Characterizing alternative splicing and long non-coding RNA with high-throughput sequencing technology

Indiana University-Purdue University Indianapolis (IUPUI)Several experimental methods has been developed for the study of the central dogma since late 20th century. Protein mass spectrometry and next generation sequencing (including DNA-Seq and RNA-Seq) forms a triangle of experimental methods, corresponding to the three vertices of the central dogma, i.e., DNA, RNA and protein. Numerous RNA sequencing and protein mass spectrometry experiments has been carried out in attempt to understand how the expression change of known genes affect biological functions in various of organisms, however, it has been once overlooked that the result data of these experiments are in fact holograms which also reveals other delicate biological mechanisms, such as RNA splicing and the expression of long non-coding RNAs. In this dissertation, we carried out five studies based on high-throughput sequencing data, in an attempt to understand how RNA splicing and differential expression of long non-coding RNAs is associated biological functions. In the first two studies, we identified and characterized 197 stimulant induced and 477 developmentally regulated alternative splicing events from RNA sequencing data. In the third study, we introduced a method for identifying novel alternative splicing events that were never documented. In the fourth study, we introduced a method for identifying known and novel RNA splicing junctions from protein mass spectrometry data. In the fifth study, we introduced a method for identifying long non-coding RNAs from poly-A selected RNA sequencing data. Taking advantage of these methods, we turned RNA sequencing and protein mass spectrometry data into an information gold mine of splicing and long non-coding RNA activities.2019-05-0

Mesoscopic packing of disk-like building blocks in calcium silicate hydrate

At 100-nanometer length scale, the mesoscopic structure of calcium silicate hydrate (C-S-H) plays a critical role in determining the macroscopic material properties, such as porosity. In order to explore the mesoscopic structure of C-S-H, we employ two effective techniques, nanoindentation test and molecular dynamics simulation. Grid nanoindentation tests find different porosity of C-S-H in cement paste specimens prepared at varied water-to-cement (w/c) ratios. The w/c-ratio-induced porosity difference can be ascribed to the aspect ratio (diameter-to-thickness ratio) of disk-like C-S-H building blocks. The molecular dynamics simulation, with a mesoscopic C-S-H model, reveals 3 typical packing patterns and relates the packing density to the aspect ratio. Illustrated with disk-like C-S-H building blocks, this study provides a description of C-S-H structures in complement to spherical-particle C-S-H models at the sub-micron scale.Croucher Foundation (Start-up Allowance for Croucher Scholars with the Grant No. 9500012)Research Grants Council (Hong Kong, China) (through the Early Career Scheme (ECS) with the Grant No. 139113