\documentclass[10pt]{article}

\usepackage{fullpage}
\usepackage{setspace}
\usepackage{parskip}
\usepackage{titlesec}
\usepackage[section]{placeins}
\usepackage{xcolor}
\usepackage{breakcites}
\usepackage{lineno}
\usepackage{hyphenat}





\PassOptionsToPackage{hyphens}{url}
\usepackage[colorlinks = true,
            linkcolor = blue,
            urlcolor  = blue,
            citecolor = blue,
            anchorcolor = blue]{hyperref}
\usepackage{etoolbox}
\makeatletter
\patchcmd\@combinedblfloats{\box\@outputbox}{\unvbox\@outputbox}{}{%
  \errmessage{\noexpand\@combinedblfloats could not be patched}%
}%
\makeatother


\usepackage{natbib}




\renewenvironment{abstract}
  {{\bfseries\noindent{\abstractname}\par\nobreak}\footnotesize}
  {\bigskip}

\titlespacing{\section}{0pt}{*3}{*1}
\titlespacing{\subsection}{0pt}{*2}{*0.5}
\titlespacing{\subsubsection}{0pt}{*1.5}{0pt}


\usepackage{authblk}


\usepackage{graphicx}
\usepackage[space]{grffile}
\usepackage{latexsym}
\usepackage{textcomp}
\usepackage{longtable}
\usepackage{tabulary}
\usepackage{booktabs,array,multirow}
\usepackage{amsfonts,amsmath,amssymb}
\providecommand\citet{\cite}
\providecommand\citep{\cite}
\providecommand\citealt{\cite}
% You can conditionalize code for latexml or normal latex using this.
\newif\iflatexml\latexmlfalse
\providecommand{\tightlist}{\setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}%

\AtBeginDocument{\DeclareGraphicsExtensions{.pdf,.PDF,.eps,.EPS,.png,.PNG,.tif,.TIF,.jpg,.JPG,.jpeg,.JPEG}}

\usepackage[utf8]{inputenc}
\usepackage[english]{babel}



\usepackage{float}








\begin{document}

\title{Differential protein expression during growth on model and commercial
mixtures of naphthenic acids in Pseudomonas fluorescens Pf-5}



\author[1]{Boyd McKew}%
\author[1]{Richard Johnson}%
\author[2]{Lindsey Clothier}%
\author[1]{Karl Skeels}%
\author[3]{Matthew Ross}%
\author[1]{Metodi Metodiev}%
\author[4]{Max Frenzel}%
\author[5]{Lisa Gieg}%
\author[6]{Jonathan Martin}%
\author[1]{Michael Hough}%
\author[1]{Corinne Whitby}%
\affil[1]{University of Essex}%
\affil[2]{Nautilus Environmental}%
\affil[3]{MacEwan University}%
\affil[4]{Oil Plus Ltd}%
\affil[5]{University of Calgary}%
\affil[6]{Stockholm University}%


\vspace{-1em}



  
  \date{May 25, 2024}


\begingroup
\let\center\flushleft
\let\endcenter\endflushleft
\maketitle
\endgroup





\selectlanguage{english}
\begin{abstract}
Naphthenic acids (NAs) are carboxylic acids with the formula (CnH2n+ZO2)
and are the toxic, persistent constituents of oil sands process-affected
waters (OSPW), produced during oil sands extraction. Currently, the
proteins and mechanisms involved in NA biodegradation are unknown. Using
LC-MS/MS shotgun proteomics, we identified proteins overexpressed during
the growth of Pseudomonas fluorescens Pf5 on a model NA
(4-n-butylphenyl)-4-butanoic acid (n-BPBA) and commercial NA mixture
(Acros). By day 11, \textgreater{}95\% of n-BPBA was degraded. With
Acros, a 17\% reduction in intensity occurred with 10-18 carbon
compounds of the Z family -2 to -14 (major NA species in this mixture).
A total of 554 proteins (n-BPBA) and 631 proteins (Acros) were
overexpressed during growth on NAs; including several transporters (e.g.
ABC transporters), suggesting a cellular protective response from NA
toxicity. Several proteins associated with fatty acid, lipid and amino
acid metabolism were also overexpressed; including acyl-CoA
dehydrogenase and acyl-CoA thioesterase II, which catalyze part of the
fatty acid beta-oxidation pathway. Indeed, multiple enzymes involved in
the fatty acid oxidation pathway were upregulated. Given the presumed
structural similarity between alkyl-carboxylic acid side chains and
fatty acids, we postulate that P. fluorescens Pf-5 was using existing
fatty acid catabolic pathways (among others) during NA degradation.%
\end{abstract}%



\sloppy


\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig1FINAL/Fig1FINAL}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig2FINAL/Fig2FINAL}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig3FINAL/Fig3FINAL}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig4FINAL/Fig4FINAL}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig5FINAL/Fig5FINAL}

\end{center}
\end{figure}\selectlanguage{english}
\begin{figure}[H]
\begin{center}
\includegraphics[width=0.70\columnwidth]{figures/Fig6FINAL/Fig6FINAL}

\end{center}
\end{figure}

\selectlanguage{english}
\FloatBarrier
\end{document}

