Skip to main content
Key Specialties
Cardiology Diabetology Endocrinology Gastroenterology Geriatrics and Gerontology Gynecology and Obstetrics Hematology Infectious Disease Internal Medicine Nephrology Neurology Oncology Pediatrics Respiratory Medicine Rheumatology Surgery
Congress Coverage
2024 ACC Congress 2023 ESMO Congress 2023 EASD Congress 2023 ERS Congress 2023 ESC Congress
Clinical Collections
Advances in Alzheimer’s

At a glance: The STEP trials

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.
ADVANCED SEARCH
Log in
Top
Malaria Journal
Published in: Malaria Journal 1/2012

Open Access 01-12-2012 | Methodology

New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community

Authors: Björn F C Kafsack, Heather J Painter, Manuel Llinás

Published in: Malaria Journal | Issue 1/2012

Login to get access

Abstract

Background

DNA microarrays have been a valuable tool in malaria research for over a decade but remain in limited use in part due their relatively high cost, poor availability, and technical difficulty. With the aim of alleviating some of these factors next-generation DNA microarrays for genome-wide transcriptome analysis for both Plasmodium falciparum and Plasmodium berghei using the Agilent 8x15K platform were designed.

Methods

Probe design was adapted from previously published methods and based on the most current transcript predictions available at the time for P. falciparum or P. berghei. Array performance and transcriptome analysis was determined using dye-coupled, aminoallyl-labelled cDNA and streamlined methods for hybridization, washing, and array analysis were developed.

Results

The new array design marks a notable improvement in the number of transcripts covered and average number of probes per transcript. Array performance was excellent across a wide range of transcript abundance, with low inter-array and inter-probe variability for relative abundance measurements and it recapitulated previously observed transcriptional patterns. Additionally, improvements in sensitivity permitted a 20-fold reduction in necessary starting RNA amounts, further reducing experimental costs and widening the range of application.

Conclusions

DNA microarrays utilizing the Agilent 8x15K platform for genome-wide transcript analysis in P. falciparum and P. berghei mark an improvement in coverage and sensitivity, increased availability to the research community, and simplification of the experimental methods.
Appendix
Available only for authorised users
Literature
1.
Limenitakis J, Soldati-Favre D: Functional genetics in Apicomplexa: Potentials and limits. FEBS Lett. 2011, 585: 1579-1588. 10.1016/j.febslet.2011.05.002.CrossRefPubMed
2.
Carvalho TG, Menard R: Manipulating the Plasmodium genome. Curr Issues Mol Biol. 2005, 7: 39-55.PubMed
3.
Gardner MJ, Hall N, Fung E, White O, Berriman M, Hyman RW, Carlton JM, Pain A, Nelson KE, Bowman S, Paulsen IT, James K, Eisen JA, Rutherford K, Salzberg SL, Craig A, Kyes S, Chan MS, Nene V, Shallom SJ, Suh B, Peterson J, Angiuoli S, Pertea M, Allen J, Selengut J, Haft D, Mather MW, Vaidya AB, Martin DM, Fairlamb AH, Fraunholz MJ, Roos DS, Ralph SA, McFadden GI, Cummings LM, Subramanian GM, Mungall C, Venter JC, Carucci DJ, Hoffman SL, Newbold C, Davis RW, Fraser CM, Barrell B: Genome sequence of the human malaria parasitePlasmodium falciparum. Nature. 2002, 419: 498-511. 10.1038/nature01097.CrossRefPubMed
4.
Carlton JM, Angiuoli SV, Suh BB, Kooij TW, Pertea M, Silva JC, Ermolaeva MD, Allen JE, Selengut JD, Koo HL, Peterson JD, Pop M, Kosack DS, Shumway MF, Bidwell SL, Shallom SJ, van Aken SE, Riedmuller SB, Feldblyum TV, Cho JK, Quackenbush J, Sedegah M, Shoaibi A, Cummings LM, Florens L, Yates JR, Raine JD, Sinden RE, Harris MA, Cunningham DA, Preiser PR, Bergman LW, Vaidya AB, van Lin LH, Janse CJ, Waters AP, Smith HO, White OR, Salzberg SL, Venter JC, Fraser CM, Hoffman SL, Gardner MJ, Carucci DJ: Genome sequence and comparative analysis of the model rodent malaria parasitePlasmodium yoelii yoelii. Nature. 2002, 419: 512-519. 10.1038/nature01099.CrossRefPubMed
5.
Carlton J: ThePlasmodium vivaxgenome sequencing project. Trends Parasitol. 2003, 19: 227-231. 10.1016/S1471-4922(03)00066-7.CrossRefPubMed
6.
Pain A, Bohme U, Berry AE, Mungall K, Finn RD, Jackson AP, Mourier T, Mistry J, Pasini EM, Aslett MA, Balasubrammaniam S, Borgwardt K, Brooks K, Carret C, Carver TJ, Cherevach I, Chillingworth T, Clark TG, Galinski MR, Hall N, Harper D, Harris D, Hauser H, Ivens A, Janssen CS, Keane T, Larke N, Lapp S, Marti M, Moule S, Meyer IM, Ormond D, Peters N, Sanders M, Sanders S, Sargeant TJ, Simmonds M, Smith F, Squares R, Thurston S, Tivey AR, Walker D, White B, Zuiderwijk E, Churcher C, Quail MA, Cowman AF, Turner CM, Rajandream MA, Kocken CH, Thomas AW, Newbold CI, Barrell BG, Berriman M: The genome of the simian and human malaria parasitePlasmodium knowlesi. Nature. 2008, 455: 799-803. 10.1038/nature07306.PubMedCentralCrossRefPubMed
7.
Hayward RE, Derisi JL, Alfadhli S, Kaslow DC, Brown PO, Rathod PK: Shotgun DNA microarrays and stage-specific gene expression inPlasmodium falciparummalaria. Mol Microbiol. 2000, 35: 6-14. 10.1046/j.1365-2958.2000.01730.x.CrossRefPubMed
8.
Ben Mamoun C, Gluzman IY, Hott C, MacMillan SK, Amarakone AS, Anderson DL, Carlton JM, Dame JB, Chakrabarti D, Martin RK, Brownstein BH, Goldberg DE: Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasitePlasmodium falciparumrevealed by microarray analysis. Mol Microbiol. 2001, 39: 26-36. 10.1046/j.1365-2958.2001.02222.x.CrossRefPubMed
9.
Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle ofPlasmodium falciparum. PLoS Biol. 2003, 1: E5-PubMedCentralCrossRefPubMed
10.
Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De La Vega P, Holder AA, Batalov S, Carucci DJ, Winzeler EA: Discovery of gene function by expression profiling of the malaria parasite life cycle. Science. 2003, 301: 1503-1508. 10.1126/science.1087025.CrossRefPubMed
11.
Llinas M, Bozdech Z, Wong ED, Adai AT, DeRisi JL: Comparative whole genome transcriptome analysis of threePlasmodium falciparumstrains. Nucleic Acids Res. 2006, 34: 1166-1173. 10.1093/nar/gkj517.PubMedCentralCrossRefPubMed
12.
Siau A, Toure FS, Ouwe-Missi-Oukem-Boyer O, Ciceron L, Mahmoudi N, Vaquero C, Froissard P, Bisvigou U, Bisser S, Coppee JY, Bischoff E, David PH, Mazier D: Whole-transcriptome analysis ofPlasmodium falciparumfield isolates: identification of new pathogenicity factors. J Inf Dis. 2007, 196: 1603-1612. 10.1086/522012.CrossRef
13.
Daily JP, Scanfeld D, Pochet N, Le Roch K, Plouffe D, Kamal M, Sarr O, Mboup S, Ndir O, Wypij D, Levasseur K, Thomas E, Tamayo P, Dong C, Zhou Y, Lander ES, Ndiaye D, Wirth D, Winzeler EA, Mesirov JP, Regev A: Distinct physiological states ofPlasmodium falciparumin malaria-infected patients. Nature. 2007, 450: 1091-1095. 10.1038/nature06311.CrossRefPubMed
14.
Mackinnon MJ, Li J, Mok S, Kortok MM, Marsh K, Preiser PR, Bozdech Z: Comparative transcriptional and genomic analysis ofPlasmodium falciparumfield isolates. PLoS Pathog. 2009, 5: e1000644-10.1371/journal.ppat.1000644.PubMedCentralCrossRefPubMed
15.
Ralph SA, Bischoff E, Mattei D, Sismeiro O, Dillies MA, Guigon G, Coppee JY, David PH, Scherf A: Transcriptome analysis of antigenic variation in Plasmodium falciparum–var silencing is not dependent on antisense RNA. Genome Biol. 2005, 6: R93-10.1186/gb-2005-6-11-r93.PubMedCentralCrossRefPubMed
16.
Le Roch KG, Johnson JR, Ahiboh H, Chung DW, Prudhomme J, Plouffe D, Henson K, Zhou Y, Witola W, Yates JR, Mamoun CB, Winzeler EA, Vial H: A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite. Plasmodium falciparum. BMC Genomics. 2008, 9: 513-10.1186/1471-2164-9-513.CrossRefPubMed
17.
Ganesan K, Ponmee N, Jiang L, Fowble JW, White J, Kamchonwongpaisan S, Yuthavong Y, Wilairat P, Rathod PK: A genetically hard-wired metabolic transcriptome inPlasmodium falciparumfails to mount protective responses to lethal antifolates. PLoS Pathog. 2008, 4: e1000214-10.1371/journal.ppat.1000214.PubMedCentralCrossRefPubMed
18.
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 parasitePlasmodium falciparum. Nat Biotechnol. 2010, 28: 91-98. 10.1038/nbt.1597.CrossRefPubMed
19.
Chaal BK, Gupta AP, Wastuwidyaningtyas BD, Luah YH, Bozdech Z: Histone deacetylases play a major role in the transcriptional regulation of thePlasmodium falciparumlife cycle. PLoS Pathog. 2010, 6: e1000737-10.1371/journal.ppat.1000737.PubMedCentralCrossRefPubMed
20.
Mok S, Imwong M, Mackinnon M, Sim J, Ramadoss R, Yi P, Mayxay M, Chotivanich K, Liong K-Y, Russell B, Socheat D, Newton P, Day N, White N, Preiser P, Nosten F, Dondorp A, Bozdech Z: Artemisinin resistance inPlasmodium falciparumis associated with an altered temporal pattern of transcription. BMC Genomics. 2011, 12: 391-10.1186/1471-2164-12-391.PubMedCentralCrossRefPubMed
21.
van Brummlen T, Becker J, Mancama D, Hoppe H: Investigating transcriptional regulation ofPlasmodium falciparumupon drug perturbation. Malar J. 2010, 9: O32-10.1186/1475-2875-9-S2-O32.PubMedCentralCrossRef
22.
Mok BW, Ribacke U, Winter G, Yip BH, Tan CS, Fernandez V, Chen Q, Nilsson P, Wahlgren M: Comparative transcriptomal analysis of isogenicPlasmodium falciparumclones of distinct antigenic and adhesive phenotypes. Mol Biochem Parasitol. 2007, 151: 184-192. 10.1016/j.molbiopara.2006.11.006.CrossRefPubMed
23.
Silvestrini F, Bozdech Z, Lanfrancotti A, Di Giulio E, Bultrini E, Picci L, Derisi JL, Pizzi E, Alano P: Genome-wide identification of genes upregulated at the onset of gametocytogenesis inPlasmodium falciparum. Mol Biochem Parasitol. 2005, 143: 100-110. 10.1016/j.molbiopara.2005.04.015.CrossRefPubMed
24.
Yuda M, Iwanaga S, Shigenobu S, Mair GR, Janse CJ, Waters AP, Kato T, Kaneko I: Identification of a transcription factor in the mosquito-invasive stage of malaria parasites. Mol Microbiol. 2009, 71: 1402-1414. 10.1111/j.1365-2958.2009.06609.x.CrossRefPubMed
25.
Le Roch KG, Johnson JR, Florens L, Zhou Y, Santrosyan A, Grainger M, Yan SF, Williamson KC, Holder AA, Carucci DJ, Yates JR, Winzeler EA: Global analysis of transcript and protein levels across thePlasmodium falciparumlife cycle. Genome Res. 2004, 14: 2308-2318. 10.1101/gr.2523904.PubMedCentralCrossRefPubMed
26.
Gissot M, Refour P, Briquet S, Boschet C, Coupe S, Mazier D, Vaquero C: Transcriptome of 3D7 and its gametocyte-less derivative F12Plasmodium falciparumclones during erythrocytic development using a gene-specific microarray assigned to gene regulation, cell cycle and transcription factors. Gene. 2004, 341: 267-277.CrossRefPubMed
27.
Young JA, Fivelman QL, Blair PL, de la Vega P, Le Roch KG, Zhou Y, Carucci DJ, Baker DA, Winzeler EA: ThePlasmodium falciparumsexual development transcriptome: a microarray analysis using ontology-based pattern identification. Mol Biochem Parasitol. 2005, 143: 67-79. 10.1016/j.molbiopara.2005.05.007.CrossRefPubMed
28.
Vontas J, Siden-Kiamos I, Papagiannakis G, Karras M, Waters AP, Louis C: Gene expression inPlasmodium bergheiookinetes and early oocysts in a co-culture system with mosquito cells. Mol Biochem Parasitol. 2005, 139: 1-13. 10.1016/j.molbiopara.2004.03.003.CrossRefPubMed
29.
Yuda M, Iwanaga S, Shigenobu S, Kato T, Kaneko I: Transcription Factor AP2-Sp and its Target Genes in Malarial Sporozoites. Mol Microbiol. 2010, 75: 854-863. 10.1111/j.1365-2958.2009.07005.x.CrossRefPubMed
30.
Mikolajczak SA, Silva-Rivera H, Peng X, Tarun AS, Camargo N, Jacobs-Lorena V, Daly TM, Bergman LW, de la Vega P, Williams J, Aly AS, Kappe SH: Distinct malaria parasite sporozoites reveal transcriptional changes that cause differential tissue infection competence in the mosquito vector and mammalian host. Mol Cell Biol. 2008, 28: 6196-6207. 10.1128/MCB.00553-08.PubMedCentralCrossRefPubMed
31.
Tarun AS, Peng X, Dumpit RF, Ogata Y, Silva-Rivera H, Camargo N, Daly TM, Bergman LW, Kappe SH: A combined transcriptome and proteome survey of malaria parasite liver stages. Proc Natl Acad Sci U S A. 2008, 105: 305-310. 10.1073/pnas.0710780104.PubMedCentralCrossRefPubMed
32.
Albuquerque S, Carret C, Grosso A, Tarun A, Peng X, Kappe S, Prudencio M, Mota M: Host cell transcriptional profiling during malaria liver stage infection reveals a coordinated and sequential set of biological events. BMC Genomics. 2009, 10: 270-10.1186/1471-2164-10-270.PubMedCentralCrossRefPubMed
33.
Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, Heiges M, Innamorato F, Iodice J, Kissinger JC, Kraemer E, Li W, Miller JA, Nayak V, Pennington C, Pinney DF, Roos DS, Ross C, Stoeckert CJ, Treatman C: Wang H: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res. 2009, 37: D539-543. 10.1093/nar/gkn814.PubMedCentralCrossRefPubMed
34.
Li F, Sonbuchner L, Kyes SA, Epp C, Deitsch KW: Nuclear non-coding RNAs are transcribed from the centromeres ofPlasmodium falciparumand are associated with centromeric chromatin. J Biol Chem. 2008, 283: 5692-5698.CrossRefPubMed
35.
Otto TD, Wilinski D, Assefa S, Keane TM, Sarry LR, Böhme U, Lemieux J, Barrell B, Pain A, Berriman M, Newbold C, Llinás M: New insights into the blood-stage transcriptome ofPlasmodium falciparumusing RNA-Seq. Mol Microbiol. 2010, 76: 12-24. 10.1111/j.1365-2958.2009.07026.x.PubMedCentralCrossRefPubMed
36.
Upadhyay R, Bawankar P, Malhotra D, Patankar S: A screen for conserved sequences with biased base composition identifies noncoding RNAs in the A–T rich genome ofPlasmodium falciparum. Mol Biochem Parasitol. 2005, 144: 149-158. 10.1016/j.molbiopara.2005.08.012.CrossRefPubMed
37.
Mourier T, Carret C, Kyes S, Christodoulou Z, Gardner PP, Jeffares DC, Pinches R, Barrell B, Berriman M, Griffiths-Jones S, Ivens A, Newbold C, Pain A: Genome-wide discovery and verification of novel structured RNAs inPlasmodium falciparum. Genome Res. 2008, 18: 281-292. 10.1101/gr.6836108.PubMedCentralCrossRefPubMed
38.
Raabe CA, Sanchez CP, Randau G, Robeck T, Skryabin BV, Chinni SV, Kube M, Reinhardt R, Ng GH, Manickam R, Kuryshev VY, Lanzer M, Brosius J, Tang TH, Rozhdestvensky TS: A global view of the nonprotein-coding transcriptome inPlasmodium falciparum. Nucleic Acids Res. 2010, 38: 608-617. 10.1093/nar/gkp895.PubMedCentralCrossRefPubMed
39.
40.
Hu G, Llinas M, Li J, Preiser P, Bozdech Z: Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy. BMC Bioinforma. 2007, 8: 350-10.1186/1471-2105-8-350.CrossRef
41.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997, 25: 3389-3402. 10.1093/nar/25.17.3389.PubMedCentralCrossRefPubMed
42.
43.
Trager W, Jensen JB: Human malaria parasites in continuous culture. Science. 1976, 193: 673-675. 10.1126/science.781840.CrossRefPubMed
44.
Haynes JD, Moch JK: Automated synchronization ofPlasmodium falciparumparasites by culture in a temperature-cycling incubator. Methods Mol Med. 2002, 72: 489-497.PubMed
45.
46.
Bozdech Z, Zhu J, Joachimiak MP, Cohen FE, Pulliam B, DeRisi JL: Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol. 2003, 4: R9-10.1186/gb-2003-4-2-r9.PubMedCentralCrossRefPubMed
47.
Branham W, Melvin C, Han T, Desai V, Moland C, Scully A, Fuscoe J: Elimination of laboratory ozone leads to a dramatic improvement in the reproducibility of microarray gene expression measurements. BMC Biotechnol. 2007, 7: 8-10.1186/1472-6750-7-8.PubMedCentralCrossRefPubMed
48.
Claessens A, Ghumra A, Gupta AP, Mok S, Bozdech Z, Rowe JA: Design of a variant surface antigen-supplemented microarray chip for whole transcriptome analysis of multiplePlasmodium falciparumcytoadherent strains, and identification of strain-transcendent rif and stevor genes. Malar J. 2011, 10: 180-10.1186/1475-2875-10-180.PubMedCentralCrossRefPubMed
49.
Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle ofPlasmodium falciparum. PLoS Biol. 2003, 1: E5-PubMedCentralCrossRefPubMed
Metadata
Title
New Agilent platform DNA microarrays for transcriptome analysis of Plasmodium falciparum and Plasmodium berghei for the malaria research community
Authors
Björn F C Kafsack
Heather J Painter
Manuel Llinás
Publication date
01-12-2012
Publisher
BioMed Central
Published in
Malaria Journal / Issue 1/2012
Electronic ISSN: 1475-2875
DOI
https://doi.org/10.1186/1475-2875-11-187

Other articles of this Issue 1/2012

Malaria Journal 1/2012 Go to the issue

Research

Changes in malaria morbidity and mortality in Mpumalanga Province, South Africa (2001- 2009): a retrospective study

Research

Relationship between treatment-seeking behaviour and artemisinin drug quality in Ghana

Research

The effects of serum lipids on the in vitro activity of lumefantrine and atovaquone against Plasmodium falciparum

Methodology

Estimating malaria parasite density: assumed white blood cell count of 10,000/μl of blood is appropriate measure in Central Ghana

Research

Molecular markers in Plasmodium falciparum linked to resistance to anti-malarial drugs in samples imported from Africa over an eight-year period (2002-2010): impact of the introduction of artemisinin combination therapy

Research

Exploring the role narrative free-text plays in discrepancies between physician coding and the InterVA regarding determination of malaria as cause of death, in a malaria holo-endemic region
Obesity Clinical Trial Summary

At a glance: The STEP trials

Read more

A round-up of the STEP phase 3 clinical trials evaluating semaglutide for weight loss in people with overweight or obesity.

Developed by: Springer Medicine

Highlights from the ACC 2024 Congress

Year in Review: Pediatric cardiology

Pediatric Cardiology Video

Watch Dr. Anne Marie Valente present the last year's highlights in pediatric and congenital heart disease in the official ACC.24 Year in Review session.

Year in Review: Pulmonary vascular disease

Cardiopulmonary Comorbidity Video

The last year's highlights in pulmonary vascular disease are presented by Dr. Jane Leopold in this official video from ACC.24.

Year in Review: Valvular heart disease

Valvular Heart Disease Video

Watch Prof. William Zoghbi present the last year's highlights in valvular heart disease from the official ACC.24 Year in Review session.

Year in Review: Heart failure and cardiomyopathies

Heart Failure Video

Watch this official video from ACC.24. Dr. Biykem Bozkurt discuss last year's major advances in heart failure and cardiomyopathies.

ACC 2024 Congress Coverage

Heart Failure Video

Year in Review: Heart failure and cardiomyopathies

Watch now

Watch this official video from ACC.24. Dr. Biykem Bozkurt discuss last year's major advances in heart failure and cardiomyopathies.

Semaglutide benefits people with type 2 diabetes and obesity-related heart failure

16-04-2024 Type 2 Diabetes News

Incentivised to exercise

11-04-2024 Lifestyle Modifications News

New intervention for STEMI-related cardiogenic shock

10-04-2024 Myocardial Infarction News

» View more highlights on the ACC 2024 congress hub page

Image Credits