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Mavridis C, Venihaki M, Dermitzaki E, Deiktakis M, Liapakis G, Mamoulakis C. mRNA expression of CRF family members in urothelial bladder cancer. Oncol Lett 2024; 27:13. [PMID: 38034485 PMCID: PMC10688464 DOI: 10.3892/ol.2023.14145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/15/2023] [Indexed: 12/02/2023] Open
Abstract
The corticotropin-releasing factor (CRF) gene family includes the three urocortins (UCN1, 2 and 3) and the two receptors (CRFR1 and 2), which play a significant role in the physiology of various organs. The expression of the CRF family of genes and its receptors are shown to participate in the pathogenesis of inflammation and even tumorigenesis. However, data regarding the human urinary tract, especially the bladder, are scarce. To the best of our knowledge, no studies are currently available on the CRF system and bladder cancer. The primary goal of the present study was to investigate the mRNA expression of the CRF family members in bladder cancer. The secondary aim was to analyze the differences with the expression of the same mRNAs in normal bladders. From August 2018 to July 2021, 43 recruited patients were divided into three groups. Group A included healthy patients, group B included patients with bladder cancer and group C included patients with a history of cancer from whom samples were taken from the normal bladder mucosa. Detection of mRNA of the CRF family of genes was performed using reverse transcription-quantitative PCR. The mRNA of the three urocortins, CRF and the two receptors were predominantly expressed in all three groups of patients. Statistical analysis using the Kruskal-Wallis test showed that UCN1 was downregulated in patients with bladder cancer and those with possible cancer compared with the healthy group (mean rank group A=24.3 vs. mean rank group B=12.58; P=0.006) and (mean rank group A=24.3 vs. mean rank group C=8.88; P=0.001). The present experiments showed that mRNA of the CRF family of genes was amplified in normal and cancer bladder tissues. Downregulation of the UCN1 gene may be associated with bladder cancer, contributing to the prognosis, diagnosis or therapy of urothelial malignancies.
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Affiliation(s)
- Charalampos Mavridis
- Department of Urology, University General Hospital of Heraklion, Medical School, University of Crete, Heraklion 71003, Greece
| | - Maria Venihaki
- Department of Clinical Chemistry, Medical School, University of Crete, Heraklion 71003, Greece
| | - Eirini Dermitzaki
- Department of Clinical Chemistry, Medical School, University of Crete, Heraklion 71003, Greece
| | - Michail Deiktakis
- Department of Clinical Chemistry, Medical School, University of Crete, Heraklion 71003, Greece
| | - Georgios Liapakis
- Department of Pharmacology, Medical School, University of Crete, Heraklion 71003, Greece
| | - Charalampos Mamoulakis
- Department of Urology, University General Hospital of Heraklion, Medical School, University of Crete, Heraklion 71003, Greece
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Mizutani Y, Chiba Y, Urayama SI, Tomaru Y, Hagiwara D, Kimura K. Detection and Characterization of RNA Viruses in Red Macroalgae (Bangiaceae) and Their Food Product (Nori Sheets). Microbes Environ 2022; 37:ME21084. [PMID: 35691910 PMCID: PMC9763034 DOI: 10.1264/jsme2.me21084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Persistent RNA viruses, which have been suggested to form symbiotic relationships with their hosts, have been reported to occur in eukaryotes, such as plants, fungi, and algae. Based on empirical findings, these viruses may also be present in commercially cultivated macroalgae. Accordingly, the present study aimed to screen red macroalgae (family Bangiaceae conchocelis and Neopyropia yezoensis thallus) and processed nori sheets (N. yezoensis) for persistent RNA viruses using fragmented and primer-ligated dsRNA sequencing (FLDS) and targeted reverse transcription PCR (RT-PCR). A Totiviridae-related virus was detected in the conchocelis of Neoporphyra haitanensis, which is widely cultivated in China, while two Mitoviridae-related viruses were found in several conchocelis samples and all N. yezoensis-derived samples (thallus and nori sheets). Mitoviridae-related viruses in N. yezoensis are widespread among cultivated species and not expected to inhibit host growth. Mitoviridae-related viruses were also detected in several phylogenetically distant species in the family Bangiaceae, which suggests that these viruses persisted and coexist in the family Bangiaceae over a long period of time. The present study is the first to report persistent RNA viruses in nori sheets and their raw materials.
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Affiliation(s)
- Yukino Mizutani
- Analytical Research Center for Experimental Sciences, Saga University, Honjo-machi 1, Saga 840–8502, Japan
| | - Yuto Chiba
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki, 305–8577, Japan
| | - Syun-ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki, 305–8577, Japan
| | - Yuji Tomaru
- Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2–17–5 Maruishi, Hatsukaichi, Hiroshima 739–0452, Japan
| | - Daisuke Hagiwara
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba, 1–1–1 Tennodai, Tsukuba, Ibaraki, 305–8577, Japan
| | - Kei Kimura
- Faculty of Agriculture, Saga University, Honjo-machi 1, Saga 840–8502, Japan, Corresponding author. E-mail: ; Tel: +81–9–5228–8496; Fax: +81–9–5228–8496
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Siddiqui ZK, Chaudhary M, Robinson ML, McCall AB, Peralta R, Esteve R, Callahan CW, Manabe YC, Campbell JD, Johnson JK, Elhabashy M, Kantsiper M, Ficke JR; CONQUER COVID Consortium. Implementation and Accuracy of BinaxNOW Rapid Antigen COVID-19 Test in Asymptomatic and Symptomatic Populations in a High-Volume Self-Referred Testing Site. Microbiol Spectr 2021; 9:e0100821. [PMID: 34851137 DOI: 10.1128/Spectrum.01008-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid antigen tests are simple to perform and provide results within 15 min. We describe our implementation and assess performance of the BinaxNOW COVID-19 Antigen Test (Abbott Laboratories) in 6,099 adults at a self-referred walk-up testing site. Participants were grouped by self-reported COVID-19 exposure and symptom status. Most (89%) were asymptomatic, of whom 17% reported potential exposure. Overall test sensitivity compared with reference laboratory reverse-transcription [RT] PCR testing was 81% (95% confidence interval [CI] 75%, 86%). It was higher in symptomatic (87%; 95% CI 80%, 91%) than asymptomatic (71%; 95% CI 61%, 80%) individuals. Sensitivity was 82% (95% CI 66%, 91%) for asymptomatic individuals with potential exposure and 64% (95% CI 51%, 76%) for those with no exposure. Specificity was greater than 99% for all groups. BinaxNOW has high accuracy among symptomatic individuals and is below the FDA threshold for emergency use authorization in asymptomatic individuals. Nonetheless, rapid antigen testing quickly identifies positive among those with symptoms and/or close contact exposure and could expedite isolation and treatment. IMPORTANCE The BinaxNOW rapid antigen COVID-19 test had a sensitivity of 87% in symptomatic and 71% asymptomatic individuals when performed by health care workers in a high-throughput setting. The performance may expedite isolation decisions or referrals for time-sensitive monoclonal antibody treatment in communities where timely COVID PCR tests are unavailable.
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Glasgow HL, Cruz K, Murphy SC. Reverse-transcription PCR increases sensitivity of broad-range fungal detection in bronchoalveolar lavage fluid. Med Mycol 2021; 60:6433194. [PMID: 34878120 DOI: 10.1093/mmy/myab061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/24/2021] [Indexed: 11/13/2022] Open
Abstract
Broad-range PCR targeting 28S D1-D2 ribosomal DNA (rDNA) identifies numerous fungi but has limited sensitivity in clinical specimens. Ribosomal RNA (rRNA) vastly outnumbers rDNA, suggesting reverse transcription (RT)-PCR could improve detection. Among contrived samples, RT-PCR decreased 28S PCR cycle threshold values by 10--12 cycles and lowered the limit of detection > 2000-fold. Among 32 bronchoalveolar lavage specimens, RT-PCR detected 12/15 (80%) fungal PCR- or culture-positive specimens, versus 6/12 (50%) by 28S PCR, 9/12 (75%) by any fungal PCR, and 13/15 (87%) by culture. RT-PCR newly identified fungi in 4/17 (24%) PCR- and culture-negative specimens. RT substantially increased 28S PCR sensitivity overall. LAY SUMMARY Fungal infection remains difficult to diagnose in the laboratory. Here, we have shown that detecting ribosomal RNA and DNA, rather than only ribosomal DNA, in a broad range fungal assay results in a significant enhancement in the ability to detect and identify fungal pathogens in clinical samples.
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Affiliation(s)
- Heather L Glasgow
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Kurtis Cruz
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA
| | - Sean C Murphy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, USA.,Department of Microbiology, University of Washington, Seattle, Washington, 98195, USA
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Chauhan S, Sen S, Chauhan SS, Pushker N, Tandon R, Kashyap S, Vanathi M, Bajaj MS. Stratifin in ocular surface squamous neoplasia and its association with p53. Acta Ophthalmol 2021; 99:e1483-e1491. [PMID: 33769712 DOI: 10.1111/aos.14844] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 06/17/2020] [Accepted: 02/23/2021] [Indexed: 11/28/2022]
Abstract
PURPOSE Sunlight-induced p53 mutations are known to contribute towards increased risk of ocular surface squamous neoplasia (OSSN). Stratifin (14-3-3σ)/HEM (human epithelial marker) is a p53-mediated inhibitor of cell cycle progression and has been shown to be a target of epigenetic deregulation in various carcinomas. In the present study, Stratifin expression, its promoter methylation status as well as expression of mutant p53 in early and advanced AJCC stages (8th edition) of OSSN, was evaluated. METHODS Sixty-four OSSN [20 conjunctival intraepithelial neoplasia (CIN) and 44 squamous cell carcinoma (SCC)] patients were registered for this study, and they were followed up for 36-58 months (mean 48 ± 3.6). Immunoexpression of Stratifin and mutant p53 protein, mRNA expression of Stratifin by reverse transcription polymerase chain reaction (PCR) and methylation status of Stratifin by methylation-specific PCR, was undertaken. RESULTS Hypermethylation of Stratifin promoter in 63% (40/64), loss of Stratifin expression in 75% (48/64) and downregulation of Stratifin mRNA in 61% (39/64) were observed. Stratifin hypermethylation was significantly associated with reduced disease-free survival in both early and advanced T stage SCC cases. Expression of mutant p53 expression was seen in 48% (31/64) OSSN cases. Of the 31 patients with mutant p53 expression, 87% (27/31) also demonstrated loss of Stratifin immunoexpression. A significant association was seen between mutant p53 expression and Stratifin loss (p = 0.01) in advanced T stage SCC cases. CONCLUSIONS Hypermethylation of Stratifin gene and its reduced mRNA expression both are potential biomarkers for identifying high-risk OSSN patients. Aberrant methylation of Stratifin and simultaneous mutant p53 expression implicates involvement of p53-Stratifin mediated signalling pathway in the pathogenesis of OSSN.
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Affiliation(s)
- Sheetal Chauhan
- Department of Ocular Pathology Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Seema Sen
- Department of Ocular Pathology Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Shyam S. Chauhan
- Department of Biochemistry All India Institute of Medical Sciences New Delhi India
| | - Neelam Pushker
- Ophthalmoplasty Service Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Radhika Tandon
- Cornea and External Disease, Cataract and Refractive Ocular Oncology and Low Vision Services, Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Seema Kashyap
- Department of Ocular Pathology Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Murugesan Vanathi
- Cornea & Ocular Surface Cataract & Refractive Services Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
| | - Mandeep S. Bajaj
- Ophthalmoplasty Service Dr. Rajendra Prasad Centre for Ophthalmic Sciences All India Institute of Medical Sciences New Delhi India
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Elsharkawy MM, Khedr AA, Mehiar F, El-Kady EM, Baazeem A, Shimizu M. Suppression of Pseudomonas syringae pv. tomato infection by rhizosphere fungi. Pest Manag Sci 2021; 77:4350-4356. [PMID: 33955671 DOI: 10.1002/ps.6468] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 08/11/2020] [Revised: 04/22/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Induced resistance against several plant pathogens was reported using different beneficial plant growth-promoting microorganisms. The potential of five fungal isolates, Trichoderma harzianum GT 3-2, Fusarium equiseti GF 18-3, F. equiseti GF 19-1, Phoma sp. GS 10-1 and Phoma sp. GS 14-1, to stimulate tomato growth and resistance against bacterial speck disease caused by Pseudomonas syringae pathovar (pv.) tomato DC3000 was evaluated. RESULTS Based on the results of disease severity and growth promotion experiments, GF 18-3 exhibited the best results among all fungal isolates. Treatment with barley grain inocula (BGI) and culture filtrate (CF) of the isolates promoted tomato growth and suppressed the pathogen in pot trials. Furthermore, expressions of the pathogenesis-related genes (PR-1, β-1,3-glucanase A, β-1,3-glucanase B and LOX) were relatively higher than the control in the leaves of tomato plants treated with both BGI and CF. The transcription levels remained consistently higher than the control plants for 6 days post-inoculation with pathogen. CONCLUSION Taken together, the results indicate that the tested fungal isolates have the potential to promote tomato growth and induce systemic resistance against the bacterial speck disease. Analysis of certain PR gene expression revealed significant activation in both BGI and CF treatments, leading to stimulated resistance against the pathogen. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Mohsen M Elsharkawy
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, Egypt
| | - Amr A Khedr
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, Egypt
| | - Farid Mehiar
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, Egypt
| | - Elsayed M El-Kady
- Department of Agricultural Botany, Faculty of Agriculture, Kafrelsheikh University, Kafr Elsheikh, Egypt
| | - Alaa Baazeem
- Department of Biology, College of Science, Taif University, Taif, Saudi Arabia
| | - Masafumi Shimizu
- Faculty of Applied Biological Sciences, Gifu University, Gifu-shi, Japan
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Gu H, Chu DKW, Chang LDJ, Cheuk SSY, Gurung S, Krishnan P, Ng DYM, Liu GYZ, Wan CKC, Xie R, Cheng SSM, Cowling BJ, Tsang DNC, Peiris M, Dhanasekaran V, Poon LLM. Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong. Emerg Infect Dis 2021; 27:2666-2668. [PMID: 34545799 PMCID: PMC8462320 DOI: 10.3201/eid2710.211028] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We sequenced 10% of imported severe acute respiratory syndrome coronavirus 2 infections detected in travelers to Hong Kong and revealed the genomic diversity of regions of origin, including lineages not previously reported from those countries. Our results suggest that international or regional travel hubs might be useful surveillance sites to monitor sequence diversity.
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Samore MH, Looney A, Orleans B, Greene T, Seegert N, Delgado JC, Presson A, Zhang C, Ying J, Zhang Y, Shen J, Slev P, Gaulin M, Yang MJ, Pavia AT, Alder SC. Probability-Based Estimates of Severe Acute Respiratory Syndrome Coronavirus 2 Seroprevalence and Detection Fraction, Utah, USA. Emerg Infect Dis 2021; 27:2786-2794. [PMID: 34469285 PMCID: PMC8544980 DOI: 10.3201/eid2711.204435] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
We aimed to generate an unbiased estimate of the incidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in 4 urban counties in Utah, USA. We used a multistage sampling design to randomly select community-representative participants >12 years of age. During May 4–June 30, 2020, we collected serum samples and survey responses from 8,108 persons belonging to 5,125 households. We used a qualitative chemiluminescent microparticle immunoassay to detect SARS-CoV-2 IgG in serum samples. We estimated the overall seroprevalence to be 0.8%. The estimated seroprevalence-to-case count ratio was 2.5, corresponding to a detection fraction of 40%. Only 0.2% of participants from whom we collected nasopharyngeal swab samples had SARS-CoV-2–positive reverse transcription PCR results. SARS-CoV-2 antibody prevalence during the study was low, and prevalence of PCR-positive cases was even lower. The comparatively high SARS-CoV-2 detection rate (40%) demonstrates the effectiveness of Utah’s testing strategy and public health response.
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Gopalkrishna V, Ganorkar N. Epidemiological and molecular characteristics of circulating CVA16, CVA6 strains and genotype distribution in hand, foot and mouth disease cases in 2017 to 2018 from Western India. J Med Virol 2021; 93:3572-3580. [PMID: 32833231 DOI: 10.1002/jmv.26454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/16/2020] [Indexed: 12/22/2022]
Abstract
Hand, Foot, and Mouth disease (HFMD) is a mild exanthematous and febrile disease occurs in children aged ≤10 years old. The present study highlights clinical, epidemiological characteristics, distribution of enterovirus (EV) types, and sub genotypes in HFMD cases reported during 2017 to 2018 in Western India. A total of 93 clinical samples collected from 68 HFMD cases were included. The presence of EV-RNA was determined by 5'UTR based nested reverse transcription polymerase chain reaction followed by molecular typing, sub genotyping by VP1/2A junction or VP1, full VP1 gene amplification, and phylogenetic analysis. The study reports 80.64% (75/93) EV positivity and 94.66% (71/75) typing rate, with a predominant circulation of CVA16 and CVA6 strains. Sequence analysis revealed the presence of coxsackievirus (CV)A16 (57.7%), CVA6 (40.8%), and Echo1 (1.4%) strains. EV infections were predominantly observed in children aged 1 to 3 years old (43.9%). Although cases were reported throughout the year, peaked in July (15.8%) and August (24.6%) months and persisted till September (19.3%). All the CVA16 and CVA6 positive strains were genotyped using full VP1 gene amplification. All CVA16 Indian strains (n = 41) were clustered with rarely reported B1c sub genotype and CVA6 strains (n = 29) with E2 sub-lineage. The study highlights the genetic characteristics of circulating CVA16, CVA6, and Echo1 strains in HFMD cases from Western India. The emergence of CVA16 B1c genotype and sub-lineage E2 of CVA6 strains and their constant circulation further demands systemic surveillance studies on HFMD from different parts of India to facilitate the rapid diagnosis of CVA16 and CVA6 strains using the molecular and serological based approach and for intervention strategies.
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Affiliation(s)
- Varanasi Gopalkrishna
- Enteric Viruses Group, Indian Council of Medical Research (ICMR), National Institute of Virology, Pune, India
| | - Nital Ganorkar
- Enteric Viruses Group, Indian Council of Medical Research (ICMR), National Institute of Virology, Pune, India
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Thomas N, White CL, Saliki J, Schuler K, Lynch D, Nielsen O, Dubey JP, Knowles S. CANINE DISTEMPER VIRUS IN THE SEA OTTER (ENHYDRA LUTRIS) POPULATION IN WASHINGTON STATE, USA. J Wildl Dis 2020; 56:873-83. [PMID: 32609600 DOI: 10.7589/JWD-D-19-00008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 03/18/2020] [Indexed: 11/20/2022]
Abstract
Before 2001, all serosurveys for morbilliviruses in sea otters (Enhydra lutris) in California, Washington, and Alaska, US, documented a 0% seroprevalence. The first published serologic detections of morbillivirus in sea otters occurred in 2001-02 in live-captured Washington sea otters, with a documented 80% seroprevalence. We conducted a retrospective study of sea otter cases from 1989 to 2010 compiled at the US Geological Survey, National Wildlife Health Center to identify cases of morbilliviral disease in Washington sea otters and to characterize the disease using immunohistochemistry, reverse transcription (RT)-PCR, genetic sequencing, virus isolation, and serology. We identified six cases of morbilliviral disease and 12 cases of morbilliviral infection in this population of sea otters during 2000-10. Significant histologic findings included inflammation in the white and gray matter of the brain characterized by lymphoplasmacytic perivascular cuffing, neuronal necrosis, and satellitosis in gray matter and by spongiosis, myelin degeneration, spheroids, and gemistocytes in white matter. Intranuclear and intracytoplasmic viral inclusion bodies were found in neurons, Purkinje cells, and glia. Immunohistochemistry for canine distemper virus (CDV) showed positive staining in neurons, glial cells, and cell processes. A pan-morbillivirus RT-PCR with subsequent restriction endonuclease digestion or sequencing identified CDV. Virus isolation was not successful. Two sea otters with morbilliviral encephalitis showed greater antibody titers to CDV than phocine distemper virus. Histologic changes were confined to the central nervous system and resembled neurologic canine distemper in domestic dogs. Cases of sea otters with morbilliviral infection without histologic changes could represent early infections or incompletely cleared sublethal infections. We found that morbillivirus was present in the Washington sea otter population as early as 2000, and we provide a description of the pathology of canine distemper in sea otters.
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Nie X, Singh M, Chen D, Gilchrist C, Soqrat Y, Shukla M, Creelman A, Dickison V, Nie B, Lavoie J, Bisht V. Development of High-Resolution DNA Melting Analysis for Simultaneous Detection of Potato Mop-Top Virus and Its Vector, Spongospora subterranea, in Soil. Plant Dis 2021; 105:948-957. [PMID: 32915119 DOI: 10.1094/pdis-06-20-1321-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, a set of duplex reverse transcription PCR (RT-PCR)-mediated high-resolution DNA melting (HRM) analyses for simultaneous detection of potato mop-virus (PMTV) and its protist vector, Spongospora subterranea f. sp. subterranea (Sss), was developed. The infestation of soil by PMTV was detected with a tobacco-based baiting system. Total RNA extracted from the soil led to successful RT-PCR gel electrophoresis detection of both PMTV and Sss. To facilitate more efficient detection, newly designed primer pairs for PMTV RNA species (i.e., RNA-Rep, RNA-CP, and RNA-TGB) were analyzed together with the existing Sss primers via real-time RT-PCR. The resulting amplicons exhibited melting profiles that could be readily differentiated. Under duplex RT-PCR format, all PMTV and Sss primer combinations led to successful detection of respective PMTV RNA species and Sss in the samples by HRM analyses. When the duplex HRM assay was applied to soil samples collected from six fields at four different sites in New Brunswick, Canada, positive detection of PMTV or Sss was found in 63 to 100% samples collected from fields in which PMTV-infected tubers had been observed. In contrast, the samples from fields where neither PMTV- nor Sss-infected tubers had been observed resulted in negative detection by the assay. Bait tobacco bioassay for PMTV and Sss produced similar results. Of the soil samples collected from PMTV-infested fields, 63 to 83% and 100% led to PMTV and Sss infections in the bait tobacco plants, respectively, whereas no PMTV- or Sss-infected plants were obtained from soil samples collected from PMTV- and Sss-free fields.
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Affiliation(s)
- Xianzhou Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Mathuresh Singh
- Agricultural Certification Services, Fredericton, NB E3B 8B7, Canada
| | - Dahu Chen
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Cassandra Gilchrist
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Yasmine Soqrat
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Biology Program, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Manisha Shukla
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Alexa Creelman
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Virginia Dickison
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
| | - Bihua Nie
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB E3B 4Z7, Canada
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jacques Lavoie
- New Brunswick Department of Agriculture, Aquaculture and Fisheries, Potato Development Centre, Wicklow, NB E7L 3S4, Canada
| | - Vikram Bisht
- Manitoba Agriculture, Carman, MB R0G 0J0, Canada
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Lewis NM, Duca LM, Marcenac P, Dietrich EA, Gregory CJ, Fields VL, Banks MM, Rispens JR, Hall A, Harcourt JL, Tamin A, Willardson S, Kiphibane T, Christensen K, Dunn AC, Tate JE, Nabity S, Matanock AM, Kirking HL. Characteristics and Timing of Initial Virus Shedding in Severe Acute Respiratory Syndrome Coronavirus 2, Utah, USA. Emerg Infect Dis 2020; 27:352-359. [PMID: 33275874 PMCID: PMC7853554 DOI: 10.3201/eid2702.203517] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Virus shedding in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can occur before onset of symptoms; less is known about symptom progression or infectiousness associated with initiation of viral shedding. We investigated household transmission in 5 households with daily specimen collection for 5 consecutive days starting a median of 4 days after symptom onset in index patients. Seven contacts across 2 households implementing no precautionary measures were infected. Of these 7, 2 tested positive for SARS-CoV-2 by reverse transcription PCR on day 3 of 5. Both had mild, nonspecific symptoms for 1–3 days preceding the first positive test. SARS-CoV-2 was cultured from the fourth-day specimen in 1 patient and from the fourth- and fifth-day specimens in the other. We also describe infection control measures taken in the households that had no transmission. Persons exposed to SARS-CoV-2 should self-isolate, including from household contacts, wear a mask, practice hand hygiene, and seek testing promptly.
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13
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Liu W, Kizu JR, Matley DR, Grant R, McCallum FJ, Moller CG, Carthew TL, Hang J, Gubala AJ, Aaskov JG. Circulation of 2 Barmah Forest Virus Lineages in Military Training Areas, Australia. Emerg Infect Dis 2020; 26:3061-3065. [PMID: 33219791 PMCID: PMC7706964 DOI: 10.3201/eid2612.191747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
During 2017–2018, Barmah Forest virus was recovered from mosquitoes trapped in military training areas in Australia and from a soldier infected at 1 of these areas. Phylogenies of the nucleotide sequences of the envelope glycoprotein gene E2 and the 3′ untranslated region suggest that 2 lineages are circulating in eastern Australia.
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14
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Chau NVV, Hong NTT, Ngoc NM, Thanh TT, Khanh PNQ, Nguyet LA, Nhu LNT, Ny NTH, Man DNH, Hang VTT, Phong NT, Que NTH, Tuyen PT, Tu TNH, Hien TT, Minh NNQ, Hung LM, Truong NT, Yen LM, Rogier van Doorn H, Dung NT, Thwaites G, Dung NT, Van Tan L. Superspreading Event of SARS-CoV-2 Infection at a Bar, Ho Chi Minh City, Vietnam. Emerg Infect Dis 2020; 27. [PMID: 33063657 PMCID: PMC7774544 DOI: 10.3201/eid2701.203480] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We report a superspreading event of severe acute respiratory syndrome coronavirus 2 infection initiated at a bar in Vietnam with evidence of symptomatic and asymptomatic transmission, based on ministry of health reports, patient interviews, and whole-genome sequence analysis. Crowds in enclosed indoor settings with poor ventilation may be considered at high risk for transmission.
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15
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Abstract
PCR has become one of the most valuable techniques currently used in bioscience, diagnostics and forensic science. Here we review the history of PCR development and the technologies that have evolved from the original PCR method. Currently, there are two main areas of PCR utilization in bioscience: high-throughput PCR systems and microfluidics-based PCR devices for point-of-care (POC) applications. We also discuss the commercialization of these techniques and conclude with a look into their modifications and use in innovative areas of biomedicine. For example, real-time reverse transcription PCR is the gold standard for SARS-CoV-2 diagnoses. It could also be used for POC applications, being a key component of the sample-to-answer system.
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Affiliation(s)
- Hanliang Zhu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Haoqing Zhang
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Ying Xu
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
| | - Soňa Laššáková
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Marie Korabečná
- Institute of Biology & Medical Genetics, First
Faculty of Medicine, Charles University & General University Hospital in
Prague, Purkyně Institute, Albertov 4, Praha 2 128 00, Czech
Republic
| | - Pavel Neužil
- Department of Microsystem Engineering, School of
Mechanical Engineering, Northwestern Polytechnical University, Xi'an,
Shaanxi 710072, PR China
- Brno University of Technology, Central European Institute
of Technology, Purkyňova 123, 612 00 Brno, Czech Republic
- Brno University of Technology, Faculty of Electrical
Engineering and Communications, Technická 3058/10, 616 00 Brno,
Czech Republic
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16
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Kim SY, Lee J, Sung H, Lee H, Han MG, Yoo CK, Lee SW, Hong KH. Pooling Upper Respiratory Specimens for Rapid Mass Screening of COVID-19 by Real-Time RT-PCR. Emerg Infect Dis 2020; 26:2469-2472. [PMID: 32844739 PMCID: PMC7510748 DOI: 10.3201/eid2610.201955] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To validate the specimen-pooling strategy for real-time reverse transcription PCR detection of severe acute respiratory syndrome coronavirus 2, we generated different pools including positive specimens, reflecting the distribution of cycle threshold values at initial diagnosis. Cumulative sensitivities of tested pool sizes suggest pooling of <6 specimens for surveillance by this method.
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17
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Borras-Bermejo B, Martínez-Gómez X, San Miguel MG, Esperalba J, Antón A, Martin E, Selvi M, Abadías MJ, Román A, Pumarola T, Campins M, Almirante B. Asymptomatic SARS-CoV-2 Infection in Nursing Homes, Barcelona, Spain, April 2020. Emerg Infect Dis 2020; 26. [PMID: 32574139 PMCID: PMC7454057 DOI: 10.3201/eid2609.202603] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
During the coronavirus disease pandemic in Spain, from April 10-24, 2020, a total of 5,869 persons were screened for severe acute respiratory syndrome coronavirus 2 at nursing homes. Among residents, 768 (23.9%) tested positive; among staff, 403 (15.2%). Of those testing positive, 69.7% of residents and 55.8% of staff were asymptomatic.
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18
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Pongpirul WA, Mott JA, Woodring JV, Uyeki TM, MacArthur JR, Vachiraphan A, Suwanvattana P, Uttayamakul S, Chunsuttiwat S, Chotpitayasunondh T, Pongpirul K, Prasithsirikul W. Clinical Characteristics of Patients Hospitalized with Coronavirus Disease, Thailand. Emerg Infect Dis 2020; 26:1580-1585. [PMID: 32267826 PMCID: PMC7323520 DOI: 10.3201/eid2607.200598] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Among 11 patients in Thailand infected with severe acute respiratory syndrome coronavirus 2, we detected viral RNA in upper respiratory specimens a median of 14 days after illness onset and 9 days after fever resolution. We identified viral co-infections and an asymptomatic person with detectable virus RNA in serial tests. We describe implications for surveillance.
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19
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Tang A, Tong ZD, Wang HL, Dai YX, Li KF, Liu JN, Wu WJ, Yuan C, Yu ML, Li P, Yan JB. Detection of Novel Coronavirus by RT-PCR in Stool Specimen from Asymptomatic Child, China. Emerg Infect Dis 2020; 26:1337-1339. [PMID: 32150527 PMCID: PMC7258461 DOI: 10.3201/eid2606.200301] [Citation(s) in RCA: 358] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
We report an asymptomatic child who was positive for a coronavirus by reverse transcription PCR in a stool specimen 17 days after the last virus exposure. The child was virus positive in stool specimens for at least an additional 9 days. Respiratory tract specimens were negative by reverse transcription PCR.
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20
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Negredo A, Habela MÁ, Ramírez de Arellano E, Diez F, Lasala F, López P, Sarriá A, Labiod N, Calero-Bernal R, Arenas M, Tenorio A, Estrada-Peña A, Sánchez-Seco MP. Survey of Crimean-Congo Hemorrhagic Fever Enzootic Focus, Spain, 2011-2015. Emerg Infect Dis 2019; 25:1177-1184. [PMID: 31107219 PMCID: PMC6537724 DOI: 10.3201/eid2506.180877] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
During 2011–2015, we conducted a Crimean-Congo hemorrhagic fever virus (CCHFV) survey in captured ticks that were feeding mainly on wild and domestic ungulates in Spain, where presence of this virus had been reported previously. We detected CCHFV RNA in Hyalomma lusitanicum and H. marginatum ticks for 3 of the 5 years. The rate of infected ticks was 2.78% (44/1,579), which was similar to those for other countries in Europe with endemic foci for CCHFV (Kosovo, Bulgaria, and Albania). These data confirm the established spread of CCHFV into western Europe. Phylogenetic study of the small RNA segment showed Africa-3 clade as the only genotype identified, although we observed cocirculation of genetic variants during 2011 and 2015. We could not rule out genetic reassortments because of lack of sequence data for the medium and large RNA segments of the virus genome.
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21
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Yan Z, Sun Q, Zhang H, Han Y, Qiao J, Niu M, Zhu S, Zhao K, Wu Q, Cheng H, Cao J, Zeng L, Li Z, Xu K. Advantages of digital PCR in the detection of low abundance BCR-ABL1 gene in patients with chronic myeloid leukemia. Oncol Lett 2019; 18:5139-5144. [PMID: 31612025 PMCID: PMC6781637 DOI: 10.3892/ol.2019.10861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 08/01/2019] [Indexed: 11/18/2022] Open
Abstract
Quantitative monitoring of BCR-ABL1IS gene using reverse transcription quantitative-PCR (RT-qPCR) is an important method for evaluating the treatment effects in patients with chronic myeloid leukemia (CML). Digital-PCR (dPCR) can be applied to detect the BCR-ABL1 gene with high sensitivity. In the present study, the results of the Clarity™ dPCR system were compared with those of the RT-qPCR in order to determine whether dPCR can be applied in the clinical setting. A total of 83 patients were included in the present study, and they were divided into two groups according to the results of BCR-ABL1IS during ongoing monitoring. A total of 43 patients with undetectable BCR-ABL1IS where enrolled in group A. BCR-ABL1 testing was performed using the dPCR system on the same peripheral blood samples of patients from group A, and the association between dPCR results and relapse was analyzed. The RT-qPCR platform and dPCR system were used simultaneously to detect the BCR-ABL1 gene of another 40 patients who achieved either partial cytogenetic response (PCyR) or further response. Among patients with undetectable BCR-ABL1IS, patients with dPCR-positive disease (BCR-ABL1 >0.1%) were more likely to undergo molecular relapse (P=0.018). The results of dPCR detection of BCR-ABL1% were consistent with the RT-qPCR results (R2=0.9510) in patients who achieved PCyR or further response. For samples with BCR-ABL1IS <1.0%, the consistency of the dPCR and RT-qPCR results was better than that of BCR-ABL1IS >1.0% (R2=0.9488 vs. R2=0.9264 for BCR-ABL1IS). The detection results of the BCR-ABL1 gene in patients with CML using dPCR matched well with those from the RT-qPCR. To conclude, the results of the dPCR system can be applied as a supplement to the RT-qPCR platform, particularly for those with BCR-ABL1IS <1.0%.
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Affiliation(s)
- Zhiling Yan
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Qian Sun
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Huanxin Zhang
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Yahui Han
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Jianlin Qiao
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Mingshan Niu
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Shengyun Zhu
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Kai Zhao
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Qingyun Wu
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Hai Cheng
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Jiang Cao
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Lingyu Zeng
- Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Zhenyu Li
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Kailin Xu
- Department of Hematology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China.,Institute of Hematology, Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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22
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Abstract
Of 103 serum samples collected from dogs in South Korea, 3 (2.9%) were positive for severe fever with thrombocytopenia syndrome virus (SFTSV) and 22 (21.4%) were positive for antibodies against SFTSV. A dog-derived isolate of SFTSV clustered with many South Korea SFTSV strains in the Japanese clade.
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23
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Tikute SS, Wangikar PB, Varanasi G. Pathological and molecular studies on Coxsackie virus A-16 isolated from hand, foot, and mouth disease cases in India: Approach using neonatal mouse model. J Med Virol 2019; 91:1765-1775. [PMID: 31237683 DOI: 10.1002/jmv.25525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 06/20/2019] [Indexed: 11/11/2022]
Abstract
The present study highlights pathogenesis and molecular aspects of Coxsackie virus A-16 (CVA-16) strains isolated from hand, foot, and mouth disease (HFMD) cases from India using a neonatal mice model. ICR mice were intraperitoneally inoculated with CVA-16/311 strain isolated from HFMD cases. Mice developed hind and forelimb paralysis on day 3 of post infection. Histopathological observations of hind limb muscles showed necrosis, dissolution of muscle fiber cells, infiltration of inflammatory cells, marked dilated ventricle, hemorrhages, and neuronal degeneration in the brain. Immunohistochemical studies revealed high expression of CVA-16/311-specific viral antigen in limb muscles, brain, heart from day 3 till day 7 of post-infection. VP1 gene-based reverse transcription polymerase chain reaction conducted in RNA samples of different tissue organs of infected mice followed by sequencing of the positive amplimers revealed presence of CVA-16/311-specific viral sequences. Phylogenetic analysis based on the VP1 gene showed the presence of B1c sub genotype of CVA-16/311 strain in targeted tissue organs. Sequence analysis revealed major genetic changes in heart, skeletal muscle tissues at the nucleotide and amino acid levels. Genetic changes occurred in organs of mice might predict some potential targets and might act as markers of virulence for neuronal tropism. Pathogenesis and molecular studies of CVA-16 strains isolated from HFMD cases using neonatal mice model was conducted for the first time from India.
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Affiliation(s)
| | - Pralhad B Wangikar
- Department of Toxicology and Pathology, Preclinical Research and Development Organization (PRADO) Pvt Ltd, Pune, India
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24
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Kim WK, No JS, Lee SH, Song DH, Lee D, Kim JA, Gu SH, Park S, Jeong ST, Kim HC, Klein TA, Wiley MR, Palacios G, Song JW. Multiplex PCR-Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats. Emerg Infect Dis 2019; 24:249-257. [PMID: 29350137 PMCID: PMC5782898 DOI: 10.3201/eid2402.171216] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens. Epidemiologic surveillance of R. norvegicus rats in South Korea during 2000-2016 demonstrated that the serologic prevalence of enzootic SEOV infections was not significant on the basis of sex, weight (age), and season. Viral loads of SEOV in rats showed wide dissemination in tissues and dynamic circulation among populations. Phylogenetic analyses showed the global diversity of SEOV and possible genomic configuration of genetic exchanges.
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25
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Abstract
Human noroviruses (HuNoVs) are one of the leading global causes of diarrhoeal diseases and are transmitted mainly from person to person but also through contaminated food, water and fomites. The possible zoonotic nature of NoVs has occasionally been discussed, although the viruses are generally considered to be host-species-specific. We investigated whether wild birds and rodents could serve as carriers of HuNoVs, thereby transmitting the virus to humans directly or indirectly by contaminating foods. All samples, 115 avian and 100 rat faeces collected in springs 2009-2013 from dump sites, and 85 faeces from yellow-necked mice trapped in late autumn 2008 and 2009 after the rodents entered human settlements due to the first night frosts, were screened for HuNoV using real-time reverse transcription PCR. HuNoVs were detected in 31 (27%) faecal samples of wild birds, in two (2%) faecal samples of rats and in no samples of mice. Most (25) of the positive bird samples and both rat samples contained genogroup II, and six positive bird samples contained genogroup I HuNoV. The avian species shedding faeces containing HuNoVs were identified as gulls and crows using DNA barcoding. Our results show that wildlife, birds and rats in particular, is capable of spreading HuNoVs in the environment.
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Affiliation(s)
- M Summa
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - H Henttonen
- Natural Resources Institute Finland, Helsinki, Finland
| | - L Maunula
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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26
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Fischer C, Torres MC, Patel P, Moreira-Soto A, Gould EA, Charrel RN, de Lamballerie X, Nogueira RMR, Sequeira PC, Rodrigues CDS, Kümmerer BM, Drosten C, Landt O, Bispo de Filippis AM, Drexler JF. Lineage-Specific Real-Time RT-PCR for Yellow Fever Virus Outbreak Surveillance, Brazil. Emerg Infect Dis 2017; 23. [PMID: 28949285 DOI: 10.3201/eid2311.171131] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The current yellow fever outbreak in Brazil prompted widespread yellow fever virus (YFV) vaccination campaigns, imposing a responsibility to distinguish between vaccine- and wild-type YFV-associated disease. We developed novel multiplex real-time reverse transcription PCRs that differentiate between vaccine and American wild-type YFV. We validated these highly specific and sensitive assays in an outbreak setting.
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27
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Chang N, Sun Q, Hu J, An C, Gao AH. Large Introns of 5 to 10 Kilo Base Pairs Can Be Spliced out in Arabidopsis. Genes (Basel) 2017; 8:genes8080200. [PMID: 28800125 PMCID: PMC5575664 DOI: 10.3390/genes8080200] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/04/2017] [Accepted: 08/07/2017] [Indexed: 11/22/2022] Open
Abstract
Most of the eukaryotic genes contain introns, which are removed from the pre-RNA during RNA processing. In contrast to the introns in animals, which are usually several kilo base pairs (kb), those in plants generally are very small, which are mostly from dozens of base pairs (bp) to a few hundred bp. According to annotation version 10.0 of the genome of Arabidopsis thaliana, there are 127,854 introns in the nuclear genes; 99.23% of them are less than 1 kb, and only 16 introns are annotated to be larger than 5 kb, which are extremely large introns (ELI) in Arabidopsis. To learn whether these introns are true introns or not and how large introns could be in Arabidopsis, RT-PCR analysis of genes containing these ELIs were carried out. The results indicated that some of these putative introns are indeed ELIs. These ELIs are mainly composed of transposons or transposable elements (TE), excepting one, whose counterparts are also very long in diverse plant species. Thus, this study confirms the existence of introns larger than 5 kb or even 10 kb in Arabidopsis.
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Affiliation(s)
- Ning Chang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Qingqing Sun
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Jinglei Hu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Chuanjing An
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - And Hongbo Gao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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28
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29
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Cifuentes SG, Trostle J, Trueba G, Milbrath M, Baldeón ME, Coloma J, Eisenberg JNS. Transition in the cause of fever from malaria to dengue, Northwestern Ecuador, 1990-2011. Emerg Infect Dis 2014; 19:1642-5. [PMID: 24047566 PMCID: PMC3810737 DOI: 10.3201/eid1910.130137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
In tropical areas, the predominant cause of fever has historically been malaria. However by 2011, among febrile patients in northwestern Ecuador, dengue was identified in 42% and malaria in none. This finding suggests a transition in the cause of fever from malaria to other illnesses, such as dengue.
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30
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Chen J, Bang WY, Lee Y, Kim S, Lee KW, Kim SW, Son YS, Kim DW, Akhter S, Bahk JD. AtObgC-AtRSH1 interaction may play a vital role in stress response signal transduction in Arabidopsis. Plant Physiol Biochem 2014; 74:176-84. [PMID: 24308987 DOI: 10.1016/j.plaphy.2013.10.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Accepted: 10/16/2013] [Indexed: 05/24/2023]
Abstract
The interaction of Obg (Spo0B-associated GTP-binding protein) GTPase and SpoT, which is a bifunctional ppGpp (guanosine 3',5'-bispyrophosphate) hydrolase/synthetase, is vital for the modulation of intracellular ppGpp levels during bacterial responses to environmental cues. It has been recently reported that the ppGpp level is also inducible by various stresses in the chloroplasts of plant cells. However, the function of the Obg-SpoT interaction in plants remains elusive. The results from the present and previous studies suggest that AtRSH1 is a putative bacterial SpoT homolog in Arabidopsis and that its transcription levels are responsive to wounding and salt stresses. In this study, we used a yeast two-hybrid analysis to map the regions required for the AtObgC-AtRSH1 interaction. Moreover, protein-protein docking simulations revealed reasonable geometric and electrostatic complementarity in the binding surfaces of the two proteins. The data support our experimental results, which suggest that the conserved domains in AtObgC and the N terminus of AtRSH1 containing the TGS domain contribute to their interaction. In addition, quantitative real-time PCR (qRT-PCR) analyses showed that the expression of AtObgC and AtRSH1 exhibit a similar inhibition pattern under wounding and salt-stress conditions, but the inhibition pattern was not greatly influenced by the presence or absence of light. Based on in vivo analyses, we further confirmed that the AtRSH1 and AtObgC proteins similarly localize in chloroplasts. Based on these results, we propose that the AtObgC-AtRSH1 interaction plays a vital role in ppGpp-mediated stress responses in chloroplasts.
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Affiliation(s)
- Ji Chen
- Agronomy College, Sichuan Agricultural University, Chengdu 611130, China; Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Woo Young Bang
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843-2133, USA
| | - Yuno Lee
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Songmi Kim
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Keun Woo Lee
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Se Won Kim
- Green Bio Research Center, Cabbage Genomics Assisted Breeding Supporting Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 305-806, Korea
| | - Young Sim Son
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Dae Won Kim
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Salina Akhter
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea
| | - Jeong Dong Bahk
- Division of Applied Life Sciences (BK21+), Graduate School of Gyeongsang National University, Jinju 660-701, Republic of Korea.
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Chen X, Qian Y, Yan F, Tu J, Yang X, Xing Y, Chen Z. 5'-triphosphate-siRNA activates RIG-I-dependent type I interferon production and enhances inhibition of hepatitis B virus replication in HepG2.2.15 cells. Eur J Pharmacol 2013; 721:86-95. [PMID: 24099962 DOI: 10.1016/j.ejphar.2013.09.050] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 09/06/2013] [Accepted: 09/22/2013] [Indexed: 12/25/2022]
Abstract
Hepatitis B virus (HBV) infection often results in acute or chronic viral hepatitis and other liver diseases including cirrhosis and hepatocellular carcinoma. Current therapies for HBV usually have severe side effects and can cause development of drug-resistant mutants. An alternative and safe immunotherapeutic approach for HBV infection is urgently needed for effective anti-HBV therapy. In this study, we propose a new strategy for anti-HBV therapy that activates type-I interferon (IFN) antiviral innate immunity through stimulating pattern-recognition receptors with RNA interference (RNAi) using a 5'-end triphosphate-modified small interfering RNA (3p-siRNA). We designed and generated a 3p-siRNA targeting overlapping region of S gene and P gene of the HBV genome at the 5'-end of pregenomic HBV RNA. Our results demonstrated that 3p-siRNA induced a RIG-I-dependent antiviral type-I IFN response when transfected into HepG2.2.15 cells that support HBV replication. The 3p-siRNA significantly inhibited HBsAg and HBeAg secretion from HepG2.2.15 cells in a RIG-I-dependent manner, and the antiviral effect of 3p-siRNA was superior to that of siRNA. Furthermore, 3p-siRNA had more pronounced inhibition effects on the replication of HBV DNA and the transcription of mRNA than that of siRNA. Finally, 3p-siRNA displayed antiviral activity with long-term suppression of HBV replication. In conclusion, our findings suggest that 3p-siRNA could act as a powerful bifunctional antiviral molecule with potential for developing a promising therapeutic against chronic HBV infection.
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Affiliation(s)
- Xiaojuan Chen
- Division of Infection and Immunity, Department of Electromagnetic and Laser Biology, Beijing Institute of Radiation Medicine, 27 Taiping Rd, Beijing 100850, China
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Kawaguchi T, Kodama T, Hikita H, Tanaka S, Shigekawa M, Nawa T, Shimizu S, Li W, Miyagi T, Hiramatsu N, Tatsumi T, Takehara T. Carbamazepine promotes liver regeneration and survival in mice. J Hepatol 2013; 59:1239-45. [PMID: 23872603 DOI: 10.1016/j.jhep.2013.07.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Revised: 07/03/2013] [Accepted: 07/05/2013] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Carbamazepine (CBZ), a widely used anticonvulsant and mood stabilizer, activates multiple proliferative and pro-survival pathways. Here, we hypothesize that CBZ may promote hepatocellular proliferation and ameliorate liver regeneration. METHODS C57BL6/J mice were orally administered CBZ or vehicle and underwent a 70% partial hepatectomy (PHx), 85% PHx or treatment with carbon tetrachloride (CCl4). Liver regeneration was determined by liver to body weight ratio, hepatocyte proliferation markers, and activation of intracellular signalling pathways. RESULTS Two to 5days after the 70% PHx, the liver to body weight ratio was significantly higher in the CBZ-treated mice than in the vehicle-treated mice. CBZ treatment upregulated the number of proliferative hepatocytes following PHx or CCl4 treatment, as assessed by intrahepatic Ki-67 staining, BrdU uptake, and PCNA protein expression. PHx surgery induced the expression of several cyclins and activated Akt/mTOR signalling pathways, all of which were enhanced by CBZ treatment. The administration of the mTOR inhibitor temsirolimus abrogated the hepato-proliferative effect of CBZ. CBZ treatment significantly improved the survival rate of the mice that underwent lethal 85% massive hepatectomy. CONCLUSIONS CBZ demonstrated a novel hepato-proliferative effect through the activation of the mTOR signalling pathway in hepatectomised mice. CBZ has the potential to be a therapeutic option for facilitating efficient liver regeneration in patients subjected to liver surgery.
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33
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Fujii T, Suzuki MG, Katsuma S, Ito K, Rong Y, Matsumoto S, Ando T, Ishikawa Y. Discovery of a disused desaturase gene from the pheromone gland of the moth Ascotis selenaria, which secretes an epoxyalkenyl sex pheromone. Biochem Biophys Res Commun 2013; 441:849-55. [PMID: 24211206 DOI: 10.1016/j.bbrc.2013.10.143] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 10/16/2013] [Accepted: 10/28/2013] [Indexed: 11/28/2022]
Abstract
Female Ascotis selenaria (Geometridae) moths use 3,4-epoxy-(Z,Z)-6,9-nonadecadiene, which is synthesized from linolenic acid, as the main component of their sex pheromone. While the use of dietary linolenic or linoleic fatty acid derivatives as sex pheromone components has been observed in moth species belonging to a few families including Geometridae, the majority of moths use derivatives of a common saturated fatty acid, palmitic acid, as their sex pheromone components. We attempted to gain insight into the differentiation of pheromone biosynthetic pathways in geometrids by analyzing the desaturase genes expressed in the pheromone gland of A. selenaria. We demonstrated that a Δ11-desaturase-like gene (Asdesat1) was specifically expressed in the pheromone gland of A. selenaria in spite of the absence of a desaturation step in the pheromone biosynthetic pathway in this species. Further analysis revealed that the presumed transmembrane domains were degenerated in Asdesat1. Phylogenetic analysis demonstrated that Asdesat1 anciently diverged from the lineage of Δ11-desaturases, which are currently widely used in the biosynthesis of sex pheromones by moths. These results suggest that an ancestral Δ11-desaturase became dysfunctional in A. selenaria after a shift in pheromone biosynthetic pathways.
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Affiliation(s)
- Takeshi Fujii
- Graduate School of Bio-Applications and Systems Engineering (BASE), Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan; Molecular Entomology Laboratory, RIKEN (The Institute of Physical and Chemical Research), Wako, Saitama 351-0198, Japan; Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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34
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Cougot N, Molza AE, Delesques J, Giudice E, Cavalier A, Rolland JP, Ermel G, Blanco C, Thomas D, Gillet R. Visualizing compaction of polysomes in bacteria. J Mol Biol 2013; 426:377-88. [PMID: 24095898 DOI: 10.1016/j.jmb.2013.09.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 10/26/2022]
Abstract
During protein synthesis, many translating ribosomes are bound together with an mRNA molecule to form polysomes (or polyribosomes). While the spatial organization of bacterial polysomes has been well studied in vitro, little is known about how they cluster when cellular conditions are highly constrained. To better understand this, we used electron tomography, template matching, and three-dimensional modeling to analyze the supramolecular network of ribosomes after induction of translational pauses. In Escherichia coli, we overexpressed an mRNA carrying a polyproline motif known to induce pausing during translation. When working with a strain lacking transfer-messenger RNA, the principle actor in the "trans-translation" rescuing system, the cells survived the hijacking of the translation machinery but this resulted in a sharp modification of the ribosomal network. The results of our experiments demonstrate that single ribosomes are replaced with large amounts of compacted polysomes. These polysomes are highly organized, principally forming hairpins and dimers of hairpins that stack together. We propose that these spatial arrangements help maintain translation efficiency when the rescue systems are absent or overwhelmed.
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Affiliation(s)
- Nicolas Cougot
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Anne-Elisabeth Molza
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jérémy Delesques
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Emmanuel Giudice
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Annie Cavalier
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Jean-Paul Rolland
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Gwennola Ermel
- Université de Rennes 1, EA 1254, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Carlos Blanco
- Université de Rennes 1, EA 1254, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Daniel Thomas
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Reynald Gillet
- Team Translation and Folding, Université de Rennes 1, UMR CNRS 6290 IGDR, Campus de Beaulieu, 35042 Rennes Cedex, France; Institut Universitaire de France.
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Tang L, Cai H, Ji W, Luo X, Wang Z, Wu J, Wang X, Cui L, Wang Y, Zhu Y, Bai X. Overexpression of GsZFP1 enhances salt and drought tolerance in transgenic alfalfa (Medicago sativa L.). Plant Physiol Biochem 2013; 71:22-30. [PMID: 23867600 DOI: 10.1016/j.plaphy.2013.06.024] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 06/20/2013] [Indexed: 05/20/2023]
Abstract
GsZFP1 encodes a Cys2/His2-type zinc-finger protein. In our previous study, when GsZFP1 was heterologously expressed in Arabidopsis, the transgenic Arabidopsis plants exhibited enhanced drought and cold tolerance. However, it is still unknown whether GsZFP1 is also involved in salt stress. GsZFP1 is from the wild legume Glycine soja. Therefore, the aims of this study were to further elucidate the functions of the GsZFP1 gene under salt and drought stress in the forage legume alfalfa and to investigate its biochemical and physiological functions under these stress conditions. Our data showed that overexpression of GsZFP1 in alfalfa resulted in enhanced salt tolerance. Under high salinity stress, greater relative membrane permeability and malondialdehyde (MDA) content were observed and more free proline and soluble sugars accumulated in transgenic alfalfa than in the wild-type (WT) plants; in addition, the transgenic lines accumulated less Na(+) and more K(+) in both the shoots and roots. Overexpression of GsZFP1 also enhanced the drought tolerance of alfalfa. The fold-inductions of stress-responsive marker gene expression, including MtCOR47, MtRAB18, MtP5CS, and MtRD2, were greater in transgenic alfalfa than those of WT under drought stress conditions. In conclusion, the transgenic alfalfa plants generated in this study could be used for farming in salt-affected as well as arid and semi-arid areas.
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Affiliation(s)
- Lili Tang
- College of Life Science, Northeast Agricultural University, Harbin 150030, China.
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Li X, Guo R, Li J, Singer SD, Zhang Y, Yin X, Zheng Y, Fan C, Wang X. Genome-wide identification and analysis of the aldehyde dehydrogenase (ALDH) gene superfamily in apple (Malus × domestica Borkh.). Plant Physiol Biochem 2013; 71:268-82. [PMID: 23978559 DOI: 10.1016/j.plaphy.2013.07.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [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: 06/20/2013] [Accepted: 07/26/2013] [Indexed: 05/01/2023]
Abstract
Aldehyde dehydrogenases (ALDHs) represent a protein superfamily encoding NAD(P)(+)-dependent enzymes that oxidize a wide range of endogenous and exogenous aliphatic and aromatic aldehydes. In plants, they are involved in many biological processes and play a role in the response to environmental stress. In this study, a total of 39 ALDH genes from ten families were identified in the apple (Malus × domestica Borkh.) genome. Synteny analysis of the apple ALDH (MdALDH) genes indicated that segmental and tandem duplications, as well as whole genome duplications, have likely contributed to the expansion and evolution of these gene families in apple. Moreover, synteny analysis between apple and Arabidopsis demonstrated that several MdALDH genes were found in the corresponding syntenic blocks of Arabidopsis, suggesting that these genes appeared before the divergence of lineages that led to apple and Arabidopsis. In addition, phylogenetic analysis, as well as comparisons of exon-intron and protein structures, provided further insight into both their evolutionary relationships and their putative functions. Tissue-specific expression analysis of the MdALDH genes demonstrated diverse spatiotemporal expression patterns, while their expression profiles under abiotic stress and various hormone treatments indicated that many MdALDH genes were responsive to high salinity and drought, as well as different plant hormones. This genome-wide identification, as well as characterization of evolutionary relationships and expression profiles, of the apple MdALDH genes will not only be useful for the further analysis of ALDH genes and their roles in stress response, but may also aid in the future improvement of apple stress tolerance.
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Affiliation(s)
- Xiaoqin Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China; Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Northwest A&F University, Yangling, Shaanxi 712100, China
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Shimokawa T, Nunomura S, Fujisawa D, Ra C. Identification of the C/EBPα C-terminal tail residues involved in the protein interaction with GABP and their potency in myeloid differentiation of K562 cells. Biochim Biophys Acta 2013; 1829:1207-17. [PMID: 24076158 DOI: 10.1016/j.bbagrm.2013.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 09/18/2013] [Accepted: 09/19/2013] [Indexed: 11/17/2022]
Abstract
The CCAAT/enhancer-binding protein α (C/EBPα) is the member of a family of related basic leucine zipper (bZIP) transcription factors and is critical for granulopoiesis. We previously demonstrated that C/EBPα interacts with the ETS domain of widely expressed GABPα, which leads to cooperative transcriptional activation of the myeloid-specific promoter for human FCAR encoding the Fc receptor for IgA (FcαR, CD89) in part by facilitating recruitment of C/EBPα to the promoter. The C/EBPα molecule contains transactivation domains (TADs) at its N-terminus and a DNA-binding and dimerization bZIP structure at its C-terminus. We demonstrate here that GABPα interacts with the last 18 residues of the C/EBPα C-terminus beyond the bZIP DNA-binding and dimerizing region. Deletion of this C-terminus resulted in loss of GABPα interaction but not affecting its DNA binding ability, indicating that it is not required for homodimer formation. Moreover, the C-terminus confers the ability to functionally synergize with GABP on a heterologous TAD when fused to the C-terminus of the VP16 TAD. We identified a three-amino acid stretch (amino acids 341-343) that is important for both functional and protein interactions with GABP. Ectopic expression in K562 cells of C/EBPα mutant incapable of interacting with GABPα does not induce expression of granulocytic differentiation markers including CD15, CD11b, GCSF-R and C/EBPε, and does not inhibit proliferation, whereas wild type does. These results demonstrate the functional importance of the C/EBPα C-terminus beyond the bZIP DNA-binding and dimerization region, which may mediate cooperative activation by C/EBPα and GABP of myeloid-specific genes involved in C/EBPα-dependent granulopoiesis.
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Affiliation(s)
- Toshibumi Shimokawa
- Division of Molecular Cell Immunology and Allergology, Department of Biomedical Sciences, Nihon University School of Medicine, Itabashi-ku, Tokyo 173-8610, Japan.
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Song YN, Lu CY, Chen J, Qiu GF. Characterization of a novel nm23 gene and its potential roles in gametogenesis in the prawn Macrobrachium rosenbergii (de Man, 1879) (Crustacea: Decapoda). Gene 2013; 531:1-7. [PMID: 23994193 DOI: 10.1016/j.gene.2013.08.064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [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: 06/25/2013] [Revised: 08/13/2013] [Accepted: 08/18/2013] [Indexed: 10/26/2022]
Abstract
Nm23 is a family of genes encoding the nucleoside diphosphate (NDP) kinase, which functions in a wide variety of biological processes, including growth, development, differentiation and tumor metastasis. In this study, a novel nm23 gene, designated as Mrnm23, was identified from the freshwater giant prawn Macrobrachium rosenbergii. The full-length cDNA was 776bp in length, encoding for a protein of 176 amino acids with one typical NDP kinase domain that harbored all the crucial residues for nucleotide binding and enzymatic activity. Like human novel nm23-H1B, the putative protein contained a unique 21-amino-acid NH2-terminal extension as compared to human nm23 (nm23-H1) homologs. Further, 3 extra amino acid residues prolonged the COOH-terminus. The Mrnm23 was ubiquitously expressed in all tissues examined, including androgenic gland, gill, heart, liver, muscle, ovary, and testis. In situ hybridization to gonad sections indicated that the Mrnm23 mRNA was localized in the cytoplasm of cup-base of differentiating spermatids, in the spike of the umbrella-shaped spermatozoa and in the cytoplasm of the early previtellogenic oocytes, suggesting that the Mrnm23 has potential roles in spermiogenesis and early differentiation of oocyte.
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Affiliation(s)
- Ya-Nan Song
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Certificated by Ministry of Education, College of Fisheries and Life Science, Shanghai Ocean University, 999 Hucheng Huan Road, Shanghai, 201306, PR China
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Ramaiah MJ, Pushpavalli SNCVL, Lavanya A, Bhadra K, Haritha V, Patel N, Tamboli JR, Kamal A, Bhadra U, Pal-Bhadra M. Novel anthranilamide-pyrazolo[1,5-a]pyrimidine conjugates modulate the expression of p53-MYCN associated micro RNAs in neuroblastoma cells and cause cell cycle arrest and apoptosis. Bioorg Med Chem Lett 2013; 23:5699-706. [PMID: 23992861 DOI: 10.1016/j.bmcl.2013.08.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [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: 05/02/2013] [Revised: 07/07/2013] [Accepted: 08/05/2013] [Indexed: 12/14/2022]
Abstract
It has previously been shown that anthranilamide-pyrazolo[1,5-a]pyrimidine conjugates activate p53 and cause apoptosis in cervical cancer cells such as HeLa and SiHa. Here we establish the role of these conjugates in activating p53 pathway by phosphorylation at Ser15, 20 and 46 residues and downregulate key oncogenic proteins such as MYCN and Mdm2 in IMR-32 neuroblastoma cells. Compounds decreased the proliferation rate of neuroblastoma cells such as IMR-32, Neuro-2a, SK-N-SH. Compound treatment resulted in G2/M cell cycle arrest. The expression of p53 dependent genes such as p21, Bax, caspases was increased with concomitant decrease of the survival proteins as well as anti-apoptotic proteins such as Akt1, E2F1 and Bcl2. In addition the expression of important microRNAs such as miR-34a, c, miR-200b, miR-107, miR-542-5p and miR-605 were significantly increased that eventually lead to the activation of apoptotic pathway. Our data revealed that conjugates of this nature cause cell cycle arrest and apoptosis in IMR-32 cells [MYCN (+) with intact wild-type p53] by activating p53 signalling and provides a lead for the development of anti-cancer therapeutics.
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Affiliation(s)
- M Janaki Ramaiah
- Department of Chemical Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India
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Abstract
Background: Hepatitis G virus (HGV) is newly identified virus, transmitted by infected blood and blood products. Effect of HGV infection on liver diseases is not well known. Aims: Co-infection of HGV with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection has been reported however; very limited data is available from India. Therefore, we have performed a pilot study for the presence of co-infection of HGV in chronic liver disease patients. Setting and Design: The study was performed in research laboratory at P.D. Hinduja National hospital and Medical research center, Mahim, Mumbai. Prospective study was designed. Methods and Materials: Forty HBV, HCV related chronic liver disease patients were studied. Forty randomly selected voluntary healthy blood donors visiting our blood bank were included as controls. Serum bilirubin, alanine aminotransferase (ALT), Aspartate aminotransferase (AST) and alkaline phosphatase (ALP) were estimated. HGV infection was detected by using reverse transcriptase molony murine leukemia virus (M-MLV) with the help of HGV 340/625IC kit (Sacace, Italy). Results and Conclusion: One HCV positive patient had infection with HGV among 40 HBV/HCV chronic liver disease patients.
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Affiliation(s)
- Amruta D Pathare
- Department of Research, Transfusion Medicine, P.D. Hinduja National Hospital and Medical Research Centre, Mumbai, India
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