Desert Agriculture Initiative

Bo Xu, Shane Waters, Caitlin S. Byrt, Darren Plett, Stephen D. Tyerman, Mark Tester, Rana Munns, Maria Hrmova, Matthew Gilliham. Structural variations in wheat HKT1;5 underpin differences in Na+ transport capacity. Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-017-2716-5

Keywords:

Gatekeeper cells, Salt exclusion, Ion transport, Structure–function Einkorn, Bread, Salt tolerance, Xenopus, Mutagenesis, Yeast, High-affinity K+ transporter

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Stephanie Saade, Burcu Kutlu, Vera Draba, Karin Förster, Erika Schumann, Mark Tester, Klaus Pillen, Andreas Maurer. A donor-specific QTL, exhibiting allelic variation for leaf sheath hairiness in a nested association mapping population, is located on barley chromosome 4H. PLOS One. https://doi.org/10.1371/journal.pone.0189446

Keywords:

N/A

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Nawar Jalal Shamaya, Yuri Shavrukov, Peter Langridge, Stuart John Roy and Mark Tester. Genetics of Na+ exclusion and salinity tolerance in Afghani durum wheat landraces. BMC Plant Biology. https://doi.org/10.1186/s12870-017-1164-6

Keywords:

Salinity tolerance, Leaf Na+ concentration, K+/Na+ ratio, Bulk Segregant analysis, SNP markers, HKT1;5

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Rozaimi Razali, Salim Bougouffa, Mitchell J. L. Morton, Damien J. Lightfoot, Intikhab Alam, Magbubah Essack, Stefan T. Arold, Allan Kamau, Sandra M. Schmöckel, Yveline Pailles, Mohammed Shahid, Craig T. Michell, Salim Al-Babili, Yung Shwen Ho, Mark Tester, Vladimir B. Bajic, Sonia Negrão. The genome sequence of the wild tomato Solanum pimpinellifolium provides insights into salinity tolerance. bioRxiv. https://doi.org/10.1101/215517

Keywords:

Wild tomato, Solanum pimpinellifolium, genome analysis, salinity tolerance, inositol 3-phosphate synthase

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Magdalena M. Julkowska, Iko T. Koevoets, Selena Mol, Huub Hoefsloot, Richard Feron, Mark A. Tester, Joost J.B. Keurentjes, Arthur Korte, Michel A. Haring, Gert-Jan de Boer, Christa Testerink. Genetic Components of Root Architecture Remodeling in Response to Salt Stress. The Plant Cell. December 2017. DOI: https://doi.org/10.1105/tpc.16.00680

Keywords:

N/A

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Zahir Ali, Ayman Eid, Shakila Ali, Magdy M. Mahfouz. Pea early-browning virus-mediated genome editing via the CRISPR/Cas9 system in Nicotiana benthamiana and Arabidopsis. Virus Research. https://doi.org/10.1016/j.virusres.2017.10.009

Keywords:

CRISPR/Cas9, Virus-mediated genome engineering, Virus-mediated genome editing, Targeted mutagenesis, Tobacco rattle virus, Pea early browning virus, Arabidopsis, Nicotiana benthamiana

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Haroon Butt, Ayman Eid, Zahir Ali, Mohamed A. M. Atia, Morad M. Mokhtar, Norhan Hassan, Ciaran M. Lee, Gang Bao and Magdy M. Mahfouz. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2017.01441

Keywords:

Genome engineering, CRISPR/Cas9, HDR, RNA-templated repair, gene editing

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Syed Shan-e-Ali Zaidi, Manal Tashkandi, Magdy M. Mahfouz. Chapter Ten - Engineering Molecular Immunity Against Plant Viruses. Progress in Molecular Biology and Translational Science. https://doi.org/10.1016/bs.pmbts.2017.03.009

Keywords:

Site-specific nuclease, Genome engineering, CRISPR/Cas9, Geminiviruses, Tobacco rattle virus

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Sahar Al Shareef, Yu Ling, Haroon Butt, Kiruthiga G. Mariappan, Moussa Benhamed and Magdy M. Mahfouz. Herboxidiene triggers splicing repression and abiotic stress responses in plants. BMC Genomics. https://doi.org/10.1186/s12864-017-3656-z

Keywords:

Alternative splicing, GEX1A, Pladienolide B, Splicing inhibitors, SR proteins, Abiotic stress responses, ABA

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Cristina Andrés-Barrao, Feras F. Lafi, Intikhab Alam, Axel de Zélicourt, Abdul A. Eida, Ameerah Bokhari, Hanin Alzubaidy, Vladimir B. Bajic, Heribert Hirt and Maged M. Saad. Complete Genome Sequence Analysis of Enterobacter sp. SA187, a Plant Multi-Stress Tolerance Promoting Endophytic Bacterium. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2017.02023

Keywords:

Indigofera argentea, root endophytes, plant–microbe interaction, plant growth-promoting bacteria (PGPB), salt stress

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Sandra M. Schmöckel, Damien J. Lightfoot, Rozaimi Razali, Mark Tester and David E. Jarvis. Identification of Putative Transmembrane Proteins Involved in Salinity Tolerance in Chenopodium quinoa by Integrating Physiological Data, RNAseq, and SNP Analyses. Frontiers in Plant Science. doi: 10.3389/fpls.2017.01023

Keywords:

Quinoa, Chenopodium quinoa, hydroponics, salinity tolerance, RNAseq, plant physiology, transporters, comparative genomics

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Joanne Tilbrook, Rhiannon K. Schilling, Bettina Berger, Alexandre F. Garcia, Christine Trittermann, Stewart Coventry, Huwaida Rabie, Chris Brien, Martin Nguyen, Mark Tester and Stuart J. Roy. Variation in shoot tolerance mechanisms not related to ion toxicity in barley. Functional Plant Biology. https://doi.org/10.1071/FP17049

Keywords:

Hordeum spp., osmotic stress, plant growth, plant phenomics, salt tolerance

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Julien Lang, Baptiste Genot, Heribert Hirt & Jean Colcombet. Constitutive activity of the Arabidopsis MAP Kinase 3 confers resistance to Pseudomonas syringae and drives robust immune responses. Plant Signaling & Behavior. http://dx.doi.org/10.1080/15592324.2017.1356533

Keywords:

Arabidopsis, MAPK, resistance protein, defense robustness, stress responses

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Teddy Jégu, Alaguraj Veluchamy, Juan S. Ramirez-Prado, Charley Rizzi-Paillet, Magalie Perez, Anaïs Lhomme, David Latrasse, Emeline Coleno, Serge Vicaire, Stéphanie Legras, Bernard Jost, Martin Rougée, Fredy Barneche, Catherine Bergounioux, Martin Crespi, Magdy M. Mahfouz, Heribert Hirt, Cécile Raynaud and Moussa Benhamed. The Arabidopsis SWI/SNF protein BAF60 mediates seedling growth control by modulating DNA accessibility. Genome Biology. https://doi.org/10.1186/s13059-017-1246-7

Keywords:

SWI/SNF, Chromatin, Morphogenesis, Phytochrome Interacting Factor, G-box, DNA accessibility, PIF4

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David Latrasse, Teddy Jégu, Huchen Li, Axel de Zelicourt, Cécile Raynaud, Stéphanie Legras, Andrea Gust, Olga Samajova, Alaguraj Veluchamy, Naganand Rayapuram, Juan Sebastian Ramirez-Prado, Olga Kulikova, Jean Colcombet, Jean Bigeard, Baptiste Genot, Ton Bisseling, Moussa Benhamed and Heribert Hirt. MAPK-triggered chromatin reprogramming by histone deacetylase in plant innate immunity. Genome Biology. https://doi.org/10.1186/s13059-017-1261-8

Keywords:

N/A

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Abdul Aziz Eida, Heribert Hirt, Maged M. Saad. Challenges Faced in Field Application of Phosphate-Solubilizing Bacteria. Rhizotrophs: Plant Growth Promotion to Bioremediation. https://doi.org/10.1007/978-981-10-4862-3_6

Keywords:

N/A

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Dongjin Kim, Mohamad E. Abdelaziz, Valentine Otang Ntui, Xiujie Guo, Salim Al-Babili. Colonization by the endophyte Piriformospora indica leads to early flowering in Arabidopsis thaliana likely by triggering gibberellin biosynthesis. Biochemical and Biophysical Research Communications. https://doi.org/10.1016/j.bbrc.2017.06.169

Keywords:

Piriformospora indica; Endophytic fungus; Early flowering; Gibberellin

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Mohamed E. Abdelaziz, Dongjin Kim, Shawkat Ali, Nina V. Fedoroff, Salim Al-Babili. The endophytic fungus Piriformospora indica enhances Arabidopsis thaliana growth and modulates Na+/K+ homeostasis under salt stress conditions. Plant Science. https://doi.org/10.1016/j.plantsci.2017.07.006

Keywords:

Salinity stress, Piriformospora indica, Arabidopsis, Lower Na+/K+ ratio

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Adil Salhi, Sónia Negrão, Magbubah Essack, Mitchell J. L. Morton, Salim Bougouffa, Rozaimi Razali , Aleksandar Radovanovic, Benoit Marchand, Maxat Kulmanov, Robert Hoehndorf, Mark Tester & Vladimir B. Bajic. DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. Scientific Reports. DOI:10.1038/s41598-017-05448-0

Keywords:

Data mining, Plant sciences

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Runxuan Zhang, Cristiane P. G. Calixto, Yamile Marquez, Peter Venhuizen, Nikoleta A. Tzioutziou, Wenbin Guo, Mark Spensley, Juan Carlos Entizne, Dominika Lewandowska, Sara ten Have, Nicolas Frei dit Frey, Heribert Hirt, Allan B. James, Hugh G. Nimmo, Andrea Barta, Maria Kalyna and John W. S. Brown. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research. https://doi.org/10.1093/nar/gkx267

Keywords:

Alternative splicing, arabidopsis, genes, genome, introns, protein isoforms, reverse transcriptase polymerase chain reaction, rna splicing, sequence analysis, rna, filters, datasets

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Baptiste Genot, Julien Lang, Souha Berriri, Marie Garmier, Françoise Gilard, Stéphanie Pateyron, Katrien Haustraete, Dominique Van Der Straeten, Heribert Hirt and Jean Colcombet. Constitutively active Arabidopsis MAP Kinase 3 triggers defense responses involving salicylic acid and SUMM2 resistance protein. Plant Physiology. http://dx.doi.org/10.1104/pp.17.00378

Keywords:

Arabidopsis, MAPK, SUMM1/2, signaling transduction, stress responses

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Camille Chardina, Sebastian T. Schenk, Heribert Hirt, Jean Colcombet, Anne Krappa. Review: Mitogen-Activated Protein Kinases in nutritional signaling in Arabidopsis. Plant Science. https://doi.org/10.1016/j.plantsci.2017.04.006

Keywords:

MAPK, Nutrients, Signaling, Gene expression, Arabidopsis thaliana

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Kasra Sabermanesh, Luke R. Holtham, Jessey George, Ute Roessner, Berin A. Boughton, Sigrid Heuer, Mark Tester, Darren C. Plett, and Trevor P. Garnett. Transition from a maternal to external nitrogen source in maize seedlings. Journal of Integrative Plant Biology. DOI: 10.1111/jipb.12525

Keywords:

Amino acids; NPF; NRT; Zea mays; nitrate uptake; nitrogen use efficiency; roots; seed; seedling

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Rui Meng, Stephanie Saade, Sebastian Kurtek, Bettina Berger, Chris Brien, Klaus Pillen, Mark Tester and Ying Sun. Growth curve registration for evaluating salinity tolerance in barley. Plant Methods. DOI 10.1186/s13007-017-0165-7

Keywords:

Functional ANOVA model, High-throughput phenotyping, Nested association mapping, Plant growth, Spatial variation, Temporal variation

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Mark Bruno, Martina Vermathen, Adrian Alder, Florian Wüst, Patrick Schaub, Rob van der Steen, Peter Beyer, Sandro Ghisla and Salim Al-Babili. Insights into the formation of carlactone from in-depth analysis of the CCD8-catalyzed reactions. FEBS Press. DOI: 10.1002/1873-3468.12593

Keywords:

Carotenoid cleavage dioxygenase, Horner–Wadsworth–Emmons, lithium diisopropylamide, normalized collision energy, strigolactones

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Eva L. Decker, Adrian Alder, Stefan Hunn, Jenny Ferguson, Mikko T. Lehtonen, Bjoern Scheler, Klaus L. Kerres, Gertrud Wiedemann, Vajiheh Safavi-Rizi, Steffen Nordzieke, Aparna Balakrishna, Lina Baz, Javier Avalos, Jari P. T. Valkonen, Ralf Reski and Salim Al-Babili. Strigolactone biosynthesis is evolutionarily conserved, regulated by phosphate starvation and contributes to resistance against phytopathogenic fungi in a moss, Physcomitrella patens. New Phytologist. doi: 10.1111/nph.14506

Keywords:

Carlactone, carotenoid cleavage dioxygenase, carotenoids, Orobanche ramosa, phosphate starvation,Physcomitrella patens, Sclerotinia sclerotiorum, strigolactones

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Magdy M. Mahfouz. Genome editing: The efficient tool CRISPR–Cpf1. Nature Plants. doi:10.1038/nplants.2017.28

Keywords:

Genetic techniques, Molecular engineering in plants

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Yveline Pailles, Shwen Ho, Inês S. Pires, Mark Tester, Sónia Negrão and Sandra M. Schmöckel. Genetic Diversity and Population Structure of Two Tomato Species from the Galapagos Islands. Frontiers in Plant Science. doi: 10.3389/fpls.2017.00138

Keywords:

Genotyping-by-sequencing, Solanum cheesmaniae, Solanum galapagense, genetic diversity, biogeography, tomato, wild relatives, Galapagos Islands

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David E. Jarvis, Yung Shwen Ho, Damien J. Lightfoot, Sandra M. Schmöckel, Bo Li, Theo J. A. Borm, Hajime Ohyanagi, Katsuhiko Mineta, Craig T. Michell, Noha Saber, Najeh M. Kharbatia, Ryan R. Rupper, Aaron R. Sharp, Nadine Dally, Berin A. Boughton, Yong H. Woo, Ge Gao, Elio G. W. M. Schijlen, Xiujie Guo, Afaque A. Momin, Sónia Negrão, Salim Al-Babili, Christoph Gehring, Ute Roessner, Christian Jung, Kevin Murphy, Stefan T. Arold, Takashi Gojobori, C. Gerard van der Linden, Eibertus N. van Loo, Eric N. Jellen, Peter J. Maughan & Mark Tester. The genome of Chenopodium quinoa. Nature. doi:10.1038/nature21370

Keywords:

N/A

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Bo Li, Mark Tester and Matthew Gilliham. Chloride on the Move. Trends in Plant Science. DOI: http://dx.doi.org/10.1016/j.tplants.2016.12.004

Keywords:

Long-distance transport, NPF2.4, SLAH1, CCC, GmSALT3, ALMT9

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Rhiannon K. Schilling, Mark Tester, Petra Marschner, Darren C. Plett, and Stuart J. Roy. AVP1: One Protein, Many Roles. Trends in Plant Science. http://dx.doi.org/10.1016/j.tplants.2016.11.012

Keywords:

H+-pyrophosphatase; vacuole; pyrophosphate; sucrose; plant growth

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Bo Li, Jiaen Qiu, Maheswari Jayakannan, Bo Xu, Yuan Li, Gwenda M. Mayo, Mark Tester, Matthew Gilliham and Stuart J. Roy. AtNPF2.5 Modulates Chloride (Cl−) Efflux from Roots of Arabidopsis thaliana. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2016.02013

Keywords:

Arabidopsis thaliana, chloride transport, MIFE, NPF2.5, salinity tolerance, TEVC

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Yu Ling, Sahar Alshareef, Haroon Butt, Jorge Lozano-Juste, Lixin Li, Aya A. Galal, Ahmed Moustafa, Afaque A. Momin, Manal Tashkandi, Dale N. Richardson, Hiroaki Fujii, Stefan Arold, Pedro L. Rodriguez, Paula Duque, Magdy M. Mahfouz. Pre-mRNA splicing repression triggers abiotic stress signaling in plants. The Plant Journal. DOI: 10.1111/tpj.13383

Keywords:

Alternative splicing, pladienolide B, splicing inhibitors, serine/arginine-rich proteins, abioticstress responses, abscisic acid

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Zahir Ali, Shakila Ali, Manal Tashkandi, Syed Shan-e-Ali Zaidi & Magdy M. Mahfouz. CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion. Scientific Reports. doi:10.1038/srep26912

Keywords:

Molecular engineering, Molecular engineering in plants

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Syed Shan-e-Ali Zaidi, Manal Tashkandi, Shahid Mansoor and Magdy M. Mahfouz. Engineering Plant Immunity: Using CRISPR/Cas9 to Generate Virus Resistance. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2016.01673

Keywords:

Plant virus, CRISPR/Cas9, genome engineering, geminivirus, virus resistance

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Ayman Eid and Magdy M. Mahfouz. Genome editing: the road of CRISPR/Cas9 from bench to clinic. Experimental & Molecular Medicine. doi:10.1038/emm.2016.111

Keywords:

N/A

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Sophia L. Samodelov, Hannes M. Beyer, Xiujie Guo, Maximilian Augustin, Kun-Peng Jia, Lina Baz, Oliver Ebenhöh, Peter Beyer, Wilfried Weber, Salim Al-Babili, and Matias D. Zurbriggen. StrigoQuant: A genetically encoded biosensor for quantifying strigolactone activity and specificity. Science Advances. DOI: 10.1126/sciadv.1601266

Keywords:

Strigolactone signaling, strigolactone quantitative biosensor, plant synthetic biology, genetically encoded strigolactone biosensor, strigolactone perception

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Nadia Al-Tamimi, Chris Brien, Helena Oakey, Bettina Berger, Stephanie Saade, Yung Shwen Ho, Sandra M. Schmockel, Mark Tester & Sonia Negrao. Salinity tolerance loci revealed in rice using high-throughput non-invasive phenotyping. Nature Communications. DOI: 10.1038/ncomms13342

Keywords:

Genome-wide association studies, Plant genetics, Salt

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Sandra Schmöckel, David Jarvis. Salt Stress. Encyclopedia of Applied Plant Sciences (Second Edition). http://dx.doi.org/10.1016/B978-0-12-394807-6.00086-1

Keywords:

Abiotic stress; Conventional crop breeding; Genetic engineering; Ionic phase; NaCl stress; Salinity tolerance mechanisms; Salt stress; Shoot ion-independent phase

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Kun-Peng Jia, Boubacar A. Kountche, Muhammad Jamil, Xiujie Guo, Valentine O. Ntui, Andreas Rüfenacht, Soizic Rochange and Salim Al-Babili. Nitro-Phenlactone, a Carlactone Analog with Pleiotropic Strigolactone Activities. Molecular Plant. http://dx.doi.org/10.1016/j.molp.2016.05.017

Keywords:

N/A

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Mark Bruno, Julian Koschmieder, Florian Wuest, Patrick Schaub, Mirjam Fehling-Kaschek, Jens Timmer, Peter Beyer and Salim Al-Babili. Enzymatic study on AtCCD4 and AtCCD7 and their potential to form acyclic regulatory metabolites. The Journal of Experimental Botany. doi:10.1093/jxb/erw356

Keywords:

Apocarotenoids, carotenoids, carotenoid cleavage dioxygenase, CCD4, CCD7, retrograde signaling

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Sonia Negrao, Sandra Schmockel and Mark Tester. Evaluating physiological responses of plants to salinity stress. Annals of Botany. doi:10.1093/aob/mcw191

Keywords:

Assessing salinity tolerance, salt-imposition systems, quantifying physiological traits, analysing salinity data, tolerance indices, salt stress phenotyping, osmotic stress

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Jessey George, Luke Holtham, Kasra Sabermanesh, Sigrid Heuer, Mark Tester, Darren Plett and Trevor Garnett. Small amounts of ammonium (NHþ4) can increase growth of maize (Zea mays). Journal of Plant Nutrition and Soil Science. DOI: 10.1002/jpln.201500625

Keywords:

Ammonium, nitrate, ion fluxes, N uptake, N budget

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Tepsuda Rungrat, Mariam Awlia, Tim Brown, Riyan Cheng, Xavier Sirault, Jiri Fajkus, Martin Trtilek, Bob Furbank, Murray Badger, Mark Tester, Barry J Pogson, Justin O Borevitz and Pip Wilson. Using Phenomic Analysis of Photosynthetic Function for Abiotic Stress Response Gene Discovery. The Arabidopsis Book 14:e0185. DOI:10.1199/tab.0185

Keywords:

N/A

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Mariam Awlia, Arianna Nigro, Jiri Fajkus, Sandra Schmockel, Sonia Negrao, Diana Santelia, Martin Trtilek, Mark Tester, Magdalena M. Julkowska and Klara Panzarova. High-throughput non-destructive phenotyping of traits that contribute to salinity tolerance in Arabidopsis thaliana. Frontiers in Plant Science. doi: 10.3389/fpls.2016.01414

Keywords:

High-throughput phenotyping, Arabidopsis thaliana, salt stress, shoot-ion independent tolerance, kinetic chlorophyll fluorescence imaging, Color segmentation

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Stephanie Saade, Andreas Maurer, Mohammed Shahid, Helena Oakey, Sandra M. Schmöckel, Sónia Negrão, Klaus Pillen & Mark Tester. Yield-related salinity tolerance traits identified in a nested association mapping (NAM) population of wild barley. Nature Scientific Reports. doi:10.1038/srep32586

Keywords:

Plant hybridization, Salt, Barley

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Darren Plett, Luke Holtham, Ute Baumann, Elena Kalashyan, Karen Francis, Akiko Enju, John Toubia, Ute Roessner, Antony Bacic, Antoni Rafalski, Kanwarpal S. Dhugga, Mark Tester, Trevor Garnett, Brent N. Kaiser. Nitrogen assimilation system in maize is regulated by developmental and tissue-specific mechanisms. Plant Molecular Biology. DOI 10.1007/s11103-016-0512-5

Keywords:

Nitrogen use efficiency, NUE, Nitrogen metabolism, Amino acids, Enzyme activity, Transcript abundance

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Ayman Eid, Zahir Ali, Magdy M. Mahfouz. High efficiency of targeted mutagenesis in arabidopsis via meiotic promoter-driven expression of Cas9 endonuclease. Plant Cell Reports. DOI: 10.1007/s00299-016-2000-4

Keywords:

CRISPR/Cas9,Genome engineering, Genome editing, Meiotic promoters, Targeted mutagenesis, Arabidopsis

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Magdy M. Mahfouz, Teodoro Cardi, C. Neal Stewart Jr. Next-generation precision genome engineering and plant biotechnology. Plant Cell Reports. DOI: 10.1007/s00299-016-2009-8

Keywords:

N/A

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Natalia Y. Rodriguez-Granados, Juan S. Ramirez-Prado, Alaguraj Veluchamy, David Latrasse, Cécile Raynaud, Martin Crespi, Federico Ariel and Moussa Benhamed. Put your 3D glasses on: plant chromatin is on show. Journal of Experimental Botany. doi: 10.1093/jxb/erw168

Keywords:

Chromatin conformation, epigenetics, genome topology, long non-coding RNAs, PRC

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Quentin Bruggeman, Christelle Mazubert, Florence Prunier, Raphaël Lugan, Kai Xun Chan, Su Yin Phua, Barry James Pogson, Anja Krieger-Liszkay, Marianne Delarue, Moussa Benhamed, Catherine Bergounioux, and Cécile Raynaud. Chloroplast Activity and 39phosphadenosine 59phosphate Signaling Regulate Programmed Cell Death in Arabidopsis1. Plant Physiology. doi: http://dx.doi.org/10.1104/pp.15.01872

Keywords:

N/A

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Sajid Mahmood, Ihsanullah Daur, Samir G. Al-Solaimani, Shakeel Ahmad, Mohamed H. Madkour, Muhammad Yasir, Heribert Hirt, Shawkat Ali and Zahir Ali. Plant Growth Promoting Rhizobacteria and Silicon Synergistically Enhance Salinity Tolerance of Mung Bean. Frontiers in Plant Science. http://dx.doi.org/10.3389/fpls.2016.00876

Keywords:

Water relation, stomatal conductance, photosynthetic pigments, salt tolerance index, rhizobacteria characterization-identification

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Heribert Hirt. Aquaporins Link ROS Signaling to Plant Immunity. Plat Physiology. doi: http://dx.doi.org/10.1104/pp.16.00433

Keywords:

N/A

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Alaguraj Veluchamy, Teddy Jégu , Federico Ariel, David Latrasse, Kiruthiga Gayathri Mariappan, Soon-Kap Kim, Martin Crespi, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed. LHP1 Regulates H3K27me3 Spreading and Shapes the Three-Dimensional Conformation of the Arabidopsis Genome. PLOS One. http://dx.doi.org/10.1371/journal.pone.0158936

Keywords:

Gene expression, Chromatin, Gene regulation, Arabidopsis thaliana, DNA transcription, Structural genomics, Sequence motif analysis

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Feras F. Lafi, Ameerah Bokhari, Intikhab Alam, Vladimir B. Bajic, Heribert Hirt, Maged M. Saad. Draft Genome Sequence of the Plant Growth-Promoting Cupriavidus gilardii Strain JZ4 Isolated from the Desert Plant Tribulus terrestris. Genome Announcements. doi: 10.1128/genomeA.00678-16

Keywords:

N/A

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Jiaen Qiu, Sam W Henderson, Mark Tester, Stuart J Roy and Mathew Gilliham. SLAH1, a homologue of the slow type anion channel SLAC1, modulates shoot Cl− accumulation and salt tolerance in Arabidopsis thaliana. Journal of Experimental Botany. doi: 10.1093/jxb/erw237

Keywords:

ABA, Arabidopsis, AtSLAH1, AtSLAH3, chloride, Cl− xylem loading, long-distance transport, nutrition, salinity, slow-type anion channel-associated homologue 1, slow-type anion channel-associated homologue 3

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Axel de Zelicourt, Jean Colcombet, Heribert Hirt. The Role of MAPK Modules and ABA during Abiotic Stress Signaling. Trends in Plant Science. doi:10.1016/j.tplants.2016.04.004

Keywords:

Abscisic acid; mitogen activated protein kinase; abiotic stress; stomata; signaling pathway

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Mark Bruno, Salim Al-Babili. On the substrate specificity of the rice strigolactone biosynthesis enzyme DWARF27. Planta (2016). doi:10.1007/s00425-016-2487-5

Keywords:

Apocarotenoids, Carotenoids, Carotenoid cleavage dioxygenase, Carotene isomerase, Carlactone, Strigolactones

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Agnieszka Piatek and Magdy M. Mahfouz. Targeted genome regulation via synthetic programmable transcriptional regulators. Critical Reviews in Biotechnology (2016). DOI:10.3109/07388551.2016.1165180

Keywords:

CRISPR/Cas9 system, functional genomics, synthetic site-specific nucleases, synthetic transcriptional regulators, targeted genome regulation, transcriptional activator-like effectors, zinc fingers

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Darren Plett, Ute Baumann, Andreas W. Schreiber, Luke Holtham, Elena Kalashyan, John Toubia, John Nau, Mary Beatty, Antoni Rafalski, Kanwarpal S. Dhugga, Mark Tester, Trevor Garnett, Brent N. Kaiser. Maize maintains growth in response to decreased nitrate supply through a highly dynamic and developmental stage-specific transcriptional response. Plant Biotechnology. doi: 10.1111/pbi.12388

Keywords:

N/A

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Bo Li, Caitlin Byrt, Jiaen Qiu, Ute Baumann, Maria Hrmova, Aurelie Evrard, Alexander A.T. Johnson, Kenneth D. Birnbaum, Gwenda M. Mayo, Deepa Jha, Sam W. Henderson, Mark Tester, Mathew Gilliham, and Stuart J. Roy. Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis. Plant Physiology. doi: 10.1104/pp.15.01163

Keywords:

N/A

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Syed Shan-e-Ali Zaidi, Shahid Mansoor, Zahir Ali, Manal Tashkandi, Magdy M. Mahfouz. Engineering Plants for Geminivirus Resistance with CRISPR/Cas9 System. Trends in Plant Science. DOI: 10.1016/j.tplants.2016.01.023

Keywords:

CRISPR/Cas9, geminiviruses, virus resistance, genome editing

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Mustapha Aouida, Ayman Eid, Zahir Ali, Thomas Cradick, Ciaran Lee, Harshavardhan Deshmukh, Ahmed Atef, Dina AbuSamra, Samah Zeineb Gadhoum, Jasmeen Merzaban, Gang Bao, Magdy M. Mahfouz. Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering. PLOS One. https://doi.org/10.1371/journal.pone.0133373

Keywords:

Genomic Medicine, Genome engineering, Cell fusion, TALENs, Genome analysis, Mutation detection, Polymerase chain reaction, Zinc finger nucleases

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Zahir Ali, Aala Abul-faraj, Lixin Li, Neha Ghosh, Marek Piatek, Ali Mahjoub, Mustapha Aouida, Agnieszka Piatek, Nicholas J. Baltes, Daniel F. Voytas, Savithramma Dinesh-Kumar, Magdy M. Mahfouz. Efficient Virus-Mediated Genome Editing in Plants Using the CRISPR/Cas9 System. Molecular Plant. https://doi.org/10.1016/j.molp.2015.02.011

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Mustapha Aouida, Lixin Li, Ali Mahjoub, Sahar Alshareef, Zahir Ali, Agnieszka Piatek, Magdy M. Mahfouz. Transcription activator-like effector nucleases mediated metabolic engineering for enhanced fatty acids production in Saccharomyces cerevisiae. Journal of Bioscience and Bioengineering. https://doi.org/10.1016/j.jbiosc.2015.02.017

Keywords:

Genome engineering; Metabolic engineering; Synthetic biology; Transcription activator-like effector nucleases; Biofuel production; Free fatty acids

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Quentin Bruggeman, Florence Pruniera, Christelle Mazubert, Linda de Bont, Marie Garmier, Raphaël Lugan, Moussa Benhamed, Catherine Bergounioux, Cécile Raynaud and Marianne Delaruea. Involvement of Arabidopsis Hexokinase1 in Cell Death Mediated by Myo-Inositol Accumulation. The Plant Cell. doi: http://dx.doi.org/10.1105/tpc.15.00068

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Federico Ariel, Natali Romero-Barrios, Teddy Je´gu, Moussa Benhamed and Martin Crespi. Battles and hijacks: noncoding transcription in plants. Trends in Plant Science. doi:10.1016/j.tplants.2015.03.003

Keywords:

lncRNAs; lncNATs; RdDM; dual noncoding transcription

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Quentin Bruggeman, Cécile Raynaud, Moussa Benhamed and Marianne Delarue. To die or not to die? Lessons from lesion mimic mutants. Frontiers in Plant Science. http://dx.doi.org/10.3389/fpls.2015.00024

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Mustapha Aouida, Ayman Eid, Magdy M. Mahfouz. CRISPR/Cas9-mediated target validation of the splicing inhibitor Pladienolide B. Biochimie Open. doi:10.1016/j.biopen.2016.02.001

Keywords:

CRIPSR/Cas9, Pladienolide B, Spliceosome, Pre-mRNA splicing, Drug target validation, Drug discovery

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Stuart Roy and Mark Tester. Salinity tolerance in plants. United States Patent

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N/A

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Teddy Jégu, Séverine Domenichini, Thomas Blein, Federico Ariel, Aurélie Christ, Soon-Kap Kim, Martin Crespi, Stéphanie Boutet-Mercey, Grégory Mouille, Mickaël Bourge, Heribert Hirt, Catherine Bergounioux, Cécile Raynaud, Moussa Benhamed. A SWI/SNF Chromatin Remodelling Protein Controls Cytokinin Production through the Regulation of Chromatin Architecture. Plos one. http://dx. doi.org/10.1371/journal.pone.0138276 (2015)

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N/A

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Violeta Díaz-Sánchez, M. Carmen Limón, Patrick Schaub, Salim Al-Babili, Javier Avalos. A RALDH-like enzyme involved in Fusarium verticillioides development. Fungal Genetics and Biology. doi:10.1016/j.fgb.2015.12.005

Keywords:

Fusarium verticillioides; RALDH enzyme; Retinoic acid; Apocarotenoids; Conidia; Hyphal development; Sexual fertility

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Andreas Savvides, Shawkat Ali, Mark Tester and Vasileios Fotopoulos. Chemical Priming of Plants Against Multiple Abiotic Stresses: Mission Possible? Trends in Plant Science. doi:10.1016/j.tplants.2015.11.003

Keywords:

Melatonin, polyamines, reactive species, stress tolerance, systemic resistance

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Zahir Ali, Aala Abulfaraj, Marek Piatek & Magdy M. Mahfouz. Activity and specificity of TRV-mediated gene editing in plants. Plant Signaling & Behavior DOI: 10.1080/15592324.2015.1044191

Keywords:

CRISPR/Cas9 system, plant genome engineering, synthetic site-specific nucleases (SSNs), TRV, viral-mediated genome editing

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Zahir Ali, Aala Abulfaraj, Ali Idris, Shakila Ali, Manal Tashkandi and Magdy M. Mahfouz. CRISPR/Cas9-mediated viral interference in plants. Genome Biology 2015, 16:238 doi:10.1186/s13059-015-0799-6

Keywords:

Plant genome engineering; CRISPR/Cas9 system; Synthetic site-specific nucleases; Viral-mediated genome editing; Virus resistance; Tomato yellow leaf curl virus ; Tobacco rattle virus

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Trevor Garnett, Darren Plett, Vanessa Conn, Simon Conn, Huwaida Rabie, J. Antoni Rafalski, Kanwarpal Dhugga, Mark A. Tester and Brent N. Kaiser.
Variation for N Uptake System in Maize: Genotypic Response to N Supply. Frontiers in Plant Science, 09 November 2015 | http://dx.doi.org/10.3389/fpls.2015.00936

Keywords:

N, nitrate, ammonium, nitrogen use efficiency, NUE, uptake, Zea mays

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Takahashi F, Tilbrook J, Trittermann C, Berger B, Roy SJ, Seki M, Shinozaki K, Tester M. (2015) Comparison of Leaf Sheath Transcriptome Profiles with Physiological Traits of Bread Wheat Cultivars under Salinity Stress. PLoS ONE 10(8): e0133322. doi:10.1371/journal.pone.0133322

Keywords:

Salinity, Gene expression, Plant resistance to abiotic stress, Wheat, Bread, Genomic databases, Rice, Microarrays

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Marie Boudsocq, Agyemang Danquah, Axel de Zélicourt, Heribert Hirt & Jean Colcombet (2015) Plant MAPK cascades: Just rapid signaling modules?, Plant Signaling & Behavior, 10:9, e1062197, DOI: 10.1080/15592324.2015.1062197

Keywords:

Abscisic acid, ABA signaling, delayed signaling, mitogen-activated pro- tein kinase, protein synthesis

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K. Shahzad, M. Rauf, M. Ahmed, Z. A. Malik, I. Habib, Z. Ahmed, K. Mahmood, R. Ali, K. Masmoudi, F. Lemtiri-Chlieh, C. Gehring, G. A. Berkowitz & N. A. Saeed. Functional characterisation of an intron retaining K+ transporter of barley reveals intron-mediated alternate splicing. Plant Biology doi:10.1111/plb.12290

Keywords:

Alternate splicing; functional complementation; HvHKT2; intron retention; transcriptional gene regulation; transporters and channels.

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Shawkat Ali , Maxime Magne, Shiyan Chen, Natasa Obradovic, Lubna Jamshaid, Xiaohong Wang, Guy Bélair and Peter Moffett. Analysis of Globodera rostochiensis effectors reveals conserved functions of SPRYSEC proteins in suppressing and eliciting plant immune responses. Frontiers in Plant Science doi: 10.3389/fpls.2015.00623

Keywords:

Globodera, plant-parasitic nematode, cyst nematodes, NB-LRR proteins, effector proteins, PAMP-triggered immunity(PTI), SPRYSEC

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Ben Ward, John Bastian, Anton van den Hengel, Daniel Pooley, Rajendra Bari, Bettina Berger, Mark Tester. A Model-Based Approach to Recovering the Structure of a Plant from Images (2015). Lectures Notes in Computer Science Doi:10. 1007/978-3-319-16220-1 16.

Keywords:

Plant phenotyping, Image processing, Plant architecture

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Shawkat Ali, Maxime Magne, Shiyan Chen, Olivier Côté, Barbara Gerič Stare, Natasa Obradovic, Lubna Jamshaid, Xiaohong Wang, Guy Bélair, Peter Moffett. Analysis of Putative Apoplastic Effectors from the Nematode, Globodera rostochiensis, and Identification of an Expansin-Like Protein That Can Induce and Suppress Host Defenses (2015). PLoS ONE 10(1): e0115042. doi:10.1371/ journal.pone.0115042

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N/A

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Zahir Ali, Aala Abulfaraj, Li L., Ghosh N., Piatek M., Ali Mahjoub, Moustafa Aouida, Piatek A., Baltes N.J., Voytas D.F., Dinesh-Kumar S., and Magdy Mahfouz (2015). Efficient Virus-Mediated Genome Editing in Plants using the CRISPR/Cas9 System. Molecular Plant. doi: 10.1016/j.molp.2015.02.011.

Keywords:

N/A

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Sandra M. Schmöckel, Alexandre F. Garcia, Bettina Berger, Mark Tester, Alex A. R. Webb, Stuart J. Roy. Different NaCl-Induced Calcium in the Arabidopsis thaliana Ecotypes Col-0 and C24. Plos One. DOI: 10.1371/journal.pone.0117564

Keywords:

Arabidopsis, NaCl, Calcium, Stress signalling

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Bigeard J, Colcombet J, Heribert Hirt, Signaling Mechanisms in Pattern-Triggered Immunity (PTI). Molecular Plant. 2015 Jan 9. pii: S1674-2052(15)00087-8. doi: 10.1016/j.molp.2014.12.022. PMID 25744358

Keywords:

plant defenses; plant immunity; PTI; signaling mechanisms; MAPKs

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Danquah A, de Zélicourt A, Boudsocq M, Neubauer J, Frei Dit Frey N, Leonhardt N, Pateyron S, Gwinner F, Tamby JP, Ortiz-Masia D, Marcote MJ, Heribert Hirt, Colc ombet J., Identification and characterization of an ABA-activated MAP kinase cascade in Arabidopsis thaliana. The Plant Journal. 2015 Feb 27. doi: 10.1111/tpj.12808

Keywords:

ABA , Arabidopsis thaliana, MAP3K18, MAPK module, MKK3, signaling pathway

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Agnieszka Piatek, Zahir Ali, Hatoon Baazim, Lixin Li, Aala Abulfaraj, Sahar Al-Shareef, Mustapha Aouida, Magdy M. Mahfouz. RNA-guided transcriptional regulation in planta via synthetic dCas9-based transcription factors. Plant Biotechnology Journal. DOI: 10.1111/pbi.12284

Keywords:

Targeted genomic regulation, synthetic transcriptional regulators, chimeric dCas9transcriptional activators andrepressors, EDLL activation domain, SRDX repressor domain

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Magdy M. Mahfouz, Agnieszka Piatek, Charles Neal Stewart Jr. Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnology Journal. DOI: 10.1111/pbi.12256

Keywords:

DNA-binding modules, TAL effectors, CRISPR/Cas9 system, synthetic site-specific nucleases (SNNs), targeted genome modifications, designer transcriptional regulators

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Mustapha Aouida, Marek J. Piatek, Dhinoth K. Bangarusamy, Magdy M. Mahfouz. Activities and specificities of homodimeric TALENs in Saccharomyces cerevisiae. Current Genetics. doi:10.1007/s00294-013-0412-z

Keywords:

Genome engineering, TALE-based nucleases TALENs, Homodimeric TALENs, Saccharomyces cerevisia, Targeted genome modification

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A. Sharkhuu, M.L. Narasimhan, J.S. Merzaban, R.A. Bressan, S. Weller and C. Gehring. A red and far-red light receptor mutation confers resistance to the herbicide glyphosate. Plant Journal, 78, 916-926, (2014)10.1111/tpj.12513.

Keywords:

Arabidopsis thaliana; circadian rhythm; glyphosate; herbicide resistance; phyB; shikimate pathway

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Khan MS, Khraiwesh B, Pugalenthi G, Gupta RS, Singh J, Duttamajumder SK, Kapur R. Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.) (2014). FEBS Open Bio. 2014 Jun 10;4:533-41. doi: 10.1016/j.fob.2014.05.007. eCollection 2014.

Keywords:

ABA, abscisic acid; ADF, actin depolymerizing factor; EST; ESTs, expressed sequence tags; Hsps, heat shock proteins; Novel miRNAs; PTGS, post-transcriptional gene silencing; REMs, remorins; SSA, snow pea pod senescence-associated; SUCEST, sugarcane EST da

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Shawkat Ali, Guus Bakkeren. Conversion of BAC Clones into Binary BAC (BIBAC) Vectors and Their Delivery into Basidiomycete Fungal Cells Using Agrobacterium tumefaciens (2014). Methods in Molecular Biology Volume 1227, 2015, pp 199-215. DOI 10.1007/978-1-4939-1652-8_9

Keywords:

Recombineering Binary vector Bacterial artificial chromosome Basidiomycete Ustilago Agrobacterium-mediated transformation

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Ilg, A., Bruno, M., Beyer, P. and Salim Al-Babili, Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles (2014). FEBS Open Bio. 4:584-93.

Keywords:

Apocarotenoids; CCD, carotenoid cleavage dioxygenase; Carotenoid cleavage dioxygenase; Carotenoids; Isoprenoids; Plants; Tomato

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Frusciante, S., Diretto, G., Bruno, M., Ferrante, P., Pietrella, M., Prado-Cabrero, A., Rubio-Moraga, A., Beyer, P., Gomez-Gomez, L., Al-Babili, S. and Giuliano, G. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis (2014). PNAS USA. 111: 12246-5

Keywords:

symmetric carotenoid cleavage; β-citraurin

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Zhang, Y., van Dijk, A.D.J., Scaffidi, A., Flematti, G. R., Hofmann, M., Charnikhova, T., Verstappen, F., Hepworth, J., van der Krol, S., Leyser, O., Smith, S.M., Zwanenburg, B., Al-Babili, S., Ruyter-Spira, C. and Bouwmeester, H.J, Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis (2014). Nature Chemical Biology 10, 1028–1033 (2014) doi:10.1038/nchembio.1660

Keywords:

Biosynthesis, Enzymes, Natural products, Plant hormones

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Magdy M. Mahfouz, Piatek A, Stewart CN Jr., Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives. Plant Biotechnolgy Journal. 2014 Oct;12(8):1006-14. doi: 10.1111/pbi.12256.

Keywords:

CRISPR/Cas9 system; DNA-binding modules; TAL effectors; designer transcriptional regulators; synthetic site-specific nucleases (SNNs); targeted genome modifications

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Yousef S. Al-Hafedh, Aftab Alam and Alejandro H. Buschmann, Bioremediation potential, growth and biomass yield of the green seaweed, Ulva lactuca in an integrated marine aquaculture system at the Red Sea coast of Saudi Arabia at different stocking densities and effluent flow rates. Aquaculture 2014, DOI: 10.1111/raq.12060.

Keywords:

Ulva lactuca, bioremediation, oreochromis niloticus, Red Sea

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Bruggeman Q, Garmier M, de Bont L, Soubigou-Taconnat L, Mazubert C, Benhamed M, Raynaud C, Bergounioux C, Delarue M.,The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis. Plant Physiology. 2014 Apr 4;165(2):732-746.

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N/A

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Federico Ariel, Teddy Jegu, David Latrasse, Natali Romero-Barrios, Aure´ lie Christ, Moussa Benhamed, and Martin Crespi. Noncoding Transcription by Alternative RNA Polymerases Dynamically Regulates an Auxin-Driven Chromatin Loop, Molecular Cell, DOI: http://dx.doi.org/10.1016/j.molcel.2014.06.011

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N/A

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Elodie Hudik, Yasushi Yoshioka, Séverine Domenichini, Mickaël Bourge, Ludivine Soubigout-Taconnat, Christelle Mazubert, Dalong Yi, Sandrine Bujaldon, Hiroyuki Hayashi, Lieven De Veylder, Catherine Bergounioux, Moussa Benhamed, and Cécile Raynaud, Chloroplast Dysfunction Causes Multiple Defects in Cell Cycle Progression in the Arabidopsis crumpled leaf Mutant, Plant Phisiology, PMID: 25037213 [PubMed - in process] PMCID: PMC4149703 [Available on 2015-09-01]

Keywords:

N/A

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Aris Hairmansis, Bettina Berger, Mark Tester and Stuart John Roy. Image-based phenotyping for non-destructive screening of different salinity tolerance traits in rice. Hairmansis et al. Rice 2014, 7:16

Keywords:

Rice (Oryza sativa L.); Salinity tolerance; Phenotyping; Image analysis; Growth; Senescence

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Caitlin Siobhan Byrt, Bo Xu, Mahima Krishnan, Damien Lightfoot, Asmini Athman, Andrew Keith Jacobs, Nathan S. Watson-Haigh, Darren Plett, Rana Munns, Mark Tester and Matthew Gilliham. The Na+ transporter, TaHKT1;5-D, limits shoot Na+ accumulation in bread wheat. The Plant Journal (2014) 80, 516–526

Keywords:

wheat, Triticum aestivum, sodium exclusion, HKT, salt tolerance, RNA interference.

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Jégu T, Latrasse D, Delarue M, Heribert Hirt, Domenichini S, Ariel F, Crespi M, Bergounioux C, Raynaud C, Benhamed M., The BAF60 Subunit of the SWI/SNF Chromatin-Remodeling Complex Directly Controls the Formation of a Gene Loop at FLOWERING LOCUS C in Arabidopsis. Plant Cell. 2014 Feb;26(2):538-51. doi: 10.1105/tpc.113.114454. PMID: 24510722

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N/A

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Ovečka M, Takáč T, Komis G, Vadovič P, Bekešová S, Doskočilová A, Smékalová V, Luptovčiak I, Samajová O, Schweighofer A, Meskiene I, Jonak C, Křenek P, Lichtscheidl I, Skultéty L, Heribert Hirt, Samaj J., Salt-induced subcellular kinase relocation and seedling susceptibility caused by overexpression of Medicago SIMKK in Arabidopsis, Molecular Cell. 2014 Jun;65(9):2335-50. doi: 10.1093/jxb/eru115. Epub 2014 Mar 19. PMID: 24648569

Keywords:

Arabidopsis, MAPK, Medicago, proteomics, salt stress, SIMK, SIMKK, subcellular relocation

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Hudik E, Berriri S, Heribert Hirt, Colcombet J., Identification of Constitutively Active AtMPK6 Mutants Using a Functional Screen in Saccharomyces cerevisiae. Methods Molecular Biology. 2014;1171:67-77. doi: 10.1007/978-1-4939-0922-3_6. PMID: 24908120

Keywords:

MAP Kinase , Functional genetic screen , Constitutive activity , Saccharomyces cerevisiae, In vivo cloning , Random mutagenesis

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Bigeard J, Pflieger D, Colcombet J, Gérard L, Mireau H, Heribert Hirt, Protein Complexes Characterization in Arabidopsis thaliana by Tandem Affi nity Purifi cation Coupled to Mass Spectrometry Analysis. Methods Molecular Biology. 2014;1171:237-50. doi: 10.1007/978-1-4939-0922-3_18. PMID: 24908132

Keywords:

Arabidopsis thaliana, Protein complexes , Tandem affi nity purifi cation , Mass spectrometry , Posttranslational modifi cations

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Neumann C, Fraiture M, Hernàndez-Reyes C, Akum FN, Virlogeux-Payant I, Chen Y, Pateyron S, Colcombet J, Kogel KH, Heribert Hirt, Brunner F, Schikora A., The Salmonella effector protein SpvC, a phosphothreonine lyase is functional in plant cells. Frontiers In Microbiology. 2014 Oct 17;5:548. doi: 10.3389/fmicb.2014.00548. eCollection 2014.

Keywords:

T3SS, trans-kingdom pathogenicity, Salmonella, plant infection

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Zourelidou M, Absmanner B, Weller B, Barbosa IC, Willige BC, Fastner A, Streit V, Port SA, Colcombet J, de la Fuente van Bentem S, Heribert Hirt, Kuster B, Schulze WX, Hammes UZ, Schwechheimer C., Auxin efflux by PIN-FORMED proteins is activated by two different protein kinases, D6 PROTEIN KINASE and PINOID. Elife. 2014 Jun 19:e02860. doi: 10.7554/eLife.02860. PMID: 24948515

Keywords:

AGC kinases, arabidopsis, auxin, auxin transport, plant biology, protein kinase

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Bigeard J, Rayapuram N, Pflieger D, Heribert Hirt. Phosphorylation-dependent regulation of plant chromatin and chromatin-associated proteins. Proteomics. 2014 May 31. doi: 10.1002/pmic.201400073. PMID: 24889195

Keywords:

Arabidopsis, Chromatin, Plant, Protein kinase, Protein phosphorylation

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Bigeard J, Rayapuram N, Bonhomme L, Heribert Hirt, Pflieger D., Proteomic and phosphoproteomic analyses of chromatin-associated proteins from Arabidopsis thaliana. Proteomics. 2014 May 31. doi: 10.1002/pmic.201400072 PMID: 24889360

Keywords:

Arabidopsis thaliana, Chromatin, Nucleus, Phosphoproteomics, Proteomics

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Frei Dit Frey N, Garcia AV, Bigeard J, Zaag R, Bueso E, Garmier M, Pateyron S, de Tauzia-Moreau ML, Brunaud V, Balzergue S, Colcombet J, Aubourg S, Martin-Magniette ML, Heribert Hirt, Functional analysis of Arabidopsis immune-related MAPKs uncovers a role for MPK3 as negative regulator of inducible defences. Genome Biology. 2014 Jun 30;15(6):R87. PMID: 24980080

Keywords:

Arabidopsis, immune-related MAPKs, MPK3

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Arvind Varsani, Jesu ́s Navas-Castillo, Enrique Moriones, Cecilia Herna ́ndez-Zepeda, Ali Idris, Judith K. Brown, F. Murilo Zerbini, Darren P. Martin, Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus, Archives of Virology, DOI 10.1007/s00705-014-2050-2, Springer Vienna

Keywords:

ssDNA viruses, geminivirus, classification

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Schilling RK, Marschner P, Shavrukov Y, Berger B, Mark Tester, Roy SJ, Plett DC. Expression of the Arabidopsis vacuolar H⁺-pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field. Plant Biotechnology Journal. 2014 Apr;12(3):378-86. doi: 10.1111/pbi.12145. Epub

Keywords:

Barley, salinity, AVP1, nondestructive imaging, grain yield, GM field trials

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Honsdorf N, March TJ, Berger B, Tester M, Pillen K. High-Throughput, Phenotyping to Detect Drought Tolerance QTL in Wild Barley Introgression Lines. PLoS One. 2014 May 13;9(5):e97047. doi: 10.1371/journal.pone.0097047. eCollection 2014. PubMed PMID: 24823485.

Keywords:

Barley, chromosomes, flowering plants, fluorescence imaging, imaging techniques, introgression, leaves, phenotypes

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Naganand Rayapuram, Ludovic Bonhomme, Jean Bigeard, Kahina Haddadou, Cédric Przybylski, Heribert Hirt, and Delphine Pflieger (2014), Identification of Novel PAMP-Triggered Phosphorylation and Dephosphorylation Events in Arabidopsis thaliana by Quantitative Phosphoproteomic Analysis, Proteome Journal, DOI 10.1021/pr401268v

Keywords:

Phosphoproteomics, arabidopsis, MAP kinase, flagellin, pathogen, electron transfer dissociation

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Bianca Kyriacou, Katie L. Moore, David Paterson, Martin D. de Jonge, Daryl L. Howard, James Stangoulis, Mark Tester, Enzo Lombi, Alexander A.T. Johnson, Localization of iron in rice grain using synchrotron X-ray fluorescence microscopy and high resolution secondary ion mass spectrometry, Journal of Cereal Science, Volume 59, Issue 2, March 2014, Pages 173-180, http://dx.doi.org/10.1016/j.jcs.2013.12.006.

Keywords:

Biofortification, phytate, IP6, bioavailability

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Alexander R. Moise, Salim Al-Babili, and Eleanore T. Wurtzel, Mechanistic Aspects of Carotenoid Biosynthesis, Chemical Reviews, 2014, 114 (1), pp 164–193, DOI: 10.1021/cr400106y.

Keywords:

N/A

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Mohammed A Al-Saleh, Ibrahim M Al-Shahwan, Judith K Brown , Ali M Idris, Molecular characterization of a naturally occurring intraspecific recombinant begomovirus with close relatives widespread in southern Arabia, Virology Journal 2014, 11:103 doi:10.1186/1743-422X-11-103

Keywords:

Geminivirus, tomato leaf curl Sudan virus, virus variability, Whitefly vector

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Bruno M, Hofmann M, Vermathen M, Alder A, Beyer P, Al-Babili S. On the substrate- and stereospecificity of the plant carotenoid cleavage dioxygenase 7. FEBS Letters. 2014 May 2;588(9):1802-7. doi: 10.1016/j.febslet.2014.03.041. Epub 2014 Mar 28. PubMed PMID: 24685691.

Keywords:

Apocarotenoid, Carlactone, Carotenoid, Carotenoid cleavage dioxygenase, Strigolactone

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Arvind Varsani, Darren P. Martin, Jesu ́s Navas-Castillo, Enrique Moriones, Cecilia Herna ́ndez-Zepeda, Ali Idris, F. Murilo Zerbini, Judith K. Brown, Revisiting the classification of curtoviruses based on genome-wide pairwise identity, Springer-Verlag Wien 2014, doi:10.1007/s00705-014-1982-x

Keywords:

ssDNA viruses, geminivirus, classification

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Ana V. García and Heribert Hirt, Salmonella enterica induces and subverts the plant immune system, Frontiers Microbiology, 04 April 2014 | doi: 10.3389/fmicb.2014.00141

Keywords:

S. enterica, flagellin, PAMP-triggered immunity, effector, plants

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Stuart J Roy, Sónia Negrão, Mark Tester, Salt resistant crop plants ,Current Opinion in Biotechnology 26C (2014),
pp. 115-124, DOI information: 10.1016/j.copbio.2013.12.004.

Keywords:

Salinity tolerance; review; abiotic stress; crop improvement; yield maintenance.

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Ali Idris, Mohammed Al-Saleh , Marek J. Piatek , Ibrahim Al-Shahwan , Shahjahan Ali and Judith K. Brown, Viral Metagenomics: Analysis of Begomoviruses by Illumina High-Throughput Sequencing, Viruses 2014, 6 1220

Keywords:

Illumina sequencing; geminivirus; ssDNA viruses; genome enrichment; viral genome assembly

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Lixin Li, Ahmed Atef, Agnieszka Piatek, Zahir Ali, Marek Piatek, Mustapha Aouida, Altanbadralt Sharakuu, Ali Mahjoub, Guangchao Wang, Suhail Khan, Nina V. Fedoroff, Jian-Kang Zhu, Magdy M. Mahfouz. Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors. Molecular Plant. https://doi.org/10.1093/mp/sst006

Keywords:

Ralstonia solanacearum, genome engineering, TAL effectors, TALE activators and repressors, TALE nucleases (TALENs), targeted genome modifications

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T. Chen, P. Cui, H. Chen, S. Ali, S. Zhang and L. Xiong. A KH-Domain RNA-Binding Protein Interacts with FIERY2/CTD Phosphatase-Like 1 and Splicing Factors and Is Important for Pre-mRNA Splicing in Arabidopsis. Plos Genetics, 9, (2013). 10.1371/journal.pgen.1003875

Keywords:

N/A

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X. Zhang, G. Yang, R. Shi, X. Han, L. Qi, R. Wang, L. Xiong and G. Li. Arabidopsis cysteine-rich receptor-like kinase 45 functions in the responses to abscisic acid and abiotic stresses. Plant Physiology and Biochemistry, 67, 189-198, (2013). 10.1016/j.plaphy.2013.03.013

Keywords:

Abscisic acid; Arabidopsis thaliana; CRK45; Drought; Early seedling establishment; Germination; Salt

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M. Aouida, K. Kim, A.R. Shaikh, J.M. Pardo, J. Eppinger, D.-J. Yun, R.A. Bressan and M.L. Narasimhan. A Saccharomyces cerevisiae Assay System to Investigate Ligand/AdipoR1 Interactions That Lead to Cellular Signaling. Plos One, 8, (2013). 10.1371/journal.pone.0065454.

Keywords:

N/A

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M.J. Van Oosten, A. Sharkhuu, G. Batelli, R.A. Bressan and A. Maggio. The Arabidopsis thaliana mutant air1 implicates SOS3 in the regulation of anthocyanins under salt stress. Plant Molecular Biology, 83, 405-415, (2013), 10.1007/s11103-013-0099-z.

Keywords:

Arabidopsis Salt stress Oxidative stress Anthocyanins Flavonoids.

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Garcia AV, Charrier A, Schikora A, Bigeard J, Pateyron S, de Tauzia-Moreau ML, Evrard A, Mithöfer A, Martin-Magniette ML, Virlogeux-Payant I, Heribert Hirt, Salmonella enterica flagellin is recognized via FLS2 and activates PAMP-triggered immunity in Arabidopsis thaliana. Molecular Plant. 2013 Nov 6. PMID: 24198231

Keywords:

Salmonella enterica; Arabidopsis thaliana; flagellin; FLS2; immunity

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Brien, C.J., Berger, B., Rabie, H. & Tester, M. (2013) Accounting for variation in designing greenhouse experiments with special reference to greenhouses containing plants on conveyor systems. Plant Methods 9: DOI: 10.1186/1746-4811-9-5

Keywords:

Automated phenotyping, conveyor system, greenhouse experiments, greenhouse experimental design, microclimate variation, plant relocation, statistical analysis, thigmomorphogensis.

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Aouida M, Piatek MJ, Bangarusamy DK, Magdy M. Mahfouz. Activities and specificities of homodimeric TALENs in Saccharomyces cerevisiae. Current Genetics. 2013 Oct 1. [Epub ahead of print] PubMed PMID: 24081604.

Keywords:

Genome engineering , TALE-based nucleases , TALENs , homodimeric TALENs , saccharomyces cerevisiae ,targeted genome modificatio,

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Mustapha Aouida, Marta Rubio Texeira, Johan M. Thevelein, Richard Poulin and Dindial Ramotar. AGP2 Encodes a Multifunctional Transceptor that Positively Regulates Polyamine Transport. PLoS One. 2013 Jun 3;8(6):e65717. doi: 10.1371/journal.pone.0065717. Print 2013

Keywords:

sensor, polyamine transporters, toxicity, transcription factors, microarray analysis, gene expression profiler

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Rodrigo MJ, Alquézar B, Alós E, Medina V, Carmona L, Bruno M, Al-Babili S, Zacarías L. A novel carotenoid cleavage activity involved in the biosynthesis of Citrus fruit-specific apocarotenoid pigments. Journal Expremental Botany. 2013 Nov;64(14):4461-78. doi: 10.1093/jxb

Keywords:

Apocarotenoid, carotenoid cleavage dioxygenase, carotenoid, β-citraurin, Citrus, fruit coloration.

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Roy, S.J., Huang, W., Wang, X., Evrard, A., Schmöckel, S., Zafar, Z.U. and Mark Tester. (2013) A novel protein kinase involved in Na+ exclusion revealed from positional cloning. Plant Cell & Environment 35: 553-568. doi: 10.1111/j.1365-3040.2012.02595.x.

Keywords:

Arabidopsis, barley, AtCIPK16, QTL mapping.

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Berger, B., de Regt, B. and Tester, M. (2013) Applications of high-throughput plant phenotyping to study nutrient use efficiency. Methods in Molecular Biology 953: 277-290. DOI: 10.1007/978-1-62703-152-3_18

Keywords:

High-throughput phenotyping, Shoot imaging, Growth analysis, Nutrient use efficiency, RGB, Leaf color

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Mustapha Aouida, Kangchang Kim, AbdulRajjak S Shaikh, Jose M. Pardo, Jorg Eppinger, Ray A. Bressan, Meena L. Narasimhan. A split luciferase method to identify Adiponectin receptors agonists using Saccharomyces cerevisiae as a model organism. PLoS One. 2013 Jun 7;8(6):e65454. doi: 10.1371/journal.pone.0065454. Print 2013

Keywords:

Adiponectin, AdipoR1,agonist screen, APPL1, osmotin, Saccharomyces cerevisiae, split luciferase

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Li, L., A. Atef, A. Piatek, Z. Ali, M. Piatek, M. Aouida, A. Sharakuu, A. Mahjoub, G. Wang, S. Khan, N. V. Fedoroff, J. K. Zhu and Magdy M. Mahfouz (2013). "Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors." Molecular Plant. (4):1318-30.

Keywords:

Ralstonia solanacearum, TAL effectors, TALE activators and repressors, TALE nucleases (TALENs), genome engineering, targeted genome modifications

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Hill, C.B., Jha, D., Bacic, A., Tester, M. & Roessner, U. (2013) Characterization of ion contents and metabolic responses to salt stress of different Arabidopsis AtHKT1;1 genotypes and their parental strains. Molecular Plant6: 350-368

Keywords:

Abiotic stress, salinity, salt tolerance, HKT, sodium transporter, metabolomics, enhancer trap system.

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Singh, R.K., Jena, S.N., Khan, M.S., Yadav, S., Banarjee, N., Raghuvanshi, S., Bhardwaj, S., Dattamajuder, S.K., Kapur, R., Soloman, S., Swapna M., Srivastava, S., and Tyagi, A.K. Development of a novel set of EST-SSR markers and their utility in revealing population structure and genetic diversity in sugarcane. Gene, 2013, 524 (2): 309-329

Keywords:

Genetically distinct groups, informative DNA markers, microsatellite markers resources, molecular tools, EST-SSR markers, population structure assayed, saccharum complex

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Iwata, Y., Takahashi, M., Fedoroff, N., and Hamdan, S. (2013). Dissecting the interactions of SERRATE with RNA and DICER-LIKE 1 in Arabidopsis microRNA precursor processing. Nucleic Acids Research. doi: 10.1093/nar/gkt667

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N/A

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Nitish Kumar, Muppala P. Reddy, Mulpuri Sujatha,Genetic Transformation of Jatropha curcas: Current Status and Future Prospects,Jatropha, Challenges for a New Energy Crop2013, pp 535-546,© Springer Science+Business Media New York 2013 .

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N/A

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Shelden, M.C., Roessner, U., Sharp, R.E., Tester, M. & Bacic, A. (2013) Genetic variation in the root growth response of barley genotypes to salinity stress. Functional Plant Biology, http://dx.doi.org/10.1071/FP12290

Keywords:

abiotic stress, cereals, osmotic stress, root elongation, salt tolerance, seminal roots.

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Shavrukov, Y., Bovill, J., Afzal, I., Hayes, J., Roy, S., Tester, M. & Collins, N. (2013) HVP10 encoding V-PPase is a prime candidate for the barley HvNax3 sodium exclusion gene: evidence from fine mapping and expression analysis. Planta. DOI: 10.1007/s00425-012-1827-3

Keywords:

HvFT, HvVRT2, Na+exclusion, salinity tolerance, vacuolar H+-pyrophosphatase.

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Nitish Kumar,Muppala P. Reddy,Jatropha, Challenges for a New Energy Crop2013Volume 2: Genetic Improvement and Biotechnology10.1007/978-1-4614-4915-7_26© Springer Science+Business Media New York 2013

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N/A

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Muppala P. Reddy , Pamidimarri D. V. N. Sudheer, Shaik. G. Mastan, Hifzur Rahman, Nicolas Carels and Bir Bahadur,Karyology and Genomics of Jatropha: Current Status and Future Prospects,10.1007/978-1-4614-4915-7_15© Springer Science+Business Media New York 2013

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N/A

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Yousef S. Al-Hafedh & Aftab Alam (2013) Replacement of Fishmeal by Single Cell Protein Derived from Yeast Grown on Date (Phoenix dactylifera) Industry Waste in the Diet of Nile Tilapia (Oreochromis niloticus) Fingerlings, Journal of Applied Aquaculture, 25:4, 346-358, DOI: 10.1080/10454438.2013.852419

Keywords:

Fishmeal, single cell protein, yeast, Nile tilapia.

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Ruyter-Spira C, Salim Al-Babili, van der Krol S, Bouwmeester H. The biology of strigolactones. Trends in Plant Science. 2013 Feb;18(2):72-83. doi: 10.1016/j.tplants.2012.10.003. Epub 2012 Nov 19. Review. PubMed PMID: 23182342.

Keywords:

Plant Development,Strigolactones,Root Parasitic Plants,Carlactone

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Garnett, T., Conn, V., Plett, D., Conn, S., Zanghellini, J., Mackenzie, N., Enju, A., Francis, K., Holtham, L., Roessner, U., Boughton, B., Bacic, A., Shirley, N., Rafalski, A., Dhugga, K., Tester, M & Kaiser, B. (2013) The response of the maize nitrate transport system to nitrogen demand and supply across the lifecycle. New Phytologist 198: 82-94

Keywords:

maize, nitrate, nitrogen, nitrogen use efficiency (NUE), uptake.

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Trautmann, Beyer, P. and Al-Babili, S. (2013) The ORF slr0091 of Synechocystis sp. PCC6803 encodes a high-light induced aldehyde dehydrogenase converting apocarotenals and alkanals. The FEBS Journal. 280, 3685-96

Keywords:

aldehyde dehydrogenase, alkanals, apocarotenoids, carotenoid cleavage, cyanobacteria.

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Díaz-Sánchez V, Estrada AF, Limón MC, Salim Al-Babili, Avalos J. The oxygenase CAO-1 of Neurospora crassa is a resveratrol cleavage enzyme. Eukaryot Cell. 2013 Sep;12(9):1305-14. doi: 10.1128/EC.00084-13. Epub 2013 Jul 26. PubMed PMID: 23893079.

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N/A

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Dong Deng, Chuangye Yan, Xiaojing Pan, Magdy M. Mahfouz, Jiawei Wang, Jian-Kang Zhu, Yigong Shi, Nieng Yan. Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors. Science. DOI: 10.1126/science.1215670

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N/A

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B. Khraiwesh, J.-K. Zhu and J. Zhu. Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms, 1819, 137-148, (2012). 10.1016/j.bbagrm.2011.05.001

Keywords:

miRNA; siRNA; Biotic; Abiotic; Stress responses; Plant

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B. Li, Q. Li, L. Xiong, H.J. Kronzucker, U. Kraemer and W. Shi. Arabidopsis Plastid AMOS1/EGY1 Integrates Abscisic Acid Signaling to Regulate Global Gene Expression Response to Ammonium Stress. Plant Physiology, 160, 2040-2051, (2012). 10.1104/pp.112.206508

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