UROP Proceedings 2020-21

School of Engineering Department of Chemical and Biological Engineering 83 Influence of Random Base in Poly(A) Tail to the Function of Mammalian mRNA Supervisor: KUANG Becki Yi / CBE Student: SHI Naiyu / BIEN Course: UROP2100, Spring Messenger ribonucleic acid (mRNA) is a single-stranded RNA. It delivers the genetic information of the DNA to the cytoplasm to synthesize proteins. To protect mRNA from degradation, a poly(A) tail is added at the 3’ end. Despite the name suggests it is a string of adenines, random insertions of guanine (G), cytosine (C) and uracil (U) inside poly(A) tails have been found. These insertions seem to have the capability of affecting the half-life and the translation efficiency of the mRNA, however, whether these insertions are the reason for the changes and how they influence the functions and properties of mRNA are not known. This project aims to investigate the influence of insertions of G and C in poly(A) tails of mammalian mRNA. RNAs with different poly(A) tails will be made in vitro and transfected into mammalian cells. Flow cytometry will be applied to analyze the transfection and protein expression rate. The Construction of Dual-Functional Synthetic RNA Control Unit Supervisor: KUANG Becki Yi / CBE Student: TSE Richard Chi Hong / BCB Course: UROP1000, Summer In this project, we have demonstrated that by using RNA-only delivery method, we could enable direct activation and repression on the translation of mRNA, our system could minimise the components needed, and it also expands the current regulatory components as in the field of synthetic biology and as a safer alternative in different medical and therapeutic applications. We demonstrated that RBP-aptamer pair PP7CP could repress translation of mRNA with a translational active 5’-cap analog with superior translational activity, whereas activates translation of mRNA with a translational inactive 5’-cap. Improving Data Analysis Methods in Proteomics Supervisor: LAM Henry Hei Ning / CBE Student: RODRIGUEZ GUTIERREZ Mauricio Antonio / MATH-PM Course: UROP1100, Fall This report will first describe common techniques applied in the field of Proteomics for the identification of peptides from mass spectrometry data. Afterwards, describe a methodology to identify features on mass spectrometry scans between matches for tryptic cut human peptides depending on their Cterminal (Lysine or Arginine). The two techniques used for analysing the features were targetdecoy database search, and the data analysed is a draft map of the human proteome submitted to the PRoteomics IDEntification Database (PRIDE). The report hopes to investigate any possible differences between the ease of identification for fragmentation patterns depending on the type of tryptic cut site. Finally, it will present the resulting data, which was filtered, processed and presented using Python library Pyteomics for the handling of .pep.xml files.