SCAPA (Spacially Addressable Protein Array) – a Novel Protein Array for the Differential Profiling of Ligand-receptor Induced Signalling

While protein microarray technology has been successful in demonstrating its usefulness for large scale high-throughput proteome profiling, performance of antibody/antigen microarrays has been only moderately productive. Immobilization of either the capture antibodies or the protein samples on solid supports has severe drawbacks. Denaturation of the immobilized proteins as well as inconsistent orientation of antibodies/ligands on the arrays can lead to erroneous results. This has prompted a number of studies to address these challenges by immobilizing proteins on biocompatible surfaces, which has met with limited success. Our strategy relates to a multiplexed, sensitive and high-throughput method for the screening quantification of intracellular signalling proteins from a complex mixture of proteins. Each signalling protein to be monitored has its capture moiety linked to a specific oligo âtag’. The array involves the oligonucleotide hybridization-directed localization and identification of different signalling proteins simultaneously, in a rapid and easy manner. Antibodies have been used as the capture moieties for specific identification of each signaling protein. The method involves covalently partnering each antibody/protein molecule with a unique DNA or DNA derivatives oligonucleotide tag that directs the antibody to a unique site on the microarray due to specific hybridization with a complementary tag-probe on the array. Particular surface modifications and optimal conditions allowed high signal to noise ratio which is essential to the success of this approach.Singapore-MIT Alliance (SMA

Protein Microarray: "Theory" to "Real Practice"

Fueled by ever-growing genomic information and rapid developments of proteomics–the large scale analysis of proteins and mapping its functional role has become one of the most important disciplines for characterizing complex cell function. For building functional linkages between the biomolecules, and for providing insight into the mechanisms of biological processes, last decade witnessed the exploration of combinatorial and chip technology for the detection of bimolecules in a high throughput and spatially addressable fashion. Among the various techniques developed, the protein chip technology has been rapid. Recently we demonstrated a new platform called “Spacially addressable protein array” (SAPA) to profile the ligand receptor interactions. To optimize the platform, the present study investigated various parameters such as the surface chemistry and role of additives for achieving high density and high-throughput detection with minimal nonspecific protein adsorption. In summary the present poster will address some of the critical challenges in protein micro array technology and the process of fine tuning to achieve the optimum system for solving real biological problems.Singapore-MIT Alliance (SMA

Design, Fabrication and Functional Analysis of a New Protein Array Based on ssDNA-based Assembly

In the post genomic era, proteomics has enormous potential in biology and medicine. Among the various bioanalytical tools developed, protein microarray is one of the recent advancements which offer high throughput profiling of cellular proteins to provide insights into the mechanisms of biological processes. Fundamentally, the protein microarray involves the immobilization of interacting elements, proteins, on a few square microns of a solid support and in principle, it is capable of detecting analytes with a higher sensitivity than conventional macroscopic immunoassays. Here in the present report we delineates the design, fabrication and functional analysis of protein microarray using semi-synthetic ssDNA tagged-proteins as capturing moiety as well as address on a solid support. Optimization of the platform has been carried out by investigating various parameters such as surface chemistry, signal amplification, and conditions for homogenous liguid phase protein-protein interaction.Singapore-MIT Alliance (SMA

DNA Directed Assembly Probe for Detecting DNA-Protein Interaction in Microarray Format

Quantifying DNA-protein interaction using DNA microarrays are gaining increasing attention due to their ability to profile specificity of interactions in a high-throughput manner. This paper describes a new approach that used the ability of ssDNA-dsDNA probe to complex with DNA binding proteins in the solution phase and then spatially immobilized onto microarray through specific DNA hybridization. In one case, the Spatially Addressable DNA Array (SADA) approach demonstrated that enzymatic cleavage in solution is more efficient than if conducted heterogeneously. In addition, binding of RNA polymerase with promoter DNA could be detected with this strategy.Singapore-MIT Alliance (SMA

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

A Preliminary Study in Rationalizing the Need for the Goldilocks Principle in Manufacturing SMEs

The Goldilocks principle has been widely used in the medical science and psychology fields. However, there appear to be many areas where this principle can be explored in social science research. The main objective of this study is to rationalize the need for the Goldilocks principle by observing the effect of fatigue and stress on human error in manufacturing SMEs. A total of 190 questionnaires were collected and analyzed in SmartPLS version 3. It was found that the alternative hypotheses were supported with p-values below 0.05. The authors suggested that manufacturing companies should set a work record of the task completion time and consider the average time as grace duration in performing the task. An organization is advised to refrain from giving extra time or too little time in completing a task. The timeframe should be based on the task complexity or task familiarity of the overall organization. This study benefits the manufacturing companies as it can serve as a guideline on HR policies and working hours

Blending a sweet pill to swallow with TRIZ and industry talks for enhanced learning during the COVID-19 pandemic

While studies have investigated relationships among learning motivation, social presence, and cognitive presence, there appear to be no studies on the inclusion of industry talks and the theory of inventive problem-solving (TRIZ) in strengthening engineering students’ learning motivation, social presence, and cognitive presence within a blended learning setting. OBJECTIVE: This study investigated the influence of industry talks and TRIZ on learning motivation, social presence, and cognitive presence in a blended learning environment. METHODS: Data samples were obtained from 98 engineering students in a blended learning course and analysed using Spearman’s correlation test, regression, ANOVA, and t-test. RESULTS: Findings suggested that TRIZ and industry talks strongly, positively, and significantly correlated with learning motivation, social presence, and cognitive presence. A well-rounded learning experience compounded of TRIZ and industry talks significantly affected learning motivation, social presence, and cognitive presence, thereby enhancing students’ programme outcome (PO) achievement. CONCLUSIONS: These findings can be attributed to the students’ independent learning capabilities with TRIZ and industry talks. Analogically, embracing TRIZ and industry talks helps turn blended learning into a “sweet instead of bitter pill to swallow” for engineering students in the face of the COVID-19 pandemic