Carmen Sands Email and Phone Number

PhD in Bioengineering. Supervised by Prof Morten Sommer in the Bacterial Synthetic Biology group at DTU Biosustain. Funded by the Novo Nordisk Foundation Initiative Copenhagen Bioscience PhD Program.During my PhD I worked on a broad range of projects, which allowed me to develop a broad range of both technical and transferable skills.Project 1 (Project lead; manuscript submitted) - Characterisation of Saccharomyces boulardii promoters for control of gene expression in vivo: comparision of S. boulardii promoter activities under lab conditions and in the mouse gastrointestinal tract. Successfully identified promoters suitable for robust peptide expression both conditions. Skills: project planning and management, leadership, prioritisationProject 2 (Strain development lead; work on-going) - Engineering human gut bacteria as a proof-of-concept microbiome therapeutic: a consortium project aiming to bring genetically engineered therapeutic bacteria to phase I clinical trials. Led the strain development, working with a previously unengineered species of gut bacteria and successfully developed a protocol for the transfer of foreign DNA to this species. Skills: independant work, inter-disciplinary communication, oral presentationProject 3 (Collaborator; manuscript submitted) - In vivo ligand-responsive gene expression in probiotic Saccharomyces boulardii: development of inducible promoters for S. boulardii. Contributed to the metabolic profiling of S. boulardii. This project formed the basis of my stay as a visiting researcher in Dr Nathan Crooks' lab at North Carolina State University. Skills: cross-cultural work experienceProject 4 (Collaborator; manuscript prepared) - Identification of probiotic bacteria capable of promoting the growth of Saccharomyces boulardii: a multidisciplinary approach to developing a robust probiotic consortium. Contributed to developing the method of co-culture analysis. Skills: teamwork

Predoctoral research assisstant year in the Bacterial Synthetic Biology group headed by Prof. Morten Sommer at DTU Biosustain. Here I engineered a probiotic yeast to produce a small molecule and worked on functionalising components for developing small molecules sensors.

Worked as part of a small team of technicians processing PCR diagnostic tests for COVID-19 at the Centre for Diagnostics at DTU Health. The role was fast-paced, processing around 1000 tests a shift.You can read more about the initiative here: https://www.dtu.dk/english/news/all-news/nyhed?id=e19f4b88-eefb-492d-a33a-04cd7e5ecba2

I worked with the Bioinformatics core facility to develop MethylationExplorer: an automated pipeline for the analysis of whole genome bisulphite sequencing data. The pipeline was assembled from a combination of R and Bash scripts. It combined three previously published analysis packages with two novel apps for the visualisation of methylation data. Bismark (1) was used for alignment and methylation calling; dmrseq (2) and DMRCaller (3) were used for calling differentially methylated regions. Links to apps, loaded with test data (4): *Note they may take up to 40s to load initially.http://bifx-rta.bio.ed.ac.uk:3838/carmen/methylation_explorer/ http://bifx-rta.bio.ed.ac.uk:3838/carmen/methylation_viewer/References: (1) Krueger, F. & Andrews, S. R., 2011. Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. (2) Korthauer, K. et al., 2018. Detection and accurate false discovery rate control of differentially methylated regions from whole genome bisulfite sequencing. Biostatistics. (3) Catoni, M. et al., 2018. DMRcaller: a versatile R/Bioconductor package for detection and visualization of differentially methylated regions in CpG and non-CpG contexts. Nucleic Acid Research.(4) Virdi, K. S. et al., 2015. Arabidopsis MSH1 mutation alters the epigenome and produces heritable changes in plant growth. Nature Communications, 27 2, Volume 6, p. 6386.

EQUATE Scotland Student Summer Internship. Supervised by Dr Leonardo Rios Solis at the Institute of Bioengineering. Used CRSIPR/Cas9 to genetically engineer Saccharomyces cerevisiae to produce intermediates in the paclitaxel (Taxol) biosynthesis pathway. Learnt the laboratory skills involved in strain engineering, including but not limited to PCR, cloning with Gibson assembly, cell transformation and sequencing. Additionally performed an extensive literature search, summarising major papers in the field, as background research for a grant application.

Funded by the James Black Prize Studentship. Supervised by Prof Kees Weijer. Ten week summer studentship. Carried out a biological imaging project, phenotyping genetic knockouts of the slime mould Dictyostelium discoideum. Learnt a range of cell culturing, staining and imaging techniques.