A5073300511- Bioinformatics and Genomic Networks
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Mitochondrial Function and Pathology
- Fungal and yeast genetics research
- Protein Structure and Dynamics
- Gene Regulatory Network Analysis
- Advanced Proteomics Techniques and Applications
- DNA Repair Mechanisms
- Genomics and Phylogenetic Studies
- Evolution and Genetic Dynamics
- Enzyme Structure and Function
- Liver Disease Diagnosis and Treatment
- Machine Learning in Bioinformatics
- Angiogenesis and VEGF in Cancer
- Bacteriophages and microbial interactions
- Heat shock proteins research
- Biotin and Related Studies
- Metabolomics and Mass Spectrometry Studies
- RNA modifications and cancer
- Parkinson's Disease Mechanisms and Treatments
- Plant-Microbe Interactions and Immunity
- Genomics, phytochemicals, and oxidative stress
- CRISPR and Genetic Engineering
University of Regina
2016-2025
Christian Medical College & Hospital
2024
Stanford University
2023-2024
Shaheed Suhrawardy Medical College
2024
JSS Dental College and Hospital
2024
Rajendra Institute of Medical Sciences
2024
Regional Institute of Medical Sciences
2024
Education and Research Institute
2024
Dr. NTR University of Health Sciences
2024
Apollo Hospitals
2024
Protein and messenger RNA (mRNA) copy numbers vary from cell to in isogenic bacterial populations. However, these molecules often exist low are difficult detect single cells. We carried out quantitative system-wide analyses of protein mRNA expression individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent fusion library for Escherichia coli. found that almost all number distributions can be described by the gamma distribution two fitting parameters...
Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based chromatographic separation cultured cell extracts into more than one thousand biochemical fractions that were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network 13,993...
One-third of the 4,225 protein-coding genes Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted E. coli, including pathogenic strains. To elucidate orphans' biological roles, we performed an extensive proteomic survey using affinity-tagged strains and generated comprehensive genomic context inferences derive a high-confidence compendium for virtually...
Autophagy is a central homeostasis and stress response pathway conserved in all eukaryotes. One hallmark of autophagy the de novo formation autophagosomes. These double-membrane vesicular structures form around deliver cargo for degradation by vacuole/lysosome. Where how autophagosomes are outstanding questions. Here we show, using proteomic, cytological, functional analyses, that spatially, physically, functionally linked to endoplasmic reticulum exit sites (ERES), which specialized regions...
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and the associated proteins (Cas) comprise a system of adaptive immunity against viruses plasmids in prokaryotes. Cas1 is CRISPR-associated protein that common to all CRISPR-containing prokaryotes but its function remains obscure. Here we show purified Escherichia coli (YgbT) exhibits nuclease activity single-stranded branched DNAs including Holliday junctions, replication forks 5'-flaps. The crystal structure YgbT...
Large-scale proteomic analyses in Escherichia coli have documented the composition and physical relationships of multiprotein complexes, but not their functional organization into biological pathways processes. Conversely, genetic interaction (GI) screens can provide insights role(s) individual gene higher order associations. Combining information from both approaches should elucidate how complexes intersect functionally at a systems level. However, such integrative analysis has been...
As the interface between a microbe and its environment, bacterial cell envelope has broad biological clinical significance. While numerous biosynthesis genes pathways have been identified studied in isolation, how these intersect functionally to ensure integrity during adaptive responses environmental challenge remains unclear. To this end, we performed high-density synthetic genetic screens generate quantitative functional association maps encompassing virtually entire biosynthetic...
Connectivity webs mediate the unique biology of mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge their underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with mass spectrometry and machine learning to survey endogenous macromolecules across adult mouse We defined a global "interactome" comprising over one thousand multi-protein complexes. These include hundreds brain-selective assemblies that have...
Knowledge of protein-metabolite interactions can enhance mechanistic understanding and chemical probing biochemical processes, but the discovery endogenous ligands remains challenging. Here, we combined rapid affinity purification with precision mass spectrometry high-resolution molecular docking to precisely map physical associations 296 chemically diverse small-molecule metabolite 69 distinct essential enzymes 45 transcription factors in gram-negative bacterium Escherichia coli. We then...
There is an emerging interest in incorporating proteomic data for environmental health risk assessments. Meanwhile, the production and use of engineered nanomaterials (ENMs) with attractive physicochemical properties are expanding potential exposure, thus necessitating toxicity information on these materials analysis, where can be informative. Here, cells (A549 human lung epithelial J774A.1 mouse monocyte/macrophage cells) were exposed to ENMs (nanoforms SiO2and TiO2) different sizes surface...
Abstract Synthesis and accumulation of seed storage proteins (SSPs) is an important aspect the maturation program. Genes encoding SSPs are specifically highly expressed in during maturation. However, mechanisms that repress expression these genes leaf tissue not well understood. To gain insight into repression mechanisms, we performed a genetic screen for mutants express leaves. Here, show mutations affecting BRAHMA (BRM), SNF2 chromatin-remodeling ATPase, cause ectopic subset other...
Improved efforts are necessary to define the functional product of cancer mutations currently being revealed through large‐scale sequencing efforts. Using genome‐scale pooled shRNA screening technology, we mapped negative genetic interactions across a set isogenic cell lines and confirmed hundreds these in orthogonal co‐culture competition assays generate high‐confidence interaction network differentially essential or differential essentiality (DiE) genes. The uncovered examples conserved...
Protein-correlation-profiling (PCP), in combination with quantitative proteomics, has emerged as a high-throughput method for the rapid identification of dynamic protein complexes native conditions. While PCP been successfully applied to soluble proteomes, characterization membrane interactome lagged, partly due necessary use detergents maintain solubility. Here, we apply peptidisc, ‘one-size fits all’ mimetic, capture Escherichia coli cell envelope proteome and its high-resolution...