Modeling metabolism and stage-specific growth of Plasmodium falciparum HB3 during the intraerythrocytic developmental cycle

2014 ◽  
Vol 10 (10) ◽  
pp. 2526-2537 ◽  
Author(s):  
Xin Fang ◽  
Jaques Reifman ◽  
Anders Wallqvist
Keyword(s):  
Gene Expression ◽  
Plasmodium Falciparum ◽  
Metabolic Network ◽  
Network Model ◽  
Specific Growth ◽  
Time Dependent ◽  
Developmental Cycle ◽  
Physiological Functions ◽  
Metabolic Network Model ◽  
Intraerythrocytic Developmental Cycle

We developed a metabolic network model that maps hourly gene expression to time-dependent metabolism and stage-specific growth, allowing us to link specific metabolites or pathways to specific physiological functions.

scholarly journals Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio

Zebrafish ◽  
2019 ◽  
Vol 16 (4) ◽  
pp. 348-362 ◽  
Author(s):  
Leonie van Steijn ◽  
Fons J. Verbeek ◽  
Herman P. Spaink ◽  
Roeland M.H. Merks
Keyword(s):  
Gene Expression ◽  
Metabolic Network ◽  
Network Model ◽  
Danio Rerio ◽  
Whole Genome ◽  
Metabolic Network Model

Metabolic design based on a coupled gene expression—metabolic network model of tryptophan production in Escherichia coli

2004 ◽  
Vol 6 (4) ◽  
pp. 364-377 ◽  
Author(s):  
Joachim W. Schmid ◽  
Klaus Mauch ◽  
Matthias Reuss ◽  
Ernst D. Gilles ◽  
Andreas Kremling
Keyword(s):  
Gene Expression ◽  
Escherichia Coli ◽  
Metabolic Network ◽  
Network Model ◽  
Metabolic Network Model ◽  
Metabolic Design

scholarly journals The Transcriptome of the Intraerythrocytic Developmental Cycle of Plasmodium falciparum

PLoS Biology ◽  
2003 ◽  
Vol 1 (1) ◽  
pp. e5 ◽  
Author(s):  
Zbynek Bozdech ◽  
Manuel Llinás ◽  
Brian Lee Pulliam ◽  
Edith D Wong ◽  
Jingchun Zhu ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Developmental Cycle ◽  
Intraerythrocytic Developmental Cycle

scholarly journals Refining the transcriptome of the human malaria parasite Plasmodium falciparum using amplification-free RNA-seq

2019 ◽  
Author(s):  
Lia Chappell ◽  
Philipp Ross ◽  
Lindsey Orchard ◽  
Thomas D. Otto ◽  
Matthew Berriman ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Malaria Parasite ◽  
Developmental Cycle ◽  
Rna Seq ◽  
Human Malaria Parasite ◽  
Human Malaria ◽  
Parasite Plasmodium ◽  
Parasite Plasmodium Falciparum ◽  
Intraerythrocytic Developmental Cycle ◽  
Transcriptional Start Sites

AbstractPlasmodium parasites undergo several major developmental transitions during their complex lifecycle, which are enabled by precisely ordered gene expression programs. Transcriptomes from the 48-hour blood stages of the major human malaria parasite Plasmodium falciparum have been described using cDNA microarrays and RNA-seq, but these assays have not always performed well within non-coding regions, where the AT-content is often 90-95%. We developed a directional, amplification-free RNA-seq protocol (DAFT-seq) to reduce bias against AT-rich cDNA, which we have applied to three strains of P. falciparum (3D7, HB3 and IT). While strain-specific differences were detected, overall there is strong conservation between the transcriptional profiles. For the 3D7 reference strain, transcription was detected from 89% of the genome, with over 75% of the genome transcribed into mRNAs. These datasets allowed us to refine the 5’ and 3’ untranslated regions (UTRs), which can be variable, long (>1,000 nt), and often overlap those of adjacent transcripts. We also find that transcription from bidirectional promoters frequently results in non-coding, antisense transcripts. By capturing the 5’ ends of mRNAs, we reveal both constant and dynamic use of transcriptional start sites across the intraerythrocytic developmental cycle resulting in an updated view of the P. falciparum transcriptome.

scholarly journals A low-complexity metabolic network model for the respiratory and fermentative metabolism of Escherichia coli

PLoS ONE ◽  
2018 ◽  
Vol 13 (8) ◽  
pp. e0202565 ◽  
Author(s):  
Ignace L. M. M. Tack ◽  
Philippe Nimmegeers ◽  
Simen Akkermans ◽  
Filip Logist ◽  
Jan F. M. Van Impe
Keyword(s):  
Escherichia Coli ◽  
Metabolic Network ◽  
Network Model ◽  
Low Complexity ◽  
Fermentative Metabolism ◽  
Metabolic Network Model

Reconstruction of a generic metabolic network model of cancer cells

2014 ◽  
Vol 10 (11) ◽  
pp. 3014-3021 ◽  
Author(s):  
Mahdieh Hadi ◽  
Sayed-Amir Marashi
Keyword(s):  
Cancer Cells ◽  
Metabolic Network ◽  
Network Model ◽  
Cancer Metabolism ◽  
Metabolic Phenotypes ◽  
Metabolic Network Model

We introduce a generic constraint-based model of cancer metabolism, which is able to successfully predict the metabolic phenotypes of cancer cells.

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