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Sun Z, Zhou Q, Yang Y, Li L, Yu M, Li H, Li A, Wang X, Jiang Y. Identification and ultrasensitive photoelectrochemical detection of LncNR_040117: a biomarker of recurrent miscarriage and antiphospholipid antibody syndrome in platelet-derived microparticles. J Nanobiotechnology 2022; 20:396. [PMID: 36045427 PMCID: PMC9429728 DOI: 10.1186/s12951-022-01608-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/22/2022] [Indexed: 05/31/2023] Open
Abstract
The abnormal expression of long non-coding RNAs (LncRNAs) in platelet-derived microparticles (PMPs) is closely related to immune disorders and may lead to antiphospholipid antibody syndrome and recurrent miscarriage. To understand the association between the LncRNAs in PMPs and RM/APS, the differences in the expression of LncRNAs in RM/APS patients and healthy controls were analyzed. Microarray analysis and RT-qPCR detection proved that RM/APS patient exhibited high levels of LncNR_040117 expression. The lentiviral silent expression transfection of HTR-8/SVneo cells indicated that LncNR_040117 downregulation decreased the activity of HTR-8/SVneo cells and inhibited the MAPK signaling pathway, further confirming the biomarker proficiency of LncNR_040117 for RM/APS. After that, we proposed a β-In2S3@g-C3N4 nanoheterojunction-based photoelectrochemical (PEC) biosensor to achieve the ultrasensitive detection of LncNR_040117. The nanoheterojunction aids in the effective separation of photogenerated carriers and significantly improve the photocurrent response of the biosensor. The conjugation of LncNR_040117 onto the PEC biosensing platform increased the steric hindrance between electrolyte and electrode, subsequently decreasing the photocurrent signal. The PEC biosensor showed a wide detection range of 0.1-106 fM and a low limit of detection of 0.025 fM. For clinical sample testing, the results of the PEC and RT-qPCR were highly consistent. Overall, LncNR_040117 in PMPs was identified as an effective biomarker for RM/APS and could be accurately detected by the proposed PEC biosensor, which is expected to provide a reliable diagnostic platform for RM/APS.
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Affiliation(s)
- Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, 250061, China
| | - Qian Zhou
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.,Department of Obstetrics and Gynecology, Liaocheng People's Hospital, Liaocheng, 252000, China.,Key Laboratory of Birth Regulation and Control Technology of National Health and Family Planning Commission of China, Maternal Child Health Hospital of Shandong Province, Jinan, 250014, China
| | - Yufei Yang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, 250061, China
| | - Lei Li
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.,Department of Obstetrics and Gynecology, Liaocheng People's Hospital, Liaocheng, 252000, China.,Key Laboratory of Birth Regulation and Control Technology of National Health and Family Planning Commission of China, Maternal Child Health Hospital of Shandong Province, Jinan, 250014, China
| | - Mengru Yu
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China.,Department of Obstetrics and Gynecology, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Hui Li
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, 250061, China
| | - Aihua Li
- Department of Obstetrics and Gynecology, Liaocheng People's Hospital, Liaocheng, 252000, China
| | - Xietong Wang
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250021, China. .,Department of Obstetrics and Gynecology, Liaocheng People's Hospital, Liaocheng, 252000, China. .,Key Laboratory of Birth Regulation and Control Technology of National Health and Family Planning Commission of China, Maternal Child Health Hospital of Shandong Province, Jinan, 250014, China.
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, 250061, China.
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2
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Li X, Lidsky PV, Xiao Y, Wu CT, Garcia-Knight M, Yang J, Nakayama T, Nayak JV, Jackson PK, Andino R, Shu X. Ethacridine inhibits SARS-CoV-2 by inactivating viral particles. PLoS Pathog 2021; 17:e1009898. [PMID: 34478458 PMCID: PMC8445489 DOI: 10.1371/journal.ppat.1009898] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 09/16/2021] [Accepted: 08/16/2021] [Indexed: 01/29/2023] Open
Abstract
The respiratory disease COVID-19 is caused by the coronavirus SARS-CoV-2. Here we report the discovery of ethacridine as a potent drug against SARS-CoV-2 (EC50 ~ 0.08 μM). Ethacridine was identified via high-throughput screening of an FDA-approved drug library in living cells using a fluorescence assay. Plaque assays, RT-PCR and immunofluorescence imaging at various stages of viral infection demonstrate that the main mode of action of ethacridine is through inactivation of viral particles, preventing their binding to the host cells. Consistently, ethacridine is effective in various cell types, including primary human nasal epithelial cells that are cultured in an air-liquid interface. Taken together, our work identifies a promising, potent, and new use of the old drug via a distinct mode of action for inhibiting SARS-CoV-2.
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Affiliation(s)
- Xiaoquan Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Peter V. Lidsky
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Yinghong Xiao
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Chien-Ting Wu
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, United States of America
| | - Miguel Garcia-Knight
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Junjiao Yang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Tsuguhisa Nakayama
- Department of Otolaryngology–Head and Neck Surgery, Stanford University, Stanford, California, United States of America
| | - Jayakar V. Nayak
- Department of Otolaryngology–Head and Neck Surgery, Stanford University, Stanford, California, United States of America
| | - Peter K. Jackson
- Department of Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University, California, United States of America
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
| | - Xiaokun Shu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California, United States of America
- Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California, United States of America
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3
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Gorji-Bahri G, Moradtabrizi N, Vakhshiteh F, Hashemi A. Validation of common reference genes stability in exosomal mRNA-isolated from liver and breast cancer cell lines. Cell Biol Int 2021; 45:1098-1110. [PMID: 33501690 DOI: 10.1002/cbin.11556] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 01/02/2021] [Accepted: 01/24/2021] [Indexed: 12/12/2022]
Abstract
Accurate relative gene expression analysis by reverse transcription-quantitative polymerase chain reaction relies on the usage of suitable reference genes for data normalization. The RNA content of small extracellular vesicles including exosomes is growingly considered as cancer biomarkers. So, reliable relative quantification of exosomal messenger RNA (mRNA) is essential for cancer diagnosis and prognosis applications. However, suitable reference genes for accurate normalization of a target gene in exosomes derived from cancer cells are not depicted yet. Here, we analyzed the expression and stability of eight well-known reference genes namely GAPDH, B2M, HPRT1, ACTB, YWHAZ, UBC, RNA18S, and TBP in exosomes-isolated from the liver (Huh7, HepG2, PLC/PRF/5) and breast (SK-BR-3) cancer cell lines using five different algorithms including geNorm, BestKeeper, Delta Ct, NormFinder, and RefFinder. Our results showed that ACTB, TBP, and HPRT1 were not expressed in exosomes-isolated from studied liver and breast cancer cell lines. The geNorm and BestKeeper algorithms indicated GAPDH and UBC as the most stable candidates. Moreover, Delta Ct and NormFinder algorithms showed YWHAZ as the most stable reference genes. Comprehensive ranking calculated by the RefFinder algorithm also pointed out GAPDH, YWHAZ, and UBC as the first three stable reference genes. Taken together, this study validated the common reference genes stability in exosomal mRNA derived from liver and breast cancer cell lines for the first time. We believe that this study would be the first step in finding more stable reference genes in exosomes that triggers more accurate detection of exosomal biomarkers.
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Affiliation(s)
- Gilar Gorji-Bahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Niloofar Moradtabrizi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Faezeh Vakhshiteh
- Nanotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Atieh Hashemi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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4
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Nebeluk N, Foster TP. Design, validation and evaluation of a SYBR green-based quantitative PCR array for comprehensive analysis of adenovirus type 5 transcriptional patterns. J Virol Methods 2020; 281:113880. [PMID: 32413477 DOI: 10.1016/j.jviromet.2020.113880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 04/14/2020] [Accepted: 04/27/2020] [Indexed: 12/13/2022]
Abstract
The adenoviral genome encodes coordinately expressed early and late gene transcriptional units that specify a complex collection of extensively spliced overlapping mRNAs. These complexities confound the generation of compatible, validated and optimized qPCR assays that permit comprehensive evaluation of adenoviral transcription. We have developed and evaluated a compilation of qPCR assays that represent the majority of the human adenovirus 5 (hAdV5) genome and allow for absolute and relative quantification of transcriptional activity. A panel of specific adenovirus gene primer pairs was designed through computational modeling to be compatible under a single reaction condition, precisely amplify spliced transcript products within each gene class, and not result in cellular or viral RNA/DNA background amplification. Primer pairs and reaction conditions were optimized to generate a single amplification product that was specific for its target amplicon with minimal intra-assay variability. The specificity of target amplicons was confirmed by dissociation curve analysis, gel electrophoresis and sequencing. In all, thirty-two primer sets representing specific gene products, as well as, pan early and late gene regions were validated under identical amplification conditions, thereby enabling a comprehensive assessment of adenoviral transcription within a single plate array. In order to generate positive control templates and to facilitate absolute quantification of gene expression, all target amplicons were cloned to create gene target-specific standards. These plasmid amplicon controls demonstrated that the SYBR qPCR assays exhibited optimal amplification efficiencies with a high sensitivity of detection to less than 10 copies and a linear amplification across at least eight orders of magnitude. The effectiveness and utility of the comprehensive adenoviral transcriptional array was assessed by investigating the changes in Ad5Wt gene expression at 72 versus 24 h post infection. Predictably, overall gene expression was globally increased at 72 h post infection; however, levels of E2 and Late transcripts exhibited the greatest increased expression, reflecting their necessity at this time point for genomic replication and virion assembly. Taken together, these data demonstrate that the adenoviral qPCR transcriptional array is a modular, scalable, and cost-effective method to comprehensively and accurately assess hAdV5 gene transcription. This array is broadly applicable to facilitate: adenoviral vector development; assessment of cell complementation of knockout viruses; antiviral mechanism of action evaluation; next-generation sequencing data validation.
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Affiliation(s)
- Nazary Nebeluk
- Department of Microbiology, Immunology, and Parasitology, USA
| | - Timothy P Foster
- Department of Microbiology, Immunology, and Parasitology, USA; Department of Ophthalmology, USA; The Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA; The Louisiana Vaccine Center, New Orleans, LA, 70112, USA.
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5
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Wu M, Zhang Q, Yi D, Wu T, Chen H, Guo S, Li S, Ji C, Wang L, Zhao D, Hou Y, Wu G. Quantitative Proteomic Analysis Reveals Antiviral and Anti-inflammatory Effects of Puerarin in Piglets Infected With Porcine Epidemic Diarrhea Virus. Front Immunol 2020; 11:169. [PMID: 32174911 PMCID: PMC7055472 DOI: 10.3389/fimmu.2020.00169] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) has caused enormous economic losses to the swine industry worldwide in recent years. Puerarin (PR), a major isoflavonoid isolated from the Chinese herb Gegen, possesses many pharmacological activities, including anti-inflammatory, and anti-viral activities. This study was conducted with both PEDV-infected African green monkey kidney cells (Vero) and neonatal pigs to determine the effect of PR on PEDV infection and to elucidate the underlying mechanisms by using proteomic analyses. Twenty-four piglets fed a milk replacer were randomly allocated into one of three groups (Control, PEDV, and PEDV + PR). After a 5-day period of adaption, piglets (n = 8/group) in the PEDV + PR were orally administered with PR (0.5 mg/kg body weight) between days 5 and 9, whereas piglets in the other two groups received the same volume of liquid milk replacer. On day 9, piglets were orally administered with either sterile saline or PEDV (Yunnan province strain) at 104.5 TCID50 (50% tissue culture infectious dose) per pig. On day 12 of the trial, jugular vein blood and intestinal samples were collected. In addition, Vero cells were assigned randomly into three groups (Control, PEDV, PEDV + PR). Cells in the PEDV and PEDV + PR groups were infected with PEDV at a multiplicity of infection of 0.01, while cells in the control group were treated with the same volume of sterile saline. One hour later, cells in the Control and PEDV groups were cultured in serum-free DMEM, while cells in the PEDV + PR group were supplemented with PR. After 36 h of culture, cells were harvested. PR attenuated the reductions in cell proliferation in vitro and growth performance in PEDV-infected piglets, and inhibited PEDV replication and the expression of several cytokines (including IL-8) both in vitro and in vivo. Proteomic analyses identified that the abundances of 29 proteins in the ileum were altered by PEDV infection and restored to the control level by PR. Pathway analyses revealed that PR restored the expression of several interferon-stimulated genes and selectively upregulated the expression of guanylate-binding proteins. Western blot analyses showed that PR supplementation inhibited the PEDV-induced NF-κB activation. Collectively, these results indicate that PR could exert antiviral and anti-inflammatory effects in piglets infected with PEDV and have the potential to be an effective antiviral feed additive.
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Affiliation(s)
- Mengjun Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Qian Zhang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Dan Yi
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Tao Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Hongbo Chen
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Shuangshuang Guo
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Siyuan Li
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Changzheng Ji
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Lei Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Di Zhao
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Yongqing Hou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China
| | - Guoyao Wu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, Wuhan Polytechnic University, Wuhan, China.,Department of Animal Science, Texas A&M University, College Station, TX, United States
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6
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Rege J, Turcu AF, Kasa-Vubu JZ, Lerario AM, Auchus GC, Auchus RJ, Smith JM, White PC, Rainey WE. 11-Ketotestosterone Is the Dominant Circulating Bioactive Androgen During Normal and Premature Adrenarche. J Clin Endocrinol Metab 2018; 103:4589-4598. [PMID: 30137510 PMCID: PMC6226603 DOI: 10.1210/jc.2018-00736] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/14/2018] [Indexed: 01/18/2023]
Abstract
CONTEXT Adrenarche refers to the rise of dehydroepiandrosterone sulfate (DHEA-S) associated with the development of a functional adrenal zona reticularis. Clinical features of adrenarche include onset of body odor, axillary hair, and pubic hair, which reflect increased androgen action. An early rise in adrenal androgens, or premature adrenarche (PremA), is a risk factor for adverse metabolic profiles in adolescence and adulthood. The bioactive androgens associated with adrenarche and PremA remain poorly understood. The adrenal gland is a potential source of testosterone (T) and the 11-oxygenated derivatives 11β-hydroxytestosterone (11OHT) and 11-ketotestosterone (11KT). OBJECTIVE The objective of this study was to characterize the adrenal androgen biome contributing to adrenarche and PremA. PARTICIPANTS AND METHODS With the use of mass spectrometry, 19 steroids including the 11-oxygenated derivatives of T were measured in sera obtained from girls with PremA (n = 37; 4 to 7 years) and age-matched girls (n = 83; 4 to 10 years). RESULTS In reference population girls, dehydroepiandrosterone, DHEA-S, androstenediol-3-sulfate, T, and 11KT all increased at the onset of adrenarche (6 to 8 years) and beyond (9 to 10 years) (P < 0.05 vs younger subjects 4 to 5 years). T, 11OHT, and 11KT were further elevated in PremA vs age-matched girls (P < 0.001). Circulating concentrations of 11KT during adrenarche and PremA exceeded those of T and 11OHT (11KT > T ≥ 11OHT). Androgen receptor activity and nuclear translocation studies demonstrated that 11KT is a potent androgen similar to T. CONCLUSIONS Our findings suggest that 11KT is the dominant bioactive androgen in children during adrenarche and PremA. Its androgenic capacity suggests that it may be responsible for the phenotypic changes seen in these phenomena.
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Affiliation(s)
- Juilee Rege
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Adina F Turcu
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | | | - Antonio M Lerario
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Gabriela C Auchus
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Richard J Auchus
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan
| | | | - Perrin C White
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - William E Rainey
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, Michigan
- Division of Metabolism, Endocrinology, and Diabetes, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
- Correspondence and Reprint Requests: William E. Rainey, PhD, Departments of Molecular and Integrative Physiology and Internal Medicine, University of Michigan, 1150 West Medical Center Drive, 2560C Medical Science Research Building II, Ann Arbor, Michigan 48109-5622. E-mail:
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7
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Kräter M, Sapudom J, Bilz NC, Pompe T, Guck J, Claus C. Alterations in Cell Mechanics by Actin Cytoskeletal Changes Correlate with Strain-Specific Rubella Virus Phenotypes for Cell Migration and Induction of Apoptosis. Cells 2018; 7:E136. [PMID: 30217036 PMCID: PMC6162683 DOI: 10.3390/cells7090136] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 02/06/2023] Open
Abstract
The cellular cytoskeleton is central for key cellular functions, and as such is a marker for diseased and infected cell states. Here we analyzed infection with rubella virus (RV) strains with respect to phenotypes in cellular mechanical properties, cell movement, and viral cytopathogenicity. Real-time deformability cytometry (RT-DC), as a high-throughput platform for the assessment of cell mechanics, revealed a correlation of an increase in cortical filamentous-actin (F-actin) with a higher cellular stiffness. The additional reduction of stress fibers noted for only some RV strains as the most severe actin rearrangement lowered cell stiffness. Furthermore, a reduced collective and single cell migration speed in a wound healing assay was detected in addition to severe changes in cell morphology. The latter was followed by activation of caspase 3/7 as a sign for induction of apoptosis. Our study emphasizes RT-DC technology as a sensitive means to characterize viral cell populations and to implicate alterations of cell mechanical properties with cell functions. These interdependent events are not only promising options to elucidate viral spread and to understand viral pathologies within the infected host. They also contribute to any diseased cell state, as exemplified by RV as a representative agent for cytoskeletal alterations involved in a cytopathological outcome.
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Affiliation(s)
- Martin Kräter
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Jiranuwat Sapudom
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
- Department of Dermatology, Venerology and Allergology, University Clinic of Leipzig, 04103 Leipzig, Germany.
| | | | - Tilo Pompe
- Institute of Biochemistry, Leipzig University, 04103 Leipzig, Germany.
| | - Jochen Guck
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Claudia Claus
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
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8
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Bilz NC, Jahn K, Lorenz M, Lüdtke A, Hübschen JM, Geyer H, Mankertz A, Hübner D, Liebert UG, Claus C. Rubella Viruses Shift Cellular Bioenergetics to a More Oxidative and Glycolytic Phenotype with a Strain-Specific Requirement for Glutamine. J Virol 2018; 92:e00934-18. [PMID: 29950419 PMCID: PMC6096829 DOI: 10.1128/jvi.00934-18] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 06/19/2018] [Indexed: 12/21/2022] Open
Abstract
The flexible regulation of cellular metabolic pathways enables cellular adaptation to changes in energy demand under conditions of stress such as posed by a virus infection. To analyze such an impact on cellular metabolism, rubella virus (RV) was used in this study. RV replication under selected substrate supplementation with glucose, pyruvate, and glutamine as essential nutrients for mammalian cells revealed its requirement for glutamine. The assessment of the mitochondrial respiratory (based on the oxygen consumption rate) and glycolytic (based on the extracellular acidification rate) rate and capacity by respective stress tests through Seahorse technology enabled determination of the bioenergetic phenotype of RV-infected cells. Irrespective of the cellular metabolic background, RV infection induced a shift of the bioenergetic state of epithelial cells (Vero and A549) and human umbilical vein endothelial cells to a higher oxidative and glycolytic level. Interestingly there was a RV strain-specific, but genotype-independent demand for glutamine to induce a significant increase in metabolic activity. While glutaminolysis appeared to be rather negligible for RV replication, glutamine could serve as donor of its amide nitrogen in biosynthesis pathways for important metabolites. This study suggests that the capacity of RVs to induce metabolic alterations could evolve differently during natural infection. Thus, changes in cellular bioenergetics represent an important component of virus-host interactions and could complement our understanding of the viral preference for a distinct host cell population.IMPORTANCE RV pathologies, especially during embryonal development, could be connected with its impact on mitochondrial metabolism. With bioenergetic phenotyping we pursued a rather novel approach in virology. For the first time it was shown that a virus infection could shift the bioenergetics of its infected host cell to a higher energetic state. Notably, the capacity to induce such alterations varied among different RV isolates. Thus, our data add viral adaptation of cellular metabolic activity to its specific needs as a novel aspect to virus-host evolution. In addition, this study emphasizes the implementation of different viral strains in the study of virus-host interactions and the use of bioenergetic phenotyping of infected cells as a biomarker for virus-induced pathological alterations.
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Affiliation(s)
- Nicole C Bilz
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - Kristin Jahn
- Institute of Virology, University of Leipzig, Leipzig, Germany
- Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | | | - Anja Lüdtke
- Institute of Virology, University of Leipzig, Leipzig, Germany
- Faculty of Life Sciences, University of Leipzig, Leipzig, Germany
| | - Judith M Hübschen
- WHO European Regional Reference Laboratory for Measles and Rubella, Department of Infection and Immunity, Luxembourg Institute of Health, Esch-Sur-Alzette, Grand-Duchy of Luxembourg
| | - Henriette Geyer
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch Institute, Berlin, Germany
| | - Annette Mankertz
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch Institute, Berlin, Germany
| | - Denise Hübner
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - Uwe G Liebert
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - Claudia Claus
- Institute of Virology, University of Leipzig, Leipzig, Germany
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9
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Kirschneck C, Batschkus S, Proff P, Köstler J, Spanier G, Schröder A. Valid gene expression normalization by RT-qPCR in studies on hPDL fibroblasts with focus on orthodontic tooth movement and periodontitis. Sci Rep 2017; 7:14751. [PMID: 29116140 PMCID: PMC5677027 DOI: 10.1038/s41598-017-15281-0] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 10/24/2017] [Indexed: 01/07/2023] Open
Abstract
Meaningful, reliable and valid mRNA expression analyses by real-time quantitative PCR (RT-qPCR) can only be achieved, if suitable reference genes are chosen for normalization and if appropriate RT-qPCR quality standards are met. Human periodontal ligament (hPDL) fibroblasts play a major mediating role in orthodontic tooth movement and periodontitis. Despite corresponding in-vitro gene expression studies being a focus of interest for many years, no information is available for hPDL fibroblasts on suitable reference genes, which are generally used in RT-qPCR experiments to normalize variability between samples. The aim of this study was to identify and validate suitable reference genes for normalization in untreated hPDL fibroblasts as well as experiments on orthodontic tooth movement or periodontitis (Aggregatibacter actinomycetemcomitans). We investigated the suitability of 13 candidate reference genes using four different algorithms (geNorm, NormFinder, comparative ΔCq and BestKeeper) and ranked them according to their expression stability. Overall PPIB (peptidylprolyl isomerase A), TBP (TATA-box-binding protein) and RPL22 (ribosomal protein 22) were found to be most stably expressed with two genes in conjunction sufficient for reliable normalization. This study provides an accurate tool for quantitative gene expression analysis in hPDL fibroblasts according to the MIQE guidelines and shows that reference gene reliability is treatment-specific.
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Affiliation(s)
- Christian Kirschneck
- Department of Orthodontics, University Medical Centre of Regensburg, Regensburg, D-93053, Germany.
| | - Sarah Batschkus
- Department of Orthodontics, University of Goettingen, Goettingen, D-37075, Germany
| | - Peter Proff
- Department of Orthodontics, University Medical Centre of Regensburg, Regensburg, D-93053, Germany
| | - Josef Köstler
- Institute of Microbiology and Hygiene, University Medical Centre of Regensburg, Regensburg, D-93053, Germany
| | - Gerrit Spanier
- Department of Cranial and Maxillo-Facial Surgery, University Medical Centre of Regensburg, Regensburg, D-93053, Germany
| | - Agnes Schröder
- Department of Orthodontics, University Medical Centre of Regensburg, Regensburg, D-93053, Germany
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10
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Claus C, Manssen L, Hübner D, Roßmark S, Bothe V, Petzold A, Große C, Reins M, Mankertz A, Frey TK, Liebert UG. Activation of the Mitochondrial Apoptotic Signaling Platform during Rubella Virus Infection. Viruses 2015; 7:6108-26. [PMID: 26703711 PMCID: PMC4690853 DOI: 10.3390/v7122928] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 11/16/2015] [Accepted: 11/17/2015] [Indexed: 12/16/2022] Open
Abstract
Mitochondria- as well as p53-based signaling pathways are central for the execution of the intrinsic apoptotic cascade. Their contribution to rubella virus (RV)-induced apoptosis was addressed through time-specific evaluation of characteristic parameters such as permeabilization of the mitochondrial membrane and subsequent release of the pro-apoptotic proteins apoptosis-inducing factor (AIF) and cytochrome c from mitochondria. Additionally, expression and localization pattern of p53 and selected members of the multifunctional and stress-inducible cyclophilin family were examined. The application of pifithrin μ as an inhibitor of p53 shuttling to mitochondria reduced RV-induced cell death to an extent similar to that of the broad spectrum caspase inhibitor z-VAD-fmk (benzyloxycarbonyl-V-A-D-(OMe)-fmk). However, RV progeny generation was not altered. This indicates that, despite an increased survival rate of its cellular host, induction of apoptosis neither supports nor restricts RV replication. Moreover, some of the examined apoptotic markers were affected in a strain-specific manner and differed between the cell culture-adapted strains: Therien and the HPV77 vaccine on the one hand, and a clinical isolate on the other. In summary, the results presented indicate that the transcription-independent mitochondrial p53 program contributes to RV-induced apoptosis.
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Affiliation(s)
- Claudia Claus
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Lena Manssen
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Denise Hübner
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Sarah Roßmark
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Viktoria Bothe
- Division of Clinical Pharmacology, Ludwig-Maximilian University Munich, 80336 Munich, Germany.
| | - Alice Petzold
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Claudia Große
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Mareen Reins
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
| | - Annette Mankertz
- WHO European Regional Reference Laboratory for Measles and Rubella, Robert Koch-Institute, 13353 Berlin, Germany.
| | - Teryl K Frey
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA.
| | - Uwe G Liebert
- Institute of Virology, University of Leipzig, 04103 Leipzig, Germany.
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11
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Garvey CE, McGowin CL, Foster TP. Development and evaluation of SYBR Green-I based quantitative PCR assays for herpes simplex virus type 1 whole transcriptome analysis. J Virol Methods 2014; 201:101-11. [PMID: 24607486 DOI: 10.1016/j.jviromet.2014.02.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 02/05/2014] [Accepted: 02/11/2014] [Indexed: 12/27/2022]
Abstract
There is an emerging need for viral gene specific quantitative PCR (qPCR) assays that validate and complement whole transcriptome level technologies, including microarray and next generation sequencing. Therefore, a compilation of qPCR assays that represented the breadth of the entire Herpes simplex virus type 1 (HSV-1) genome were developed and evaluated. SYBR Green-I-based quantitation of each of the 74 HSV-1 lytic genes enabled accurate and reproducible detection of viral genes using a minimal number of reaction conditions. The amplification specificity of these assays for HSV-1 target genes was confirmed by amplicon size and purity determination on agarose gels, melt temperature dissociation curve analysis, and direct DNA sequencing of amplified products. Analysis of representative target genes demonstrated that these assays accurately and reproducibly quantified target gene expression across a wide and linear range of detection. In addition, minimal intra- and inter-assay variability was observed with significant well-to-well and plate-to-plate/assay-to-assay precision. To evaluate the utility of the developed qPCR assay system, kinetic profiles of viral gene expression were determined for an array of representative genes from all HSV-1 transcriptional gene classes. Collectively, these data demonstrate that the compiled optimized qPCR assays is a scalable and cost-effective method to assess HSV-1 gene expression with broad application potential, including investigation of pathogenesis and antiviral therapies. In addition, they can be employed to validate and complement evolving technologies for genome-wide transcriptome analysis.
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Affiliation(s)
- Cathryn E Garvey
- Department of Microbiology, Immunology, and Parasitology, New Orleans, LA 70112, USA; The Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; The Louisiana Vaccine Center, New Orleans, LA 70112, USA
| | - Chris L McGowin
- Department of Microbiology, Immunology, and Parasitology, New Orleans, LA 70112, USA; The Louisiana Vaccine Center, New Orleans, LA 70112, USA
| | - Timothy P Foster
- Department of Microbiology, Immunology, and Parasitology, New Orleans, LA 70112, USA; The Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA 70112, USA; The Louisiana Vaccine Center, New Orleans, LA 70112, USA.
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12
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Claus C, Schönefeld K, Hübner D, Chey S, Reibetanz U, Liebert UG. Activity increase in respiratory chain complexes by rubella virus with marginal induction of oxidative stress. J Virol 2013; 87:8481-92. [PMID: 23720730 PMCID: PMC3719815 DOI: 10.1128/jvi.00533-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 05/14/2013] [Indexed: 02/07/2023] Open
Abstract
Mitochondria are important for the viral life cycle, mainly by providing the energy required for viral replication and assembly. A highly complex interaction with mitochondria is exerted by rubella virus (RV), which includes an increase in the mitochondrial membrane potential as a general marker for mitochondrial activity. We aimed in this study to provide a more comprehensive picture of the activity of mitochondrial respiratory chain complexes I to IV. Their activities were compared among three different cell lines. A strong and significant increase in the activity of mitochondrial respiratory enzyme succinate:ubiquinone oxidoreductase (complex II) and a moderate increase of ubiquinol:cytochrome c oxidoreductase (complex III) were detected in all cell lines. In contrast, the activity of mitochondrial respiratory enzyme cytochrome c oxidase (complex IV) was significantly decreased. The effects on mitochondrial functions appear to be RV specific, as they were absent in control infections with measles virus. Additionally, these alterations of the respiratory chain activity were not associated with an elevated transcription of oxidative stress proteins, and reactive oxygen species (ROS) were induced only marginally. Moreover, protein and/or mRNA levels of markers for mitochondrial biogenesis and structure were elevated, such as nuclear respiratory factors (NRFs) and mitofusin 2 (Mfn2). Together, these results establish a novel view on the regulation of mitochondrial functions by viruses.
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Affiliation(s)
- C. Claus
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - K. Schönefeld
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - D. Hübner
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - S. Chey
- Institute of Virology, University of Leipzig, Leipzig, Germany
| | - U. Reibetanz
- Institute for Medical Physics and Biophysics, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - U. G. Liebert
- Institute of Virology, University of Leipzig, Leipzig, Germany
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13
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Graham RL, Becker MM, Eckerle LD, Bolles M, Denison MR, Baric RS. A live, impaired-fidelity coronavirus vaccine protects in an aged, immunocompromised mouse model of lethal disease. Nat Med 2012; 18:1820-6. [PMID: 23142821 PMCID: PMC3518599 DOI: 10.1038/nm.2972] [Citation(s) in RCA: 187] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 09/14/2012] [Indexed: 12/21/2022]
Abstract
Attenuated viruses can be highly effective vaccines. In this issue, Ralph Baric and colleagues report that inactivating mutations in the exonuclease ExoN of a mouse-adapted SARS coronavirus impair replication fidelity and cause a mutator phenotype. The resulting attenuated virus protected mice against a lethal coronavirus challenge. Live, attenuated RNA virus vaccines are efficacious but subject to reversion to virulence. Among RNA viruses, replication fidelity is recognized as a key determinant of virulence and escape from antiviral therapy; increased fidelity is attenuating for some viruses. Coronavirus (CoV) replication fidelity is approximately 20-fold greater than that of other RNA viruses and is mediated by a 3′→5′ exonuclease (ExoN) activity that probably functions in RNA proofreading. In this study we demonstrate that engineered inactivation of severe acute respiratory syndrome (SARS)-CoV ExoN activity results in a stable mutator phenotype with profoundly decreased fidelity in vivo and attenuation of pathogenesis in young, aged and immunocompromised mice. The ExoN inactivation genotype and mutator phenotype are stable and do not revert to virulence, even after serial passage or long-term persistent infection in vivo. ExoN inactivation has potential for broad applications in the stable attenuation of CoVs and, perhaps, other RNA viruses.
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Affiliation(s)
- Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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14
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Too IHK, Ling MHT. Signal Peptidase Complex Subunit 1 and Hydroxyacyl-CoA Dehydrogenase Beta Subunit Are Suitable Reference Genes in Human Lungs. ISRN BIOINFORMATICS 2011; 2012:790452. [PMID: 25969744 PMCID: PMC4407196 DOI: 10.5402/2012/790452] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/10/2011] [Accepted: 10/27/2011] [Indexed: 11/24/2022]
Abstract
Lung cancer is a common cancer, and expression profiling can provide an accurate indication to advance the medical intervention. However, this requires the availability of stably expressed genes as reference. Recent studies had shown that genes that are stably expressed in a tissue may not be stably expressed in other tissues suggesting the need to identify stably expressed genes in each tissue for use as reference genes. DNA microarray analysis has been used to identify those reference genes with low fluctuation. Fourteen datasets with different lung conditions were employed in our study. Coefficient of variance, followed by NormFinder, was used to identify stably expressed genes. Our results showed that classical reference genes such as GAPDH and HPRT1 were highly variable; thus, they are unsuitable as reference genes. Signal peptidase complex subunit 1 (SPCS1) and hydroxyacyl-CoA dehydrogenase beta subunit (HADHB), which are involved in fundamental biochemical processes, demonstrated high expression stability suggesting their suitability in human lung cell profiling.
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Affiliation(s)
- Issac H K Too
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Maurice H T Ling
- Department of Zoology, The University of Melbourne, Parkville, Victoria 3010, Australia
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15
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Involvement of p32 and microtubules in alteration of mitochondrial functions by rubella virus. J Virol 2011; 85:3881-92. [PMID: 21248045 DOI: 10.1128/jvi.02492-10] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interaction of the rubella virus (RV) capsid (C) protein and the mitochondrial p32 protein is believed to participate in virus replication. In this study, the physiological significance of the association of RV with mitochondria was investigated by silencing p32 through RNA interference. It was demonstrated that downregulation of p32 interferes with microtubule-directed redistribution of mitochondria in RV-infected cells. However, the association of the viral C protein with mitochondria was not affected. When cell lines either pretreated with respiratory chain inhibitors or cultivated under (mild) hypoxic conditions were infected with RV, viral replication was reduced in a time-dependent fashion. Additionally, RV infection induces increased activity of mitochondrial electron transport chain complex III, which was associated with an increase in the mitochondrial membrane potential. These effects are outstanding among the examples of mitochondrial alterations caused by viruses. In contrast to the preferential localization of p32 to the mitochondrial matrix in most cell lines, RV-permissive cell lines were characterized by an almost exclusive membrane association of p32. Conceivably, this contributes to p32 function(s) during RV replication. The data presented suggest that p32 fulfills an essential function for RV replication in directing trafficking of mitochondria near sites of viral replication to meet the energy demands of the virus.
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