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Research

Biological systems - including the simplest cells - exhibit a broad range of functions to thrive in their environment. Research in the Imperial College Centre for Synthetic Biology is focused on the possibility of engineering the underlying biochemical processes to solve many of the challenges facing society, from healthcare to sustainable energy. In particular, we model, analyse, design and build biological and biochemical systems in living cells and/or in cell extracts, both exploring and enhancing the engineering potential of biology.

As part of our research we develop novel methods to accelerate the celebrated Design-Build-Test-Learn synthetic biology cycle. As such research in the Centre for Synthetic Biology highly multi- and interdisciplinary covering computational modelling and machine learning approaches; automated platform development and genetic circuit engineering ; multi-cellular and multi-organismal interactions, including gene drive and genome engineering; metabolic engineering; in vitro/cell-free synthetic biology; engineered phages and directed evolution; and biomimetics, biomaterials and biological engineering.

Publications

Citation

BibTex format

@article{Witmer:2020:10.1038/s41598-020-63121-5,
author = {Witmer, K and Fraschka, S and Vlachou, D and Bartfai, R and Christophides, G},
doi = {10.1038/s41598-020-63121-5},
journal = {Scientific Reports},
title = {An epigenetic map of malaria parasite development from host to vector},
url = {http://dx.doi.org/10.1038/s41598-020-63121-5},
volume = {10},
year = {2020}
}

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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - The malaria parasite replicates asexually in the red blood cells of its vertebrate host employing epigenetic mechanisms to regulate gene expression in response to changes in its environment. We used chromatin immunoprecipitation followed by sequencing in conjunction with RNA sequencing to create an epigenomic and transcriptomic map of the developmental transition from asexual blood stages to male and female gametocytes and to ookinetes in the rodent malaria parasite Plasmodium berghei. Across the developmental stages examined, heterochromatin protein 1 associates with variantly expressed gene families localised at subtelomeric regions and variant gene expression based on heterochromatic silencing is observed only in some genes. Conversely, the euchromatin mark histone 3 lysine 9 acetylation (H3K9ac) is abundant in non-heterochromatic regions across all developmental stages. H3K9ac presents a distinct pattern of enrichment around the start codon of ribosomal protein genes in all stages but male gametocytes. Additionally, H3K9ac occupancy positively correlates with transcript abundance in all stages but female gametocytes suggesting that transcription in this stage is independent of H3K9ac levels. This finding together with known mRNA repression in female gametocytes suggests a multilayered mechanism operating in female gametocytes in preparation for fertilization and zygote development, coinciding with parasite transition from host to vector.
AU  - Witmer,K
AU  - Fraschka,S
AU  - Vlachou,D
AU  - Bartfai,R
AU  - Christophides,G
DO  - 10.1038/s41598-020-63121-5
PY  - 2020///
SN  - 2045-2322
TI  - An epigenetic map of malaria parasite development from host to vector
T2  - Scientific Reports
UR  - http://dx.doi.org/10.1038/s41598-020-63121-5
UR  - http://hdl.handle.net/10044/1/79012
VL  - 10
ER  -