Plasmodium falciparum 3D7
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ABSTRACT:
PROVIDER: PRJNA377430 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Transcriptional profiling of transgenic P. falciparum blood stage parasites expressing an ectopic copy of GDV1-GFP-DD (3D7/GDV1-GFP-DD). The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in response to induced GDV1 overexpression.
2017-03-02 | GSE95547 | GEO
Project description:Transcriptional profiling of transgenic Plasmodium falciparum blood stage parasites expressing the telomere repeat-binding factor PfTRF as a C-terminal GFP-DD fusion (3D7/TRFGFP-ON). The DD (FKBP destabilisation domain) allows for the conditional depletion of fusion proteins in absence of the stabilising ligand Shield-1 (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in response to PfTRF depletion.
2016-07-14 | GSE84342 | GEO
Project description:Periodic fever is the most characteristic clinical feature of human malaria. However, how parasites survive malarial febrile episodes, which often involve temperatures of >40ºC, is not known. To understand the molecular basis of heat shock (HS) resistance in Plasmodium falciparum, we took advantage of previously developed P. falciparum lines adapted to periodic HS (3D7-A-HS) and their non-selected controls maintained in parallel (3D7-A). Their ability to adapt in only a few cycles suggested that the parental parasite population contained a selectable subset of parasites resistant to HS. Transcriptomic analysis of both 3D7-A-HS and 3D7-A was used to study the differences at a transcriptional level that could be related with the HS-resistant phenotype.
2021-05-17 | GSE149393 | GEO
Project description:Transcriptional profiling of transgenic P. falciparum asexual blood stage parasites of the transgenic strain 3D7/DDGFP-PfAP2-HC at five time points during intra-erythrocytic parasite development. The DD (FKBP destabilisation domain) allows for the conditional expression of fusion proteins: DD fusion proteins are rapidly degraded or stably expressed in absence or presence of the stabilising ligand Shield-1, respectively (Banaszynski LA, Chen LC, Maynard-Smith LA, Ooi AG, Wandless TJ. A rapid, reversible, and tunable method to regulate protein function in living cells using synthetic small molecules.Cell. 2006 Sep 8;126(5):995-1004). The goal of this experiment was to identify genes differentially expressed in DDGFP-PfAP2-HC-expressing compared to DDGFP-PfAP2-HC-depleted parasites during the intra-erythtrocytic cell cycle.
2020-10-06 | GSE159061 | GEO
Project description:The malaria parasite Plasmodium falciparum relies on clonally variant gene expression in order to escape immune recognition and secure continuous proliferation during blood stage infection. Here, we studied the role of heterochromatin protein 1 (HP1), an evolutionary conserved regulator of heritable gene silencing, in the biology of P. falciparum blood stage parasites. We demonstrate that conditional PfHP1 depletion de-represses hundreds of heterochromatic virulence genes and disrupts the elusive mechanism underlying mutually exclusive expression and antigenic variation of PfEMP1. Intriguingly, we also discovered that the PfHP1-dependent regulation of an ApiAP2 transcription factor controls the switch from asexual parasite proliferation to sexual differentiation. This uncovers the first mechanistic insight into the unknown pathway triggering gametocyte conversion and establishes a new concept of HP1-dependent cell fate decision in unicellular eukaryotes. P. falciparum 3D7 parasites expressing endogenous PfHP1-GFP-DD were grown in presence of 4nM WR/625nM Shield-1 (3D7/HP1ON) or 4nM WR (3D7/HP1OFF). RNA extracted from these samples at eleven consecutive time points each was processed for microarray analysis.
2014-07-09 | E-GEOD-53176 | biostudies-arrayexpress
Project description:Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of control Plasmodium falciparum asexual blood stages not treated with the calcium ionophores, A23187 and ionomycin has been presented here. P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the untreated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.
2012-07-14 | E-GEOD-33795 | biostudies-arrayexpress
Project description:This experiment studies the effect of knocking out the transcriptional regulator SIR2 in 3D7 parasites. RNA was harvested from ring-stage parasites at 8 hours post-infection. Keywords = SIR2 Keywords = epigenetic regulation Keywords = antigenic variation Keywords = var Keywords = Plasmodium falciparum Keywords: other
2005-03-08 | GSE2369 | GEO
Project description:ChIP-seq experiments were performed for the putative telomere repeat-binding factor (PfTRF) in the malaria parasite Plasmodium falciparum strain 3D7. The gene encoding this factor (PF3D7_1209300) was endogenously tagged with either a GFP- or a 3xHA-tag and these transgenic parasite lines were used in ChIP-sequencing experiments. Sequencing of the ChIP and input libraries showed enrichment of PfTRF at all telomere-repeat containing chromosome ends (reference genome Plasmodium falciparum 3D7 from PlasmoDB version 6.1) as well as in all upsB var promoters.In addition,PfTRF was enriched at seven additional, intra-chromosomal sites and called in the PfTRF-HA ChIP-seq only. Plasmodium falciparum 3D7 parasites were generated with -GFP or -3xHA C-terminal tagged TRF (PF3D7_1209300). Nuclei were isolated from formaldehyde cross-linked schizont-stage transgenic parasites and used to prepare chromatin. Chromatin immunoprecipitations were performed using mouse anti-GFP (Roche Diagnostics, #11814460001) or rat anti-HA 3F10 (Roche Diagnostics, #12158167001). Sequencing libraries were prepared according to a Plasmodium-optimized library preparation procedure including KAPA polymerase-mediated PCR amplification.
2016-07-15 | E-GEOD-76537 | biostudies-arrayexpress
Project description:Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for extracellular calcium chelation of the control Plasmodium falciparum asexual blood stages not treated with the calcium ionophore ionomycin and EGTA has been presented here. P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the untreated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.
2012-07-14 | E-GEOD-33834 | biostudies-arrayexpress
Project description:Calcium is a universal second messenger molecule which plays a significant role in several biological processes. Presence of calcium sensors (calmodulins) and calcium-dependent protein kinases in Plasmodium species suggests an important role of calcium-dependent signaling pathways in the regulation of cellular processes in the malaria parasites. Evidence for the transcriptional response of Plasmodium falciparum asexual blood stages to the well-known calcium ionophore A23187 has been presented here. P. falciparum 3D7 strain was cultured as described by Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. Calcium ionophore treatment was done as follows. Parasites at schizont stage were treated with 5 μM of calcium ionophore, A23187 for 30 minutes, 1 hour, 2 hours, 4 hours and 6 hours. Total RNA from each of the time points was isolated and aminoallyl-cDNA was synthesized using reverse transcriptase system (Fermentas). cDNA made from the treated parasites were labeled with Cy5 (GE-Amersham). A reference pool was made by mixing equal amount of cDNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham). The samples were then hybridized on a spotted cDNA chip platform comprising 10166 MOEs representing 5363 coding sequences as described in Hu G, Cabrera A, Kono M, Mok S, Chaal BK, Haase S, Engelberg K, Cheemadan S, Spielmann T, Preiser PR, Gilberger TW, Bozdech Z: Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum. Nat Biotechnol, 2009. 28(1): p. 91-8. The data was normalized and filtered with the condition, signal intensity>background intensity + 2 SD of background intensity) using NOMAD.
2012-07-14 | E-GEOD-33797 | biostudies-arrayexpress