1
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Chacón RD, Sánchez-Llatas CJ, L Pajuelo S, Diaz Forero AJ, Jimenez-Vasquez V, Médico JA, Soto-Ugaldi LF, Astolfi-Ferreira CS, Piantino Ferreira AJ. Molecular characterization of the meq oncogene of Marek's disease virus in vaccinated Brazilian poultry farms reveals selective pressure on prevalent strains. Vet Q 2024; 44:1-13. [PMID: 38465827 DOI: 10.1080/01652176.2024.2318198] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 02/05/2024] [Indexed: 03/12/2024] Open
Abstract
Marek's disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek's disease (MD) outbreaks in recent years. Our study aimed to analyze the complete meq gene sequences to understand the molecular epidemiological basis of MD outbreaks in Brazilian vaccinated layer farms. We detected a high incidence rate of visceral MD (67.74%) and multiple circulating MDV strains. The most prevalent and geographically widespread genotype presented several clinical and molecular characteristics of a highly virulent strain and evolving under positive selective pressure. Phylogenetic and phylogeographic analysis revealed a closer relationship with strains from the USA and Japan. This study sheds light on the circulation of MDV strains capable of infecting vaccinated birds. We emphasize the urgency of adopting preventive measures to manage MDV outbreaks threatening the poultry farming industry.
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Affiliation(s)
- Ruy D Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | | | - Andrea J Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | | | - Jack A Médico
- Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA
| | - Luis F Soto-Ugaldi
- Tri-Institutional Program in Computational Biology and Medicine, New York, NY, USA
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2
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Wang Z, Wang Y, Zhou T, Chen S, Morris D, Magalhães RDM, Li M, Wang S, Wang H, Xie Y, McSwiggin H, Oliver D, Yuan S, Zheng H, Mohammed J, Lai EC, McCarrey JR, Yan W. The rapidly evolving X-linked MIR-506 family fine-tunes spermatogenesis to enhance sperm competition. eLife 2024; 13:RP90203. [PMID: 38639482 PMCID: PMC11031087 DOI: 10.7554/elife.90203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Despite rapid evolution across eutherian mammals, the X-linked MIR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (SLITRK2 and FMR1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked MIR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernible defects, but simultaneous ablation of five clusters containing 19 members of the MIR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility, and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked MIR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the MIR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.
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Affiliation(s)
- Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Sheng Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Dayton Morris
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | | | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Shawn Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Hetan Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
| | - Jaaved Mohammed
- Developmental Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering InstituteNew YorkUnited States
| | - John R McCarrey
- Department of Neuroscience, Developmental and Regenerative Biology, University of Texas at San AntonioSan AntonioUnited States
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of MedicineRenoUnited States
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical CenterTorranceUnited States
- Department of Medicine, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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3
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Wu D, Fu W, Fan G, Huang D, Wu K, Zhan Y, Tu X, He J. Characteristics and Comparative Analysis of the Special-Structure (Non-Single-Circle) Mitochondrial Genome of Capsicum pubescens Ruiz & Pav. Genes (Basel) 2024; 15:152. [PMID: 38397142 PMCID: PMC10888363 DOI: 10.3390/genes15020152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/25/2024] Open
Abstract
Chilean peppers, cultivated from Capsicum pubescens, are globally renowned as popular vegetable and spice crops. C. pubescens belongs to the Capsicum L. (pepper) family and is one of the five pepper cultivars grown in China. In this study, we assembled and annotated the complete mt genome of C. pubescens. We investigated several aspects of its genome, including characteristics, codon usage, RNA editing sites, repeat sequences, selective pressure, gene clusters, and phylogenetic relationships. Furthermore, we compared it with other plant mt genomes. The data we obtained will provide valuable information for studying evolutionary processes in the Capsicum genus and will assist in the functional analysis of Capsicum mitogenomes.
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Affiliation(s)
- Di Wu
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Wenting Fu
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Gaoling Fan
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Dongfu Huang
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Kangyun Wu
- Key Laboratory of Crop Genetic Resources and Germplasm Innovation in Karst Mountain Areas, Ministry of Agriculture and Rural Affairs, Huaxi District, Guiyang 550025, China;
| | - Yongfa Zhan
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Xiangmin Tu
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
| | - Jianwen He
- Research Institute of Pepper, Guizhou Academy of Agricultural Science, Huaxi District, Guiyang 550025, China; (D.W.); (W.F.); (G.F.); (D.H.); (Y.Z.); (X.T.)
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4
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Wang Z, Wang Y, Zhou T, Chen S, Morris D, Magalhães RDM, Li M, Wang S, Wang H, Xie Y, McSwiggin H, Oliver D, Yuan S, Zheng H, Mohammed J, Lai EC, McCarrey JR, Yan W. The Rapidly Evolving X-linked miR-506 Family Finetunes Spermatogenesis to Enhance Sperm Competition. bioRxiv 2024:2023.06.14.544876. [PMID: 37398484 PMCID: PMC10312769 DOI: 10.1101/2023.06.14.544876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Despite rapid evolution across eutherian mammals, the X-linked miR-506 family miRNAs are located in a region flanked by two highly conserved protein-coding genes (Slitrk2 and Fmr1) on the X chromosome. Intriguingly, these miRNAs are predominantly expressed in the testis, suggesting a potential role in spermatogenesis and male fertility. Here, we report that the X-linked miR-506 family miRNAs were derived from the MER91C DNA transposons. Selective inactivation of individual miRNAs or clusters caused no discernable defects, but simultaneous ablation of five clusters containing nineteen members of the miR-506 family led to reduced male fertility in mice. Despite normal sperm counts, motility and morphology, the KO sperm were less competitive than wild-type sperm when subjected to a polyandrous mating scheme. Transcriptomic and bioinformatic analyses revealed that these X-linked miR-506 family miRNAs, in addition to targeting a set of conserved genes, have more targets that are critical for spermatogenesis and embryonic development during evolution. Our data suggest that the miR-506 family miRNAs function to enhance sperm competitiveness and reproductive fitness of the male by finetuning gene expression during spermatogenesis.
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Affiliation(s)
- Zhuqing Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Sheng Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Dayton Morris
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | | | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shawn Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hetan Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Yeming Xie
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Hayden McSwiggin
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Daniel Oliver
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Shuiqiao Yuan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Jaaved Mohammed
- Department of Developmental Biology, Memorial Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - Eric C. Lai
- Department of Developmental Biology, Memorial Sloan-Kettering Institute, 1275 York Ave, Box 252, New York, NY 10065, USA
| | - John R. McCarrey
- Department of Biology, University of Texas at San Antonio, San Antonio, TX, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
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5
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Peters L, Venkatachalam A, Ben-Neriah Y. Tissue-Predisposition to Cancer Driver Mutations. Cells 2024; 13:106. [PMID: 38247798 PMCID: PMC10814991 DOI: 10.3390/cells13020106] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Driver mutations are considered the cornerstone of cancer initiation. They are defined as mutations that convey a competitive fitness advantage, and hence, their mutation frequency in premalignant tissue is expected to exceed the basal mutation rate. In old terms, that translates to "the survival of the fittest" and implies that a selective process underlies the frequency of cancer driver mutations. In that sense, each tissue is its own niche that creates a molecular selective pressure that may favor the propagation of a mutation or not. At the heart of this stands one of the biggest riddles in cancer biology: the tissue-predisposition to cancer driver mutations. The frequency of cancer driver mutations among tissues is non-uniform: for instance, mutations in APC are particularly frequent in colorectal cancer, and 99% of chronic myeloid leukemia patients harbor the driver BCR-ABL1 fusion mutation, which is rarely found in solid tumors. Here, we provide a mechanistic framework that aims to explain how tissue-specific features, ranging from epigenetic underpinnings to the expression of viral transposable elements, establish a molecular basis for selecting cancer driver mutations in a tissue-specific manner.
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Affiliation(s)
| | | | - Yinon Ben-Neriah
- Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research (IMRIC), The Faculty of Medicine, Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 91120, Israel; (L.P.); (A.V.)
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6
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Chacón RD, Sánchez-Llatas CJ, Diaz Forero AJ, Guimarães MB, Pajuelo SL, Astolfi-Ferreira CS, Ferreira AJP. Evolutionary Analysis of a Parrot Bornavirus 2 Detected in a Sulphur-Crested Cockatoo ( Cacatua galerita) Suggests a South American Ancestor. Animals (Basel) 2023; 14:47. [PMID: 38200778 PMCID: PMC10778322 DOI: 10.3390/ani14010047] [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: 10/20/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Parrot bornavirus (PaBV) is an RNA virus that causes Proventricular Dilatation Disease (PDD), neurological disorders, and death in Psittaciformes. Its diversity in South America is poorly known. We examined a Cacatua galerita presenting neuropathies, PDD, and oculopathies as the main signs. We detected PaBV through reverse transcription polymerase chain reaction (RT-PCR) and partial sequencing of the nucleoprotein (N) and matrix (M) genes. Maximum likelihood and Bayesian phylogenetic inferences classified it as PaBV-2. The nucleotide identity of the sequenced strain ranged from 88.3% to 90.3% against genotype PaBV-2 and from 80.2% to 84.4% against other genotypes. Selective pressure analysis detected signs of episodic diversifying selection in both the N and M genes. No recombination events were detected. Phylodynamic analysis estimated the time to the most recent common ancestor (TMRCA) as the year 1758 for genotype PaBV-2 and the year 1049 for the Orthobornavirus alphapsittaciforme species. Substitution rates were estimated at 2.73 × 10-4 and 4.08 × 10-4 substitutions per year per site for N and M, respectively. The analysis of population dynamics showed a progressive decline in the effective population size during the last century. Timescale phylogeographic analysis revealed a potential South American ancestor as the origin of genotypes 1, 2, and 8. These results contribute to our knowledge of the evolutionary origin, diversity, and dynamics of PaBVs in South America and the world. Additionally, it highlights the importance of further studies in captive Psittaciformes and the potential impact on endangered wild birds.
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Affiliation(s)
- Ruy D. Chacón
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Christian J. Sánchez-Llatas
- Department of Genetics, Physiology, and Microbiology, Faculty of Biology, Complutense University of Madrid (UCM), 28040 Madrid, Spain;
| | - Andrea J. Diaz Forero
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Marta B. Guimarães
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Sarah L. Pajuelo
- Faculty of Biological Sciences, National University of Trujillo, Trujillo 13001, La Libertad, Peru;
| | - Claudete S. Astolfi-Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
| | - Antonio J. Piantino Ferreira
- Department of Pathology, School of Veterinary Medicine, University of São Paulo, Av. Prof. Orlando Marques de Paiva, 87, São Paulo 05508-900, Brazil; (R.D.C.); (A.J.D.F.); (M.B.G.); (C.S.A.-F.)
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7
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Liu Q, Zeng H, Wu X, Yang X, Wang G. Global Prevalence and Hemagglutinin Evolution of H7N9 Avian Influenza Viruses from 2013 to 2022. Viruses 2023; 15:2214. [PMID: 38005891 PMCID: PMC10674656 DOI: 10.3390/v15112214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 11/26/2023] Open
Abstract
H7N9 avian influenza viruses have caused severe harm to the global aquaculture industry and human health. For further understanding of the characteristics of prevalence and hemagglutinin evolution of H7N9 avian influenza viruses, we generated the global epidemic map of H7N9 viruses from 2013 to 2022, constructed a phylogenetic tree, predicted the glycosylation sites and compared the selection pressure of the hemagglutinin. The results showed that although H7N9 avian influenza appeared sporadically in other regions worldwide, China had concentrated outbreaks from 2013 to 2017. The hemagglutinin genes were classified into six distinct lineages: A, B, C, D, E and F. After 2019, H7N9 viruses from the lineages B, E and F persisted, with the lineage B being the dominant. The hemagglutinin of highly pathogenic viruses in the B lineage has an additional predicted glycosylation site, which may account for their persistent pandemic, and is under more positive selection pressure. The most recent ancestor of the H7N9 avian influenza viruses originated in September 1991. The continuous evolution of hemagglutinin has led to an increase in virus pathogenicity in both poultry and humans, and sustained human-to-human transmission. This study provides a theoretical basis for better prediction and control of H7N9 avian influenza.
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Affiliation(s)
- Qianshuo Liu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Haowen Zeng
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Xinghui Wu
- College of Life Sciences, Nanjing Normal University, Nanjing 210023, China; (Q.L.); (H.Z.); (X.W.)
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Xuelian Yang
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
| | - Guiqin Wang
- Nanjing Advanced Academy of Life and Health, Nanjing 211135, China;
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8
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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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9
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Attili I, Corvaja C, Spitaleri G, Del Signore E, Trillo Aliaga P, Passaro A, de Marinis F. New Generations of Tyrosine Kinase Inhibitors in Treating NSCLC with Oncogene Addiction: Strengths and Limitations. Cancers (Basel) 2023; 15:5079. [PMID: 37894445 PMCID: PMC10605462 DOI: 10.3390/cancers15205079] [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: 09/29/2023] [Revised: 10/17/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Tyrosine kinase inhibitors (TKIs) revolutionized the treatment of patients with advanced or metastatic non-small cell lung cancer (NSCLC) harboring most driver gene alterations. Starting from the first generation, research rapidly moved to the development of newer, more selective generations of TKIs, obtaining improved results in terms of disease control and survival. However, the use of novel generations of TKIs is not without limitations. We reviewed the main results obtained, as well as the ongoing clinical trials with TKIs in oncogene-addicted NSCLC, together with the biology underlying their potential strengths and limitations. Across driver gene alterations, novel generations of TKIs allowed delayed resistance, prolonged survival, and improved brain penetration compared to previous generations, although with different toxicity profiles, that generally moved their use from further lines to the front-line treatment. However, the anticipated positioning of novel generation TKIs leads to abolishing the possibility of TKI treatment sequencing and any role of previous generations. In addition, under the selective pressure of such more potent drugs, resistant clones emerge harboring more complex and hard-to-target resistance mechanisms. Deeper knowledge of tumor biology and drug properties will help identify new strategies, including combinatorial treatments, to continue improving results in patients with oncogene-addicted NSCLC.
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Affiliation(s)
- Ilaria Attili
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Via G. Ripamonti 435, 20141 Milan, Italy
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10
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Feng P, Liang X, Yu H, Dong X, Liang Q, Dai C. The evolution of bitter taste receptor gene in primates: Gene duplication and selection. Ecol Evol 2023; 13:e10610. [PMID: 37841228 PMCID: PMC10571502 DOI: 10.1002/ece3.10610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 09/08/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Bitter taste perception plays an important role in preventing animals from digesting poisonous and harmful substances. In primates, especially the Cercopithecidae species, most species feed on plants; thus, it is reasonable to speculate that most of the bitter taste receptor genes (T2Rs) of primates are under purifying selection to maintain the functional stability of bitter taste perception. Gene duplication has happened in T2Rs frequently, and what will be the fate of T2Rs copies is another question we are concerned about. To answer these questions, we selected the T2Rs of primates reported in another study and conducted corresponding selective pressure analyses to determine what kind of selective pressure was acting on them. Further, we carried out selective pressure analyses on gene copies and their corresponding ancestors by considering several possible situations. The results showed that among the 25 gene groups examined here, 15 groups are subject to purifying selection and others are under relaxed selection, with many positively selected sites detected. Gene copies existed in several groups, but only some groups (clade1_a1-b2, clade1_c-c2, clade1_d1-d3, clade1_f1-f2, T2R10, T2R13, and T2R42) have positively selected sites, inferring that they may have some relation to functional divergence. Taken together, T2Rs in primates are under diverse selective pressures, and most gene copies are subject to the same selective pressures. In such cases, the copies may be just to keep the function conservative, and more copies can increase the quantity of the bitter taste receptor, raise the efficiency of bitter substance recognition, and finally enhance the fitness of feeding during the evolutionary course of primates. This study can improve our understanding of T2Rs evolution in primates.
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Affiliation(s)
- Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xinyue Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Hongling Yu
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
| | - Chuanyin Dai
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education of the People's Republic of ChinaGuangxi Normal UniversityGuilinGuangxiChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinGuangxiChina
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11
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Chacón JL, Chacón RD, Sánchez-Llatas CJ, Morín JG, Astolfi-Ferreira CS, Piantino Ferreira AJ. Antigenic and molecular characterization of isolates of the Brazilian genotype BR-I (GI-11) of infectious bronchitis virus supports its recognition as BR-I serotype. Avian Pathol 2023; 52:323-338. [PMID: 37477586 DOI: 10.1080/03079457.2023.2228725] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/22/2023]
Abstract
The antigenic and molecular characteristics of BR-I infectious bronchitis viruses (IBVs) isolated from Brazil are reported. IBVs isolated from commercial flocks with different clinical manifestations between 2003 and 2019 were submitted to antigenic and molecular characterization. The complete S1 glycoprotein gene of 11 field isolates was amplified and sequenced. The virus neutralization (VN) test showed 94.75% neutralization with a BR-I isolate and 30% or less against other worldwide reference strains. The nucleotide and amino acid sequence analyses revealed 84.3-100% and 83.5-100% identity among them, respectively. The identity values ranged from 57.1 to 82.6% for nucleotides and from 46.6-84.4% for amino acids compared with those of other genotypes. By phylogenetic tree analysis, the Brazilian isolates were branched into the BR-I genotype (lineage GI-11), which was differentiated from foreign reference strains. Selective pressure analyses of BR-I IBVs revealed evolution under purifying selection (negative pressure) for the complete S1 gene but four specific sites (87, 121, 279, and 542) under diversifying selection (positive pressure). Profiles of cleavage sites and potential N-glycosylation sites differed from those of other genotypes. The low molecular relationship among the Brazilian viruses and foreign serotypes was concordant with the VN test results. The low antigenic relatedness (ranging from 5.3-30% between Brazilian genotype BR-I and reference IBV serotypes of North America, Europe, and Asia) indicates that the BR-I genotype is a different serotype, referred to for the first time and hereafter as serotype BR-I. RESEARCH HIGHLIGHTSStrains of the BR-I genotype presented robust antigenic and molecular similarity.BR-I strains evolved under purifying selection mode (negative pressure).The BR-I genotype originated in Brazil and dispersed to other countries.BR-I genotype viruses can be referred to as the BR-I serotype.
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Affiliation(s)
- Jorge L Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Ruy D Chacón
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Christian J Sánchez-Llatas
- Faculty of Biology, Department of Genetics, Physiology, and Microbiology, Complutense University of Madrid, Madrid, Spain
| | - Jaime G Morín
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Claudete S Astolfi-Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
| | - Antonio J Piantino Ferreira
- Laboratory of Avian Diseases, Department of Pathology, School of Veterinary Medicine, University of São Paulo, São Paulo, Brazil
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12
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Flore L, Francalacci P, Massidda M, Robledo R, Calò CM. Influence of Different Evolutive Forces on GDF5 Gene Variability. Genes (Basel) 2023; 14:1895. [PMID: 37895244 PMCID: PMC10606091 DOI: 10.3390/genes14101895] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
The GDF5 gene is involved in the development of skeletal elements, synovial joint formation, tendons, ligaments, and cartilage. Several polymorphisms are present within the gene, and two of them, rs143384 and 143383, were reported to be correlated with osteoarticular disease or muscle flexibility. The aim of this research is to verify if the worldwide distribution of the rs143384 polymorphism among human populations was shaped by selective pressure, or if it was the result of random genetic drift events. Ninety-four individuals of both the male and female sexes, 18-28 years old, from Sardinia were analyzed. We observed the following genotype frequencies: 28.72% of AA homozygotes, 13.83% of GG homozygotes, and 57.45% of AG heterozygotes. The allele frequencies were 0.574 for allele A and 0.426 for allele G. The relationships between the populations were verified via Multidimensional Scaling (MDS). Our data show (i) a clear heterogeneity within the African populations; (ii) a strong differentiation between the African populations and the other populations; and that (iii) the Sardinian population is placed within the European cluster. To reveal possible traces of selective pressure, the Population Branch Statistic (PBS) was calculated; both the rs143384 and 143383 SNPs have low PBS values, suggesting that there are no signals of selective pressure in those areas of the gene.
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Affiliation(s)
- Laura Flore
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Paolo Francalacci
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
| | - Myosotis Massidda
- Department of Medical Sciences and Public Health, University of Cagliari, 09042 Cagliari, Italy;
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, 09042 Cagliari, Italy
| | - Carla Maria Calò
- Department of Life and Environment Sciences, University of Cagliari, 09042 Cagliari, Italy; (L.F.); (P.F.); (C.M.C.)
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13
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Bonnet PL, Hoffmann CV, Le Nan N, Bellamy L, Hoarau G, Flori P, Demar M, Argy N, Morio F, Le Gal S, Nevez G. Atovaquone exposure and Pneumocystis jirovecii cytochrome b mutations: French data and review of the literature. Med Mycol 2023; 61:myad095. [PMID: 37656874 DOI: 10.1093/mmy/myad095] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/18/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023] Open
Abstract
Pneumocystis jirovecii is a transmissible fungus responsible for severe pneumonia (Pneumocystis pneumonia [PCP]) in immunocompromised patients. Missense mutations due to atovaquone selective pressure have been identified on cytochrome b (CYB) gene of P. jirovecii. It was recently shown that atovaquone prophylaxis can lead to the selection of specific P. jirovecii CYB mutants potentially resistant to atovaquone among organ transplant recipients. In this context, our objectives were to provide data on P. jirovecii CYB mutants and the putative selective pressure exerted by atovaquone on P. jirovecii organisms in France. A total of 123 patients (124 P. jirovecii specimens) from four metropolitan hospitals and two overseas hospitals were retrospectively enrolled. Fourteen patients had prior exposure to atovaquone, whereas 109 patients did not at the time of P. jirovecii detection. A 638 base-pair fragment of the CYB gene of P. jirovecii was amplified and sequenced. A total of 10 single nucleotide polymorphisms (SNPs) were identified. Both missense mutations C431T (Ala144Val) and C823T (Leu275Phe), located at the Qo active site of the enzyme, were significantly associated with prior atovaquone exposure, these mutations being conversely incidental in the absence of prior atovaquone exposure (P < 0.001). Considering that the aforementioned hospitals may be representative of the national territory, these findings suggest that the overall presence of P. jirovecii CYB mutants remains low in France.
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Affiliation(s)
- Pierre L Bonnet
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Claire V Hoffmann
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Nathan Le Nan
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Lorenn Bellamy
- Clinical Data Center, Brest University Hospital, 29609 Brest, France
| | - Gautier Hoarau
- Ophthalmology Department, OPHTARA Network, Bicêtre Paris Saclay University Hospital, AP-HP, 94276 Le Kremlin-Bicêtre, France
| | - Pierre Flori
- Laboratory of Infectious Agents, Parasitology Section, GIMAP, Faculty of Medicine, 42055 Saint-Etienne, France
| | - Magalie Demar
- University Hospital Laboratory of Parasitology-Mycology, Cayenne Hospital Center, 97306 Cayenne, French Guiana
| | - Nicolas Argy
- IRD, MERIT, University of Paris Cité, 75006 Paris, France
| | - Florent Morio
- Laboratory of Parasitology and Medical Mycology, Nantes University Hospital, 44000 Nantes, France
| | - Solène Le Gal
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
| | - Gilles Nevez
- Laboratory of Parasitology and Mycology, Brest University Hospital, 29609 Brest, France
- Fungal Respiratory Infections Research Unit (FRI), University of Angers, University of Western Brittany, 29238 Brest, France
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14
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Devaux CA, Fantini J. ACE2 receptor polymorphism in humans and animals increases the risk of the emergence of SARS-CoV-2 variants during repeated intra- and inter-species host-switching of the virus. Front Microbiol 2023; 14:1199561. [PMID: 37520374 PMCID: PMC10373931 DOI: 10.3389/fmicb.2023.1199561] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Like other coronaviruses, SARS-CoV-2 has ability to spread through human-to-human transmission and to circulate from humans to animals and from animals to humans. A high frequency of SARS-CoV-2 mutations has been observed in the viruses isolated from both humans and animals, suggesting a genetic fitness under positive selection in both ecological niches. The most documented positive selection force driving SARS-CoV-2 mutations is the host-specific immune response. However, after electrostatic interactions with lipid rafts, the first contact between the virus and host proteins is the viral spike-cellular receptor binding. Therefore, it is likely that the first level of selection pressure impacting viral fitness relates to the virus's affinity for its receptor, the angiotensin I converting enzyme 2 (ACE2). Although sufficiently conserved in a huge number of species to support binding of the viral spike with enough affinity to initiate fusion, ACE2 is highly polymorphic both among species and within a species. Here, we provide evidence suggesting that when the viral spike-ACE2 receptor interaction is not optimal, due to host-switching, mutations can be selected to improve the affinity of the spike for the ACE2 expressed by the new host. Notably, SARS-CoV-2 is mutation-prone in the spike receptor binding domain (RBD), allowing a better fit for ACE2 orthologs in animals. It is possibly that this may also be true for rare human alleles of ACE2 when the virus is spreading to billions of people. In this study, we present evidence that human subjects expressing the rare E329G allele of ACE2 with higher allele frequencies in European populations exhibit a improved affinity for the SARS-CoV-2 spike N501Y variant of the virus. This may suggest that this viral N501Y variant emerged in the human population after SARS-CoV-2 had infected a human carrying the rare E329G allele of ACE2. In addition, this viral evolution could impact viral replication as well as the ability of the adaptive humoral response to control infection with RBD-specific neutralizing antibodies. In a shifting landscape, this ACE2-driven genetic drift of SARS-CoV-2 which we have named the 'boomerang effect', could complicate the challenge of preventing COVID with a SARS-CoV-2 spike-derived vaccine.
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Affiliation(s)
- Christian A. Devaux
- Laboratory Microbes Evolution Phylogeny and Infection (MEPHI), Aix-Marseille Université, IRD, APHM, MEPHI, IHU–Méditerranée Infection, Marseille, France
- Centre National de la Recherche Scientifique (CNRS-SNC5039), Marseille, France
| | - Jacques Fantini
- INSERM UMR_S1072, Marseille, France, Aix-Marseille Université, Marseille, France
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15
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Chukwu KB, Abafe OA, Amoako DG, Essack SY, Abia ALK. Antibiotic, Heavy Metal, and Biocide Concentrations in a Wastewater Treatment Plant and Its Receiving Water Body Exceed PNEC Limits: Potential for Antimicrobial Resistance Selective Pressure. Antibiotics (Basel) 2023; 12:1166. [PMID: 37508262 PMCID: PMC10376008 DOI: 10.3390/antibiotics12071166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Although the rise in antimicrobial resistance has been attributed mainly to the extensive and indiscriminate use of antimicrobials such as antibiotics and biocides in humans, animals and on plants, studies investigating the impact of this use on water environments in Africa are minimal. This study quantified selected antibiotics, heavy metals, and biocides in an urban wastewater treatment plant (WWTP) and its receiving water body in Kwazulu-Natal, South Africa, in the context of the predicted no-effect concentrations (PNEC) for the selection of antimicrobial resistance (AMR). Water samples were collected from the WWTP effluent discharge point and upstream and downstream from this point. Heavy metals were identified and quantified using the United States Environmental Protection Agency (US EPA) method 200.7. Biocides and antibiotic residues were determined using validated ultra-high-performance liquid chromatography with tandem mass spectrometry-based methods. The overall highest mean antibiotic, metal and biocide concentrations were observed for sulfamethoxazole (286.180 µg/L), neodymium (Nd; 27.734 mg/L), and benzalkonium chloride (BAC 12) (7.805 µg/L), respectively. In decreasing order per sampling site, the pollutant concentrations were effluent > downstream > upstream. This implies that the WWTP significantly contributed to the observed pollution in the receiving water. Furthermore, most of the pollutants measured recorded values exceeding the recommended predicted no-effect concentration (PNEC) values, suggesting that the microbes in such water environments were at risk of developing resistance due to the selection pressure exerted by these antimicrobials. Further studies are required to establish such a relationship.
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Affiliation(s)
- Kelechi B Chukwu
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Ovokeroye A Abafe
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Residue Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research Campus, Onderstepoort 0110, South Africa
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Department of Integrative Biology and Bioinformatics, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Akebe L K Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
- Environmental Research Foundation, Westville 3630, South Africa
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16
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Wang Z, Zheng Y, Zhao X, Xu X, Xu Z, Cui C. Molecular Phylogeny and Evolution of the Tuerkayana (Decapoda: Brachyura: Gecarcinidae) Genus Based on Whole Mitochondrial Genome Sequences. Biology (Basel) 2023; 12:974. [PMID: 37508404 PMCID: PMC10376310 DOI: 10.3390/biology12070974] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/06/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023]
Abstract
Tuerkayana is of particular interest because it has been separated, in recent years, from Cardisoma and Discoplax but studies of its taxonomic status, especially from a whole mitochondrial genome perspective, have been lacking. In this study, the mitogenomes of four species (Tuerkayana magnum, Tuerkayana rotundum, Tuerkayana hirtipes, and Tuerkayana celeste) of Tuerkayana are sequenced and contrasted with other species in Brachyura for the first time. The phylogenetic tree of Brachyura, which includes 206 crab species (189 species of Brachyuran and 17 Anomura species) with a complete mitogenome, was constructed to evaluate the phylogenetic position of Tuerkayana and Gecarcinidae within Brachyuran, and explore the monophyly of Gecarcinidae. Furthermore, two single gene trees based on cox1 and 16SrRNA separately within interspecies of Gecarcinidae were reconstructed, providing molecular evidence for Tuerkayana and further clarifying the division of genera in Gecarcinidae. Based on the mitogenome dataset of 206 crabs, the branch-site model was utilized to explore selective pressure in individual codons with CodeML. The strong selective pressure shown in nad6 indicates that it may have played a significant role in the evolution of Gecarcinidae.
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Affiliation(s)
- Zhengfei Wang
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Yuqing Zheng
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Xinyue Zhao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Xinyi Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200000, China
| | - Zhiwen Xu
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
| | - Chong Cui
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-Agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Wetlands, Yancheng Teachers University, Yancheng 224001, China
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
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17
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Satari L, Iglesias A, Porcar M. The Microbiome of Things: Appliances, Machines, and Devices Hosting Artificial Niche-Adapted Microbial Communities. Microorganisms 2023; 11:1507. [PMID: 37375009 DOI: 10.3390/microorganisms11061507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/25/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
As it is the case with natural substrates, artificial surfaces of man-made devices are home to a myriad of microbial species. Artificial products are not necessarily characterized by human-associated microbiomes; instead, they can present original microbial populations shaped by specific environmental-often extreme-selection pressures. This review provides a detailed insight into the microbial ecology of a range of artificial devices, machines, and appliances, which we argue are specific microbial niches that do not necessarily fit in the "build environment" microbiome definition. Instead, we propose here the Microbiome of Things (MoT) concept analogous to the Internet of Things (IoT) because we believe it may be useful to shed light on human-made, but not necessarily human-related, unexplored microbial niches.
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Affiliation(s)
- Leila Satari
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Alba Iglesias
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Manuel Porcar
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
- Darwin Bioprospecting Excellence SL., Parc Científic, Universitat de València, 46980 Paterna, Spain
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Del Duca S, Vassallo A, Semenzato G, Fani R. Mimicking the last step of gene elongation: hints from the bacterial hisF gene. Gene 2023:147533. [PMID: 37279865 DOI: 10.1016/j.gene.2023.147533] [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: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/31/2023] [Indexed: 06/08/2023]
Abstract
Gene elongation consists in an in-tandem duplication of a gene and divergence and fusion of the two copies, resulting in a gene constituted by two divergent paralogous modules. Many present-day proteins show internal repeats of amino acid sequences, generated by gene elongation events; however, gene elongation is still a poorly studied evolutionary molecular mechanism. The most documented case is that of the histidine biosynthetic genes hisA and hisF, which derive from the gene elongation of an ancestral gene half the size of the extant ones. The aim of this work was to experimentally simulate the possible last step of the gene elongation event occurred during hisF gene evolution under selective pressure conditions. Azospirillum brasilense hisF gene, carrying a single nucleotide mutation that generates a stop codon between the two halves of the gene, was used to transform the histidine-auxotrophic Escherichia coli strain FB182 (hisF892). The transformed strain was subjected to selective pressure (i.e., low concentration/absence of histidine in the growth medium) and the obtained mutants were characterized. The restoration of prototrophy was strongly dependent on the time of incubation and on the strength of the selective pressure. The mutations involved the introduced stop codon with a single base substitution and none of the mutants restored the wild-type codon. Possible correlations between the different mutations and i) E. coli codon usage, ii) three-dimensional structures of the mutated HisF proteins, and iii) growth ability of the mutants were investigated. On the contrary, when the experiment was repeated by mutating a more conserved codon, only a synonymous substitution was obtained. Thus, experiments performed in this study allowed to mimic a possible gene elongation event occurred during the evolution of hisF gene, evidencing the ability of bacterial cells to modify their genome in short times under selective conditions.
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Affiliation(s)
- Sara Del Duca
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy; Research Centre for Agriculture and Environment, Council for Agricultural Research and Economics (CREA-AA), Via di Lanciola 12/A, 50125, Cascine del Riccio (FI), Italy
| | - Alberto Vassallo
- School of Biosciences and Veterinary Medicine, University of Camerino, Via Gentile III Da Varano 1, 62032, Camerino (MC) Italy
| | - Giulia Semenzato
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy
| | - Renato Fani
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino (FI), Italy.
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Guo J, He Y, Wang X, Merits A, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Gao Q, Sun D, Tian B, Cheng A, Chen S. Attenuation of Avian Flavivirus by Rewiring the Leucine and Serine Codons of Its E-NS1 Protein toward Stop Mutation To Redirect Virus Evolution. Microbiol Spectr 2023; 11:e0292122. [PMID: 36625643 PMCID: PMC9927255 DOI: 10.1128/spectrum.02921-22] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently, a new strategy for attenuating RNA viruses by redirecting their evolution in sequence space was confirmed for Enterovirus and Influenza viruses. Using avian flavivirus as a model, the 69 serine and 53 leucine codons on the E-NS1 genes were modified to change evolutionary direction of the viral sequence space. This means that all codons encoding serine or leucine residues were substituted with codons that are only one base different from the three stop codons, resulting in the initial position of the virus genome in sequence space being closer to the detrimental areas to achieve attenuation by reducing viral adaptability. The growth curve and plaque size of CQW1-one-to-stop (CQW1-OTS) were similar to those of CQW1-wild type (CQW1-WT) in vitro, but attenuated proliferation was detected when treated with a mutagenic reagent (ribavirin). However, comparably high CQW1-OTS and CQW1-WT lethality rates were detected in 9-day-old duck embryos and 5-day-old ducklings, suggesting that this strategy works but with limitations. With that in mind, homologous hosts in nonsensitive age (25-day-old ducks) and heterologous hosts (3-week-old Kunming mice) were employed to investigate if CQW1-OTS was attenuated under host selection pressure. Minimal attenuation of CQW1-OTS in elder ducks and apparent attenuation in mice were reported, providing reduced viral titers, mild clinical signs, and lower specific infectivity. Collectively, we experimentally demonstrate that the attenuation strategy of redirecting virus evolution in sequence space works for flavivirus. Redirection of the virus is attenuated only under some outside pressure, such as heterologous hosts or antiviral drugs treatment, limiting its usage in flaviviruses. IMPORTANCE Flaviviruses are medically important arboviruses that threaten public health, but no approved treatments are currently available. Vaccines prevent flavivirus infection. We employed duck Tembusu virus (TMUV), a mosquito-borne flavivirus, to evaluate virus redirection. TMUV is native to birds and could infect mice by intracerebral injection, making it an experimental animal model to study flavivirus characteristics in vivo. The 69 serine and 53 leucine codons on the E-NS1 proteins of CQW1 were synonymously substituted to change evolutionary direction of the virus in sequence space. In vitro mutagen reagent treatment suppressed CQW1-OTS viral multiplication, but in vivo attenuation depended on host selective pressure. CQW1-OTS viral attenuation was observed in older ducks but not sensitive ducklings; considerable attenuation was also observed in heterogenous host (mice), which provides more selective pressure on viruses. Collectively, these data indicated that there are very important preconditions for application of evaluating whether this strategy shows application prospects in novel flavivirus vaccine development.
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Affiliation(s)
- Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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Chen X, Sun Z, Xu X, Jiang J, Su J. Genomic characterization of colistin resistance in Klebsiella spp. under the pressure of colistin. J Med Microbiol 2023; 72. [PMID: 36748641 DOI: 10.1099/jmm.0.001647] [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] [Indexed: 01/12/2023] Open
Abstract
Introduction. Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a serious threat to global public health. Colistin is regarded as the last-resort antibiotic for CRKP infections, but colistin resistance among CRKP is increasingly being reported, making clinical treatment for CRKP infections more difficult.Hypothesis/Gap Statement. The molecular mechanisms of colistin resistance in Klebsiella spp. under the pressure of colistin have not been fully investigated.Aim. We aimed to investigate the phenotypic and genetic variation in two colistin-susceptible Klebsiella spp. strains under selective pressure of colistin.Methodology. One hundred microlitres of overnight cultures of the CRKP clinical strain CRKP12-130 and of ATCC 700603 was spread on five Mueller-Hinton Agar (MHA) plates with colistin concentrations of 2, 4, 8, 16 and 32 µg ml-1, and growth of colonies was observed for five consecutive days. Colonies collected from plates were passaged daily for 10 days on MHA plates without colistin and susceptibility testing of colistin was performed by broth microdilution. Thirty-four colistin-resistant strains randomly selected were submitted to whole genome sequencing (WGS). Transcriptional levels of genes involved in colistin resistance (mgrB, phoP, phoQ, pmrA, pmrB, pmrD, pmrE and pmrK) were measured by quantitative real-time PCR.Results. A total of 114 and 119 colistin-resistant colonies were obtained from CRKP12-130 and ATCC 700603 in this study, among which 16 and 18 colonies were submitted to WGS, respectively. Among these 34 sequenced isolates, mutation in phoQ (13/16, 81.25 %) was the main genetic factor mediating colistin resistance in strains from CRKP12-130, while for strains from ATCC 700603, mutation associated with mgrB (8/18, 44.44 %) was found to be the commonest. Mutation of mgrB led to a significant increase in the MIC for colistin (from 64 to >128 µg ml-1), and a novel mutation C28R in mgrB was first reported in this study.Conclusion. Colistin-resistant Klebsiella spp. could be easily selected under pressure of different concentrations of colistin. Mutations of mgrB, phoP, phoQ and pmrB genes were the main mechanisms leading to chromosomally mediated colistin resistance in Klebsiella spp.
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Affiliation(s)
- Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Zhewei Sun
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Jianping Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Jiachun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
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Tian L, Yang W, Si C, Guo X, Zhang B. Complete Mitogenome Analysis of Five Leafhopper Species of Idiocerini (Hemiptera: Cicadellidae). Genes (Basel) 2022; 13:2000. [PMID: 36360236 PMCID: PMC9690763 DOI: 10.3390/genes13112000] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/26/2022] [Accepted: 10/27/2022] [Indexed: 10/03/2023] Open
Abstract
Insect mitochondrial genomes (mitogenomes) are of great interest in exploring molecular evolution, phylogenetics, and biogeography. So far, only 12 mitogenomes of the leafhopper tribe Idiocerini have been released in GenBank, although the tribe comprises 488 known species including some agricultural, forestry, and horticultural pests. In order to compare and analyze the mitochondrial genome structure of Idiocerini and even the selective pressure of 13 protein-coding genes (PCGs) of the family Cicadellidae, the complete mitogenomes of five species including Nabicerus dentimus, Sahlbergotettix salicicola, Podulmorinus opacus, Podulmorinus consimilis, and a new species of a new genus were determined by next-generation sequencing. The size of the newly determined mitogenomes ranged from 14,733 bp to 15,044 bp, comprising the standard set of 13 PCGs, 22 transfer RNA genes, two ribosomal RNA genes, and a long non-coding control region (CR). The extent of purifying selection presented different pictures in the tribe and the family. The less pronounced genes (0.5 < dN/dS < 1) were nad5 and nad4l in Idiocerin, whereas in the family Cicadellidae including the sequences of Idiocerin, nad1-nad6 and cox1 genes were less pronounced. The codon encoding leucine was the most common in all species, and the codon encoding serine 1 was the most common in all species except for P. opacus. Interestingly, in P. opacus, another of the most common codons is that encoding serine 2. Among the 17 examined species of the Idiocerini, 14 species contained the tandem repeats, and 11 species of them contained the motif "TTATA". These findings will promote research on the structure and evolution of the mitochondrial genome and highlight the need for more mitogenomes in Cicadellidae.
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Affiliation(s)
- Lili Tian
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxin Yang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Chengyan Si
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
| | - Xianguang Guo
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bin Zhang
- College of Life Sciences & Technology, Inner Mongolia Normal University, Hohhot 010022, China
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Song H, Guo Z, Zhang X, Sui J. De novo genes in Arachis hypogaea cv. Tifrunner: systematic identification, molecular evolution, and potential contributions to cultivated peanut. Plant J 2022; 111:1081-1095. [PMID: 35748398 DOI: 10.1111/tpj.15875] [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] [Received: 01/08/2021] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 06/15/2023]
Abstract
De novo genes are derived from non-coding sequences, and they can play essential roles in organisms. Cultivated peanut (Arachis hypogaea) is a major oil and protein crop derived from a cross between Arachis duranensis and Arachis ipaensis. However, few de novo genes have been documented in Arachis. Here, we identified 381 de novo genes in A. hypogaea cv. Tifrunner based on comparison with five closely related Arachis species. There are distinct differences in gene expression patterns and gene structures between conserved and de novo genes. The identified de novo genes originated from ancestral sequence regions associated with metabolic and biosynthetic processes, and they were subsequently integrated into existing regulatory networks. De novo paralogs and homoeologs were identified in A. hypogaea cv. Tifrunner. De novo paralogs and homoeologs with conserved expression have mismatching cis-acting elements under normal growth conditions. De novo genes potentially have pluripotent functions in responses to biotic stresses as well as in growth and development based on quantitative trait locus data. This work provides a foundation for future research examining gene birth processes and gene function in Arachis and related taxa.
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Affiliation(s)
- Hui Song
- Grassland Agri-husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Zhonglong Guo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Life Sciences and School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Jiongming Sui
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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Pottier M, Le Thi VA, Primard-Brisset C, Marion J, Wolf Bianchi M, Victor C, Déjardin A, Pilate G, Thomine S. Duplication of NRAMP3 gene in poplars generated two homologous transporters with distinct functions. Mol Biol Evol 2022; 39:msac129. [PMID: 35700212 PMCID: PMC9234761 DOI: 10.1093/molbev/msac129] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 05/28/2022] [Accepted: 06/02/2022] [Indexed: 12/02/2022] Open
Abstract
Transition metals are essential for a wealth of metabolic reactions, but their concentrations need to be tightly controlled across cells and cell compartments, as metal excess or imbalance has deleterious effects. Metal homeostasis is achieved by a combination of metal transport across membranes and metal binding to a variety of molecules. Gene duplication is a key process in evolution, as emergence of advantageous mutations on one of the copies can confer a new function. Here, we report that the poplar genome contains two paralogues encoding NRAMP3 metal transporters localized in tandem. All Populus species analyzed had two copies of NRAMP3, whereas only one could be identified in Salix species indicating that duplication occurred when the two genera separated. Both copies are under purifying selection and encode functional transporters, as shown by expression in the yeast heterologous expression system. However, genetic complementation revealed that only one of the paralogues has retained the original function in release of metals stored in the vacuole previously characterized in A. thaliana. Confocal imaging showed that the other copy has acquired a distinct localization to the Trans Golgi Network (TGN). Expression in poplar suggested that the copy of NRAMP3 localized on the TGN has a novel function in the control of cell-to-cell transport of manganese. This work provides a clear case of neo-functionalization through change in the subcellular localization of a metal transporter as well as evidence for the involvement of the secretory pathway in cell-to-cell transport of manganese.
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Affiliation(s)
- Mathieu Pottier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Van Anh Le Thi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Catherine Primard-Brisset
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Jessica Marion
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Michele Wolf Bianchi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Cindy Victor
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | | | | | - Sébastien Thomine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
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Jahant-Miller C, Miller R, Parry D. Size-dependent flight capacity and propensity in a range-expanding invasive insect. Insect Sci 2022; 29:879-888. [PMID: 34351047 DOI: 10.1111/1744-7917.12950] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/28/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
For capital-breeding insects, all resources available for adult metabolic needs are accumulated during larval feeding. Therefore, body size at adult eclosion represents the total energetic capacity of the individual. For female capital breeders, body size is strongly correlated with lifetime fecundity, while in males, body size, which correlates with fitness, is less understood. In capital-breeding species with wingless, flightless, or dispersal-limited females, flight potential for male Lepidoptera has important implications for mate-finding and may be correlated with body size. At low population densities, failure to mate has been identified as an important Allee effect and can drive the success or failure of invasive species at range edges and in species of conservation concern. Th capital-breeding European subspecies of Lymantria dispar (L.), was introduced to North America in 1869 and now ranges across much of eastern North America. In L. dispar, females are flightless and mate-finding is entirely performed by males. We quantified male L. dispar flight capacity and propensity relative to morphological and physiological characteristics using fixed-arm flight mills. A range of male body sizes was produced by varying the protein content of standard artificial diets while holding other dietary components constant. Wing length, a proxy for body size, relative thorax mass, and forewing aspect were all important predictors of total flight distance and maximum speed. These results have important implications for mate-finding and invasion dynamics in L. dispar and may apply broadly to other capital-breeding insects.
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Affiliation(s)
- Chelsea Jahant-Miller
- Forest Health Protection, U.S. Forest Service, Coeur d'Alene, ID, 83815, USA
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
| | - Russell Miller
- School for Environment and Sustainability, Cooperative Institute for Great Lakes Research, University of Michigan, Ann Arbor, MI, 48106, USA
| | - Dylan Parry
- Department of Environmental and Forest Biology, College of Environmental Science and Forestry, State University of New York, Syracuse, NY, 13210, USA
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Fan W, Chen J, Zhang Y, Deng Q, Wei L, Zhao C, Lv D, Lin L, Zhang B, Wei T, Huang T, Wei P, Mo M. Phylogenetic and Spatiotemporal Analyses of the Complete Genome Sequences of Avian Coronavirus Infectious Bronchitis Virus in China During 1985-2020: Revealing Coexistence of Multiple Transmission Chains and the Origin of LX4-Type Virus. Front Microbiol 2022; 13:693196. [PMID: 35444624 PMCID: PMC9013971 DOI: 10.3389/fmicb.2022.693196] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Infectious bronchitis (IB) virus (IBV) causes considerable economic losses to poultry production. The data on transmission dynamics of IBV in China are limited. The complete genome sequences of 212 IBV isolates in China during 1985–2020 were analyzed as well as the characteristics of the phylogenetic tree, recombination events, dN/dS ratios, temporal dynamics, and phylogeographic relationships. The LX4 type (GI-19) was found to have the highest dN/dS ratios and has been the most dominant genotype since 1999, and the Taiwan-I type (GI-7) and New type (GVI-1) showed an increasing trend. A total of 59 recombinants were identified, multiple recombination events between the field and vaccine strains were found in 24 isolates, and the 4/91-type (GI-13) isolates were found to be more prone to being involved in the recombination. Bayesian phylogeographic analyses indicated that the Chinese IBVs originated from Liaoning province in the early 1900s. The LX4-type viruses were traced back to Liaoning province in the late 1950s and had multiple transmission routes in China and two major transmission routes in the world. Viral phylogeography identified three spread regions for IBVs (including LX4 type) in China: Northeastern China (Heilongjiang, Liaoning, and Jilin), north and central China (Beijing, Hebei, Shanxi, Shandong, and Jiangsu), and Southern China (Guangxi and Guangdong). Shandong has been the epidemiological center of IBVs (including LX4 type) in China. Overall, our study highlighted the reasons why the LX4-type viruses had become the dominant genotype and its origin and transmission routes, providing more targeted strategies for the prevention and control of IB in China.
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Affiliation(s)
- Wensheng Fan
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Jiming Chen
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Yu Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Qiaomu Deng
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Lanping Wei
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Changrun Zhao
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Di Lv
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Liting Lin
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Bingsha Zhang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Tianchao Wei
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Teng Huang
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Ping Wei
- College of Animal Science and Technology, Guangxi University, Nanning, China
| | - Meilan Mo
- College of Animal Science and Technology, Guangxi University, Nanning, China
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Li J, Xiao Y, Qiu M, Li X, Li S, Lin H, Li X, Zhu J, Chen N. A Systematic Investigation Unveils High Coinfection Status of Porcine Parvovirus Types 1 through 7 in China from 2016 to 2020. Microbiol Spectr 2021; 9:e0129421. [PMID: 34851175 DOI: 10.1128/Spectrum.01294-21] [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: 02/07/2023] Open
Abstract
Porcine parvovirus genotype 1 (PPV1) causes reproductive disorder in swine and is prevalent in China. Recently, six new genotypes of PPVs (PPV2 through PPV7) have also been detected in Chinese swine herds. However, the coinfection status of all these seven genotypes of PPVs (PPV1-7) in China was not clarified yet. In this study, we developed a panel of PPV1–7 PCR assays with satisfied specificity, sensitivity and reproducibility and then applied to the detection of PPV1–7 in 435 clinical samples collected from eight provinces of China in 2016–2020. A total of 55.40% samples (241 out of 435) were PPV positive, while PPV2 and PPV3 (both 22.53%) belonging to the genus of Tetraparvovirus were the most prevalent genotypes. Noticeably, PPV1–7 strains were more prevalent in nursery and finishing pigs than in suckling pigs. In addition, coinfection could be detected in all eight provinces and 27.36% (119/435) samples were coinfected with two to five genotypes of PPVs. Meanwhile, the coinfection of PPVs with PCV2 was 22.30% (97/435). Twenty complete genomes of representative PPV1–7 were determined, and phylogenetic analysis confirmed the genotyping results by sequence comparisons and PCR assays. Remarkably, the PPV7 HBTZ20180519-152 strain from domestic pig was recombined from parental JX15-like and JX38-like isolates from wild boars. Selective pressure analysis based on VP2 sequences of PPV1–7 showed that they were predominantly under negative selection, while few positive selection sites could be detected in VP2 of PPV7. Overall, this systematic investigation unveils high prevalence and coinfection of PPV1–7 in China from 2016 to 2020. IMPORTANCE Porcine parvoviruses (PPVs) are prevalent in China associating with reproductive failure in swine. The coinfection of seven genotypes of PPVs (PPV1-7) might have synergistic effects on PPV1 associated SMEDI syndrome. However, the coinfection status of PPV1–7 in China is not clear yet. This study showed that PPV1–7 strains are highly prevalent (55.40%) in China and mainly in nursery and finishing pigs in recent years. In addition, the coinfections of different genotypes of PPVs (27.36%) and PPVs with PCV2 (22.30%) are common. Geographic analysis indicated that different genotypes of PPVs are widely cocirculating in China. Intriguingly, a PPV7 strain from the domestic pig was detected as a recombinant from two wild boar isolates. Selective pressure analyses showed that PPV1–7 are mainly under purifying selection. Our findings provide the first systematic investigation on the prevalence, coinfection, and evolution of PPV1 through PPV7 in Chinese swineherds from 2016 to 2020.
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27
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Gao R, Zu W, Liu Y, Li J, Li Z, Wen Y, Wang H, Yuan J, Cheng L, Zhang S, Zhang Y, Zhang S, Liu W, Lan X, Liu L, Li F, Zhang Z. Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis. Virulence 2021; 12:1209-1226. [PMID: 34030593 PMCID: PMC8158041 DOI: 10.1080/21505594.2021.1911477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/28/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022] Open
Abstract
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies' composition varies with time during the early onset of symptoms, which implicates viral evolution during infection. Network analysis of co-occurring SNPs revealed the most abundant non-synonymous SNP 22,638 in the S glycoprotein RBD region and 28,144 in the ORF8 region. Furthermore, SARS-CoV-2 variations differ in an individual's respiratory tissue (nose, throat, BALF, or sputum), suggesting independent compartmentalization of SARS-CoV-2 populations in patients. The positive selection analysis of the SARS-CoV-2 genome uncovered the positive selected amino acid G251V on ORF3a. Alternative allele frequency spectrum (AAFS) of all variants revealed that ORF8 could bear alternate alleles with high frequency. Overall, the results show the quasispecies' profile of SARS-CoV-2 in the respiratory tract in the first two months after the outbreak.
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Affiliation(s)
- Rongsui Gao
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Wenhong Zu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yang Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Junhua Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Zeyao Li
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Yanling Wen
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Haiyan Wang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Jing Yuan
- Department of Infectious Diseases, Shenzhen Third People’s Hospital, National Clinical Research Center for Infectious Disease, Shenzhen, Guangdong Province, China
| | - Lin Cheng
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengyuan Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Yu Zhang
- National Supercomputing Center in Shenzhen (Shenzhen Cloud Computing Center), Shenzhen, China
| | - Shuye Zhang
- Shanghai Public Health Clinical Center, Institute of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weilong Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Xun Lan
- Department of Basic Medical Sciences at School of Medicine, Tsinghua University, Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing, China
| | - Lei Liu
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Feng Li
- Guangzhou Eighth People’s Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zheng Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, the Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
- Shenzhen Research Center for Communicable Disease Diagnosis and Treatment of Chinese Academy of Medical Science, Shenzhen, Guangdong Province, China
- Guangdong Key Laboratory for Anti-infection Drug Quality Evaluation, Shenzhen, Guangdong Province, China
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28
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Li X, Li Y, Sylvester SP, Zang M, El‐Kassaby YA, Fang Y. Evolutionary patterns of nucleotide substitution rates in plastid genomes of Quercus. Ecol Evol 2021; 11:13401-13414. [PMID: 34646478 PMCID: PMC8495791 DOI: 10.1002/ece3.8063] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Molecular evolution, including nucleotide substitutions, plays an important role in understanding the dynamics and mechanisms of species evolution. Here, we sequenced whole plastid genomes (plastomes) of Quercus fabri, Quercus semecarpifolia, Quercus engleriana, and Quercus phellos and compared them with 14 other Quercus plastomes to explore their evolutionary relationships using 67 shared protein-coding sequences. While many previously identified evolutionary relationships were found, our findings do not support previous research which retrieve Quercus subg. Cerris sect. Ilex as a monophyletic group, with sect. Ilex found to be polyphyletic and composed of three strongly supported lineages inserted between sections Cerris and Cyclobalanposis. Compared with gymnosperms, Quercus plastomes showed higher evolutionary rates (Dn/Ds = 0.3793). Most protein-coding genes experienced relaxed purifying selection, and the high Dn value (0.1927) indicated that gene functions adjusted to environmental changes effectively. Our findings suggest that gene interval regions play an important role in Quercus evolution. We detected greater variation in the intergenic regions (trnH-psbA, trnK_UUU-rps16, trnfM_CAU-rps14, trnS_GCU-trnG_GCC, and atpF-atpH), intron losses (petB and petD), and pseudogene loss and degradation (ycf15). Additionally, the loss of some genes suggested the existence of gene exchanges between plastid and nuclear genomes, which affects the evolutionary rate of the former. However, the connective mechanism between these two genomes is still unclear.
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Affiliation(s)
- Xuan Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yongfu Li
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Steven Paul Sylvester
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Mingyue Zang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
| | - Yousry A. El‐Kassaby
- Department of Forest and Conservation Sciences Faculty of ForestryThe University of British ColumbiaVancouverBCCanada
| | - Yanming Fang
- Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity ConservationCollege of Biology and the EnvironmentCo‐Innovation Center for Sustainable Forestry in Southern ChinaNanjing Forestry UniversityNanjingChina
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29
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Bradley IM, Li Y, Guest JS. Solids Residence Time Impacts Carbon Dynamics and Bioenergy Feedstock Potential in Phototrophic Wastewater Treatment Systems. Environ Sci Technol 2021; 55:12574-12584. [PMID: 34478624 DOI: 10.1021/acs.est.1c02590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/13/2023]
Abstract
The use of wastewater-grown microalgae has the potential to reduce the cost of algae-derived biofuels while simultaneously advancing nutrient recovery at water resource recovery facilities (WRRFs). However, a significant barrier has been the low yield and high protein content of phototrophic biomass. Here, we examine the use of solids residence time (SRT) as a selective pressure in driving biochemical composition, yield, biofuel production, and WRRF nutrient management cost. We cultivated mixed phototrophic communities in controlled, laboratory-scale photobioreactors on the local WRRF secondary effluent to link SRT with biochemical composition and techno-economic analysis to yield insights into biomass composition and downstream processing effects on minimum fuel selling price. SRT significantly impacted biochemical composition, with total and dynamic carbohydrates the highest at low SRT (total carbohydrates being 0.60 and 0.32 mg-carbohydrate·mg-protein-1 at SRT 5 and 15 days, respectively). However, there were distinct differences between extant, steady-state performance and intrinsic potential, and longer SRT communities were able to accumulate significant fractions (51% on an ash-free dry weight basis, AFDW %) of carbohydrate reserves under nutrient starvation. Overall, hydrothermal liquefaction (HTL) was found to be more suitable than lipid extraction for hydrotreating (LEH) and combined algal processing (CAP) for conversion of biomass to fuels, but LEH and CAP became more competitive when intrinsic carbon storage potential was realized. The results suggest that the use of algae for nutrient recovery could reduce the nutrient management cost at WRRFs through revenue from algal biofuels, with HTL resulting in a net revenue.
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Affiliation(s)
- Ian M Bradley
- Department of Civil, Structural and Environmental Engineering, University at Buffalo, 212 Ketter Hall, Buffalo, New York 14260, United States
- Research and Education in Energy, Environment and Water Institute, University at Buffalo, 112 Cooke Hall, Buffalo, New York 14260, United States
| | - Yalin Li
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, 1101 West Peabody Drive, Urbana, Illinois 61801, United States
| | - Jeremy S Guest
- Institute for Sustainability, Energy, and Environment, University of Illinois at Urbana-Champaign, 1101 West Peabody Drive, Urbana, Illinois 61801, United States
- Department of Civil and Environmental Engineering, University of Illinois at Urbana-Champaign, 205 North Mathews Avenue, Urbana, Illinois 61801, United States
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30
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Ghorbani A, Samarfard S, Eskandarzade N, Afsharifar A, Eskandari MH, Niazi A, Izadpanah K, Karbanowicz TP. Comparative phylogenetic analysis of SARS-CoV-2 spike protein-possibility effect on virus spillover. Brief Bioinform 2021; 22:bbab144. [PMID: 33885726 PMCID: PMC8083239 DOI: 10.1093/bib/bbab144] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 has developed into a dramatic pandemic with tremendous global impact. The receptor-binding motif (RBM) region of the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), binds to host angiotensin-converting enzyme 2 (ACE2) receptors for infection. As ACE2 receptors are highly conserved within vertebrate species, SARS-CoV-2 can infect significant animal species as well as human populations. An analysis of SARS-CoV-2 genotypes isolated from human and significant animal species was conducted to compare and identify mutation and adaptation patterns across different animal species. The phylogenetic data revealed seven distinct phylogenetic clades with no significant relationship between the clades and geographical locations. A high rate of variation within SARS-CoV-2 mink isolates implies that mink populations were infected before human populations. Positions of most single-nucleotide polymorphisms (SNPs) within the spike (S) protein of SARS-CoV-2 genotypes from the different hosts are mostly accumulated in the RBM region and highlight the pronounced accumulation of variants with mutations in the RBM region in comparison with other variants. These SNPs play a crucial role in viral transmission and pathogenicity and are keys in identifying other animal species as potential intermediate hosts of SARS-CoV-2. The possible roles in the emergence of new viral strains and the possible implications of these changes, in compromising vaccine effectiveness, deserve urgent considerations.
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Affiliation(s)
- Abozar Ghorbani
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Samira Samarfard
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
- Department of Primary Industries and Regional Development, DPIRD Diagnostic Laboratory Services, South Perth, WA, Australia
| | - Neda Eskandarzade
- Department of Basic Sciences, School of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Alireza Afsharifar
- Plant Virology Research Centre, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Mohammad Hadi Eskandari
- Department of Food Science and Technology, College of Agriculture, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, College of Agriculture, Shiraz University, Shiraz, Iran
| | | | - Thomas P Karbanowicz
- Queensland Biosciences Precinct, The University of Queensland, St Lucia 4072, Queensland, Australia
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31
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Carlson HK, Vuono DC, Glass JB, Adams MWW. Editorial: Selective Controls on Microbial Energy Metabolisms: From the Microscale to the Macroscale. Front Microbiol 2021; 12:728705. [PMID: 34421884 PMCID: PMC8377807 DOI: 10.3389/fmicb.2021.728705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Hans K Carlson
- Lawrence Berkeley National Laboratory, Environmental Genomics and Systems Biology Division, Berkeley, CA, United States
| | - David C Vuono
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, CO, United States.,Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, NV, United States
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, United States
| | - Michael W W Adams
- Department of Biochemistry and Molecular Biology, University of Georgia, Atlanta, GA, United States
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32
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Kwak Y. An Update on Trichoderma Mitogenomes: Complete De Novo Mitochondrial Genome of the Fungal Biocontrol Agent Trichoderma harzianum (Hypocreales, Sordariomycetes), an Ex-Neotype Strain CBS 226.95, and Tracing the Evolutionary Divergences of Mitogenomes in Trichoderma. Microorganisms 2021; 9:1564. [PMID: 34442643 PMCID: PMC8401334 DOI: 10.3390/microorganisms9081564] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/08/2021] [Accepted: 07/19/2021] [Indexed: 12/13/2022] Open
Abstract
Members of the genus Trichoderma (Hypocreales), widely used as biofungicides, biofertilizers, and as model fungi for the industrial production of CAZymes, have actively been studied for the applications of their biological functions. Recently, the study of the nuclear genomes of Trichoderma has expanded in the directions of adaptation and evolution to gain a better understanding of their ecological traits. However, Trichoderma's mitochondria have received much less attention despite mitochondria being the most necessary element for sustaining cell life. In this study, a mitogenome of the fungus Trichoderma harzianum CBS 226.95 was assembled de novo. A 27,632 bp circular DNA molecule was revealed with specific features, such as the intronless of all core PCGs, one homing endonuclease, and a putative overlapping tRNA, on a closer phylogenetic relationship with T. reesei among hypocrealean fungi. Interestingly, the mitogenome of T. harzianum CBS 226.95 was predicted to have evolved earlier than those of other Trichoderma species and also assumed with a selection pressure in the cox3. Considering the bioavailability, both for the ex-neotype strain of the T. harzianum species complex and the most globally representative commercial fungal biocontrol agent, our results on the T. harzianum CBS 226.95 mitogenome provide crucial information which will be helpful criteria in future studies on Trichoderma.
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Affiliation(s)
- Yunyoung Kwak
- Écologie, Systématique et Évolution, CNRS, Université Paris Sud (Paris XI), Université Paris Saclay, AgroParisTech, 91400 Orsay, France;
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
- Institute for Quality and Safety Assessment of Agricultural Products, Kyungpook National University, Daegu 41566, Korea
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33
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Abstract
A new codon-pair bias present in the genomes of different types of influenza virus is described. Codons with fewer network interactions are more frequency paired together than other codon-pairs in influenza A, B, and C genomes. A shared feature among three different influenza types suggests an evolutionary bias. Codon-pair preference can affect both speed of protein translation and RNA structure. This newly identified bias may provide insight into drivers of virus evolution.
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Affiliation(s)
- Ewan P Plant
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccines Research and Review, CBER, FDA, Silver Spring, MD, United States
| | - Zhiping Ye
- Laboratory of Pediatric and Respiratory Viral Disease, Office of Vaccines Research and Review, CBER, FDA, Silver Spring, MD, United States
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34
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Seth-Smith HMB, Bénard A, Bruisten SM, Versteeg B, Herrmann B, Kok J, Carter I, Peuchant O, Bébéar C, Lewis DA, Puerta T, Keše D, Balla E, Zákoucká H, Rob F, Morré SA, de Barbeyrac B, Galán JC, de Vries HJC, Thomson NR, Goldenberger D, Egli A. Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains. Microb Genom 2021; 7. [PMID: 34184981 PMCID: PMC8461462 DOI: 10.1099/mgen.0.000599] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 11/18/2022] Open
Abstract
Lymphogranuloma venereum (LGV), the invasive infection of the sexually transmissible infection (STI) Chlamydia trachomatis, is caused by strains from the LGV biovar, most commonly represented by ompA-genotypes L2b and L2. We investigated the diversity in LGV samples across an international collection over seven years using typing and genome sequencing. LGV-positive samples (n=321) from eight countries collected between 2011 and 2017 (Spain n=97, Netherlands n=67, Switzerland n=64, Australia n=53, Sweden n=37, Hungary n=31, Czechia n=30, Slovenia n=10) were genotyped for pmpH and ompA variants. All were found to contain the 9 bp insertion in the pmpH gene, previously associated with ompA-genotype L2b. However, analysis of the ompA gene shows ompA-genotype L2b (n=83), ompA-genotype L2 (n=180) and several variants of these (n=52; 12 variant types), as well as other/mixed ompA-genotypes (n=6). To elucidate the genomic diversity, whole genome sequencing (WGS) was performed from selected samples using SureSelect target enrichment, resulting in 42 genomes, covering a diversity of ompA-genotypes and representing most of the countries sampled. A phylogeny of these data clearly shows that these ompA-genotypes derive from an ompA-genotype L2b ancestor, carrying up to eight SNPs per isolate. SNPs within ompA are overrepresented among genomic changes in these samples, each of which results in an amino acid change in the variable domains of OmpA (major outer membrane protein, MOMP). A reversion to ompA-genotype L2 with the L2b genomic backbone is commonly seen. The wide diversity of ompA-genotypes found in these recent LGV samples indicates that this gene is under immunological selection. Our results suggest that the ompA-genotype L2b genomic backbone is the dominant strain circulating and evolving particularly in men who have sex with men (MSM) populations.
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Affiliation(s)
- Helena M B Seth-Smith
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.,SIB Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Angèle Bénard
- Present address: Healthcare Systems Research Group, VHIR, Universitat Autònoma de Barcelona, Passeig de la Vall d'Hebron 119-129, 08035 Barcelona, Spain.,Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sylvia M Bruisten
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Bart Versteeg
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Björn Herrmann
- Section of Clinical Bacteriology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Olivia Peuchant
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Cécile Bébéar
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - David A Lewis
- Western Sydney Sexual Health Centre, Western Sydney Local Health District, Parramatta, New South Wales, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity & Westmead Clinical School, University of Sydney, Sydney, New South Wales, Australia
| | - Teresa Puerta
- Unidad de ITS/VIH, Centro Sanitario Sandoval, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria San Carlos (IdISSC), Madrid, Spain
| | - Darja Keše
- University of Ljubljana, Faculty of Medicine, Institute of Microbiology and Immunology, Ljubljana, Slovenia
| | - Eszter Balla
- Bacterial STI Reference Laboratory, National Public Health Center (former National Center for Epidemiology), Budapest, Hungary
| | - Hana Zákoucká
- National Reference Laboratory for Diagnostics of Syphilis and Chlamydia Infections, National Institute of Public Health, Srobarova 48, 100 42, Prague 10, Czech Republic
| | - Filip Rob
- Department of Dermatovenereology, Second Faculty of Medicine, Charles University and Hospital Bulovka, Budinova 2, 180 81, Prague 8, Czech Republic
| | - Servaas A Morré
- Laboratory of Immunogenetics, Department of Medical Microbiology and Infection Control, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.,Institute for Public Health Genomics (IPHG), Department of Genetics and Cell Biology, Research Institute GROW, University of Maastricht, Maastricht, The Netherlands
| | - Bertille de Barbeyrac
- CHU Bordeaux, Department of Bacteriology, French National Reference Center for bacterial STIs, Bordeaux, France
| | - Juan Carlos Galán
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal. Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain. CIBER en Epidemiología y Salud Pública (CIBERESP)
| | - Henry J C de Vries
- Department of Infectious Diseases, GGD Public Health Service of Amsterdam, Amsterdam, The Netherlands.,Amsterdam UMC, University of Amsterdam, Amsterdam Institute for Infection and Immunity (AII), Location Academic Medical Centre, Amsterdam, The Netherlands
| | - Nicholas R Thomson
- Wellcome Trust Sanger Institute, Cambridge, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Daniel Goldenberger
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland
| | - Adrian Egli
- Clinical Bacteriology & Mycology, University Hospital Basel, University of Basel, Switzerland.,Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
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Rovida AFDS, Costa G, Santos MI, Silva CR, Freitas PNN, Oliveira EP, Pileggi SAV, Olchanheski RL, Pileggi M. Herbicides Tolerance in a Pseudomonas Strain Is Associated With Metabolic Plasticity of Antioxidative Enzymes Regardless of Selection. Front Microbiol 2021; 12:673211. [PMID: 34239509 PMCID: PMC8258386 DOI: 10.3389/fmicb.2021.673211] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 05/10/2021] [Indexed: 11/19/2022] Open
Abstract
Agriculture uses many food production chains, and herbicides participate in this process by eliminating weeds through different biochemical strategies. However, herbicides can affect non-target organisms such as bacteria, which can suffer damage if there is no efficient control of reactive oxygen species. It is not clear, according to the literature, whether the efficiency of this control needs to be selected by the presence of xenobiotics. Thus, the Pseudomonas sp. CMA 6.9 strain, collected from biofilms in an herbicide packaging washing tank, was selected for its tolerance to pesticides and analyzed for activities of different antioxidative enzymes against the herbicides Boral®, absent at the isolation site, and Heat®, present at the site; both herbicides have the same mode of action, the inhibition of the enzyme protoporphyrinogen oxidase. The strain showed tolerance to both herbicides in doses up to 45 times than those applied in agriculture. The toxicity of these herbicides, which is greater for Boral®, was assessed by means of oxidative stress indicators, growth kinetics, viability, and amounts of peroxide and malondialdehyde. However, the studied strain showed two characteristic antioxidant response systems for each herbicide: glutathione-s-transferase acting to control malondialdehyde in treatments with Boral®; and catalase, ascorbate peroxidase, and guaiacol peroxidase in the control of peroxide induced by Heat®. It is possible that this modulation of the activity of different enzymes independent of previous selection characterizes a system of metabolic plasticity that may be more general in the adaptation of microorganisms in soil and water environments subjected to chemical contaminants. This is relevant to the impact of pesticides on the diversity and abundance of microbial species as well as a promising line of metabolic studies in microbial consortia for use in bioremediation.
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Affiliation(s)
| | - Gessica Costa
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Mariana Inglês Santos
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Caroline Rosa Silva
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Paloma Nathane Nunes Freitas
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Elizangela Paz Oliveira
- Department of Biotechnology, Genetics and Cell Biology, State University of Maringá, Maringá, Brazil
| | - Sônia Alvim Veiga Pileggi
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Ricardo Luiz Olchanheski
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
| | - Marcos Pileggi
- Laboratory of Environmental Microbiology, Biological and Health Sciences Sector, Department of Structural and Molecular Biology and Genetics, State University of Ponta Grossa, Ponta Grossa, Brazil
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Wang L, Zhu L, Tang K, Liu M, Xue X, Wang G, Wang Z. Population genetic structure of sharpbelly Hemiculter leucisculus (Basilesky, 1855) and morphological diversification along climate gradients in China. Ecol Evol 2021; 11:6798-6813. [PMID: 34141257 PMCID: PMC8207360 DOI: 10.1002/ece3.7528] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/08/2022] Open
Abstract
Sharpbelly Hemiculter leucisculus (Basilewski, 1855) is a small, widespread, and native cyprinid fish with prominent habitat suitability and high invasive potential and is becoming the dominant species in freshwater ecosystems under intensified environmental disturbances. But how H. leucisculus acclimates to extremely heterogeneous environments remains unclear. In current study, the genetic structure of H. leucisculus was analyzed using Bayesian phylogenetic inference, haplotype network, and STRUCTURE base on cytb gene across 18 populations spanning 20 degrees of latitude and 18 degrees of longitude in China. The morphological diversification of body size and shape for H. leucisculus along the climate gradient was studied. The results showed that the 18 H. leucisculus populations were divided into 3 clusters: one cluster mainly from Huanghe River Basin, another cluster mainly from Yangzi River Basin, and H cluster containing Hainan and Beihai populations. The fish from southern populations were deeper bodied while individuals from northern populations were more slender. Inland individuals were more streamlined while coastal individuals were of deeper body. The partial Mantel test predicts that the potential mechanism underlining the intraspecies morphological diversification along climate gradients is primarily the divergent selection pressures among different environments, while genetic variation had less contribution to morphological differentiation. The formation of the Nanling Mountain Range could drive genetic differentiation between Beihai population and those from Yangzi River Basin. The present results highlight strong selective pressures of climate on widespread species and enrich morphological differentiation basis of acclimation for species with high habitat suitability and invasive potential.
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Affiliation(s)
- Lihong Wang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Long Zhu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Kui Tang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Mengyu Liu
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Xue Xue
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Gaoxue Wang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
| | - Zaizhao Wang
- College of Animal Science and TechnologyNorthwest A&F UniversityYanglingChina
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Zhang M, Li Q, Wu F, Ou Z, Li Y, You F, Chen Q. Epidemiology, Genetic Characterization, and Evolution of Hunnivirus Carried by Rattus norvegicus and Rattus tanezumi: The First Epidemiological Evidence from Southern China. Pathogens 2021; 10:661. [PMID: 34071186 DOI: 10.3390/pathogens10060661] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/22/2021] [Accepted: 05/24/2021] [Indexed: 11/17/2022] Open
Abstract
Hunnivirus is a novel member of the family Picornaviridae. A single species, Hunnivirus A, is currently described. However, there is limited information on the identification of Hunnivirus to date, and thereby the circulation of Hunnivirus is not fully understood. Thus, the objective of this study was to investigate the prevalence, genomic characteristics, and evolution of rat hunnivirus in southern China. A total of 404 fecal samples were subjected to detection of Hunnivirus from urban rats (Rattus norvegicus and Rattus tanezumi) using PCR assay based on specific primers targeted to partial 3D regions, with the prevalence of 17.8% in Rattus norvegicus and 15.6% in Rattus tanezumi. An almost full-length rat hunnivirus sequence (RatHuV/YY12/CHN) and the genome structure were acquired in the present study. Phylogenetic analysis of the P1 coding regions suggested the RatHuV/YY12/CHN sequence was found to be within the genotype of Hunnivirus A4. The negative selection was further identified based on analysis of non-synonymous to synonymous substitution rates. The present findings suggest that hunniviruses are common in urban rats. Further research is needed for increased surveillance and awareness of potential risks to human health.
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Dong X, Liang Q, Li J, Feng P. Positive selection drives the evolution of a primate bitter taste receptor gene. Ecol Evol 2021; 11:5459-5467. [PMID: 34026020 PMCID: PMC8131804 DOI: 10.1002/ece3.7440] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/20/2021] [Accepted: 02/24/2021] [Indexed: 12/22/2022] Open
Abstract
Bitter taste perception is important in food choice of animals, and it is mediated by bitter taste receptor (T2R) containing three regions: extracellular regions (ECs), transmembrane regions (TMs), and intracellular regions (ICs). It is hypothesized that ECs, TMs, and ICs are under different selective pressures, with ECs being unstable while TMs and ICs being constrained. To test this hypothesis, we examined the selective pressures on one of the bitter taste receptor genes-T2R1 and its different areas from 35 primates and found that T2R1 was under neutral evolution but with some positively selected sites in it. Further analyses suggested that TMs, ICs, and the concatenated transmembrane region TM1237 were under purifying selection; in contrast, extracellular regions, the first and second extracellular loop (EL1, EL2), were subject to positive selection with several positively selected sites in them. Therefore, this study supported the above-mentioned hypothesis. The reason why EL1 and EL2 of T2R1 have positively selected sites is probably due to their participation in forming the cap-like structure involved in ligand binding. Positive selection acts as a driving force of the T2R1 functional differentiation and confers the ability to discern various bitter substances for primates, which could help them to adapt to the changing environment during the evolutionary course.
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Affiliation(s)
- Xiaoyan Dong
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Qiufang Liang
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Jiaping Li
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
| | - Ping Feng
- Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection (Guangxi Normal University)Ministry of EducationGuilinChina
- Guangxi Key Laboratory of Rare and Endangered Animal EcologyGuangxi Normal UniversityGuilinChina
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Wu Y, Zhu Z, Wu J, Bi W, Xu W, Xia X, Han D. Evolutionary Analysis of Pre-S/S Mutations in HBeAg-Negative Chronic Hepatitis B With HBsAg < 100 IU/ml. Front Public Health 2021; 9:633792. [PMID: 33981663 PMCID: PMC8107265 DOI: 10.3389/fpubh.2021.633792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 03/29/2021] [Indexed: 01/12/2023] Open
Abstract
Background: Hepatitis B surface antigen (HBsAg) and viral load are important clinical indicators for antiviral therapy. Few studies have evaluated viral sequence biomarkers predicting the risk of hepatocellular carcinoma (HCC) in the stage, which show a low serological response (HBsAg < 100 IU/ml) and high viral levels (HBV DNA > 2,000 IU/ml). This study aims to determine the trend of the biological prevalence within the pre-S/S regions of special model of inactive CHB infection. Methods: We used Sanger sequencing, quantitative HBV serology (HBeAg and HBsAg), and liver function index to identify whether HBV genome sequences are associated with long-term risk of further HCC progression in special inactive CHB infection. Results: HBV sequencing analysis of 28 CHB patients with special infectious pattern showed higher genetic diversity among four opening reading frames (ORFs) (p < 0.001). However, dN/dS ratios of HBsAg and pre-C/C regions in the experimental group showed no significantly different from those in the HCC group (p = 0.06), while significantly lower in polymerase and HBxAg regions of the experimental group (p < 0.001). In addition, seven positively selected sites were identified in pre-S1, five in pre-S2, and four in S, in which five sites (128H/135Q/135R/139L/141P) were among "α" determinant. Conclusions: These mutations in the pre-S/S region might be associated with the HCC phenotype of low HBsAg expression, with the P region possibly impacting high viral loads. Increased viral diversity across the HBV genome is also associated with low levels of HBsAg. The cumulative evolutionary changes in the HBV pre-S/S regions shows that facilitate immune evasion should be monitored individually. Due to the similarity of evolutionary characteristics in HCC, low serological responses and high viremia may be associated with the risk of further disease progression.
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Affiliation(s)
- Yingping Wu
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Zhiqiang Zhu
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Jianyong Wu
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Wenzi Bi
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Wei Xu
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Xiaoping Xia
- Department of Clinical Laboratory, Fourth Affiliated Hospital of Zhejiang University School of Medicine, Jinhua, China
| | - Dongsheng Han
- Clinical Medical Examination Center, Northern Jiangsu People's Hospital, Yangzhou, China
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40
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Kinnunen-Grubb M, Sapkota R, Vignola M, Nunes IM, Nicolaisen M. Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome. FEMS Microbiol Ecol 2021; 96:5911094. [PMID: 32970821 DOI: 10.1093/femsec/fiaa196] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 07/09/2020] [Accepted: 09/22/2020] [Indexed: 12/22/2022] Open
Abstract
Plants-microbiome associations are the result of millions of years of co-evolution. Due to breeding-accelerated plant evolution in non-native and highly managed soil, plant-microbe links could have been lost. We hypothesized that post-domestication breeding of wheat changed the root-associated microbiome. To test this, we analyzed root-associated fungal and bacterial communities shortly after emergence of seedlings representing a transect of wheat evolution including modern wheat, landraces and ancestors. Numbers of observed microbial taxa were highest in landraces bred in low-input agricultural systems, and lowest in ancestors that had evolved in native soils. The microbial communities of modern cultivars were different from those of landraces and ancestors. Old wheat accessions enriched Acidobacteria and Actinobacteria, while modern cultivars enriched OTUs from Candidatus Saccharibacteria, Verrucomicrobia and Firmicutes. The fungal pathogens Fusarium, Neoascochyta and Microdochium enriched in modern cultivars. Both bacterial and fungal communities followed a neutral assembly model when bulk soil was considered as the source community, but accessions of the ancient Triticum turgidum and T. monococcum created a more isolated environment in their roots. In conclusion, wheat root-associated microbiomes have dramatically changed through a transect of breeding history.
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Affiliation(s)
- Marta Kinnunen-Grubb
- Novozymes A/S, Microbiomics and Microbe Discovery Denmark, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Rumakanta Sapkota
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
| | - Marta Vignola
- School of Engineering, University of Glasgow, 78 Oakfield Ave, Glasgow G12 8LS, United Kingdom
| | - Inês Marques Nunes
- Novozymes A/S, Microbiomics and Microbe Discovery Denmark, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Mogens Nicolaisen
- Department of Agroecology, Aarhus University, Forsøgsvej 1, 4200 Slagelse, Denmark
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Rodrigo AP, Grosso AR, Baptista PV, Fernandes AR, Costa PM. A Transcriptomic Approach to the Recruitment of Venom Proteins in a Marine Annelid. Toxins (Basel) 2021; 13:toxins13020097. [PMID: 33525375 PMCID: PMC7911839 DOI: 10.3390/toxins13020097] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/21/2021] [Accepted: 01/23/2021] [Indexed: 12/19/2022] Open
Abstract
The growing number of known venomous marine invertebrates indicates that chemical warfare plays an important role in adapting to diversified ecological niches, even though it remains unclear how toxins fit into the evolutionary history of these animals. Our case study, the Polychaeta Eulalia sp., is an intertidal predator that secretes toxins. Whole-transcriptome sequencing revealed proteinaceous toxins secreted by cells in the proboscis and delivered by mucus. Toxins and accompanying enzymes promote permeabilization, coagulation impairment and the blocking of the neuromuscular activity of prey upon which the worm feeds by sucking pieces of live flesh. The main neurotoxins ("phyllotoxins") were found to be cysteine-rich proteins, a class of substances ubiquitous among venomous animals. Some toxins were phylogenetically related to Polychaeta, Mollusca or more ancient groups, such as Cnidaria. Some toxins may have evolved from non-toxin homologs that were recruited without the reduction in molecular mass and increased specificity of other invertebrate toxins. By analyzing the phylogeny of toxin mixtures, we show that Polychaeta is uniquely positioned in the evolution of animal venoms. Indeed, the phylogenetic models of mixed or individual toxins do not follow the expected eumetazoan tree-of-life and highlight that the recruitment of gene products for a role in venom systems is complex.
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Whitmer SLM, Lo MK, Sazzad HMS, Zufan S, Gurley ES, Sultana S, Amman B, Ladner JT, Rahman MZ, Doan S, Satter SM, Flora MS, Montgomery JM, Nichol ST, Spiropoulou CF, Klena JD. Inference of Nipah virus evolution, 1999-2015. Virus Evol 2021; 7:veaa062. [PMID: 34422315 PMCID: PMC7947586 DOI: 10.1093/ve/veaa062] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Despite near-annual human outbreaks of Nipah virus (NiV) disease in Bangladesh, typically due to individual spillover events from the local bat population, only twenty whole-genome NiV sequences exist from humans and ten from bats. NiV whole-genome sequences from annual outbreaks have been challenging to generate, primarily due to the low viral load in human throat swab and serum specimens. Here, we used targeted enrichment with custom NiV-specific probes and generated thirty-five additional unique full-length genomic sequences directly from human specimens and viral isolates. We inferred the temporal and geographic evolutionary history of NiV in Bangladesh and expanded a tool to visualize NiV spatio-temporal spread from a Bayesian continuous diffusion analysis. We observed that strains from Bangladesh segregated into two distinct clades that have intermingled geographically in Bangladesh over time and space. As these clades expanded geographically and temporally, we did not observe evidence for significant branch and site-specific selection, except for a single site in the Henipavirus L polymerase. However, the Bangladesh 1 and 2 clades are differentiated by mutations initially occurring in the polymerase, with additional mutations accumulating in the N, G, F, P, and L genes on external branches. Modeling the historic geographical and temporal spread demonstrates that while widespread, NiV does not exhibit significant genetic variation in Bangladesh. Thus, future public health measures should address whether NiV within in the bat population also exhibits comparable genetic variation, if zoonotic transmission results in a genetic bottleneck and if surveillance techniques are detecting only a subset of NiV.
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Affiliation(s)
- Shannon L M Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Michael K Lo
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Hossain M S Sazzad
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- Kirby Institute, University of New South Wales, Sydney, NSW, Australia
| | - Sara Zufan
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Emily S Gurley
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Sharmin Sultana
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Brian Amman
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Mohammed Ziaur Rahman
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr, b), Dhaka, Bangladesh
| | - Stephanie Doan
- The Center for Global Health, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329
| | - Syed M Satter
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Meerjady S Flora
- Institute of Epidemiology, Disease Control and Research, Bangladesh
| | - Joel M Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Stuart T Nichol
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - Christina F Spiropoulou
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
| | - John D Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, 1600 Clifton Rd. NE, Atlanta, GA 30329, USA
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Zhang WM, Fang D, Cheng XZ, Cao J, Tan XL. Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes in Brassica napus. Front Plant Sci 2021; 12:714305. [PMID: 34567028 PMCID: PMC8458767 DOI: 10.3389/fpls.2021.714305] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/19/2021] [Indexed: 05/13/2023]
Abstract
AT-hook motif nuclear localization (AHL) proteins belong to a family of transcription factors, and play important roles in plant growth and development and response to various stresses through protein-DNA and protein-protein interactions. To better understand the Brassica napus AHL gene family, AHL genes in B. napus and related species were analyzed. Using Arabidopsis as a reference, 122 AHL gene family members were first identified in B. napus. According to the phylogenetic tree and gene organization, the BnaAHLs were classified into two clades (Clade-A and Clade-B) and three types (Type-I, Type-II, and Type-III). Gene organization and motif distribution analysis suggested that the AHL gene family is relatively conserved during evolution. These BnaAHLs are unevenly distributed on 38 chromosomes and expanded by whole-genome duplication (WGD) or segmental duplication. And large-scale loss events have also occurred in evolution. All types of BnaAHLs are subject to purification or neutral selection, while some positive selection sites are also identified in Type-II and Type-III groups. At the same time, the purification effect of Type-I members are stronger than that of the others. In addition, RNA-seq data and cis-acting element analysis also suggested that the BnaAHLs play important roles in B. napus growth and development, as well as in response to some abiotic and biotic stresses. Protein-protein interaction analysis identified some important BnaAHL-binding proteins, which also play key roles in plant growth and development. This study is helpful to fully understand the origin and evolution of the AHL gene in B. napus, and lays the foundation for their functional studies.
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Narbona E, Arista M, Whittall JB, Camargo MGG, Shrestha M. Editorial: The Role of Flower Color in Angiosperm Evolution. Front Plant Sci 2021; 12:736998. [PMID: 34603361 PMCID: PMC8484755 DOI: 10.3389/fpls.2021.736998] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 08/24/2021] [Indexed: 05/20/2023]
Affiliation(s)
- Eduardo Narbona
- Department of Molecular Biology and Biochemical Engineering, Pablo de Olavide University, Seville, Spain
- *Correspondence: Eduardo Narbona
| | - Montserrat Arista
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain
| | - Justen B. Whittall
- Department of Biology, College of Arts and Sciences, Santa Clara University, Santa Clara, CA, United States
| | - Maria Gabriela Gutierrez Camargo
- Laboratory of Ecology and Evolution of Plant-Animal Interactions, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Mani Shrestha
- Disturbance Ecology, Bayreuth Center for Ecology and Environmental Research, University of Bayreuth, Bayreuth, Germany
- School of Media and Communication, Royal Melbourne Institute of Technology University, Melbourne, VIC, Australia
- Faculty of Information Technology, Monash University, Melbourne, VIC, Australia
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45
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Rezasoltani S, Yadegar A, Hatami B, Asadzadeh Aghdaei H, Zali MR. Antimicrobial Resistance as a Hidden Menace Lurking Behind the COVID-19 Outbreak: The Global Impacts of Too Much Hygiene on AMR. Front Microbiol 2020; 11:590683. [PMID: 33384670 PMCID: PMC7769770 DOI: 10.3389/fmicb.2020.590683] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [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: 08/02/2020] [Accepted: 11/13/2020] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a new coronavirus that was recently discovered in 2019. While the world is working hard to overcome and control the coronavirus disease 2019 (COVID-19) pandemic, it is also crucial to be prepared for the great impacts of this outbreak on the development of antimicrobial resistance (AMR). It is predicted that inappropriate and too much use of antibiotics, biocides, and disinfectants during this pandemic may raise disastrous effects on antibiotic stewardship programs and AMR control all around the world. Furthermore, the use of certain antibiotics alone or in combination with antiviral agents or other medications for the treatment of secondary bacterial infections among COVID-19 patients may be regarded as a major factor that negatively affects host immune response by disrupting mitochondrial function and activity. Herein, we suggest that the current management strategies to control AMR and prioritize antibiotic stewardship schemes should be extremely highlighted in relation to the COVID-19 outbreak. The rising concerns about excessive use of antimicrobials and biocides and taking too much hygiene also need to be addressed during this pandemic due to their impacts on AMR, public health, and the environment.
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Affiliation(s)
- Sama Rezasoltani
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Behzad Hatami
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Amsalu A, Sapula SA, De Barros Lopes M, Hart BJ, Nguyen AH, Drigo B, Turnidge J, Leong LE, Venter H. Efflux Pump-Driven Antibiotic and Biocide Cross-Resistance in Pseudomonas aeruginosa Isolated from Different Ecological Niches: A Case Study in the Development of Multidrug Resistance in Environmental Hotspots. Microorganisms 2020; 8:E1647. [PMID: 33114277 DOI: 10.3390/microorganisms8111647] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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] [Received: 09/23/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/11/2022] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen displaying high intrinsic antimicrobial resistance and the ability to thrive in different ecological environments. In this study, the ability of P. aeruginosa to develop simultaneous resistance to multiple antibiotics and disinfectants in different natural niches were investigated using strains collected from clinical samples, veterinary samples, and wastewater. The correlation between biocide and antimicrobial resistance was determined by employing principal component analysis. Molecular mechanisms linking biocide and antimicrobial resistance were interrogated by determining gene expression using RT-qPCR and identifying a potential genetic determinant for co- and cross-resistance using whole-genome sequencing. A subpopulation of P. aeruginosa isolates belonging to three sequence types was resistant against the common preservative benzalkonium chloride and showed cross-resistance to fluoroquinolones, cephalosporins, aminoglycosides, and multidrug resistance. Of these, the epidemiological high-risk ST235 clone was the most abundant. The overexpression of the MexAB-OprM drug efflux pump resulting from amino acid mutations in regulators MexR, NalC, or NalD was the major contributing factor for cross-resistance that could be reversed by an efflux pump inhibitor. This is the first comparison of antibiotic-biocide cross-resistance in samples isolated from different ecological niches and serves as a confirmation of laboratory-based studies on biocide adapted isolates. The isolates from wastewater had a higher incidence of multidrug resistance and biocide-antibiotic cross-resistance than those from clinical and veterinary settings.
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47
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Duan W, Huang Z, Li Y, Song X, Sun X, Jin C, Wang Y, Wang J. Molecular Evolutionary and Expression Pattern Analysis of AKR Genes Shed New Light on GalUR Functional Characteristics in Brassica rapa. Int J Mol Sci 2020; 21:ijms21175987. [PMID: 32825292 PMCID: PMC7503288 DOI: 10.3390/ijms21175987] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/31/2022] Open
Abstract
The aldo-keto reductase (AKR) superfamily plays a major role in oxidation-reduction in plants. D-galacturonic acid reductase (GalUR), an ascorbic acid (AsA) biosynthetic enzyme, belongs to this superfamily. However, the phylogenetic relationship and evolutionary history of the AKR gene family in plants has not yet been clarified. In this study, a total of 1268 AKR genes identified in 36 plant species were used to determine this phylogenetic relationship. The retention, structural characteristics, and expression patterns of AKR homologous genes in Brassica rapa and Arabidopsis thaliana were analyzed to further explore their evolutionary history. We found that the AKRs originated in algae and could be divided into A and B groups according to the bootstrap value; GalURs belonged to group A. Group A AKR genes expanded significantly before the origin of angiosperms. Two groups of AKR genes demonstrated functional divergence due to environmental adaptability, while group A genes were more conservative than those in group B. All 12 candidate GalUR genes were cloned, and their expression patterns under stress were analyzed, in Pak-choi. These genes showed an obvious expression divergence under multiple stresses, and BrcAKR22 exhibited a positive correlation between its expression trend and AsA content. Our findings provide new insights into the evolution of the AKR superfamily and help build a foundation for further investigations of GalUR’s functional characteristics.
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Affiliation(s)
- Weike Duan
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing 210095, China
| | - Zhinan Huang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
- Correspondence: (Z.H.); (Y.L.); Tel.: +86-0517-8355-9216 (Z.H.); +86-025-8439-5756 (Y.L.)
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture of Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (Z.H.); (Y.L.); Tel.: +86-0517-8355-9216 (Z.H.); +86-025-8439-5756 (Y.L.)
| | - Xiaoming Song
- School of Life Science and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan 063210, China;
| | - Xiaochuan Sun
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Cong Jin
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Yunpeng Wang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
| | - Jizhong Wang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huai’an 223003, China; (W.D.); (X.S.); (C.J.); (Y.W.); (J.W.)
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Yu X, Zheng B, Xiao F, Jin Y, Guo L, Xu H, Luo Q, Xiao Y. Effect of Short-Term Antimicrobial Therapy on the Tolerance and Antibiotic Resistance of Multidrug-Resistant Staphylococcus capitis. Infect Drug Resist 2020; 13:2017-2026. [PMID: 32636655 PMCID: PMC7335296 DOI: 10.2147/idr.s254141] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/26/2020] [Indexed: 11/28/2022] Open
Abstract
Background Bacteria undergo adaptive mutation in the host. However, the specific effect of antimicrobial use on bacterial evolution and genome mutations related to bacterial survival within a patient is unclear. Materials and Methods Three S. capitis strains were sequentially isolated from cerebrospinal fluid of a clinical inpatient. Antimicrobial susceptibility, growth rate, biofilm formation and whole blood survival of these strains were measured. Relative fitness was calculated. The virulence was examined in the Galleria mellonella model. Whole-genome sequencing and in silico analysis were performed to explore the genetic mechanisms of the changes in antimicrobial resistance phenotype. Hypothetical proteins are cloned, expressed and characterized by detection the susceptibility to gentamycin. Results The first isolate was susceptible to rifampin (MIC=0.25 μg/mL), resistant to gentamicin (MIC=16 μg/mL), while the later two isolates were resistant to rifampin (MIC >64 μg/mL), susceptible to gentamicin (MIC=4 μg/mL). For the latter two strains, compared to the first, frameshift mutation in a hypothetical protein encoding gene and base substitutions (in genes saeR, moaA and rpoB) were discovered. The mutation of rpoB gene caused rifampicin resistance. Mutations in saeR, moaA and hypothetical gene are associated with changes in other biological traits. Amino acid sequence-based structure and function identification of the hypothetical protein indicated that a mutation in the encoding gene might be associated with altered aminoglycoside susceptibility. Growth curve showed that the later two isolates grew faster than the first isolate with a positive fitness advantage of 13.5%, and 14.8%, accordingly. Biofilm form ability and whole blood survival of the derivative mutants were also enhanced. No significant differences of virulence in the G. mellonella model were observed. Conclusion We report here for the first time that short-term clinical antibiotic use was associated with resistance mutations, collateral sensitivity, and positive in vivo fitness advantages to S. capitis during infection.
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Affiliation(s)
- Xiao Yu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Feng Xiao
- Neurosurgery Department, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Ye Jin
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Lihua Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Qixia Luo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People's Republic of China
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Rohaim MA, El Naggar RF, Abdelsabour MA, Mohamed MHA, El-Sabagh IM, Munir M. Evolutionary Analysis of Infectious Bronchitis Virus Reveals Marked Genetic Diversity and Recombination Events. Genes (Basel) 2020; 11:E605. [PMID: 32486006 DOI: 10.3390/genes11060605] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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] [Received: 04/03/2020] [Revised: 05/24/2020] [Accepted: 05/27/2020] [Indexed: 01/18/2023] Open
Abstract
In the last 5 years, frequent outbreaks of infectious bronchitis virus (IBV) are observed in both broiler and layer chicken flocks in the Kingdom of Saudi Arabia (KSA) in spite of extensive usage of vaccines. The IBV is a widespread avian coronavirus affecting both vaccinated and unvaccinated chicken flocks and is attributed to significant economic losses, around the globe. In the present study, 58 (n = 58) samples were collected from four different commercial poultry flocks from 8 KSA districts during 2019. A total of nine positive isolates (9/58; 15.5%), based on real-time reverse transcriptase PCR targeting nucleocapsid (N) gene, were used for further genetic characterization and evolutionary analysis. Genetic characterization of the partial spike (S1) gene revealed the clustering of the reported isolates into three different genotypes, whereas four additional isolates were grouped within 4/91 genotype, two isolates within IS/885 genotype, one isolate was closely related to IS/1494/06, and two isolates were grouped within classic serotype (vaccine-like strains). Phylodynamic revealed clustering of four isolated viruses within GI-13 lineage, three isolates within GI-23 lineage, and two isolates within GI-1 lineage. Results indicate that there are high evolutionary distances between the newly identified IBV strains in this study and the commercially used vaccines (GI-1), suggesting that IBV strains circulating in the KSA are under constant evolutionary pressures. Selective pressure biostatistics analyses consistently demonstrate the presence of a higher positive score which highlights the role of natural selection, a mechanism of virus evolution on sites located on the protein surface, within or nearby domains involved in viral attachment or related functions. Recombination analysis revealed emergence of two isolates through recombination events resulting in new recombinant viruses. Taken together, these finding demonstrate the genetic and evolutionary insights into the currently circulating IBV genotypes in KSA, which could help to better understand the origin, spread, and evolution of infectious bronchitis viruses, and to ascertain the importance of disease monitoring as well as re-evaluation for the currently used vaccines and vaccination programs.
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50
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Ward-Smith H, Arbuckle K, Naude A, Wüster W. Fangs for the Memories? A Survey of Pain in Snakebite Patients Does Not Support a Strong Role for Defense in the Evolution of Snake Venom Composition. Toxins (Basel) 2020; 12:E201. [PMID: 32235759 DOI: 10.3390/toxins12030201] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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] [Received: 02/13/2020] [Revised: 03/16/2020] [Accepted: 03/19/2020] [Indexed: 12/17/2022] Open
Abstract
Animals use venoms for multiple purposes, most prominently for prey acquisition and self-defense. In snakes, venom composition often evolves as a result of selection for optimization for local diet. However, whether selection for a defensive function has also played a role in driving the evolution of venom composition has remained largely unstudied. Here, we use an online survey of snakebite victims to test a key prediction of a defensive function, that envenoming should result in the rapid onset of severe pain. From the analysis of 584 snakebite reports, involving 192 species of venomous snake, we find that the vast majority of bites do not result in severe early pain. Phylogenetic comparative analysis shows that where early pain after a bite evolves, it is often lost rapidly. Our results, therefore, do not support the hypothesis that natural selection for antipredator defense played an important role in the origin of venom or front-fanged delivery systems in general, although there may be intriguing exceptions to this rule.
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