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Arnold MT, Temte JL, Barlow SK, Bell CJ, Goss MD, Temte EG, Checovich MM, Reisdorf E, Scott S, Guenther K, Wedig M, Shult P, Uzicanin A. Comparison of participant-collected nasal and staff-collected oropharyngeal specimens for human ribonuclease P detection with RT-PCR during a community-based study. PLoS One 2020; 15:e0239000. [PMID: 33027284 PMCID: PMC7540885 DOI: 10.1371/journal.pone.0239000] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/27/2020] [Indexed: 11/24/2022] Open
Abstract
We analyzed 4,352 participant- and staff-collected respiratory specimens from 2,796 subjects in the Oregon Child Absenteeism due to Respiratory Disease Study. Trained staff collected oropharyngeal specimens from school-aged children with acute respiratory illness while household participants of all ages collected their own midturbinate nasal specimens in year one and anterior nasal specimens in year two. Human ribonuclease P levels were measured using RT-PCR for all staff- and participant-collected specimens to determine adequacy, defined as Cycle threshold less than 38. Overall, staff- and participant-collected specimens were 99.9% and 96.4% adequate, respectively. Participant-collected midturbinate specimens were 95.2% adequate in year one, increasing to 97.2% in year two with anterior nasal collection. The mean human ribonuclease P Cycle threshold for participant-collected specimens was 31.18 in year one and 28.48 in year two. The results from this study suggest that community-based participant collection of respiratory specimens is comparable to staff-collected oropharyngeal specimens, is feasible, and may be optimal with anterior nasal collection.
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Affiliation(s)
- Mitchell T. Arnold
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
- * E-mail:
| | - Jonathan L. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Shari K. Barlow
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Cristalyne J. Bell
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Maureen D. Goss
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Emily G. Temte
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Mary M. Checovich
- Department of Family Medicine and Community Health, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI, United States of America
| | - Erik Reisdorf
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Samantha Scott
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Kyley Guenther
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Mary Wedig
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Peter Shult
- Wisconsin State Laboratory of Hygiene, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Amra Uzicanin
- US Centers for Disease Control and Prevention, Atlanta, GA, United States of America
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Yan Y, Chang L, Wang L. Laboratory testing of SARS-CoV, MERS-CoV, and SARS-CoV-2 (2019-nCoV): Current status, challenges, and countermeasures. Rev Med Virol 2020; 30:e2106. [PMID: 32302058 PMCID: PMC7235496 DOI: 10.1002/rmv.2106] [Citation(s) in RCA: 188] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/20/2020] [Accepted: 03/20/2020] [Indexed: 01/08/2023]
Abstract
Emerging and reemerging infectious diseases are global public concerns. With the outbreak of unknown pneumonia in Wuhan, China in December 2019, a new coronavirus, SARS-CoV-2 has been attracting tremendous attention. Rapid and accurate laboratory testing of SARS-CoV-2 is essential for early discovery, early reporting, early quarantine, early treatment, and cutting off epidemic transmission. The genome structure, transmission, and pathogenesis of SARS-CoV-2 are basically similar to SARS-CoV and MERS-CoV, the other two beta-CoVs of medical importance. During the SARS-CoV and MERS-CoV epidemics, a variety of molecular and serological diagnostic assays were established and should be referred to for SARS-CoV-2. In this review, by summarizing the articles and guidelines about specimen collection, nucleic acid tests (NAT) and serological tests for SARS-CoV, MERS-CoV, and SARS-CoV-2, several suggestions are put forward to improve the laboratory testing of SARS-CoV-2. In summary, for NAT: collecting stool and blood samples at later periods of illness to improve the positive rate if lower respiratory tract specimens are unavailable; increasing template volume to raise the sensitivity of detection; putting samples in reagents containing guanidine salt to inactivate virus as well as protect RNA; setting proper positive, negative and inhibition controls to ensure high-quality results; simultaneously amplifying human RNase P gene to avoid false-negative results. For antibody test, diverse assays targeting different antigens, and collecting paired samples are needed.
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Affiliation(s)
- Ying Yan
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
| | - Lunan Wang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of GerontologyInstitute of Geriatric Medicine, Chinese Academy of Medical SciencesBeijingChina
- Beijing Engineering Research Center of Laboratory MedicineBeijing HospitalBeijingChina
- Graduate School, Peking Union Medical CollegeChinese Academy of Medical SciencesBeijingChina
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Abstract
RNase P, which catalyzes the magnesium-dependent 5'-end maturation of tRNAs in all three domains of life, is composed of one essential RNA and a varying number of protein subunits depending on the source: at least one in bacteria, four in archaea, and nine in eukarya. To address why multiple protein subunits are needed for archaeal/eukaryal RNase P catalysis, in contrast to their bacterial relative, in vitro reconstitution of these holoenzymes is a prerequisite. Using recombinant subunits, we have reconstituted in vitro the RNase P holoenzyme from the thermophilic archaeon Pyrococcus furiosus (Pfu) and furthered our understanding regarding its functional organization and assembly pathway(s). Whereas Pfu RNase P RNA (RPR) alone is capable of multiple turnover, addition of all four RNase P protein (Rpp) subunits to Pfu RPR results in a 25-fold increase in its k(cat) and a 170-fold decrease in K(m). In fact, even in the presence of only one of two specific pairs of Rpps, the RPR displays activity at lower substrate and magnesium concentrations. Moreover, a pared-down, mini-Pfu RNase P was identified with an RPR deletion mutant. Results from our kinetic and footprinting studies on Pfu RNase P, together with insights from recent structures of bacterial RPRs, provide a framework for appreciating the role of multiple Rpps in archaeal RNase P.
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Affiliation(s)
- Hsin-Yue Tsai
- *Molecular, Cellular and Developmental Biology Graduate Program
- Department of Biochemistry, Ohio State University, Columbus, OH 43210
| | - Dileep K. Pulukkunat
- Ohio State Biochemistry Program, and
- Department of Biochemistry, Ohio State University, Columbus, OH 43210
| | - Walter K. Woznick
- Department of Biochemistry, Ohio State University, Columbus, OH 43210
| | - Venkat Gopalan
- *Molecular, Cellular and Developmental Biology Graduate Program
- Ohio State Biochemistry Program, and
- Department of Biochemistry, Ohio State University, Columbus, OH 43210
- To whom correspondence should be addressed. E-mail:
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Salinas K, Wierzbicki S, Zhou L, Schmitt ME. Characterization and purification of Saccharomyces cerevisiae RNase MRP reveals a new unique protein component. J Biol Chem 2005; 280:11352-60. [PMID: 15637077 DOI: 10.1074/jbc.m409568200] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In the yeast Saccharomyces cerevisiae, RNase mitochondrial RNA processing (MRP) is an essential endoribonuclease that consists of one RNA component and at least nine protein components. Characterization of the complex is complicated by the fact that eight of the known protein components are shared with a related endoribonuclease, RNase P. To fully characterize the RNase MRP complex, we purified it to apparent homogeneity in a highly active state using tandem affinity purification. In addition to the nine known protein components, both Rpr2 and a protein encoded by the essential gene YLR145w were present in our preparations of RNase MRP. Precipitation of a tagged version of Ylr145w brought with it the RNase MRP RNA, but not the RNase P RNA. A temperature-sensitive ylr145w mutant was generated and found to exhibit a rRNA processing defect identical to that seen in other RNase MRP mutants, whereas no defect in tRNA processing was observed. Homologues of the Ylr145w protein were found in most yeasts, fungi, and Arabidopsis. Based on this evidence, we propose that YLR145w encodes a novel protein component of RNase MRP, but not RNase P. We recommend that this gene be designated RMP1, for RNase MRP protein 1.
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Affiliation(s)
- Kelly Salinas
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, New York 13210, USA
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Gao MY, Chen R, Liu SG, Feng JN. [Experimental study on phenotypic conversion of clinical chloromycetin-resistant strains of E. coli to drug-sensitive strains by using EGS technique in vitro]. Zhonghua Yi Xue Za Zhi 2004; 84:1294-8. [PMID: 15387969] [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: 04/30/2023]
Abstract
OBJECTIVE To explore the possibility of phenotypic conversion of clinical chloromycetin (Cm)-resistant isolates of E.coli to drug-sensitive ones with external guide sequences (EGS) in vitro. METHODS Recombinant EGS plasmids directed against Cm acetyl transferase (cat) and containing kanamycin (Km) drug-resistance gene and control plasmids only containing kanamycin-resistance gene without EGS were constructed. By using CaCl(2) method, the recombinant plasmids were introduced into the clinically isolated Cm-resistant E.coli strains. Extraction of plasmids and PCR were applied to identify the EGS positive clones; The growth rate in liquid broth culture of Cm-resistant bacteria after EGS containing plasmid transformation was determined by spectrophotometer A(600). Drug sensitivity was tested in solid culture by using KB method. RESULTS Transformation studies were carried out on 16 clinically isolated Cm-resistant E.coli strains with pEGFP-C1-EGS + cat1 + cat2 recombinant plasmid. Transformants were screened on LB-agar plates containing Km after transformation using EGS. In 4 tested strains of them, transformants with specific EGS plasmid showed growth inhibition when grown in liquid broth culture containing 100 approximately 200 micro g/ml of Cm. They were sensitive to Cm on LB-agar plates containing 100 approximately 200 micro g/ml of Cm in drug-sensitivity test. Extraction of plasmids showed the existence of EGS bands. PCR amplified products of EGS. The above facts indicated that the 4 strains out of the 16 clinical isolates had been converted to drug-sensitive phenotype, and Cm-resistant clinically isolated E. coli resumed sensitivity to Cm. CONCLUSION EGS has the capability of converting the phenotype of clinical drug-resistant isolates to drug sensitivity.
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Affiliation(s)
- Mei-ying Gao
- Department of Infectious Diseases, Tongji Hospital and Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Dunn W, Liu F. RNase P-mediated inhibition of viral growth by exogenous administration of short oligonucleotide external guide sequence. Methods Mol Biol 2004; 252:425-36. [PMID: 15017068 DOI: 10.1385/1-59259-746-7:425] [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] [Indexed: 04/29/2023]
Abstract
The use of external guide sequence (EGS) in directing endogenous ribonuclease P (RNase P) for inhibition of viral propagation is described in this chapter, with an emphasis on chemically modified EGSs and their extracellular delivery. Targeting of the mRNA-encoding human cytomegalovirus (HCMV) protease by DNA-based EGSs is presented as an example of how to design chemically modified EGSs for antiviral applications. General information about the EGS-based technology is included, followed by detailed protocols for EGS design, human RNase P purification, in vitro assay of EGS activity, liposome-mediated delivery of chemically modified EGSs and detection of their distribution in cells, and an assay of EGS activity for blocking growth of HCMV in cultured cells.
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Affiliation(s)
- Walter Dunn
- Division of Infectious Diseases, School of Public Health, University of California, Berkeley, USA
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