The silicon trypanosome: a test case of iterative model extension in systems biology (Q36638615)

15 August 2017

The silicon trypanosome: a test case of iterative model extension in systems biology (English)

1 reference

15 August 2017

0 references

10

Michael P Barrett

0 references

Eduard J Kerkhoven

Eduard J Kerkhoven

4

0 references

Fiona Achcar

Fiona Achcar

1

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Alejandro Leroux

Alejandro E Leroux

6

0 references

Theodore Papamarkou

Theodore Papamarkou

7

0 references

Dong-Hyun Kim

Dong-Hyun Kim

5

0 references

Abeer Fadda

Abeer Fadda

2

0 references

Jurgen R. Haanstra

Jurgen R Haanstra

3

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Barbara Marleen Bakker

Barbara M Bakker

9

0 references

Rainer Breitling

Rainer Breitling

15

0 references

Christine Clayton

Christine Clayton

11

0 references

Federico Rojas

Federico Rojas

8

0 references

Mark Girolami

12

Mark Girolami

1 reference

15 August 2017

Michael P Barrett

10

1 reference

PMCID

4773886

15 August 2017

R Luise Krauth-Siegel

13

1 reference

PMCID

4773886

15 August 2017

Keith R Matthews

14

1 reference

15 August 2017

1 January 2014

1 reference

Advances in Microbial Physiology

15 August 2017

1 reference

15 August 2017

64

1 reference

15 August 2017

115-143

1 reference

Explicit consideration of topological and parameter uncertainty gives new insights into a well-established model of glycolysis

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

The roles of 3'-exoribonucleases and the exosome in trypanosome mRNA degradation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Modeling challenges in the synthetic biology of secondary metabolism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Metabolomics guides rational development of a simplified cell culture medium for drug screening against Trypanosoma brucei.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Secreted proteases of Trypanosoma brucei gambiense: possible targets for sleeping sickness control?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Mathematical modelling of polyamine metabolism in bloodstream-form Trypanosoma brucei: an application to drug target identification

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Current trends and challenges in sample preparation for global metabolomics using liquid chromatography-mass spectrometry.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Untargeted metabolomics reveals a lack of synergy between nifurtimox and eflornithine against Trypanosoma brucei

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Channel-forming activities in the glycosomal fraction from the bloodstream form of Trypanosoma brucei

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Gene expression in Trypanosoma brucei: lessons from high-throughput RNA sequencing

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Metabolomic systems biology of trypanosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Exocytosis and protein secretion in Trypanosoma.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Chemical validation of trypanothione synthetase: a potential drug target for human trypanosomiasis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

RNA interference-mediated silencing of ornithine decarboxylase and spermidine synthase genes in Trypanosoma brucei provides insight into regulation of polyamine biosynthesis

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Compartmentation prevents a lethal turbo-explosion of glycolysis in trypanosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Glyoxalase II does not support methylglyoxal detoxification but serves as a general trypanothione thioesterase in African trypanosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Depletion of the thioredoxin homologue tryparedoxin impairs antioxidative defence in African trypanosomes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Tagging a T. brucei RRNA locus improves stable transfection efficiency and circumvents inducible expression position effects

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Peroxisomes, glyoxysomes and glycosomes (review).

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Phenotypic analysis of trypanothione synthetase knockdown in the African trypanosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Experimental and in silico analyses of glycolytic flux control in bloodstream form Trypanosoma brucei

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Validation of Trypanosoma brucei trypanothione synthetase as drug target

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Ion suppression in mass spectrometry

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

RNA interference identifies two hydroperoxide metabolizing enzymes that are essential to the bloodstream form of the african trypanosome.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei

30 September 2017

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

30 September 2017

12 December 2020

Compartmentation protects trypanosomes from the dangerous design of glycolysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Trypanosomes lacking trypanothione reductase are avirulent and show increased sensitivity to oxidative stress

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Contribution of glucose transport to the control of the glycolytic flux in Trypanosoma brucei

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Import of a DHFR hybrid protein into glycosomes in vivo is not inhibited by the folate-analogue aminopterin

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Hydrogen ion gradients across the mitochondrial, endosomal and plasma membranes in bloodstream forms of trypanosoma brucei solving the three-compartment problem

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Peptidase in the plasma of mice infected with Trypanosoma brucei brucei.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Maintenance of internal pH and an electrochemical gradient in Trypanosoma brucei

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Drug target validation of the trypanothione pathway enzymes through metabolic modelling.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Inhibition of Trypanosoma brucei glucose-6-phosphate dehydrogenase by human steroids and their effects on the viability of cultured parasites.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Quantitative metabolome analysis using liquid chromatography-high-resolution mass spectrometry.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Bayesian ranking of biochemical system models.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Control and regulation of gene expression: quantitative analysis of the expression of phosphoglycerate kinase in bloodstream form Trypanosoma brucei

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

MIRACLE: mass isotopomer ratio analysis of U-13C-labeled extracts. A new method for accurate quantification of changes in concentrations of intracellular metabolites

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Properties of trypanothione synthetase from Trypanosoma brucei

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Gene knockdown of gamma-glutamylcysteine synthetase by RNAi in the parasitic protozoa Trypanosoma brucei demonstrates that it is an essential enzyme

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Arginases in parasitic diseases

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Silencing of the thioredoxin gene in Trypanosoma brucei brucei

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

Phosphoglycerate mutase from Trypanosoma brucei is hyperactivated by cobalt in vitro, but not in vivo

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4773886

What Controls Glycolysis in Bloodstream FormTrypanosoma brucei?

4 December 2018

1 reference

12 December 2020

Determination of ornithine in human plasma by hydrophilic interaction chromatography–tandem mass spectrometry

1 reference

12 December 2020

Factors that determine the plasma-membrane potential in bloodstream forms of Trypanosoma brucei

1 reference

12 December 2020

31P NMR spectroscopy of Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. Evidence for high levels of condensed inorganic phosphates

1 reference

12 December 2020

In vivo effects of difluoromethylornithine on trypanothione and polyamine levels in bloodstream forms of Trypanosoma brucei

1 reference

12 December 2020

6-Phosphogluconate Dehydrogenase from Trypanosoma Brucei. Kinetic Analysis and Inhibition by Trypanocidal Drugs

1 reference

12 December 2020

10.1016/B978-0-12-800143-1.00003-8

Identifiers

DOI

1 reference

15 August 2017

1 reference

15 August 2017

1 reference

PMCID

4773886