cnor_pub

Description

This repository includes the experimental data collected for the reduction of NO to N₂O by purified Paracoccus denitrificans cytochrome c nitric oxide reductase (cNOR) and the R code used to analyze these data.

Getting started

To clone the remote repository to your local drive and create a new directory on your local drive at the same time:

• Go to the parent directory where you want to put this repository:

  cd parent_directory
  

• Clone this remote repo into a new sub-directory and navigate to that sub-directory.

  • For GitHub (non-GLBRC) users:

  git clone https://github.com/GLBRC/cnor_pub
  cd cnor_pub
  

  • For GLBRC users:

  git clone https://gitpub.wei.wisc.edu/rivettel/cnor_pub.git
  cd cnor_pub
  

Cloning the repository will create three sub-directories under cnor_pub:

• code includes markdown (.qmd) files with code written in R
  • exp_cNOR_pub - code for analyzing the experimental isotopic (GC-IRMS) data presented in the main text
  • controls_cNOR_pub - code for analyzing the control GC-ECD and GC-IRMS data
• data includes: experimental data (.csv files) under input, and output (initially empty)
• graphs (initially empty)

Running the code will create additional files that will be stored in these sub-directories. To write files properly, the package here has to be loaded in cnor_pub.

Data

exp_cNOR_pub

• cNOR_all_raw.csv
  • All isotopic data from the first set of experiments
  • Includes data collected after N₂O production plateaued
• cNOR_raw.csv
  • The isotopic data presented in the main text and used to determine KIEs (Figures 1-3, Table 1, Figures S5-6, Table S1)
  • Excludes data collected after N₂O production plateaued
  • Note that this file can also be generated using cNOR_all_raw.csv as input and running the controls_cNOR_pub code.

controls_cNOR_pub

• no_enzyme_GC-ECD.csv
  • GC-ECD data for no-enzyme negative controls (Figure S7)
• controls_all.csv
  • All isotopic data from the second set of experiments (N₂O production measured in the presence or absence of H₂¹⁸O-enriched water)
  • Includes data where f is greater than or equal to 0.9
  • Includes data collected after N₂O production plateaued
  • Includes outliers
• controls.csv
  • The isotopic data from the second set of experiments presented in Figures S1-4 and Table S2 (N₂O production measured in the presence or absence of H₂¹⁸O-enriched water)
  • Excludes data where f is greater than or equal to 0.9
  • Excludes data collected after N₂O production plateaued
  • Excludes outliers identified with Grubbs' test
  • Note that this file can also be generated using controls_all.csv as input and running the exp_cNOR_pub code.

General outline for analyzing experimental data

• Load packages
• Load data
• Calculate additional values needed for analysis
• Remove observations
  • Where f is greater than or equal to 0.9
  • After N₂O production plateaued
• Combine (pool) data from all replicates
• Apply standard Rayleigh model to bulk N
  • Perform Grubbs' test for outliers
  • Remove outlier and reapply standard Rayleigh model if necessary
• Plot data
• Apply Expanded Rayleigh model to determine KIE_alpha and KIE_beta
• Combine results in summary table(s)
• Bootstrapping (if needed)

Authors

Elise Rivett

References

Grubbs, F. E. (1950) Sample criteria for testing outlying observations, Ann Math Stat 21, 27-58.

Komsta, L. (2006) Processing data for outliers, R News 6, 10-13.

Rivett, E. D., Ma, W., Ostrom, N. E., and Hegg, E. L. (2024) Position-specific kinetic isotope effects for nitrous oxide: a new expansion of the Rayleigh model, Biogeosciences 21, 4549-4567.