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Abstract
Malaria is a life-threatening parasitic disease caused by members of the genus Plasmodium. The development and spread of drug-resistant strains of Plasmodium parasites represent a major challenge to malaria control and elimination programmes. Evaluating genetic polymorphism in a drug target improves our understanding of drug resistance and facilitates drug design. Approximately 450 and 19 whole-genome assemblies of Plasmodium falciparum and Plasmodium vivax, respectively, are currently available, and numerous sequence variations have been found due to the presence of single nucleotide polymorphism (SNP). In the study reported here, we analysed global SNPs in the malaria parasite aminoacyl-tRNA synthetases (aaRSs). Our analysis revealed 3182 unique SNPs in the 20 cytoplasmic P. falciparum aaRSs. Structural mapping of SNPs onto the three-dimensional inhibitor-bound complexes of the three advanced drug targets within aaRSs revealed a remarkably low mutation frequency in the crucial aminoacylation domains, low overall occurrence of mutations across samples and high conservation in drug/substrate binding regions. In contrast to aaRSs, dihydropteroate synthase (DHPS), also a malaria drug target, showed high occurrences of drug resistance-causing mutations. Our results show that it is pivotal to screen potent malaria drug targets against global SNP profiles to assess genetic variances to ensure success in designing drugs against validated targets and tackle drug resistance early on.
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Affiliation(s)
- Jasmita Gill
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India
| | - Amit Sharma
- ICMR-National Institute of Malaria Research, Sector 8, Dwarka, 110077, New Delhi, India. .,International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Tornyigah B, Ndam NT. Preservation of Parasite RNA in the Field. Methods Mol Biol 2022; 2470:19-25. [PMID: 35881335 DOI: 10.1007/978-1-0716-2189-9_3] [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] [Indexed: 06/15/2023]
Abstract
The pathogenesis of malaria is largely attributable to the parasite's ability to modulate its cytoadhesion phenotype. This relates to the multigenic families comprising dozens to hundreds of members, whose expression, often mutually exclusive, allows the parasite to vary its adhesive properties and antigenic appearance. This phenomenon is mainly described for the variant surface antigens that the parasite expresses on the infected erythrocyte. In order to decipher these gene expression spectra and identify potential antigenic candidates and/or targets of therapeutic interest, the analysis of the transcriptomes of the parasites directly isolated from patients with well-defined clinical presentation is important. RNA stabilization is an absolute prerequisite for a precise and accurate transcriptome profiling. Immediate stabilization of RNA of biological samples is therefore necessary to prevent degradation by ribonucleases (RNase) or cellular changes. This chapter described methodology for preserving parasite RNA samples from malaria patients in the field for transcriptome studies.
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Affiliation(s)
- Bernard Tornyigah
- Université de Paris, MERIT, IRD, Paris, France
- Department of Immunology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Legon, Ghana
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Hviid L, Lopez-Perez M. Analysis by Flow Cytometry of α 2-Macroglobulin and Nonimmune IgM-Binding to Plasmodium falciparum-Infected Erythrocytes. Methods Mol Biol 2022; 2470:435-444. [PMID: 35881364 DOI: 10.1007/978-1-0716-2189-9_32] [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] [Indexed: 06/15/2023]
Abstract
Several members of the Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family can bind human serum proteins such as IgM and α2-macroglobulin (α2M). This binding seems to play a role in pathogenesis and immune evasion by improving the avidity of PfEMP1-mediated binding to erythrocyte receptors and/or by masking antibody epitopes in PfEMP1. In this protocol, we describe a flow cytometry-based protocol to evaluate IgM- and α2M-binding to intact and unfixed mature-stage IEs. The method can be used for laboratory clones and field isolates.
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Affiliation(s)
- Lars Hviid
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
- Department of Infectious Diseases, Centre for Medical Parasitology, Rigshospitalet, Copenhagen, Denmark
| | - Mary Lopez-Perez
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark.
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Reis-Cunha JL, Baptista RP, Rodrigues-Luiz GF, Coqueiro-Dos-Santos A, Valdivia HO, de Almeida LV, Cardoso MS, D'Ávila DA, Dias FHC, Fujiwara RT, Galvão LMC, Chiari E, Cerqueira GC, Bartholomeu DC. Whole genome sequencing of Trypanosoma cruzi field isolates reveals extensive genomic variability and complex aneuploidy patterns within TcII DTU. BMC Genomics 2018; 19:816. [PMID: 30424726 PMCID: PMC6234542 DOI: 10.1186/s12864-018-5198-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 10/23/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Trypanosoma cruzi, the etiologic agent of Chagas disease, is currently divided into six discrete typing units (DTUs), named TcI-TcVI. TcII is among the major DTUs enrolled in human infections in South America southern cone, where it is associated with severe cardiac and digestive symptoms. Despite the importance of TcII in Chagas disease epidemiology and pathology, so far, no genome-wide comparisons of the mitochondrial and nuclear genomes of TcII field isolates have been performed to track the variability and evolution of this DTU in endemic regions. RESULTS In the present work, we have sequenced and compared the whole nuclear and mitochondrial genomes of seven TcII strains isolated from chagasic patients from the central and northeastern regions of Minas Gerais, Brazil, revealing an extensive genetic variability within this DTU. A comparison of the phylogeny based on the nuclear or mitochondrial genomes revealed that the majority of branches were shared by both sequences. The subtle divergences in the branches are probably consequence of mitochondrial introgression events between TcII strains. Two T. cruzi strains isolated from patients living in the central region of Minas Gerais, S15 and S162a, were clustered in the nuclear and mitochondrial phylogeny analysis. These two strains were isolated from the other five by the Espinhaço Mountains, a geographic barrier that could have restricted the traffic of insect vectors during T. cruzi evolution in the Minas Gerais state. Finally, the presence of aneuploidies was evaluated, revealing that all seven TcII strains have a different pattern of chromosomal duplication/loss. CONCLUSIONS Analysis of genomic variability and aneuploidies suggests that there is significant genomic variability within Minas Gerais TcII strains, which could be exploited by the parasite to allow rapid selection of favorable phenotypes. Also, the aneuploidy patterns vary among T. cruzi strains and does not correlate with the nuclear phylogeny, suggesting that chromosomal duplication/loss are recent and frequent events in the parasite evolution.
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Affiliation(s)
- João Luís Reis-Cunha
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo P Baptista
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,The University of Georgia, Athens, USA
| | - Gabriela F Rodrigues-Luiz
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina, Florianópolis, Brazil
| | | | - Hugo O Valdivia
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.,U.S. Naval Medical Research, Lima, Peru
| | - Laila Viana de Almeida
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana Santos Cardoso
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Lúcia M C Galvão
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Egler Chiari
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Daniella C Bartholomeu
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
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Xu MY, Lin SY, Zhao Y, Jin JH, Tang N, Zhang GZ. Characteristics of very virulent infectious bursal disease viruses isolated from Chinese broiler chickens (2012-2013). Acta Trop 2015; 141:128-34. [PMID: 25312336 DOI: 10.1016/j.actatropica.2014.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 09/30/2014] [Accepted: 10/03/2014] [Indexed: 11/27/2022]
Abstract
The objective of this study was to characterize the infectious bursal disease viruses (IBDVs) circulating in broiler chicken farms in China between 2012 and 2013. The VP2 gene sequences of nine newly isolated IBDVs, obtained using reverse transcriptase polymerase chain reaction, were determined and compared with worldwide reference isolates, which have been previously well characterized. Phylogenetic analysis revealed that the nine broiler IBDV isolates are closely related to very virulent IBDV (vvIBDV) strains. Analysis of the predicted amino acid sequences of VP2 from the nine vvIBDVs isolated from the broilers revealed that they share 99.2 to 100% sequence similarity. Additionally, amino acids A222, I242, I256, I294 and S299 of VP2 that are conserved among previously characterized vvIBDV strains are also encoded by the nine isolates. This study confirms the circulation of vvIBDVs in Chinese broiler chicken farms experienced slow evolution and was relatively stable in China.
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