@article{matthiadis_long_2016, title={Further insight into BRUTUS domain composition and functionality}, volume={11}, ISSN={["1559-2324"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84986575665&partnerID=MN8TOARS}, DOI={10.1080/15592324.2016.1204508}, abstractNote={ABSTRACT BRUTUS (BTS) is a hemerythrin (HHE) domain containing E3 ligase that facilitates the degradation of POPEYE-like (PYEL) proteins in a proteasomal-dependent manner. Deletion of BTS HHE domains enhances BTS stability in the presence of iron and also complements loss of BTS function, suggesting that the HHE domains are critical for protein stability but not for enzymatic function. The RING E3 domain plays an essential role in BTS' capacity to both interact with PYEL proteins and to act as an E3 ligase. Here we show that removal of the RING domain does not complement loss of BTS function. We conclude that enzymatic activity of BTS via the RING domain is essential for response to iron deficiency in plants. Further, we analyze possible BTS domain structure evolution and predict that the combination of domains found in BTS is specific to photosynthetic organisms, potentially indicative of a role for BTS and its orthologs in mitigating the iron-related challenges presented by photosynthesis.}, number={8}, journal={PLANT SIGNALING & BEHAVIOR}, author={Matthiadis, Anna and Long, Terri A.}, year={2016} }
 @article{koryachko_matthiadis_muhammad_foret_brady_ducoste_tuck_long_williams_2015, title={Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response}, volume={10}, ISSN={["1932-6203"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84943338816&partnerID=MN8TOARS}, DOI={10.1371/journal.pone.0136591}, abstractNote={Time course transcriptome datasets are commonly used to predict key gene regulators associated with stress responses and to explore gene functionality. Techniques developed to extract causal relationships between genes from high throughput time course expression data are limited by low signal levels coupled with noise and sparseness in time points. We deal with these limitations by proposing the Cluster and Differential Alignment Algorithm (CDAA). This algorithm was designed to process transcriptome data by first grouping genes based on stages of activity and then using similarities in gene expression to predict influential connections between individual genes. Regulatory relationships are assigned based on pairwise alignment scores generated using the expression patterns of two genes and some inferred delay between the regulator and the observed activity of the target. We applied the CDAA to an iron deficiency time course microarray dataset to identify regulators that influence 7 target transcription factors known to participate in the Arabidopsis thaliana iron deficiency response. The algorithm predicted that 7 regulators previously unlinked to iron homeostasis influence the expression of these known transcription factors. We validated over half of predicted influential relationships using qRT-PCR expression analysis in mutant backgrounds. One predicted regulator-target relationship was shown to be a direct binding interaction according to yeast one-hybrid (Y1H) analysis. These results serve as a proof of concept emphasizing the utility of the CDAA for identifying unknown or missing nodes in regulatory cascades, providing the fundamental knowledge needed for constructing predictive gene regulatory networks. We propose that this tool can be used successfully for similar time course datasets to extract additional information and infer reliable regulatory connections for individual genes.}, number={8}, journal={PLOS ONE}, author={Koryachko, Alexandr and Matthiadis, Anna and Muhammad, Durreshahwar and Foret, Jessica and Brady, Siobhan M. and Ducoste, Joel J. and Tuck, James and Long, Terri A. and Williams, Cranos}, year={2015}, month={Aug} }
 @article{selote_samira_matthiadis_gillikin_long_2015, title={Iron-Binding E3 Ligase Mediates Iron Response in Plants by Targeting Basic Helix-Loop-Helix Transcription Factors}, volume={167}, ISSN={["1532-2548"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84920141665&partnerID=MN8TOARS}, DOI={10.1104/pp.114.250837}, abstractNote={Abstract}, number={1}, journal={PLANT PHYSIOLOGY}, author={Selote, Devarshi and Samira, Rozalynne and Matthiadis, Anna and Gillikin, Jeffrey W. and Long, Terri A.}, year={2015}, month={Jan}, pages={273-+} }
 @misc{gonzalez-guerrero_matthiadis_saez_long_2014, title={Fixating on metals: new insights into the role of metals in nodulation and symbiotic nitrogen fixation}, volume={5}, ISSN={["1664-462X"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84901021951&partnerID=MN8TOARS}, DOI={10.3389/fpls.2014.00045}, abstractNote={Symbiotic nitrogen fixation is one of the most promising and immediate alternatives to the overuse of polluting nitrogen fertilizers for improving plant nutrition. At the core of this process are a number of metalloproteins that catalyze and provide energy for the conversion of atmospheric nitrogen to ammonia, eliminate free radicals produced by this process, and create the microaerobic conditions required by these reactions. In legumes, metal cofactors are provided to endosymbiotic rhizobia within root nodule cortical cells. However, low metal bioavailability is prevalent in most soils types, resulting in widespread plant metal deficiency and decreased nitrogen fixation capabilities. As a result, renewed efforts have been undertaken to identify the mechanisms governing metal delivery from soil to the rhizobia, and to determine how metals are used in the nodule and how they are recycled once the nodule is no longer functional. This effort is being aided by improved legume molecular biology tools (genome projects, mutant collections, and transformation methods), in addition to state-of-the-art metal visualization systems.}, number={FEB}, journal={FRONTIERS IN PLANT SCIENCE}, author={Gonzalez-Guerrero, Manuel and Matthiadis, Anna and Saez, Angela and Long, Terri A.}, year={2014}, month={Feb} }