Category: systems biology

Recap of my research journey (2004 to present)

April 19, 2024

My research journey started in May 2004 with a UROP (Undergraduate Research Opportunities Programme) project on biosorption of copper using local marine seaweed in Prof. Chen Jiaping’s lab at National University of Singapore. Currently, I am working on developing quantitative polymerase chain reaction (qPCR) assay and device for detecting Helicobacter pylori in stomach gastric samples. … More Recap of my research journey (2004 to present)

Yeast extract is a rich source of vitamins and growth factors for microbial culture

April 1, 2024

In the formulation of many microbial culture medium, it is inevitable to find yeast extract as a significant component of the complex medium. In simple terms, yeast extract is a rich source of vitamins and growth factors that enhance the microbiological medium, enabling it to culture more types of microbes, as well as take the … More Yeast extract is a rich source of vitamins and growth factors for microbial culture

Cost of synthesis is the main barrier to longer read RNA-sequencing

March 24, 2024

Modern RNA-sequencing relies on next-generation short read sequencing technologies to profile for the total ensemble of mRNA molecules in the sample. Conceptually, it is a formidable challenge as there are literally millions of mRNA molecules that need to be sequenced. The cost of this endeavour is also hefty. To reduce the cost to a manageable … More Cost of synthesis is the main barrier to longer read RNA-sequencing

RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

March 21, 2024

Understanding gene expression pattern of cells in different health and disease conditions have evolved from an academic curiosity 20 years ago into an almost essential aspect of many biological research workflows. The reason is our newfound ability at correlating gene expression pattern with cellular behaviour and phenotype. To this end, one technique stands out amongst … More RNA-seq is a label-free, unbiased genome scale transcriptome profiling technique

Expressing plant genes in yeast provides a platform for expedited elucidation of gene function

March 20, 2024

Plants have a long life cycle that meant months and often years are needed to elucidate gene function and their effect on plant cell physiology. However, the alternative approach of expressing plant genes in yeast provides a useful platform for expediting discovery of novel functions of genes. Specifically, the approach entails the molecular cloning of … More Expressing plant genes in yeast provides a platform for expedited elucidation of gene function

The need for more investment in bioseparation research in support of metabolic engineering and biotechnology

March 16, 2024

Metabolic engineering research has seen tremendous growth over the past 25 years, and has realised the production of many drugs and fuel compounds at least at the lab scale level. It uses a carefully choreographed series of genetic manipulations to endow microbial chassis cells with new and improved metabolic capabilities in aid of product formation. … More The need for more investment in bioseparation research in support of metabolic engineering and biotechnology

SDS-PAGE is the cheapest coarse proteomics tool

March 3, 2024

Interrogating the ensemble of proteins in a cellular system has become an important tool if we want to link gene expression pattern and observed phenotype. The method to do this is known broadly as proteomics, and the most popular proteomics approach is liquid chromatography mass spectrometry (LC-MS). However, LC-MS runs are time-consuming and costly. Hence, … More SDS-PAGE is the cheapest coarse proteomics tool

Evolution is often a necessary step in metabolic engineering research seeking to implement a new pathway into a species

February 6, 2024

Desire to optimise endogenous cellular metabolism or to prod a microbe to use a new unconventional substrate often requires the implementation of new metabolic pathway in a microbial chassis. While this can be done through a combination of gene overexpression and deletions, the new metabolic pathway often only allows slow growth for the species. This … More Evolution is often a necessary step in metabolic engineering research seeking to implement a new pathway into a species

Carbon-13 isotope labelling experiments can be implemented in two different ways to track the metabolic route in utilisation of a substrate

February 2, 2024

To show that metabolic flux flows along a designated path in heterologous metabolic engineering or to understand carbon flow within endogenous carbon metabolism, one needs a method for tracking carbon flow along particular pathways. The dominant approach for achieving this task is through carbon-13 isotope labelling. In this method, substrates with labelled carbon-13 atoms provided … More Carbon-13 isotope labelling experiments can be implemented in two different ways to track the metabolic route in utilisation of a substrate

Focus on a few biotechnology workhorse and model organisms have led us to neglect the rich microbial diversity represented by environmental microbiology

January 12, 2024

Much of fundamental and applied microbiology research has focused on model organism or biotechnology chassis workhorse. Focus on these organisms comes about due to the availability of tools for interrogating the experimental systems as well as the ability to translate findings from model organism to other species. However, biology is marked by diversity, and while … More Focus on a few biotechnology workhorse and model organisms have led us to neglect the rich microbial diversity represented by environmental microbiology