Currently I’m a PhD student at the University of Bath doing an interdisciplinary project between the Departments of Biology and Biochemistry and Mathematical Sciences. My project is a mixture of Developmental Biology, Systems Biology and Mathematical Biology, and it aims to develop the Gene Regulatory Network of melanocyte development. The abstract of my project is the following:
Multicellular organisms are formed by different cell types produced using a common genome. The process that regulated the change from a stem cell to a differentiated cell involved a large number of genes and complex interactions between them forming an intricate network called gene regulatory network (GRN).
Work carried out by Greenhill et al. (2011) used experimental evidence and mathematical modelling approaches to build a GRN that describes the interactions of some of the main genes involved in melanocyte development and predicts its behaviour.
The aim of my project is to continue the development of the melanocyte GRN including more genes involved in this process and getting quantitative information of gene expression levels to improve the mathematical model underlying the GRN, making it more realistic.
You can learn more about my project in this post: My research: understanding melanocyte development, which I published some time ago.
From Wikipedia
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Before the PhD I did a MSc in Applied Bioinformatics at Cranfield University. My MSc thesis title was: Molecular dynamics of the preQ1 riboswitch: towards in silico design. The abstract is bellow:
Riboswitches are gene control elements located in the 5’-untranslated region of some mRNAs. These elements are composed by two domains: a natural aptamer where the ligand binds and an expression platform that interacts with RNA elements which regulate the gene expression. Ligand binding produces structural changes which regulate the expression of the downstream genes through three mechanisms: transcription elongation, translation initiation and splicing processing. There are several types of riboswitches depending on the ligand they recognise. The preQ1 riboswitch has been studied in this project because it has the smallest natural aptamer domain keeping a high affinity and selectivity for its ligand, which makes it very interesting for drug development and molecular engineering.
The aim of this project was to use molecular dynamics simulations for understanding the molecular structure and dynamics behaviour of the preQ1 riboswitch in the presence and absence of its ligand. The information obtained from it was used for designing a modified riboswitch sequence to recognise a selected target.
Three molecular dynamics simulations were performed, two with the ligand-free riboswitch conformation and one with the ligand-bound. The results have drawn that the ligand-free conformation is very variable and unstable, allowing the access of the ribosome to the RBS (part of the aptamer sequence), and the translation of the downstream gene. However, the ligand-bound structure is very compact and stable, blocking the ribosome access and preventing the gene expression.
Furthermore, the riboswitch ligand binding sequence was subjected to an in silico mutagenesis process. The objective was to create a riboswitch structure with a higher affinity for a novel ligand than for the natural one. Three of the mutated structures presented this characteristic. A short molecular dynamics equilibration was performed with them to prove if this characteristic was stable.
PreQ1 riboswitch
If you want to know more about my research don’t hesitate to contact me.
Sciplexity 