Challenges of protein identification by MALDI-TOF mass spectrometry

The gold standard approach for identifying a protein is Western blot, which uses a primary antibody to recognize the target protein for subsequent visualization of the protein band by chemiluminescence. More recently, various mass spectrometry-based methods have been developed for the detection and identification of proteins.   These techniques could be classified into fragmentation-based methods … More Challenges of protein identification by MALDI-TOF mass spectrometry

Endosymbiosis may have occurred more than once

Multiple theories exist to explain the occurrence of endosymbiosis, which is the leading theory outlining the sequence of events that led to the formation of modern cells. Specifically, modern cells are ancestral prokaryotic cells nestled within an eukaryotic host cell. For example, mitochondrion in cells have been identified as ancestral prokaryotic cells that evolved into … More Endosymbiosis may have occurred more than once

Computer modelling for fitting possible structures to diffraction data

Modern structural biology is a combination of diffraction experiments using X-rays or electron, and computer simulation for fitting possible structures to the diffraction data.   Specifically, after protein crystallization and determination of structure through X-ray diffraction or cryo-electron microscopy, the resulting data remains difficult to understand. Thus, molecular simulation tools such as molecular dynamics are … More Computer modelling for fitting possible structures to diffraction data

Inability to achieve atomic resolution structure for molecular complexes such as ribosome through molecular dynamics simulation

Contemporary state-of-the-art structure elucidation studies typically employ molecular dynamics simulation to provide an atomistic view of the molecules under study. While useful in providing guidance to the potential structural conformation space available to the molecule, molecular dynamics data remains an educated guess of the true conformations of the molecules. More importantly, atomistic molecular dynamics simulations … More Inability to achieve atomic resolution structure for molecular complexes such as ribosome through molecular dynamics simulation

Cryo electron microscopy’s increasingly important role in structural biology

Cryo electron microscopy has been increasingly used in determining the structure of biomolecules such as proteins down to the atomic resolution level of 2 to 4 Angstrom. More importantly, capable of determining the native structure of proteins in frozen solutions, the method is finding increasing use in protein structure elucidation. Specifically, cryo electron microscopy find … More Cryo electron microscopy’s increasingly important role in structural biology

How to confirm that a microbe could grow in minimal salts medium?

Growth in a minimal salts medium signifies that a microbe has a competitive advantage over other microbial species for nutrients and, more importantly, environmental habitats. But, how should one confirm that a microbe could grow in minimal salts medium? Specifically, should the inoculum contain any trace of a rich medium? The answer to the latter … More How to confirm that a microbe could grow in minimal salts medium?

Gut microbiome changes in sync with food intake pattern

Gut microbiome is the consortium of microorganisms that inhabit the mucous membrane lining the large and small intestines, and is responsible for many body functions such as digestion of food and regulation of overall intestinal health. A recent study reported in the New York Times (Link) reveals that the gut microbiome of a population in … More Gut microbiome changes in sync with food intake pattern

Field deployable DNA sequencers

Since its inception in the 1990s, multiple revolutions have occurred in the field of DNA sequencing, where successive iterations of the technology enabled more reliable and less error prone sequencing of increasingly larger segments of DNA from a variety of sources such as human, bacteria, fungi, viruses etc. Indeed, DNA sequencing technology has revolutionized biology … More Field deployable DNA sequencers

Utility of co-expression analysis

In biology, researchers often seek to understand the factors that underpin a particular cellular process or diseased state. Thus, this line of thinking necessarily result in experiment design that seek to correlate molecular events with cellular processes, which could be readout experimentally, either through microscopy techniques or enzymatic biochemical assays. More generally, co-expression analysis is … More Utility of co-expression analysis