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Home / Archives for BMC Genomics

Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance

  • Authors: Oppong YEA, Phelan J, Perdigão J, Machado D, Miranda A, Portugal I, Viveiros M, Clark TG, Hibberd ML
  • Publication Year: 2019
  • Journal: BMC Genomics
  • Link: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5615-3

Background Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to […]
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Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

  • Authors: Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG
  • Publication Year: 2018
  • Journal: BMC Genomics
  • Link: https://www.ncbi.nlm.nih.gov/pubmed/30107785

Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and […]
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Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

  • Authors: Alves A, Anthony RM, Bergval I, Bessa TB, Campino S, Clark TG, Coll F, Crampin AC, de Oliveira Sousa E, Dheda K, Gey van Pittius NC, Glynn JR, Grandjean L, Hasan R, Hasan Z, Hibberd ML, McNerney R, Miranda A, Moore D, Pain A, Panaiotov S, Perdigão J, Phelan JE, Portugal I, Sampson SL, Sheen P, Streicher EM, van Helden PD, Viveiros M, Warren R
  • Publication Year: 2016
  • Journal: BMC Genomics
  • Link: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2467-y

Background Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised […]
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Experimental evolution, genetic analysis and genome re-sequencing reveal the mutation conferring artemisinin resistance in an isogenic lineage of malaria parasites

  • Authors: Beraldi D, Blaxter M, Borges S, Cravo P, Creasey A, Fawcett R, Hunt P, Kumar S, Loewe L, Martinelli A, Modrzynska K, Otto TD, Pain A, Rodrigues L, Thomson M, Trivedi U
  • Journal: BMC Genomics
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Experimental+evolution%2C+genetic+analysis+and+genome+re-sequencing+reveal+the+mutation+conferring+artemisinin+resistance+in+an+isogenic+lineage+of+malaria+parasites

BACKGROUND: Classical and quantitative linkage analyses of genetic crosses have traditionally been used to map genes of interest, such as those conferring chloroquine or quinine resistance in malaria parasites. Next-generation sequencing technologies now present the possibility of determining genome-wide genetic variation at single base-pair resolution. Here, we combine in vivo experimental evolution, a rapid genetic […]
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Plasmodium infection alters Anopheles gambiae detoxification gene expression

  • Authors: Felix RC, Müller P, Ranson H, Ribeiro V, Silveira H
  • Journal: BMC Genomics
  • Link: http://www.ncbi.nlm.nih.gov/pubmed/?term=Plasmodium+infection+alters+Anopheles+gambiae+detoxification+gene+expression

BACKGROUND: Anopheles gambiae has been shown to change its global gene expression patterns upon Plasmodium infection. While many alterations are directly related to the mosquito’s innate immune response, parasite invasion is also expected to generate toxic by-products such as free radicals. The current study aimed at identifying which loci coding for detoxification enzymes are differentially […]
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About GHTM

GHTM is a R&D Unit that brings together researchers with a track record in Tropical Medicine and International & Global Health. It aims at strengthening Portugal's role as a leading partner in the development and implementation of a global health research agenda. Our evidence-based interventions contribute to the promotion of equity in health and to improve the health of populations.

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