ABSTRACT: Barcoding project of insect and plant trypanosomatids availables at Fiocruz Protozoa Culture Collection http://colprot.fiocruz.br/ Phenotype or genotype
Project description:Enhancing Trypanosomatids Identification and Genotyping with Oxford Nanopore Sequencing: Development and Validation of an 18S rRNAs Amplicon-Based Method.
Project description:We developed a novel method for RNA-seq in Trypanosomatids called ‘Spliced-Leader Sequencing’ (SL-seq). The method is based on the fact that the 5’ end of Trypanosomatid mRNA is starts with a SL-sequence, and specifically enriches SL-containing RNA prior to sequencing. In this study we compared the performance and functional results obtained with SL-seq to those generated with conventional Illumina Stranded mRNA prep. Therefore we sequenced mRNA of Leishmania donovani logarithmic phase promastigotes, stationary phase promastigotes and intracellular amastigotes with both methods. We also sequenced controlled dilutions of Leishmania RNA with human RNA.
Project description:Amplification of small subunit rRNA sequences of trypanosomatids from human samples of a patient diagnosed with visceral leishmaniasis.
Project description:The 43S pre-initiation complex (PIC) assembly requires establishment of numerous interactions among eukaryotic initiation factors (eIFs), Met-tRNAiMet and the small ribosomal subunit (40S). Owing to several differences in the structure and composition of kinetoplastidian 40S compared to their mammalian counterparts, translation initiation in trypanosomatids is suspected to display substantial variability. Here, we determined the structure of the 43S PIC from Trypanosoma cruzi, the Chagas disease parasite, showing numerous specific features, such as different eIF3 structure and interactions with the large rRNA expansion segments 9S, 7S and 6S, and the association of a kinetoplastid-specific ~245 kDa DDX60-like helicase. We also revealed a previously undetermined binding site of the eIF5 C-terminal domain, and terminal tails of eIF2β, eIF1, eIF1A and eIF3 c and d subunits, uncovering molecular details of their critical activities.
Project description:Interventions: Intravenous adminstration of CPT-11 100 mg/m2 on Days 1, 8, and 15, every 4 weeks
Primary outcome(s): 1)Tumor response rate 2)Genotype-phenotype association (CYP3A4,CES1,2, UGT1A1, ABCG2, ABCB1, and ABCC1,2 vs toxicity), mutation -phenotype association (TOP1A, ABCG2 vs tumor response), and expression-phenotype association (TOP1A, ABCG2 vs tumor response)
Study Design: Single arm Non-randomized
Project description:RNA-seq from human tissue samples from the Genotype-Tissue Expression (GTEx) Project (http://www.gtexportal.org/home/). This dataset is part of the TransQST collection.
