Bacterial Chromatin

<p>1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Determination of the 3D Genome Organization of Bacteria using Hi-C</p>

<p>Frédéric G. Crémazy, Fatema-Zahra M. Rashid, James R. Haycocks, Lisa E. Lamberte, David C. Grainger, and Remus T. Dame</p>

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<p>2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Overview of Processing and Analyzing Hi-C Data on Bacteria</p>

<p>Andreas Hofmann and Dieter W. Heermann </p>

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<p>3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; GeF-seq：A Simple Procedure for Base Pair Resolution ChIP-seq</p>

<p>Onuma Chumsakul,Kensuke Nakamura, Shu Ishikawa, and Taku Oshima</p>

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<p>4.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Genomic SELEX Screening of Regulatory Targets of Escherichia coli Transcription Factors</p>

<p>Tomohiro Shimada, Hiroshi Ogasawara, and Akira Ishihama</p>

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<p>5.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Modular assembly of Synthetic Secondary Chromosomes</p>

<p>Celine Zumkeller, Daniel Schindler, and Torsten Waldminghaus</p>

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<p>6.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; High-resolution Characterization of DNA/Protein Complexes in Living Bacteria</p>

<p>Nicole A. Becker, Justin P. Peters, and L. James Maher, III</p>

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<p>7.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Imaging of Transcription and Replication in the Bacterial Chromosome with Multicolor Three-dimensional Superresolution Structured Illumination Microscopy </p>

<p>Carmen Mata Martin, Cedric Cagliero, Zhe Sun, and Ding Jun Jin </p>

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<p>8.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Genetic Approaches to Study the Interplay Between Transcription and Nucleoid-associated Proteins in Escherichia coli</p>

<p>Karin Schnetz</p>

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<p>Part I: In vitro approaches</p>

<p>9.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Atomic Force Microscopy Imaging and Analysis of Prokaryotic Genome Organization</p>

<p>Ryosuke L. Ohniwa, Hugo Maruyama, Kazuya Morikawa, and Kunio Takeyasu</p>

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<p>10.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Dynamic Light Scattering of DNA-ligand Complexes</p>

Guangcan Yang and Yanwei Wang<p></p>

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<p>11.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Microscale Thermophoresis Analysis of Chromatin Interactions</p>

Ivan Corbeski, Velten Horn, Ramon A. van der Valk, Ulric le Paige, Remus T. Dame,and Hugo van Ingen<p></p>

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<p>12.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Quantitative Determination of DNA Bridging Efficiency of Chromatin Proteins</p>

<p>Ramon A. van der Valk, Qin Liang, Geri F. Moolenaar, ^&nbsp;and Remus T. Dame</p>

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<p>13.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Approaches for Determining DNA Persistence Length using Atomic Force Microscopy</p>

<p>Justin P. Peters and L. James Maher, III</p>

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<p>14.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Quantitation of DNA Binding Affinity using Tethered Particle Motion</p>

<p>Bram Henneman, Joost Heinsman, Julius Battjes, and Remus T. Dame</p>

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<p>15.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Observing Bacterial Chromatin Protein-DNA Interactions by Combining DNA Flow-stretching with Single-molecule Imaging</p>

<p>HyeongJun Kim and Joseph J. Loparo</p>

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<p>16.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Unravelling the Biophysical Properties of Chromatin Proteins and DNA using Acoustic Force Spectroscopy<br> Szu-Ning Lin, Liang Qin, Gijs J. L. Wuite and Remus T. Dame</p>

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17.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Unravelling DNA organization with single-molecule Force Spectroscopy using Magnetic Tweezers<br> Thomas B. Brouwer, Artur Kaczmarczyk, Chi Pham, and John van Noort<p></p>

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<p>18.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; In Vitro Transcription Assay to Quantify Effects of H-NS Filaments on RNA Chain Elongation by RNA Polymerase<br> Beth A. Boudreau, Matthew V. Kotlajich, and Robert Landick</p>

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<p>Part II: In Silico Approaches</p>

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<p>19.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Deciphering 3D Organization Of Chromosomes using Hi-C Data</p>

<p>Andreas Hofmann and Dieter W. Heermann </p>

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<p>20.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Molecular Dynamics Simulation of a Feather-boa Model of Bacterial Chromosome</p>

<p>Debasish Chaudhuri and Bela M. Mulder </p>