23
DOI: https://doi.org/10.1186/s43141-023-00515-8
English
eng
Wimalagunasekara, Samadhi S.
Contributor
<p><ul id="issue-navigation" class="issue-navigation u-margin-s-bottom u-bg-grey1" style="box-sizing: border-box; margin-top: 0px; margin-right: 0px; margin-bottom: 16px !important; margin-left: 0px; padding: 0px; list-style: none; background-color: rgb(245, 245, 245) !important; overflow: hidden; font-size: 16px; line-height: 24px; color: rgb(31, 31, 31); font-family: ElsevierSans, Arial, Helvetica, Roboto, "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", STIXGeneral, "Cambria Math", "Arial Unicode MS", sans-serif; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;"><li class="previous move-left u-padding-s-ver u-padding-s-left" style="box-sizing: border-box; margin: 0px; padding-top: 16px !important; padding-right: 0px; padding-bottom: 16px !important; padding-left: 16px !important; float: left; left: 0px;"><a class="button-alternative button-alternative-tertiary u-display-flex button-alternative-icon-left" href="https://www.sciencedirect.com/science/article/pii/S1687157X23010521" style="box-sizing: border-box; margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; --sd-ui-button-alt-border-bottom-colour: transparent; --sd-ui-button-alt-border-bottom-colour-hover: #eb6500; --sd-ui-button-alt-border-bottom-width: 2px; --sd-ui-button-alt-colour: #1f1f1f; --sd-ui-button-alt-colour-focus: #eb6500; --sd-ui-button-alt-cursor: pointer; --sd-ui-button-alt-font-size: 1em; --sd-ui-button-alt-gap: calc(0.5em - 2px); --sd-ui-button-alt-min-width: 5.5rem; --sd-ui-button-alt-icon-background-colour: transparent; --sd-ui-button-alt-icon-background-colour-hover: transparent; --sd-ui-button-alt-icon-border-colour: #1f1f1f; --sd-ui-button-alt-icon-border-colour-hover: #eb6500; --sd-ui-button-alt-icon-fill: #1f1f1f; --sd-ui-button-alt-icon-fill-hover: #1f1f1f; --sd-ui-button-alt-icon-padding: 0.5rem; --sd-ui-button-alt-icon-size: 2.5rem; --sd-ui-button-alt-icon-external-link-size: 0.625rem; -webkit-box-align: baseline; align-items: baseline; border: none; color: rgb(31, 31, 31); cursor: pointer; display: flex !important; font-family: inherit; font-size: 16px; gap: 6px; line-height: 24px; min-width: 88px; text-decoration: none; user-select: text;"><svg focusable="false" viewBox="0 0 54 128" height="20" class="icon icon-navigate-left"><path d="M1 61l45-45 7 7-38 38 38 38-7 7z"></path></svg></a></li></ul></p><div class="Abstracts u-font-serif" id="abstracts" style="box-sizing: border-box; margin: 0px; padding: 0px; --sd-ui-line-height: calc(1em + 10px); line-height: 26px; font-family: ElsevierGulliver, Georgia, "Times New Roman", Times, STIXGeneral, "Cambria Math", "Lucida Sans Unicode", "Microsoft Sans Serif", "Segoe UI Symbol", "Arial Unicode MS", serif, sans-serif !important; color: rgb(31, 31, 31); font-size: 16px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal; orphans: 2; text-align: start; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; white-space: normal; text-decoration-thickness: initial; text-decoration-style: initial; text-decoration-color: initial;"><div class="abstract author" id="ab0005" style="box-sizing: border-box; margin: 0px 0px 8px; padding: 0px;"><div id="abs0005" style="box-sizing: border-box; margin: 0px; padding: 0px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0010" style="box-sizing: border-box; margin-top: 24px !important; margin-right: 0px; margin-bottom: 8px !important; margin-left: 0px; padding: 0px; font-weight: normal !important; font-size: 20px !important; line-height: 30px !important;">Background</h3><div class="u-margin-s-bottom" id="sp0080" style="box-sizing: border-box; margin-top: 0px; margin-right: 0px; margin-bottom: 16px !important; margin-left: 0px; padding: 0px;">The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved<span> </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/varietas" class="topic-link" style="box-sizing: border-box; margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">plant varieties</a><span style="box-sizing: border-box; margin: 0px; padding: 0px;">. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve<span> </span><a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/stress" class="topic-link" style="box-sizing: border-box; margin: 0px; padding: 0px; background-color: rgba(0, 0, 0, 0); word-break: break-word; text-decoration: underline 1px rgb(31, 31, 31); color: rgb(31, 31, 31); text-underline-offset: 1px;">stress tolerance</a>.</span></div></div><div id="abs0010" style="box-sizing: border-box; margin: 0px; padding: 0px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0015" style="box-sizing: border-box; margin-top: 24px !important; margin-right: 0px; margin-bottom: 8px !important; margin-left: 0px; padding: 0px; font-weight: normal !important; font-size: 20px !important; line-height: 30px !important;">Results</h3><div class="u-margin-s-bottom" id="sp0085" style="box-sizing: border-box; margin-top: 0px; margin-right: 0px; margin-bottom: 16px !important; margin-left: 0px; padding: 0px;">Here, the network module for root development was extracted from the global<span> </span><em style="box-sizing: border-box; margin: 0px; padding: 0px;">Oryza sativa</em><span> </span>PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs.</div></div><div id="abs0015" style="box-sizing: border-box; margin: 0px; padding: 0px;"><h3 class="u-h4 u-margin-m-top u-margin-xs-bottom" id="sect0020" style="box-sizing: border-box; margin-top: 24px !important; margin-right: 0px; margin-bottom: 8px !important; margin-left: 0px; padding: 0px; font-weight: normal !important; font-size: 20px !important; line-height: 30px !important;">Conclusions</h3><div class="u-margin-s-bottom" id="sp0090" style="box-sizing: border-box; margin-top: 0px; margin-right: 0px; margin-bottom: 16px !important; margin-left: 0px; padding: 0px;">These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.</div></div></div></div>
Elsevier
December 2023
pdf
Journal of Genetic Engineering and Biotechnology
Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa)
mixed material
Elsevier