ParaFuGe Lab Parasite Functional Genetics Laboratory

Research

Our current quest is to understand how malaria parasites reproduce asexually within red blood cells. The parasite undergoes an extraordinary form of cell division called schizogony, where the parasite’s nucleus divides multiple times before the entire cell splits all at once, producing up to 24 daughter parasites. Many features of this process remain a mystery. How does the parasite know when to start dividing? How does it time each step in this process? And how does it know when to stop after making a certain number of daughter parasites? We want to understand how these crucial decisions are made and identify the molecules and mechanisms involved. We hope that this will lead to new insights into how the parasite proliferates in the blood - the primary cause of clinical symptoms - and eventually to developing new drugs to combat this devastating disease.

Replication cycle of the malaria parasite within a red blood cell
Replication cycle of the malaria parasite within a red blood cell

To survive and multiply within red blood cells, the malaria parasite relies on nearly half of its ~5000 protein-coding genes. However, we still do not know what many of these important genes do. Studying these essential genes is difficult because of the parasite’s haploid nature. We use the inducible Dimerisable Cre (DiCre)-lox system to precisely knock out target genes at desired stages of the replication cycle in the most lethal human malaria parasite, Plasmodium falciparum. This enables us to analyse the resulting phenotypes in a population of mutant parasites in a controlled manner through multi-omics strategies, live-cell time-lapse imaging, and detailed biochemical and molecular analyses. Recently, we developed a scalable refinement of this system called frameshift-based trackable inducible knockout (SHIFTiKO) that now allows us to conduct targeted inducible knockout screens of groups of essential genes, thereby speeding up gene function discovery.

SHIFTiKO workflow
SHIFTiKO workflow

Publications

Highlighted

A scaleable inducible knockout system for studying essential gene function in the malaria parasite
A scaleable inducible knockout system for studying essential gene function in the malaria parasite
Abhinay Ramaprasad, Michael J Blackman
Nucleic Acids Research  ·  31 Dec 2024  ·  doi:10.1093/nar/gkae1274
This paper introduces SHIFTiKO, a novel inducible gene knockout system to study essential gene function at scale in P. falciparum.

All

2024

A scaleable inducible knockout system for studying essential gene function in the malaria parasite
A scaleable inducible knockout system for studying essential gene function in the malaria parasite
Abhinay Ramaprasad, Michael J Blackman
Nucleic Acids Research  ·  31 Dec 2024  ·  doi:10.1093/nar/gkae1274
This paper introduces SHIFTiKO, a novel inducible gene knockout system to study essential gene function at scale in P. falciparum.

2023

A patatin-like phospholipase is important for mitochondrial function in malaria parasites
A patatin-like phospholipase is important for mitochondrial function in malaria parasites
Emma Pietsch, Abhinay Ramaprasad, Sabrina Bielfeld, Yvonne Wohlfarter, Bohumil Maco, …, Markus A. Keller, Dominique Soldati-Favre, Michael J. Blackman, Tim-Wolf Gilberger, Paul-Christian Burda
mBio  ·  19 Dec 2023  ·  doi:10.1128/mbio.01718-23
This paper describes the function of a patatin-like phospholipase 2 (PF3D7_1358000) in P. falciparum.
Global analysis of putative phospholipases in i Plasmodium falciparum i reveals an essential role of the phosphoinositide-specific phospholipase C in parasite maturation
Global analysis of putative phospholipases in Plasmodium falciparum reveals an essential role of the phosphoinositide-specific phospholipase C in parasite maturation
Paul-Christian Burda, Abhinay Ramaprasad, Sabrina Bielfeld, Emma Pietsch, Anna Woitalla, …, Aaron Sait, Lucy M. Collinson, Dominik Schwudke, Michael J. Blackman, Tim-Wolf Gilberger
mBio  ·  25 Jul 2023  ·  doi:10.1128/mbio.01413-23
This paper describes a global knockout screen of phospholipases and the function of a phosphoinositide-specific phospholipase C (PF3D7_1013500) in P. falciparum.
A malaria parasite phospholipase facilitates efficient asexual blood stage egress
A malaria parasite phospholipase facilitates efficient asexual blood stage egress
Abhinay Ramaprasad, Paul-Christian Burda, Konstantinos Koussis, James A Thomas, Emma Pietsch, …, Steven A Howell, James I MacRae, Ambrosius P Snijders, Tim-Wolf Gilberger, Michael J Blackman
PLoS pathogens  ·  23 Jun 2023  ·  doi:10.1371/journal.ppat.1011449
This paper describes the functions of perforin-like proteins and a lecithin:cholesterol acyltransferase (PF3D7_0629300) in P. falciparum.

2022

A choline-releasing glycerophosphodiesterase essential for phosphatidylcholine biosynthesis and blood stage development in the malaria parasite
A choline-releasing glycerophosphodiesterase essential for phosphatidylcholine biosynthesis and blood stage development in the malaria parasite
Abhinay Ramaprasad, Paul-Christian Burda, Enrica Calvani, Aaron J Sait, Susana Alejandra Palma-Duran, …, Fiona Hackett, James Macrae, Lucy Collinson, Tim Wolf Gilberger, Michael J Blackman
eLife  ·  28 Dec 2022  ·  doi:10.7554/eLife.82207
This paper describes the function of a phosphodiester glycerophosphodiesterase (PF3D7_1406300) in P. falciparum.
A song for the unsung: The relevance of Plasmodium vinckei as a laboratory rodent malaria system
A song for the unsung: The relevance of Plasmodium vinckei as a laboratory rodent malaria system
Abhinay Ramaprasad, Richard Culleton
Parasitology International  ·  21 Sep 2022  ·  doi:10.1016/j.parint.2022.102680
Pangenome analysis of the soilborne fungal phytopathogen i Rhizoctonia solani i and development of a comprehensive web resource: RsolaniDB
Pangenome analysis of the soilborne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB
Abhinav Kaushik, Daniel P Roberts, Abhinay Ramaprasad, Sara Mfarrej, Mridul Nair, Dilip K Lakshman, Arnab Pain
Frontiers in microbiology  ·  25 Mar 2022  ·  doi:10.3389/fmicb.2022.839524

2021

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.
Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.
Joel Hellewell, Timothy W Russell, The SAFER Investigators and Field Study Team, The Crick COVID-19 Consortium, CMMID COVID-19 working group, Rupert Beale, Gavin Kelly, Catherine Houlihan, Eleni Nastouli, Adam J Kucharski
BMC medicine  ·  27 Apr 2021  ·  doi:10.1186/s12916-021-01982-x
Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites
Plasmodium vinckei genomes provide insights into the pan-genome and evolution of rodent malaria parasites
Abhinay Ramaprasad, Severina Klaus, Olga Douvropoulou, Richard Culleton, Arnab Pain
BMC Biology  ·  23 Apr 2021  ·  doi:10.1186/s12915-021-00995-5
This paper describes a genetic resource for the rodent malaria parasite P. vinckei.

2020

MRE11 is crucial for malaria parasite transmission and its absence affects expression of interconnected networks of key genes essential for life
MRE11 is crucial for malaria parasite transmission and its absence affects expression of interconnected networks of key genes essential for life
David S. Guttery, Abhinay Ramaprasad, David J. P. Ferguson, Mohammad Zeeshan, Rajan Pandey, Declan Brady, Anthony A. Holder, Arnab Pain, Rita Tewari
Cells  ·  03 Dec 2020  ·  doi:10.3390/cells9122590
Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy.
Clinical outcomes of COVID-19 in long-term care facilities for people with epilepsy.
Simona Balestrini, Matthias J Koepp, Sonia Gandhi, Hannah M Rickman, Gee Yen Shin, …, Eleni Nastouli, Charles Swanton, Josemir W Sander, Sanjay M Sisodiya, Crick COVID Consortium
Epilepsy & Behavior  ·  05 Nov 2020  ·  10.1016/j.yebeh.2020.107602
Scalable and robust SARS-CoV-2 testing in an academic center.
Scalable and robust SARS-CoV-2 testing in an academic center.
Jim Aitken, Karen Ambrose, Sam Barrell, Rupert Beale, Ganka Bineva-Todd, …, Sophia Ward, Wai Keong Wong, Joshua Wright, Mary Wu, Crick COVID Consortium
Nature biotechnology  ·  01 Aug 2020  ·  doi:10.1038/s41587-020-0588-y
Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers.
Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers.
Catherine F Houlihan, Nina Vora, Thomas Byrne, Dan Lewer, Gavin Kelly, …, Charles Swanton, Crick COVID Consortium, Andrew Hayward, Eleni Nastouli, SAFER Investigators
Lancet  ·  09 Jul 2020  ·  doi:10.1016/S0140-6736(20)31484-7
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms
Malaria parasites regulate intra-erythrocytic development duration via serpentine receptor 10 to coordinate with host rhythms
Amit K. Subudhi, Aidan J. O’Donnell, Abhinay Ramaprasad, Hussein M. Abkallo, Abhinav Kaushik, …, Fathia Ben Rached, Osamu Kaneko, Richard Culleton, Sarah E. Reece, Arnab Pain
Nature Communications  ·  02 Jun 2020  ·  doi:10.1038/s41467-020-16593-y

2019

Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations
Whole genome sequencing of amplified Plasmodium knowlesi DNA from unprocessed blood reveals genetic exchange events between Malaysian Peninsular and Borneo subpopulations
Ernest Diez Benavente, Ana Rita Gomes, Jeremy Ryan De Silva, Matthew Grigg, Harriet Walker, …, Sarah Auburn, Lau Yee Ling, Nicholas M. Anstey, Taane G. Clark, Susana Campino
Scientific Reports  ·  08 Jul 2019  ·  doi:10.1038/s41598-019-46398-z
A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites.
A fast and cost-effective microsampling protocol incorporating reduced animal usage for time-series transcriptomics in rodent malaria parasites.
Abhinay Ramaprasad, Amit Kumar Subudhi, Richard Culleton, Arnab Pain
Malaria Journal  ·  25 Jan 2019  ·  doi:10.1186/s12936-019-2659-4

2018

Phenomics, Genomics and Genetics in Plasmodium vinckei
Phenomics, Genomics and Genetics in Plasmodium vinckei
Abhinay Ramaprasad
KAUST Research Repository  ·  05 Nov 2018  ·  doi:10.25781/KAUST-T1M05
Proteomic profiling of the plasma of Gambian children with cerebral malaria
Proteomic profiling of the plasma of Gambian children with cerebral malaria
Ehab M. Moussa, Honglei Huang, Marie L. Thézénas, Roman Fischer, Abhinay Ramaprasad, …, Muminatou Jallow, Arnab Pain, Dominic Kwiatkowski, Benedikt M. Kessler, Climent Casals-Pascual
Malaria Journal  ·  24 Sep 2018  ·  doi:10.1186/s12936-018-2487-y
Timing of host feeding drives rhythms in parasite replication
Timing of host feeding drives rhythms in parasite replication
Kimberley F. Prior, Daan R. van der Veen, Aidan J. O’Donnell, Katherine Cumnock, David Schneider, …, Amit Subudhi, Abhinay Ramaprasad, Samuel S. C. Rund, Nicholas J. Savill, Sarah E. Reece
PLOS Pathogens  ·  26 Feb 2018  ·  doi:10.1371/journal.ppat.1006900

2017

Rapid identification of genes controlling virulence and immunity in malaria parasites
Rapid identification of genes controlling virulence and immunity in malaria parasites
Hussein M. Abkallo, Axel Martinelli, Megumi Inoue, Abhinay Ramaprasad, Phonepadith Xangsayarath, …, Osamu Kaneko, Ville Mustonen, Christopher J. R. Illingworth, Arnab Pain, Richard Culleton
PLOS Pathogens  ·  12 Jul 2017  ·  doi:10.1371/journal.ppat.1006447
Emergence of indigenous artemisinin-resistant Plasmodium falciparum in Africa.
Emergence of indigenous artemisinin-resistant Plasmodium falciparum in Africa.
Feng Lu, Richard Culleton, Meihua Zhang, Abhinay Ramaprasad, Lorenz von Seidlein, …, Didier Menard, Arnab Pain, Haitao Yang, Qingfeng Zhang, Jun Cao
The New England Journal of Medicine  ·  22 Feb 2017  ·  doi:10.1056/NEJMc1612765

2016

Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species
Genome-scale comparison of expanded gene families in Plasmodium ovale wallikeri and Plasmodium ovale curtisi with Plasmodium malariae and with other Plasmodium species
Hifzur Rahman Ansari, Thomas J. Templeton, Amit Kumar Subudhi, Abhinay Ramaprasad, Jianxia Tang, …, Colin J. Sutherland, John W. Barnwell, Richard Culleton, Jun Cao, Arnab Pain
International Journal for Parasitology  ·  01 Oct 2016  ·  doi:10.1016/j.ijpara.2016.05.009
Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite i Plasmodium knowlesi i
Normocyte-binding protein required for human erythrocyte invasion by the zoonotic malaria parasite Plasmodium knowlesi
Robert W. Moon, Hazem Sharaf, Claire H. Hastings, Yung Shwen Ho, Mridul B. Nair, …, Neil Almond, Yee Ling Lau, Arnab Pain, Michael J. Blackman, Anthony A. Holder
Proceedings of the National Academy of Sciences  ·  14 Jun 2016  ·  doi:10.1073/pnas.1522469113

2015

Plasmodium P-Type Cyclin CYC3 modulates endomitotic growth during oocyst development in mosquitoes
Plasmodium P-Type Cyclin CYC3 modulates endomitotic growth during oocyst development in mosquitoes
Magali Roques, Richard J. Wall, Alexander P. Douglass, Abhinay Ramaprasad, David J. P. Ferguson, …, Hiroyuki Yamano, Anthony A. Holder, Arnab Pain, Bill Wickstead, Rita Tewari
PLOS Pathogens  ·  13 Nov 2015  ·  doi:10.1371/journal.ppat.1005273
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites
Yong H Woo, Hifzur Ansari, Thomas D Otto, Christen M Klinger, Martin Kolisko, …, Thomas J Templeton, Ross F Waller, Julius Lukeš, Miroslav Oborník, Arnab Pain
eLife  ·  15 Jul 2015  ·  doi:10.7554/eLife.06974
Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate
Endosymbiosis undone by stepwise elimination of the plastid in a parasitic dinoflagellate
Sebastian G. Gornik, Febrimarsa, Andrew M. Cassin, James I. MacRae, Abhinay Ramaprasad, …, Malcolm J. McConville, Antony Bacic, Geoffrey I. McFadden, Arnab Pain, Ross F. Waller
Proceedings of the National Academy of Sciences  ·  20 Apr 2015  ·  doi:10.1073/pnas.1423400112
Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features
Comprehensive evaluation of Toxoplasma gondii VEG and Neospora caninum LIV genomes with tachyzoite stage transcriptome and proteome defines novel transcript features
Abhinay Ramaprasad, Tobias Mourier, Raeece Naeem, Tareq B. Malas, Ehab Moussa, Aswini Panigrahi, Sarah J. Vermont, Thomas D. Otto, Jonathan Wastling, Arnab Pain
PLOS ONE  ·  13 Apr 2015  ·  doi:10.1371/journal.pone.0124473

2014

Genome-wide functional analysis of Plasmodium protein phosphatases reveals key regulators of parasite development and differentiation
Genome-wide functional analysis of Plasmodium protein phosphatases reveals key regulators of parasite development and differentiation
David S. Guttery, Benoit Poulin, Abhinay Ramaprasad, Richard J. Wall, David J.P. Ferguson, …, Edward W. Tate, Anthony A. Holder, Bill Wickstead, Arnab Pain, Rita Tewari
Cell Host & Microbe  ·  01 Jul 2014  ·  doi:10.1016/j.chom.2014.05.020
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction
The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction
A. P. Jackson, T. D. Otto, A. Darby, A. Ramaprasad, D. Xia, …, B. Shiels, A. Tait, M. Berriman, D. R. Allred, A. Pain
Nucleic Acids Research  ·  05 May 2014  ·  doi:10.1093/nar/gku322
Interleukin-10 regulates hepcidin in Plasmodium falciparum malaria
Interleukin-10 regulates hepcidin in Plasmodium falciparum malaria
Honglei Huang, Abigail A. Lamikanra, Matthew S. Alkaitis, Marie L. Thézénas, Abhinay Ramaprasad, Ehab Moussa, David J. Roberts, Climent Casals-Pascual
PLoS ONE  ·  10 Feb 2014  ·  doi:10.1371/journal.pone.0088408

2013

PfHPRT: A new biomarker candidate of acute i Plasmodium falciparum i infection
PfHPRT: A new biomarker candidate of acute Plasmodium falciparum infection
Marie L. Thézénas, Honglei Huang, Madi Njie, Abhinay Ramaprasad, Davis C. Nwakanma, …, Katalin Digleria, Michael Walther, David J. Conway, Benedikt M. Kessler, Climent Casals-Pascual
Journal of Proteome Research  ·  12 Feb 2013  ·  doi:10.1021/pr300858g

2012

Defining the protein interaction network of human malaria parasite Plasmodium falciparum
Defining the protein interaction network of human malaria parasite Plasmodium falciparum
Abhinay Ramaprasad, Arnab Pain, Timothy Ravasi
Genomics  ·  01 Feb 2012  ·  doi:10.1016/j.ygeno.2011.11.006
Studying Different Clinical Syndromes Of Paediatric Severe Malaria Using Plasma Proteomics
Studying Different Clinical Syndromes Of Paediatric Severe Malaria Using Plasma Proteomics
Abhinay Ramaprasad
KAUST Research Repository  ·  01 Jan 2012  ·  doi:10.25781/KAUST-1XW71