Mould D, Song G, Kinley J, Venkatakrishnan K. BRENTUXIMAB VEDOTIN POPULATION PHARMACOKINETIC (POPPK) MODELLING IN ADULT AND PAEDIATRIC PATIENTS (PTS) WITH RELAPSED/REFRACTORY (R/R) HEMATOLOGIC MALIGNANCIES. Hematol Oncol 2019. [DOI: 10.1002/hon.209_2631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- A. Suri
- Quantitative Clinical Pharmacology; Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited Inc.; Cambridge United States
| | - D.R. Mould
- Projections Research, Inc.; Phoenixville United States
| | - G. Song
- Oncology Statistics; Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited Inc.; Cambridge United States
| | - J. Kinley
- Oncology Clinical Research; Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited Inc.; Cambridge United States
| | - K. Venkatakrishnan
- Quantitative Clinical Pharmacology; Millennium Pharmaceuticals, a wholly owned subsidiary of Takeda Pharmaceutical Company Limited Inc.; Cambridge United States
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44
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Lieow JLM, Chen FSM, Song G, Tang PS, Kowitlawakul Y, Mukhopadhyay A. Effectiveness of an advanced practice nurse-led delirium education and training programme. Int Nurs Rev 2019; 66:506-513. [PMID: 31066049 DOI: 10.1111/inr.12519] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [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: 12/18/2022]
Abstract
AIM To develop an education and training programme to enhance bedside nurses' knowledge, competency and compliance in accurately performing delirium screening in intensive care units. BACKGROUND Delirium in intensive care units is associated with several poor patient outcomes. Delirium detection can be improved by enhancing nurses' knowledge, competency and compliance in accurately performing delirium screening. METHODS A descriptive quantitative study with pretest-post-test design was adopted. There were 245 nurses from five intensive care units who participated in the study. Multiple-choice questions were used to assess nurses' knowledge change before and after the education programme. Competency was assessed before and 2 months after the programme by simulation with a standardized patient, followed by real patients at the bedside. Compliance data on screening were collected from the documentation of the Richmond Agitation-Sedation Scale and the Confusion Assessment Method for the ICU before and 3 and 10 months after the programme. Data collection took 1 year, from June 2014 to May 2015. RESULTS Despite nurses' improved knowledge and good competency, delirium screening documentations after 3 months were poor. However, screening documentations subsequently improved when measured at 10 months, following further emphasis by the senior nursing staff. IMPLICATIONS FOR NURSING PRACTICE AND POLICY Nursing administrators and bedside nurses need to be involved in the policy-making process and plan a training programme for the new nursing staff in the high-risk areas. A short refreshment course should be offered to the nursing staff 3 months after the initial training programme. CONCLUSIONS Improved knowledge and competency in assessment did not improve compliance and documentation of delirium screening. Therefore, it is important to reinforce nurses' compliance of delirium screening over time.
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Affiliation(s)
- J L M Lieow
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University of Singapore, Singapore City, Singapore
| | - F S M Chen
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University of Singapore, Singapore City, Singapore
| | - G Song
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University of Singapore, Singapore City, Singapore
| | - P S Tang
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University of Singapore, Singapore City, Singapore
| | - Y Kowitlawakul
- Alice Lee Centre for Nursing Studies, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - A Mukhopadhyay
- Division of Respiratory and Critical Care Medicine, University Medicine Cluster, National University Hospital, National University of Singapore, Singapore City, Singapore
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45
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Abstract
The condition of the placenta is a determinant of the short- and long-term health of the mother and the fetus. However, critical processes occurring in early placental development, such as trophoblast invasion and establishment of placental metabolism, remain poorly understood. To gain a better understanding of the genes involved in regulating these processes, we utilized a multiomics approach, incorporating transcriptome, proteome, and phosphoproteome data generated from mouse placental tissue collected at two critical developmental time points. We found that incorporating information from both the transcriptome and proteome identifies genes associated with time point-specific biological processes, unlike using the proteome alone. We further inferred genes upregulated on the basis of the proteome data but not the transcriptome data at each time point, leading us to identify 27 genes that we predict to have a role in trophoblast migration or placental metabolism. Finally, using the phosphoproteome data set, we discovered novel phosphosites that may play crucial roles in the regulation of placental transcription factors. By generating the largest proteome and phosphoproteome data sets in the developing placenta, and integrating transcriptome analysis, we uncovered novel aspects of placental gene regulation.
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Affiliation(s)
- Majd Abdulghani
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Gaoyuan Song
- Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Haninder Kaur
- Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Justin W Walley
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Plant Pathology and Microbiology , Iowa State University , Ames , Iowa 50011-1079 , United States
| | - Geetu Tuteja
- Interdepartmental Genetics and Genomics , Iowa State University , Ames , Iowa 50011-1079 , United States.,Department of Genetics, Development, and Cell Biology , Iowa State University , Ames , Iowa 50011-1079 , United States
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46
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Song G, Sun G, Kong X, Jia M, Wang K, Ye X, Zhou Y, Geng S, Mao L, Li A. The soft glumes of common wheat are sterile-lemmas as determined by the domestication gene Q. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2018.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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47
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Wu LC, Zhang Y, Steinberg G, Qu H, Huang S, Cheng M, Bliss T, Du F, Rao J, Song G, Pisani L, Doyle T, Conolly S, Krishnan K, Grant G, Wintermark M. A Review of Magnetic Particle Imaging and Perspectives on Neuroimaging. AJNR Am J Neuroradiol 2019; 40:206-212. [PMID: 30655254 DOI: 10.3174/ajnr.a5896] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Magnetic particle imaging is an emerging tomographic technique with the potential for simultaneous high-resolution, high-sensitivity, and real-time imaging. Magnetic particle imaging is based on the unique behavior of superparamagnetic iron oxide nanoparticles modeled by the Langevin theory, with the ability to track and quantify nanoparticle concentrations without tissue background noise. It is a promising new imaging technique for multiple applications, including vascular and perfusion imaging, oncology imaging, cell tracking, inflammation imaging, and trauma imaging. In particular, many neuroimaging applications may be enabled and enhanced with magnetic particle imaging. In this review, we will provide an overview of magnetic particle imaging principles and implementation, current applications, promising neuroimaging applications, and practical considerations.
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Affiliation(s)
- L C Wu
- From the Departments of Bioengineering (L.C.W.)
| | - Y Zhang
- Radiology (Y.Z., H.Q., S.H., M.W.)
| | - G Steinberg
- Neurosurgery (G.S., M.C., T.B., F.D., G.G.).,Neuroradiology Section, Radiology (J.R., G.S., L.P.)
| | - H Qu
- Radiology (Y.Z., H.Q., S.H., M.W.)
| | - S Huang
- Radiology (Y.Z., H.Q., S.H., M.W.).,Chongqing Medical University (S.H.), Traditional Chinese Medicine College, Chongqing, China
| | - M Cheng
- Neurosurgery (G.S., M.C., T.B., F.D., G.G.)
| | - T Bliss
- Neurosurgery (G.S., M.C., T.B., F.D., G.G.)
| | - F Du
- Neurosurgery (G.S., M.C., T.B., F.D., G.G.)
| | - J Rao
- Neuroradiology Section, Radiology (J.R., G.S., L.P.)
| | - G Song
- From the Departments of Bioengineering (L.C.W.)
| | - L Pisani
- Neuroradiology Section, Radiology (J.R., G.S., L.P.)
| | - T Doyle
- Pediatrics (T.D.), Stanford University, Stanford, California
| | - S Conolly
- Department of Electrical Engineering and Computer Sciences (S.C.), University of California Berkeley, Berkeley, California
| | - K Krishnan
- Departments of Materials Sciences and Engineering and Physics (K.K.), University of Washington, Seattle, Washington
| | - G Grant
- Neurosurgery (G.S., M.C., T.B., F.D., G.G.)
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48
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Geng S, Kong X, Song G, Jia M, Guan J, Wang F, Qin Z, Wu L, Lan X, Li A, Mao L. DNA methylation dynamics during the interaction of wheat progenitor Aegilops tauschii with the obligate biotrophic fungus Blumeria graminis f. sp. tritici. New Phytol 2019; 221:1023-1035. [PMID: 30256420 PMCID: PMC6586159 DOI: 10.1111/nph.15432] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [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: 05/28/2018] [Accepted: 08/06/2018] [Indexed: 05/23/2023]
Abstract
DNA methylation is dynamically involved in plant immunity, but little information is known about its roles in plant interactions with biotrophic fungi, especially in temperate grasses such as wheat (Triticum aestivum). Using wheat diploid progenitor Aegilops tauschii accession AL8/78, the genome of which has been sequenced, we assessed the extent of DNA methylation in response to infection with Blumeria graminis f. sp. tritici (Bgt), which causes powdery mildew. Upon Bgt infection, ARGONAUTE4a (AGO4a) was significantly downregulated in A. tauschii, which was accompanied by a substantial reduction in AGO4a-sorted 24-nt siRNA levels, especially for genes near transposable elements (TAGs). Bisulfite sequencing revealed abundant differentially methylated regions (DMRs) with CHH hypomethylation. TAGs bearing CHH-hypomethylated DMRs were enriched for 'response to stress' functions, including receptor kinase, peroxidase, and pathogenesis-related genes. Virus-induced gene silencing (VIGS) of a DOMAINS REARRANGED METHYLASE 2 (DRM2) homolog enhanced plant resistance to Bgt. The effect of CHH hypomethylation was exemplified by the upregulation of a pathogenesis-related β-1,3-glucanse gene implicated in Bgt defense. These findings support the idea that dynamic DNA methylation represents a regulatory layer in the complex mechanism of plant immunity, which could be exploited to improve disease resistance in common wheat.
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Affiliation(s)
- Shuaifeng Geng
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Xingchen Kong
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuan611130China
| | - Gaoyuan Song
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Meiling Jia
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Jiantao Guan
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Fang Wang
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Zhengrui Qin
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Liang Wu
- Department of AgronomyCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhou310058China
| | - Xiujin Lan
- Triticeae Research InstituteSichuan Agricultural UniversityChengduSichuan611130China
| | - Aili Li
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
| | - Long Mao
- National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop ScienceChinese Academy of Agricultural SciencesBeijing100081China
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49
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Song G, Brachova L, Nikolau BJ, Jones AM, Walley JW. Heterotrimeric G-Protein-Dependent Proteome and Phosphoproteome in Unstimulated Arabidopsis Roots. Proteomics 2018; 18:e1800323. [PMID: 30407730 PMCID: PMC6298806 DOI: 10.1002/pmic.201800323] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 10/09/2018] [Indexed: 12/19/2022]
Abstract
The G-protein complex is a cytoplasmic on-off molecular switch that is set by plasma membrane receptors that activate upon binding of its cognate extracellular agonist. In animals, the default setting is the "off" resting state, while in plants, the default state is constitutively "on" but repressed by a plasma membrane receptor-like protein. De-repression appears to involve specific phosphorylation of key elements of the G-protein complex and possibly target proteins that are positioned downstream of this complex. To address this possibility, protein abundance and phosphorylation state are quantified in wild type and G-protein deficient Arabidopsis roots in the unstimulated resting state. A total of 3246 phosphorylated and 8141 non-modified protein groups are identified. It has been found that 428 phosphorylation sites decrease and 509 sites increase in abundance in the G-protein quadrupole mutant lacking an operable G-protein-complex. Kinases with known roles in G-protein signaling including MAP KINASE 6 and FERONIA are differentially phosphorylated along with many other proteins now implicated in the control of G-protein signaling. Taken together, these datasets will enable the discovery of novel proteins and biological processes dependent on G-protein signaling.
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Affiliation(s)
- Gaoyuan Song
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
| | - Libuse Brachova
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Basil J. Nikolau
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Alan M. Jones
- Department of Biology and Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Justin W. Walley
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA USA
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Sarosiek I, Song G, Sun Y, Sandoval H, Sands S, Chen J, McCallum R. Central and Peripheral Effects of Transcutaneous Acupuncture Treatment for Nausea in Patients With Diabetic Gastroparesis. J Acupunct Meridian Stud 2018. [DOI: 10.1016/j.jams.2018.10.005] [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: 11/25/2022] Open
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