Maryam holds an MSc in Bioinformatics and is currently enrolled as a PhD student at King's College London, UK. Her project lies at the interface of developmental biology and bioinformatics with the major aim to uncover gene regulatory networks (GRNs) that control and define the hierarchy of events that commit progenitor cells to an ear lineage.
During development, the coordinated and sequential action of signals and regulatory factors controls how cells become different from each other and acquire specific fates. This information can be integrated in gene regulatory networks (GRNs) that model these processes over time and consider temporal and spatial changes of gene expression and how these are regulated. The inner ear is responsible for hearing and balance and its progenitors are specified during early development. This project uses a bioinformatics approach to establish a GRN to model how multipotent progenitors transition through sequential regulatory states until they are committed to the ear lineage. Using RNAseq we have identified new ear-specific genes and established their epistatic relationships by iterating systematic perturbation experiments with network building. This has enriched a preliminary literature-based GRN and predicts new interactions. Using alignment and motif discovery algorithms combined with histone ChIP-seq we have characterized the dynamic enhancer changes as cell acquire ear identity. Focusing on the earliest steps that initiate this process, we have identified two novel enhancers of a known otic specifier, Foxi3. These enhancers show spatially and temporally distinct activity in vivo, and integrate different transcriptional inputs. Together, we establish the first GRN for otic specification and reveal novel regulatory interactions
Suliman Alsagaby has finished his MSc degree in molecular medicine from Essex University in the UK 2009. Then he joined the chronic lymphocytic leukaemia (CLL) research group in Cardiff University in the UK where he studied the proteome of patients CLL cells and obtained his PhD degree in 2013. Alsagaby has published 6 research abstracts/posters in different conferences in the UK. Currently, Alsagaby serves in Mjmaah University college of Science as an assistant professor and supervisor of the biotechnology research centre in the college.
Chronic lymphocytic leukaemia (CLL) is incurable disease with heterogeneous clinical outcomes. Identification of proteins expressed in CLL cells has the potential to better our understanding of the disease. A cellular fractionation method was developed to extract cytosolic proteins enriched fraction and nuclear proteins enriched fraction (termed NP40 fraction and SDS fraction respectively) from CLL patients samples. Protein fractions were independently subjected to trypsin- digestion followed by separation using two-dimensional nano liquid chromatography (2D nano-LC) and peptide identification by matrix-assisted laser desorption/ionization time of flight tandem mass spectrometry (MALDI TOF/TOF MS). We report the largest and most conserved protein set identified in primary CLL cells; 900 proteins were detected with false discovery rate (FDR) < 1%. Of these proteins 625 were identified using 2 or more different peptides (ion score ≥ 95% C.I.) and 375 proteins were identified based on single peptides (ion score > 99% C.I.). From the NP40 fractions 729 proteins were detected and 326 proteins were identified in the SDS fractions; 221 proteins were common in both fractions. Protein localisation analysis using Gene Ontology data and Quick GO-EBI tool showed that 50% of the proteins found in the NP40 fractions was cytosolic proteins, while 82% of proteins detected in the SDS fractions was nuclear proteins. This study showed the benefit of proteomics especially when combined with cellular fractionation to identify proteins associated with a disease