The Genotypic and Phenotypic Stability of Plasmodium falciparum Field Isolates in Continuous In Vitro Culture
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{"title"=>"The genotypic and phenotypic stability of plasmodium falciparum field isolates in continuous in vitro culture", "type"=>"journal", "authors"=>[{"first_name"=>"Redemptah", "last_name"=>"Yeda", "scopus_author_id"=>"55506059500"}, {"first_name"=>"Luicer A.", "last_name"=>"Ingasia", "scopus_author_id"=>"55695955700"}, {"first_name"=>"Agnes C.", "last_name"=>"Cheruiyot", "scopus_author_id"=>"42861216600"}, {"first_name"=>"Charles", "last_name"=>"Okudo", "scopus_author_id"=>"55389389900"}, {"first_name"=>"Lorna J.", "last_name"=>"Chebon", "scopus_author_id"=>"56227126000"}, {"first_name"=>"Jelagat", "last_name"=>"Cheruiyot", "scopus_author_id"=>"6506169680"}, {"first_name"=>"Hoseah M.", "last_name"=>"Akala", "scopus_author_id"=>"35612411100"}, {"first_name"=>"Edwin", "last_name"=>"Kamau", "scopus_author_id"=>"8703610800"}], "year"=>2016, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "pui"=>"607726768", "doi"=>"10.1371/journal.pone.0143565", "sgr"=>"84954421981", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"26751382", "scopus"=>"2-s2.0-84954421981"}, "id"=>"5bf00b76-22eb-3377-afd1-38931fd8d65c", "abstract"=>"The Plasmodium falciparum in vitro culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate ex vivo or in vitro culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24-48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC50) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC50s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long-term cultures, which indicates parasite genetic information obtained even in short cultures is likely to be different from the natural infection parasites.", "link"=>"http://www.mendeley.com/research/genotypic-phenotypic-stability-plasmodium-falciparum-field-isolates-continuous-vitro-culture", "reader_count"=>22, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>5, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>5, "Student > Master"=>3, "Student > Bachelor"=>4, "Professor"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>6, "Medicine and Dentistry"=>4, "Veterinary Science and Veterinary Medicine"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>1, "Immunology and Microbiology"=>1, "Economics, Econometrics and Finance"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Chemistry"=>{"Chemistry"=>1}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Economics, Econometrics and Finance"=>{"Economics, Econometrics and Finance"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>6}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>1}}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2624842"], "description"=>"<p>Diagram showing relationship of the different parasite generations in H63 parasite-line samples. The multilocus MS haplotypes profiles were constructed for each of the parasite generations using the 12 MS markers located across the <i>P</i>. <i>falciparum</i> genome. The 26 generations of the cultured <i>P</i>. <i>falciparum</i> field isolates analyzed formed 18 unique 12-loci microsatellite haplotypes. For allele sizes please refer to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143565#pone.0143565.s004\" target=\"_blank\">S4 Table</a>. Each circle in the network represents a unique MS haplotype with the size of the circle being proportional to the number of isolates showing that particular haplotype. The red dots are hypothetical median vectors generated by the software to connect existing haplotypes within the network with maximum parsimony.</p>", "links"=>[], "tags"=>["parasite biology studies", "Plasmodium falciparum Field Isolates", "snp", "patient blood sample", "ms", "dna", "culture adaptation process", "genotypic", "phenotypic profiles", "ic", "analysis", "23 drug resistance markers"], "article_id"=>1635762, "categories"=>["Uncategorised"], "users"=>["Redemptah Yeda", "Luicer A. Ingasia", "Agnes C. Cheruiyot", "Charles Okudo", "Lorna J. Chebon", "Jelagat Cheruiyot", "Hoseah M. Akala", "Edwin Kamau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143565.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Median_joining_network_diagram_for_MS_data_/1635762", "title"=>"Median-joining network diagram for MS data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:13:08"}
  • {"files"=>["https://ndownloader.figshare.com/files/2624843"], "description"=>"<p>Phylogeny tree constructed using SNP haplotypes of samples in H63 parasite-line. The SNP haplotype profiles are shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0143565#pone.0143565.s003\" target=\"_blank\">S3 Table</a>. Bayesian algorithm was used to infer the number of genetically related clusters from the individual SNP haplotype profiles generated using the 30-drug resistance SNPs.</p>", "links"=>[], "tags"=>["parasite biology studies", "Plasmodium falciparum Field Isolates", "snp", "patient blood sample", "ms", "dna", "culture adaptation process", "genotypic", "phenotypic profiles", "ic", "analysis", "23 drug resistance markers"], "article_id"=>1635763, "categories"=>["Uncategorised"], "users"=>["Redemptah Yeda", "Luicer A. Ingasia", "Agnes C. Cheruiyot", "Charles Okudo", "Lorna J. Chebon", "Jelagat Cheruiyot", "Hoseah M. Akala", "Edwin Kamau"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0143565.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phylogeny_tree_diagram_for_SNP_data_/1635763", "title"=>"Phylogeny tree diagram for SNP data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2016-01-18 15:13:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/2624845", "https://ndownloader.figshare.com/files/2624846", "https://ndownloader.figshare.com/files/2624847", "https://ndownloader.figshare.com/files/2624848", "https://ndownloader.figshare.com/files/2624849", "https://ndownloader.figshare.com/files/2624850"], "description"=>"<div><p>The <i>Plasmodium falciparum in vitro</i> culture system is critical for genotypic and phenotypic analyses of the parasites. For genotypic analysis, the genomic DNA can be obtained directly from the patient blood sample or from culture adapted parasites whereas for phenotypic analysis, immediate <i>ex vivo</i> or <i>in vitro</i> culture adapted parasites are used. However, parasite biology studies have not investigated whether culture adaptation process affects genotypic and/or phenotypic characteristics of the parasites in short- or long-term cultures. Here, we set out to study the dynamics and stability of parasite genetic and phenotypic profiles as field isolate parasites were adapted in continuous cultures. Parasites collected from three different patients presenting with uncomplicated malaria were adapted and maintained in drug-free continuous cultures. Aliquots from the continuous cultures were collected every 24–48 hours for analyses. Each aliquot was treated as a separate parasite sample. For genetic analysis, microsatellite (MS) typing and single nucleotide polymorphism (SNP) analyses of 23 drug resistance markers were done. The 50% inhibitory concentrations (IC<sub>50</sub>) for some of the samples were also established for four antimalarial drugs. Samples from each patient (parasite-line) were compared as they were passed through the continuous culture. Data revealed genotypic and phenotypic profiles for the three parasite-lines fluctuated from one generation to the next with no specific pattern or periodicity. With few exceptions, multilocus analysis revealed samples from each parasite-line had high genetic diversity with unique haplotypes. Interestingly, changes in MS and SNP profiles occurred simultaneously. The difference in the IC<sub>50</sub>s of samples in each parasite-line reached statistical significance. However, phenotypic changes did not correspond or correlate to genotypic changes. Our study revealed parasite genetic and phenotypic characteristics fluctuates in short- and long-term cultures, which indicates parasite genetic information obtained even in short cultures is likely to be different from the natural infection parasites.</p></div>", "links"=>[], "tags"=>["parasite biology studies", "Plasmodium falciparum Field Isolates", "snp", "patient blood sample", "ms", "dna", "culture adaptation process", "genotypic", "phenotypic profiles", "ic", "analysis", "23 drug resistance markers"], "article_id"=>1635765, "categories"=>["Uncategorised"], "users"=>["Redemptah Yeda", "Luicer A. Ingasia", "Agnes C. Cheruiyot", "Charles Okudo", "Lorna J. Chebon", "Jelagat Cheruiyot", "Hoseah M. Akala", "Edwin Kamau"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0143565.s001", "https://dx.doi.org/10.1371/journal.pone.0143565.s002", "https://dx.doi.org/10.1371/journal.pone.0143565.s003", "https://dx.doi.org/10.1371/journal.pone.0143565.s004", "https://dx.doi.org/10.1371/journal.pone.0143565.s005", "https://dx.doi.org/10.1371/journal.pone.0143565.s006"], "stats"=>{"downloads"=>1, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Genotypic_and_Phenotypic_Stability_of_Plasmodium_falciparum_Field_Isolates_in_Continuous_In_Vitro_Culture/1635765", "title"=>"The Genotypic and Phenotypic Stability of <i>Plasmodium falciparum</i> Field Isolates in Continuous <i>In Vitro</i> Culture", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2016-01-18 15:13:06"}

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  • {"unique-ip"=>"10", "full-text"=>"8", "pdf"=>"3", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"6", "cited-by"=>"0", "year"=>"2019", "month"=>"9"}
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  • {"unique-ip"=>"10", "full-text"=>"7", "pdf"=>"5", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"12"}

Relative Metric

{"start_date"=>"2016-01-01T00:00:00Z", "end_date"=>"2016-12-31T00:00:00Z", "subject_areas"=>[]}
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