A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.

Here we describe an analytical platform for systems-level quantitative analysis of modified ribonucleosides in any RNA species, with a focus on stress-induced reprogramming of tRNA as part of a system of translational control of cell stress response. This chapter emphasizes strategies and caveats for each of the seven steps of the platform workflow: (1) RNA isolation, (2) RNA purification, (3) RNA hydrolysis to individual ribonucleosides, (4) chromatographic resolution of ribonucleosides, (5) identification of the full set of modified ribonucleosides, (6) mass spectrometric quantification of ribonucleosides, (6) interrogation of ribonucleoside datasets, and (7) mapping the location of stress-sensitive modifications in individual tRNA molecules. We have focused on the critical determinants of analytical sensitivity, specificity, precision, and accuracy in an effort to ensure the most biologically meaningful data on mechanisms of translational control of cell stress response.

Micromagnetic resonance relaxometry for rapid label-free malaria diagnosis.

We report a new technique for sensitive, quantitative and rapid detection of Plasmodium spp.-infected red blood cells (RBCs) by means of magnetic resonance relaxometry (MRR). During the intraerythrocytic cycle, malaria parasites metabolize large amounts of cellular hemoglobin and convert it into hemozoin crystallites.

A multidimensional platform for the purification of non-coding RNA species.

A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species.

iTRAQ-based quantitative proteomic analysis of Thermobifida fusca reveals metabolic pathways of cellulose utilization.

Thermobifida fusca is an aerobic, thermophilic, cellulose degrading bacterium identified in heated organic materials. This study applied iTRAQ quantitative proteomic analysis to the cellular and membrane proteomes of T. fusca grown in presence and absence of cellulose to elucidate the cellular processes induced by cellulose nutrient.

Quantitative iTRAQ secretome analysis of cellulolytic Thermobifida fusca.

Thermobifida fusca, a thermophilic bacterium belonging to Actinobacteria, is a major degrader of plant cell walls. The protein profiles of the secretome produced by T. fusca grown in cellulose, lignin, and mixture of cellulose and lignin containing culture media, promoting production of respective substrate hydrolyzing enzymes, was explored using a proteomics approach with high throughput isobaric tag for relative and absolute quantification (iTRAQ) technique using liquid chromatography-tandem mass spectrometry (LC-MS/MS).