The Bacterial Nucleoid

Homologous Recombineering to Generate Chromosomal Deletions in Escherichia coli.- Measuring In Vivo Supercoil Dynamics and Transcription Elongation Rates in Bacterial Chromosomes.- Revealing Sister Chromatid Interactions with the loxP/Cre Recombination Assay.- Transposon Insertion Site Sequencing for Synthetic Lethal Screening.- WGADseq: Whole Genome Affinity Determination of Protein-DNA Binding Sites.- High Resolution Chromatin Immunoprecipitation: ChIP-Sequencing.- Generation and Analysis of Chromosomal Contact Maps of Bacteria.- Nucleoid Associated Proteins: Genome Level Occupancy and Expression Analysis.- Isolation and Analysis of RNA Polymerase Supramolecular Complex with Associated Proteins.- A chromosome Co-Entrapment Assay to Study Topological Protein-DNA Interactions.- Tethered Particle Motion Analysis of the DNA Binding Properties of Architectural Proteins.- Biochemical Analysis of Bacterial Condensins.- Exploring Condensins with Magnetic Tweezers.- Applications of Magnetic Tweezers to Studies of NAPs.- A User-Friendly DNA Modeling Software for the Interpretation of Cryo-Electron Microscopy Data.- Multi-Locus Imaging of the E. coli Chromosome by Fluorescent In Situ Hybridization.- Imaging the Cell Cycle of Pathogen E. coli During Growth in Macrophage.- Measuring In Vivo Protein Dynamics throughout the Cell Cycle using Microfluidics.- Imaging of Bacterial Chromosome Organization by 3D Super-Resolution Microscopy.- Sequential Super-Resolution Imaging of Bacterial Regulatory Proteins, the Nucleoid and the Cell Membrane in Single, Fixed E. coli Cells.- Procedures for Model-Guided Data Analysis of Chromosomal Loci Dynamics at Short Time Scales.- Isolation and Characterization of Bacterial Nucleoids in Microuidic Devices.- Modeling Bacterial DNA: Simulation of Self-Avoiding Supercoiled Worm-Like Chains Including Structural Transitions of the Helix.- Molecular Dynamics Simulation of Supercoiled, Knotted and Catenated DNA Molecules, Including Modeling of Action of DNA Gyrase.