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Nam Y, Kang KM, Sung SR, Park JE, Shin YJ, Song SH, Seo JT, Yoon TK, Shim SH. The association of stromal antigen 3 (STAG3) sequence variations with spermatogenic impairment in the male Korean population. Asian J Androl 2020; 22:106-111. [PMID: 31115363 PMCID: PMC6958972 DOI: 10.4103/aja.aja_28_19] [Citation(s) in RCA: 5] [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] [Indexed: 12/12/2022] Open
Abstract
The stromal antigen 3 (STAG3) gene, encoding a meiosis-specific cohesin component, is a strong candidate for causing male infertility, but little is known about this gene so far. We identified STAG3 in patients with nonobstructive azoospermia (NOA) and normozoospermia in the Korean population. The coding regions and their intron boundaries of STAG3 were identified in 120 Korean men with spermatogenic impairments and 245 normal controls by using direct sequencing and haplotype analysis. A total of 30 sequence variations were identified in this study. Of the total, seven were exonic variants, 18 were intronic variants, one was in the 5’-UTR, and four were in the 3’-UTR. Pathogenic variations that directly caused NOA were not identified. However, two variants, c.3669+35C>G (rs1727130) and +198A>T (rs1052482), showed significant differences in the frequency between the patient and control groups (P = 0.021, odds ratio [OR]: 1.79, 95% confidence interval [CI]: 1.098–2.918) and were tightly linked in the linkage disequilibrium (LD) block. When pmir-rs1052482A was cotransfected with miR-3162-5p, there was a substantial decrease in luciferase activity, compared with pmir-rs1052482T. This result suggests that rs1052482 was located within a binding site of miR-3162-5p in the STAG3 3’-UTR, and the minor allele, the rs1052482T polymorphism, might offset inhibition by miR-3162-5p. We are the first to identify a total of 30 single-nucleotide variations (SNVs) of STAG3 gene in the Korean population. We found that two SNVs (rs1727130 and rs1052482) located in the 3’-UTR region may be associated with the NOA phenotype. Our findings contribute to understanding male infertility with spermatogenic impairment.
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Affiliation(s)
- Yeojung Nam
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea
| | - Kyung Min Kang
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
| | - Se Ra Sung
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
| | - Ji Eun Park
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
| | - Yun-Jeong Shin
- Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
| | - Seung Hun Song
- Department of Urology, CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
| | - Ju Tae Seo
- Department of Urology, Cheil General Hospital, Seoul 04619, Korea
| | - Tae Ki Yoon
- Department of Obstetrics and Gynecology, CHA Gangnam Medical Center, Seoul 04637, Korea
| | - Sung Han Shim
- Department of Biomedical Science, College of Life Science, CHA University, Seongnam 13488, Korea.,Genetics Laboratory, Fertility Center of CHA Gangnam Medical Center, CHA University, Seoul 06135, Korea
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McNamara RP, Caro-Vegas C, Landis JT, Moorad R, Pluta LJ, Eason AB, Thompson C, Bailey A, Villamor FCS, Lange PT, Wong JP, Seltzer T, Seltzer J, Zhou Y, Vahrson W, Juarez A, Meyo JO, Calabre T, Broussard G, Rivera-Soto R, Chappell DL, Baric RS, Damania B, Miller MB, Dittmer DP. High-Density Amplicon Sequencing Identifies Community Spread and Ongoing Evolution of SARS-CoV-2 in the Southern United States. Cell Rep 2020; 33:108352. [PMID: 33113345 PMCID: PMC7574689 DOI: 10.1016/j.celrep.2020.108352] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 06/16/2020] [Revised: 09/04/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is constantly evolving. Prior studies focused on high-case-density locations, such as the northern and western metropolitan areas of the United States. This study demonstrates continued SARS-CoV-2 evolution in a suburban southern region of the United States by high-density amplicon sequencing of symptomatic cases. 57% of strains carry the spike D614G variant, which is associated with higher genome copy numbers, and its prevalence expands with time. Four strains carry a deletion in a predicted stem loop of the 3' UTR. The data are consistent with community spread within local populations and the larger continental United States. The data instill confidence in current testing sensitivity and validate "testing by sequencing" as an option to uncover cases, particularly nonstandard coronavirus disease 2019 (COVID-19) clinical presentations. This study contributes to the understanding of COVID-19 through an extensive set of genomes from a non-urban setting and informs vaccine design by defining D614G as a dominant and emergent SARS-CoV-2 isolate in the United States.
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Affiliation(s)
- Ryan P McNamara
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Carolina Caro-Vegas
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Justin T Landis
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Razia Moorad
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Linda J Pluta
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Anthony B Eason
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Cecilia Thompson
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA
| | - Aubrey Bailey
- Kuopio Center for Gene and Cell Therapy, Kuopio, Finland
| | - Femi Cleola S Villamor
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Philip T Lange
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Jason P Wong
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Tischan Seltzer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Jedediah Seltzer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Yijun Zhou
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | | | - Angelica Juarez
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - James O Meyo
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
| | - Tiphaine Calabre
- École supérieure de Chimie Physique Électronique (CPE), Lyon, France
| | - Grant Broussard
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
| | - Ricardo Rivera-Soto
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Genetics Curriculum, Chapel Hill, NC 27599, USA
| | - Danielle L Chappell
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ralph S Baric
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA; Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Blossom Damania
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA
| | - Melissa B Miller
- Department of Pathology and Laboratory Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Clinical Microbiology Laboratory, UNC Medical Center, Chapel Hill, NC 27599, USA.
| | - Dirk P Dittmer
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599, USA.
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Sekizuka T, Kuramoto S, Nariai E, Taira M, Hachisu Y, Tokaji A, Shinohara M, Kishimoto T, Itokawa K, Kobayashi Y, Kadokura K, Kamiya H, Matsui T, Suzuki M, Kuroda M. SARS-CoV-2 Genome Analysis of Japanese Travelers in Nile River Cruise. Front Microbiol 2020; 11:1316. [PMID: 32582136 PMCID: PMC7291780 DOI: 10.3389/fmicb.2020.01316] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 04/06/2020] [Accepted: 05/25/2020] [Indexed: 11/13/2022] Open
Abstract
Japan has reported 26 cases of coronavirus disease 2019 (COVID-19) linked to cruise tours on the River Nile in Egypt between March 5 and 15, 2020. Here, we characterized the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome of isolates from 10 travelers who returned from Egypt and from patients possibly associated with these travelers. We performed haplotype network analysis of SARS-CoV-2 isolates using genome-wide single-nucleotide variations. Our analysis identified two potential Egypt-related clusters from these imported cases, and these clusters were related to globally detected viruses in different countries.
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Affiliation(s)
- Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Sanae Kuramoto
- Ishikawa Prefectural Institute of Public Health and Environmental Science, Kanazawa, Japan
| | - Eri Nariai
- Ishikawa Prefectural Institute of Public Health and Environmental Science, Kanazawa, Japan
| | | | - Yushi Hachisu
- Chiba Prefectural Institute of Public Health, Chiba, Japan
| | - Akihiko Tokaji
- Kochi Prefectural Institute of Public Health, Kochi, Japan
| | | | | | - Kentaro Itokawa
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yusuke Kobayashi
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Keisuke Kadokura
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hajime Kamiya
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tamano Matsui
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Motoi Suzuki
- Infectious Disease Surveillance Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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Chen L, Luo J, Li JX, Li JJ, Wang DQ, Tian Y, Lu LZ. Transcriptome analysis of adiposity in domestic ducks by transcriptomic comparison with their wild counterparts. Anim Genet 2015; 46:299-307. [PMID: 25917302 DOI: 10.1111/age.12294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 01/28/2023]
Abstract
Excessive adiposity is a major problem in the duck industry, but its molecular mechanisms remain unknown. Genetic comparisons between domestic and wild animals have contributed to the exploration of genetic mechanisms responsible for many phenotypic traits. Significant differences in body fat mass have been detected between domestic and wild ducks. In this study, we used the Peking duck and Anas platyrhynchos as the domestic breed and wild counterpart respectively and performed a transcriptomic comparison of abdominal fat between the two breeds to comprehensively analyze the transcriptome basis of adiposity in ducks. We obtained approximately 350 million clean reads; assembled 61 250 transcripts, including 23 699 novel ones; and identified alternative 5' splice sites, alternative 3' splice sites, skipped exons and retained intron as the main alternative splicing events. A differential expression analysis between the two breeds showed that 753 genes exhibited differential expression. In Peking ducks, some lipid metabolism-related genes (IGF2, FABP5, BMP7, etc.) and oncogenes (RRM2, AURKA, CYR61, etc.) were upregulated, whereas genes related to tumor suppression and immunity (TNFRSF19, TNFAIP6, IGSF21, NCF1, etc.) were downregulated, suggesting adiposity might closely associate with tumorigenesis in ducks. Furthermore, 280 576 single-nucleotide variations were found differentiated between the two breeds, including 8641 non-synonymous ones, and some of the non-synonymous ones were found enriched in genes involved in lipid-associated and immune-associated pathways, suggesting abdominal fat of the duck undertakes both a metabolic function and immune-related function. These datasets enlarge our genetic information of ducks and provide valuable resources for analyzing mechanisms underlying adiposity in ducks.
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Affiliation(s)
- L Chen
- Institute of Animal Sciences and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
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