List of base-pair substitutions in "The symmetrical pattern of base-pair substitutions rates across the chromosome in Escherichia coli has multiple causes"
There are two files: a README describing the main data file, and a main data file.
The main data file is plain ASCII, tab delimited, with header comments.
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Data set for article "Links among inflammation, sexual activity and ovulation: Evolutionary trade-offs and clinical implications"
These matlab files were produced by a Macintosh computer running Matlab version 2015. Files with the extension *.m are unformatted text files that can be opened with any text editor. They are Matlab scripts and functions that can be opened and executed by Matlab. Files with the extension *.mat are binary data files that can be opened only by Matlab. These Matlab files are intended for readers of the monograph “Fourier Analysis for Beginners” who wish to review numerical examples and exercises mentioned in the text. The full text of the book can be downloaded at http://hdl.handle.net/2022/21365 .
The Bedrock Geologic Map of the Southern Half of the Knox 30- X 60-Minute Quadrangle was created to provide digital access to the bedrock geology of southern half of the Knox quadrangle in northern Indiana. This geodatabase presents basic bedrock geological information that contributes to the characterization of potential mineral resources and bedrock aquifer systems. The data are synthesized from archived public domain geological data obtained from many different sources, original data obtained from fieldwork conducted by the authors, and contract drilling supported by project funds. Archive data sources include petroleum-well records, water-well records, refraction seismic surveys, and the geological literature. Project data includes measurements from quarry exposures, drill cores, drill cuttings, geophysical logs, chemostratigraphic analysis via portable X-ray fluorescence and stable isotope ratio mass spectrometry, conodont biostratigraphy, and horizontal-to-vertical spectral ratio geophysical surveys. This database is, in large part, the result of a cooperative mapping agreement between the U.S. Geological Survey (USGS) and the Indiana Geological and Water Survey through the STATEMAP program of the USGS.
The Quaternary Geology of the Indiana Portion of the Eastern Extent of the South Bend 30- x 60-Minute Quadrangle was created to provide digital access to the Quaternary geology of the eastern extent of the South Bend 30- x 60-minute quadrangle in Indiana. This geodatabase presents basic Quaternary geological information that contributes to the development of a three-dimensional framework of the state of Indiana. The data are synthesized from archived public domain geological data obtained from many different sources, original data obtained from fieldwork conducted by the authors, and contract drilling supported by project funds. Archive data sources include water-well records, refraction seismic surveys, borehole descriptions and geophysical logs, and the geological literature. Project data includes observations and measurements from drilled and sampled boreholes and estimated bedrock depths from analysis of horizontal-vertical spectral ratios (HVSR) seismic measurements. This database is, in large part, the result of a cooperative mapping agreement between the U.S. Geological Survey (USGS) and the Indiana Geological and Water Survey through the STATEMAP program of the USGS.
Antinao, J. L., and Rupp, R. F., 2021, Quaternary geology of the Indiana portion of the eastern extent of the South Bend 30- x 60-minute quadrangle: Indiana Geological and Water Survey, Indiana Journal of Earth Sciences, v. 3, scale 1:100,000. doi: 10.14434/ijes.v3i0.31698
Title:
Quaternary Geology of the Indiana Portion of the Eastern Extent of the South Bend 30- x 60-Minute Quadrangle
To gain insight into how the POP scaffold might give rise to the observed ArM selectivity, molecular dynamics simulations were conducted on models of 5-G that involved different starting coordination states of dirhodium cofactor 1. Three starting coordination states (5-G apo, 5-G with parameterized Rh-His bond, 5-G without Rh-His bond) were studied. The initial structure of 5-G apo was constructed from the crystal structure of POP, with the following amino acids mutations made using VMD17: S477F/E104A/F146A/K199A/D202A/S301G/G99S/Y326H/Q98P/S99H/V71G/E283G. The 5-G with Rh-His and 5-G without Rh-His bond models were constructed by mutating S477Z (Z is azidophenylalanine, where dirhodium cofactor 1 covalently links to the protein), which is the only other mutation from 5-G apo. No other changes where made to the model without a Rh-His bond. The Rh-His model contains a parameterized H326 bond to one of the dirhodium atoms, as shown in Figure 2D.
MD simulations were performed for the 5-G apo, with Rh-His and no Rh-His POP enzymes. All three structures were bathed in a 0.15M KCl solution using the Solution Builder Module in CHARMM-GUI.18 These systems were roughly 100 100 100 Å3 in dimension and contained ~ 110,000 atoms. The periodic boundary conditions were counted using the particle-mesh Ewald method with an automatic generated grid size.
Once the simulation systems were generated, they were subjected to equilibration at 358.15 K. The system was first equilibrated in an NVT ensemble for 10 ns. The equilibration simulations were performed using NAMD2.14 GPU acceleration version package19 on Nvidia’s P100 GPUs. After equilibration, the systems were simulated for 1000 ns each in an NPT ensemble with temperature set to 358.15 K and the isotropic pressure set to 1 atm. Langevin thermostats with a damping coefficient of 1 ps-1 were used to keep the temperature constant. The cutoff of the van der Waals interactions and short-range electrostatic interactions were set to ~25 Å as suggested by the guesser script. The additive C36 force field was used in all the simulations performed here.20,21,22,23 The force field parameters for the covalently linked dirhodium cofactor 1 were generated using the GAAMP server.24
