Data4UrbanMobility presented the paper “Data4UrbanMobility: Towards Holistic Data Analytics for Mobility Applications in Urban Regions” at the 5th International Smart City Workshop at the Web Conference 2019. The workshop focused on enhancing every day life in urban environments using digital technologies. Thank you very much for the fruitful discussions!

• Seed DNA damage responses promote germination and growth in textitArabidopsis thaliana. Waterworth, Wanda M.; Latham, Rosalind; Wang, Dapeng; Alsharif, Mona; West, Christopher E. (2022). 119(30) e2202172119.

  The desiccated, quiescent state of seeds confers extended survival of the embryonic plant. However, accumulation of striking levels of genome damage in quiescence impairs germination and threatens plant survival. The mechanisms by which seeds mitigate this damage remain unclear. Here, we reveal that imbibed Arabidopsis seeds display high resistance to DNA damage, which is lost as seeds advance to germination, coincident with increasing cell cycle activity. In contrast to seedlings, we show that seeds minimize the impact of DNA damage by reducing meristem disruption and delaying SOG1-dependent programmed cell death. This promotes root growth early postgermination. In response to naturally accumulated DNA damage in aging seeds, SOG1 activates cell death postgermination. SOG1 activities are also important for promoting successful seedling establishment. These distinct cellular responses of seeds and seedlings are reflected by different DNA damage transcriptional profiles. Comparative analysis of DNA repair mutants identifies roles of the major genome maintenance pathways in germination but that the repair of cytotoxic chromosomal breaks is the most important for seed longevity. Collectively, these results indicate that high levels of DNA damage incurred in seeds are countered by low cell cycle activity, cell cycle checkpoints, and DNA repair, promoting successful seedling establishment. Our findings reveal insight into both the physiological significance of plant DNA damage responses and the mechanisms which maintain seed longevity, important for survival of plant populations in the natural environment and sustainable crop production under changing climates.
• Origins of the seed: The “golden-trio hypothesis”. Bai, Shu-Nong; Rao, Guang-Yuan; Yang, Ji (2022). 13 965000.

  The seed is an evolutionary innovation in the plant kingdom. While human civilization depends heavily on seed production, how the seed trait emerged remains elusive. In this opinion article, a “golden-trio hypothesis” is proposed based on our investigations of LEC1 gene functions in Adiantum capillus-veneris . This hypothesis posits that a “seed program” arose from spatiotemporal integration of three key components: assimilate flow, ABA-mediated stress responses, and stress-induced LEC1 expression. Thus, the evolutionary innovation of seeds should be considered not a simple event resulting from new genes; rather, it represents the outcome of a series of physiological and morphological innovations that emerged prior to and regardless of the origin of the seed program. This new perspective could help us tackle some long-standing questions around the puzzling origin of seeds.
• Uncovering salt tolerance mechanisms in pepper plants: a physiological and transcriptomic approach. López-Serrano, Lidia; Calatayud, Ángeles; López-Galarza, Salvador; Serrano, Ramón; Bueso, Eduardo (2021). 21(1) 169.

  Abstract Background Pepper is one of the most cultivated crops worldwide, but is sensitive to salinity. This sensitivity is dependent on varieties and our knowledge about how they can face such stress is limited, mainly according to a molecular point of view. This is the main reason why we decided to develop this transcriptomic analysis. Tolerant and sensitive accessions, respectively called A25 and A6, were grown for 14 days under control conditions and irrigated with 70 mM of NaCl. Biomass, different physiological parameters and differentially expressed genes were analysed to give response to differential salinity mechanisms between both accessions. Results The genetic changes found between the accessions under both control and stress conditions could explain the physiological behaviour in A25 by the decrease of osmotic potential that could be due mainly to an increase in potassium and proline accumulation, improved growth (e.g. expansins), more efficient starch accumulation (e.g. BAM1), ion homeostasis (e.g. CBL9, HAI3, BASS1), photosynthetic protection (e.g. FIB1A, TIL, JAR1) and antioxidant activity (e.g. PSDS3, SnRK2.10). In addition, misregulation of ABA signalling (e.g. HAB1, ERD4, HAI3) and other stress signalling genes (e.g. JAR1) would appear crucial to explain the different sensitivity to NaCl in both accessions. Conclusions After analysing the physiological behaviour and transcriptomic results, we have concluded that A25 accession utilizes different strategies to cope better salt stress, being ABA-signalling a pivotal point of regulation. However, other strategies, such as the decrease in osmotic potential to preserve water status in leaves seem to be important to explain the defence response to salinity in pepper A25 plants.
• Correlation between seed longevity and RNA integrity in the embryos of rice seeds. Saighani, Kalimullah; Kondo, Daiki; Sano, Naoto; Murata, Kazumasa; Yamada, Tetsuya; Kanekatsu, Motoki (2021). 38(2) 277–283.
• RBR-Type E3 Ligases and the Ubiquitin-Conjugating Enzyme UBC26 Regulate Abscisic Acid Receptor Levels and Signaling. Fernandez, Maria Angeles; Belda-Palazon, Borja; Julian, Jose; Coego, Alberto; Lozano-Juste, Jorge; Iñigo, Sabrina; Rodriguez, Lesia; Bueso, Eduardo; Goossens, Alain; Rodriguez, Pedro L. (2020). 182(4) 1723–1742.
• A matter of life and death: Molecular, physiological, and environmental regulation of seed longevity. Zhou, Wenguan; Chen, Feng; Luo, Xiaofeng; Dai, Yujia; Yang, Yingzeng; Zheng, Chuan; Yang, Wenyu; Shu, Kai (2020). 43(2) 293–302.
• Trichoderma-functional metabolomics to genetic engineering. Saravanakumar, Kandasamy; Rathnayake, Anuruddhika Udayangani; Sathiyaseelan, Anbazhagan; Selvakumar, Vijayalakshmi; Vijaya Anand, Mariadoss Arokia; Adeyemi, Damilare Emmanuel; Kathiresan, Kandasamy; Byun, Hee-Guk; Wang, Myeong-Hyeon (2020). 209–220.
• Cutin and suberin: assembly and origins of specialized lipidic cell wall scaffolds. Philippe, Glenn; Sørensen, Iben; Jiao, Chen; Sun, Xuepeng; Fei, Zhangjun; Domozych, David S; Rose, Jocelyn KC (2020). 55 11–20.
• Overexpression of the trehalose-6-phosphate phosphatase family gene AtTPPF improves the drought tolerance of Arabidopsis thaliana. Lin, Qingfang; Yang, Jiao; Wang, Qiongli; Zhu, Hong; Chen, Zhiyong; Dao, Yihang; Wang, Kai (2019). 19(1) 381.
• Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model. Hsu, Bryan B.; Gibson, Travis E.; Yeliseyev, Vladimir; Liu, Qing; Lyon, Lorena; Bry, Lynn; Silver, Pamela A.; Gerber, Georg K. (2019). 25(6) 803–814.e5.
• Regulation of K+ Nutrition in Plants. Ragel, Paula; Raddatz, Natalia; Leidi, Eduardo O.; Quintero, Francisco J.; Pardo, José M. (2019). 10
• Transcriptome Changes Induced by Different Potassium Levels in Banana Roots. He, Yingdui; Li, Ruimei; Lin, Fei; Xiong, Ying; Wang, Lixia; Wang, Bizun; Guo, Jianchun; Hu, Chengxiao (2019). 9(1) 11.
• Wheat seed ageing viewed through the cellular redox environment and changes in pH. Nagel, Manuela; Seal, Charlotte E.; Colville, Louise; Rodenstein, Axel; Un, Sun; Richter, Josefine; Pritchard, Hugh W.; Börner, Andreas; Kranner, Ilse (2019). 53(6) 641–654.
• A role for auxin signaling in the acquisition of longevity during seed maturation. Pellizzaro, Anthoni; Neveu, Martine; Lalanne, David; Ly Vu, Benoit; Kanno, Yuri; Seo, Mitsunori; Leprince, Olivier; Buitink, Julia (2019).
• Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. Chauffour, Frédéric; Bailly, Marlène; Perreau, François; Cueff, Gwendal; Suzuki, Hiromi; Collet, Boris; Frey, Anne; Clément, Gilles; Soubigou-Taconnat, Ludivine; Balliau, Thierry; Krieger-Liszkay, Anja; Rajjou, Loïc; Marion-Poll, Annie (2019). 180(2) 1198–1218.
• The Effect of Storage Condition and Duration on the Deterioration of Primed Rice Seeds. Wang, Weiqin; He, Aibin; Peng, Shaobing; Huang, Jianliang; Cui, Kehui; Nie, Lixiao (2018). 9 172.
• An overview of textitBacillus proteases: from production to application. Contesini, Fabiano Jares; Melo, Ricardo Rodrigues de; Sato, Hélia Harumi (2018). 38(3) 321–334.
• The MYB107 Transcription Factor Positively Regulates Suberin Biosynthesis. Gou, Mingyue; Hou, Guichuan; Yang, Huijun; Zhang, Xuebin; Cai, Yuanheng; Kai, Guoyin; Liu, Chang-Jun (2017). 173(2) 1045–1058.
• Transcriptome Analysis of Differentially Expressed Genes Induced by Low and High Potassium Levels Provides Insight into Fruit Sugar Metabolism of Pear. Shen, Changwei; Wang, Jie; Shi, Xiaoqian; Kang, Yalong; Xie, Changyan; Peng, Lirun; Dong, Caixia; Shen, Qirong; Xu, Yangchun (2017). 8
• Aldehyde Oxidase 4 Plays a Critical Role in Delaying Silique Senescence by Catalyzing Aldehyde Detoxification. Srivastava, Sudhakar; Brychkova, Galina; Yarmolinsky, Dmitry; Soltabayeva, Aigerim; Samani, Talya; Sagi, Moshe (2017). 173(4) 1977–1997.
• Brassinosteroid Biosynthesis Is Modulated via a Transcription Factor Cascade of COG1, PIF4, and PIF5. Wei, Zhuoyun; Yuan, Tong; Tarkowská, Danuše; Kim, Jeongsik; Nam, Hong Gil; Novák, Ondřej; He, Kai; Gou, Xiaoping; Li, Jia (2017). 174(2) 1260–1273.
• Exogenous gibberellin enhances secondary xylem development and lignification in carrot taproot. Wang, Guang-Long; Que, Feng; Xu, Zhi-Sheng; Wang, Feng; Xiong, Ai-Sheng (2017). 254(2) 839–848.
• Galactinol as marker for seed longevity. de Souza Vidigal, Deborah; Willems, Leo; van Arkel, Jeroen; Dekkers, Bas J.W.; Hilhorst, Henk W.M.; Bentsink, Leónie (2016). 246 112–118.
• Multiple criteria-based screening of Trichoderma isolates for biological control of Botrytis cinerea on tomato. You, Jiaqi; Zhang, Jing; Wu, Mingde; Yang, Long; Chen, Weidong; Li, Guoqing (2016). 101 31–38.
• Differentially expressed galactinol synthase(s) in chickpea are implicated in seed vigor and longevity by limiting the age induced ROS accumulation. Salvi, Prafull; Saxena, Saurabh Chandra; Petla, Bhanu Prakash; Kamble, Nitin Uttam; Kaur, Harmeet; Verma, Pooja; Rao, Venkateswara; Ghosh, Shraboni; Majee, Manoj (2016). 6(1)
• MYB107 and MYB9 Homologs Regulate Suberin Deposition in Angiosperms. Lashbrooke, Justin; Cohen, Hagai; Levy-Samocha, Dorit; Tzfadia, Oren; Panizel, Irina; Zeisler, Viktoria; Massalha, Hassan; Stern, Adi; Trainotti, Livio; Schreiber, Lukas; Costa, Fabrizio; Aharoni, Asaph (2016). 28(9) 2097–2116.
• Differentially expressed seed aging responsive heat shock protein OsHSP18.2 implicates in seed vigor, longevity and improves germination and seedling establishment under abiotic stress. Kaur, Harmeet; Petla, Bhanu P.; Kamble, Nitin U.; Singh, Ajeet; Rao, Venkateswara; Salvi, Prafull; Ghosh, Shraboni; Majee, Manoj (2015). 6
• Suberin: biosynthesis, regulation, and polymer assembly of a protective extracellular barrier. Vishwanath, Sollapura J.; Delude, Camille; Domergue, Frédéric; Rowland, Owen (2015). 34(4) 573–586.
• HISAT: a fast spliced aligner with low memory requirements. Kim, Daehwan; Langmead, Ben; Salzberg, Steven L (2015). 12(4) 357–360.
• The importance of safeguarding genome integrity in germination and seed longevity. Waterworth, Wanda M.; Bray, Clifford M.; West, Christopher E. (2015). 66(12) 3549–3558.
• What Is Stress? Dose-Response Effects in Commonly Used in Vitro Stress Assays. Claeys, Hannes; Van Landeghem, Sofie; Dubois, Marieke; Maleux, Katrien; Inzé, Dirk (2014). 165(2) 519–527.
• Expression of textitPRX36 , textitPMEI6 and textitSBT1.7 is controlled by complex transcription factor regulatory networks for proper seed coat mucilage extrusion. Ranocha, Philippe; Francoz, Edith; Burlat, Vincent; Dunand, Christophe (2014). 9(11) e977734.
• Trimmomatic: a flexible trimmer for Illumina sequence data. Bolger, Anthony M.; Lohse, Marc; Usadel, Bjoern (2014). 30(15) 2114–2120.
• AtMYB41 activates ectopic suberin synthesis and assembly in multiple plant species and cell types. Kosma, Dylan K.; Murmu, Jhadeswar; Razeq, Fakhria M.; Santos, Patricia; Bourgault, Richard; Molina, Isabel; Rowland, Owen (2014). 80(2) 216–229.
• The Impact of Horizontal Gene Transfer on the Biology of Clostridium difficile. Roberts, Adam P.; Allan, Elaine; Mullany, Peter (2014). (Vol. 65) 63–82.
• Applications of Trichoderma in Plant Growth Promotion. Stewart, Alison; Hill, Robert (2014). 415–428.
• The single-subunit RING-type E3 ubiquitin ligase RSL1 targets PYL4 and PYR1 ABA receptors in plasma membrane to modulate abscisic acid signaling. Bueso, Eduardo; Rodriguez, Lesia; Lorenzo-Orts, Laura; Gonzalez-Guzman, Miguel; Sayas, Enric; Muñoz-Bertomeu, Jesús; Ibañez, Carla; Serrano, Ramón; Rodriguez, Pedro L. (2014). 80(6) 1057–1071.
• Coexistence but Independent Biosynthesis of Catechyl and Guaiacyl/Syringyl Lignin Polymers in Seed Coats. Tobimatsu, Y.; Chen, F.; Nakashima, J.; Escamilla-Trevino, L. L.; Jackson, L.; Dixon, R. A.; Ralph, J. (2013). 25(7) 2587–2600.
• Differential analysis of gene regulation at transcript resolution with RNA-seq. Trapnell, Cole; Hendrickson, David G; Sauvageau, Martin; Goff, Loyal; Rinn, John L; Pachter, Lior (2013). 31(1) 46–53.
• A Regulatory Network-Based Approach Dissects Late Maturation Processes Related to the Acquisition of Desiccation Tolerance and Longevity of Medicago truncatula Seeds. Verdier, J.; Lalanne, D.; Pelletier, S.; Torres-Jerez, I.; Righetti, K.; Bandyopadhyay, K.; Leprince, O.; Chatelain, E.; Vu, B. L.; Gouzy, J.; Gamas, P.; Udvardi, M. K.; Buitink, J. (2013). 163(2) 757–774.
• Relationships between antioxidant enzymes and physiological variations occur during ageing of pepper seeds. Demirkaya, Mustafa (2013). 54(2) 97–102.
• A Quartet of PIF bHLH Factors Provides a Transcriptionally Centered Signaling Hub That Regulates Seedling Morphogenesis through Differential Expression-Patterning of Shared Target Genes in Arabidopsis. Zhang, Yu; Mayba, Oleg; Pfeiffer, Anne; Shi, Hui; Tepperman, James M.; Speed, Terence P.; Quail, Peter H. (G. P. Copenhaver, ed.) (2013). 9(1) e1003244.
• Suberin-Associated Fatty Alcohols in Arabidopsis: Distributions in Roots and Contributions to Seed Coat Barrier Properties. Vishwanath, S. J.; Kosma, D. K.; Pulsifer, I. P.; Scandola, S.; Pascal, S.; Joubes, J.; Dittrich-Domergue, F.; Lessire, R.; Rowland, O.; Domergue, F. (2013). 163(3) 1118–1132.
• Using Tablet for visual exploration of second-generation sequencing data. Milne, I.; Stephen, G.; Bayer, M.; Cock, P. J. A.; Pritchard, L.; Cardle, L.; Shaw, P. D.; Marshall, D. (2013). 14(2) 193–202.
• Solving the puzzles of cutin and suberin polymer biosynthesis. Beisson, Fred; Li-Beisson, Yonghua; Pollard, Mike (2012). 15(3) 329–337.
• Plasmids foster diversification and adaptation of bacterial populations in soil. Heuer, Holger; Smalla, Kornelia (2012). 36(6) 1083–1104.
• Distant Activation of Transcription: Mechanisms of Enhancer Action. Kulaeva, O. I.; Nizovtseva, E. V.; Polikanov, Y. S.; Ulianov, S. V.; Studitsky, V. M. (2012). 32(24) 4892–4897.
• α-Tocopherol levels in natural and artificial aging of soybean seeds. Giurizatto, Maria Izabel Krüger; Ferrarese-Filho, Osvaldo; Ferrarese, Maria de Lourdes Lucio; Robaina, Antonio Dias; Gonçalves, Manoel Carlos; Cardoso, Cláudia Andréia Lima (2012). 34(3) 339–343.
• Peppers vegetable and spice capsicums Bosland, Paul W; Votava, Eric J (2012). CABI, Wallingford.

  This book provides an introduction to and overview of vegetable and spice peppers and consolidates the many aspects of pepper research, i.e. taxonomy, breeding and biotechnology, production, harvesting, postharvest handling and disorders, pests and diseases, among others. The chemical composition of various Capsicum species are also presented.
• Conservation of Salmonella Infection Mechanisms in Plants and Animals. Schikora, Adam; Virlogeux-Payant, Isabelle; Bueso, Eduardo; Garcia, Ana V.; Nilau, Theodora; Charrier, Amélie; Pelletier, Sandra; Menanteau, Pierrette; Baccarini, Manuela; Velge, Philippe; Hirt, Heribert (M. Hensel, ed.) (2011). 6(9) e24112.
• Chromatin Immunoprecipitation to Verify or to Identify In Vivo Protein–DNA Interactions. Zheng, Yumei; Perry, Sharyn E. L. Yuan, S. E. Perry (eds.) (2011). (Vol. 754) 277–291.
• The reduction of seed-specific dehydrins reduces seed longevity in Arabidopsis thaliana. Hundertmark, Michaela; Buitink, Julia; Leprince, Olivier; Hincha, Dirk K. (2011). 21(03) 165–173.
• Cytochromes P450. Bak, Søren; Beisson, Fred; Bishop, Gerard; Hamberger, Björn; Höfer, René; Paquette, Suzanne; Werck-Reichhart, Danièle (2011). 9 e0144.
• Developmental regulation of CYCA2s contributes to tissue-specific proliferation in textitArabidopsis: Developmental control of CYCA2. Vanneste, Steffen; Coppens, Frederik; Lee, EunKyoung; Donner, Tyler J; Xie, Zidian; Van Isterdael, Gert; Dhondt, Stijn; De Winter, Freya; De Rybel, Bert; Vuylsteke, Marnik; De Veylder, Lieven; Friml, Jiří; Inzé, Dirk; Grotewold, Erich; Scarpella, Enrico; Sack, Fred; Beemster, Gerrit T S; Beeckman, Tom (2011). 30(16) 3430–3441.
• Phloroglucinol Stain for Lignin. Liljegren, S. (2010). 2010(1) pdb.prot4954-pdb.prot4954.
• Activation of the plasma membrane H (+) -ATPase by acid stress: antibodies as a tool to follow the phosphorylation status of the penultimate activating Thr. Bobik, Krzysztof; Boutry, Marc; Duby, Geoffrey (2010). 5(6) 681–683.

  Tight regulation of the plasma membrane proton pump ATPase (H (+) -ATPase) is necessary for controlling the membrane potential that energizes secondary transporters. This regulation relies on the phosphorylation of the H (+) -ATPase penultimate residue, a theonine, and the subsequent binding of regulatory 14-3-3 proteins, which results in enzyme activation. Using phospho-specific antibodies directed against the phosphorylable Thr of either PMA2 (Plasma membrane H (+) -ATPase from N. plumbaginifolia) or PMA4, we showed that the kinetics and extent of phosphorylation differ between both isoforms according to the growth or environmental conditions like cold stress. (1) Here, we used phospho-specific antibodies to follow PMA2 Thr phosphorylation upon acidification of the cytosol by incubating N. tabacum BY2 cells with four different weak organic acids. Increased PMA2 phosphorylation was observed for three of them, thus highlighting the role of the H (+) -ATPase in cell pH homeostasis.
• Identification of an Arabidopsis Feruloyl-Coenzyme A Transferase Required for Suberin Synthesis. Molina, Isabel; Li-Beisson, Yonghua; Beisson, Fred; Ohlrogge, John B.; Pollard, Mike (2009). 151(3) 1317–1328.
• Effects of APETALA2 on embryo, endosperm, and seed coat development determine seed size in Arabidopsis. Ohto, Masa-aki; Floyd, Sandra K.; Fischer, Robert L.; Goldberg, Robert B.; Harada, John J. (2009). 22(4) 277–289.
• Mutations in UDP-Glucose:Sterol Glucosyltransferase in Arabidopsis Cause Transparent Testa Phenotype and Suberization Defect in Seeds. DeBolt, S.; Scheible, W.-R.; Schrick, K.; Auer, M.; Beisson, F.; Bischoff, V.; Bouvier-Nave, P.; Carroll, A.; Hematy, K.; Li, Y.; Milne, J.; Nair, M.; Schaller, H.; Zemla, M.; Somerville, C. (2009). 151(1) 78–87.
• Specific functions of individual class III peroxidase genes. Cosio, C.; Dunand, C. (2009). 60(2) 391–408.
• Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Amann, Rudolf; Fuchs, Bernhard M. (2008). 6(5) 339–348.
• DNA-free RNA isolation protocols for Arabidopsis thaliana, including seeds and siliques. Oñate-Sánchez, Luis; Vicente-Carbajosa, Jesús (2008). 1(1) 93.
• Building lipid barriers: biosynthesis of cutin and suberin. Pollard, Mike; Beisson, Fred; Li, Yonghua; Ohlrogge, John B. (2008). 13(5) 236–246.
• Seed longevity: Survival and maintenance of high germination ability of dry seeds. Rajjou, Loïc; Debeaujon, Isabelle (2008). 331(10) 796–805.
• LECs go crazy in embryo development. Braybrook, S; Harada, J (2008). 13(12) 624–630.
• Deposition and localization of lipid polyester in developing seeds of Brassica napus and Arabidopsis thaliana: Lipid polyesters in seed coats. Molina, Isabel; Ohlrogge, John B.; Pollard, Mike (2007). 53(3) 437–449.
• Development of series of gateway binary vectors, pGWBs, for realizing efficient construction of fusion genes for plant transformation. Nakagawa, Tsuyoshi; Kurose, Takayuki; Hino, Takeshi; Tanaka, Katsunori; Kawamukai, Makoto; Niwa, Yasuo; Toyooka, Kiminori; Matsuoka, Ken; Jinbo, Tetsuro; Kimura, Tetsuya (2007). 104(1) 34–41.
• Differential Gene Expression and Subcellular Targeting of Arabidopsis Glutathione textitS -Transferase F8 Is Achieved through Alternative Transcription Start Sites. Thatcher, Louise F.; Carrie, Chris; Andersson, Carol R.; Sivasithamparam, Krishnapillai; Whelan, James; Singh, Karam B. (2007). 282(39) 28915–28928.
• Gene Annotation and Pathway Mapping in KEGG. Aoki-Kinoshita, Kiyoko F; Kanehisa, Minoru J. M. Walker, N. H. Bergman (eds.) (2007). (Vol. 396) 71–91.
• Improved Gateway Binary Vectors: High-Performance Vectors for Creation of Fusion Constructs in Transgenic Analysis of Plants. Nakagawa, Tsuyoshi; Suzuki, Takamasa; Murata, Satoko; Nakamura, Shinya; Hino, Takeshi; Maeo, Kenichiro; Tabata, Ryo; Kawai, Tsutae; Tanaka, Katsunori; Niwa, Yasuo; Watanabe, Yuichiro; Nakamura, Kenzo; Kimura, Tetsuya; Ishiguro, Sumie (2007). 71(8) 2095–2100.
• The gibberellin biosynthetic genes AtGA20ox1 and AtGA20ox2 act, partially redundantly, to promote growth and development throughout the Arabidopsis life cycle: GA20ox function in Arabidopsis. Rieu, Ivo; Ruiz-Rivero, Omar; Fernandez-Garcia, Nieves; Griffiths, Jayne; Powers, Stephen J.; Gong, Fan; Linhartova, Terezie; Eriksson, Sven; Nilsson, Ove; Thomas, Stephen G.; Phillips, Andrew L.; Hedden, Peter (2007). 53(3) 488–504.
• The FOX hunting system: an alternative gain-of-function gene hunting technique. Ichikawa, Takanari; Nakazawa, Miki; Kawashima, Mika; Iizumi, Haruko; Kuroda, Hirofumi; Kondou, Youichi; Tsuhara, Yumi; Suzuki, Kumiko; Ishikawa, Akie; Seki, Motoaki; Fujita, Miki; Motohashi, Reiko; Nagata, Noriko; Takagi, Tomoko; Shinozaki, Kazuo; Matsui, Minami (2006). 48(6) 974–985.
• The Arabidopsis Zinc Finger-Homeodomain Genes Encode Proteins with Unique Biochemical Properties That Are Coordinately Expressed during Floral Development. Tan, Q. K.-G.; Irish, V. F. (2006). 140(3) 1095–1108.
• Flavonoid diversity and biosynthesis in seed of Arabidopsis thaliana. Routaboul, Jean-Marc; Kerhoas, Lucien; Debeaujon, Isabelle; Pourcel, Lucille; Caboche, Michel; Einhorn, Jacques; Lepiniec, Loïc (2006). 224(1) 96–107.
• Apoplastic polyesters in Arabidopsis surface tissues – A typical suberin and a particular cutin. Franke, Rochus; Briesen, Isabel; Wojciechowski, Tobias; Faust, Andrea; Yephremov, Alexander; Nawrath, Christiane; Schreiber, Lukas (2005). 66(22) 2643–2658.
• Genetic analysis of seed coat development in Arabidopsis. Haughn, George; Chaudhury, Abed (2005). 10(10) 472–477.
• Glycerol-insensitive Arabidopsis mutants: gli1 seedlings lack glycerol kinase, accumulate glycerol and are more resistant to abiotic stress. Eastmond, Peter J. (2004). 37(4) 617–625.

  The aim of this study was to investigate the process of glycerol catabolism in germinating Arabidopsis seed. A genetic screen was performed to isolate glycerol-insensitive (gli) mutant seedlings. Three separate mutant loci were identified (gli1, gli2 and gli3). Of these, only gli1 is unable to utilise glycerol. Following germination, gli1 seedlings transiently accumulate glycerol derived from the breakdown of storage oil and are more resistant to hyperosmotic stress, salt stress, oxidative stress, freezing and desiccation. Enzyme assays revealed that gli1 lacks glycerol kinase activity. GLI1 mapped to chromosome 1 near the putative glycerol kinase gene NHO1. Mutations in this gene were identified in three independent gli1 alleles. A cDNA encoding GLI1 was cloned and its function was proven by complementation of an Escherichia coli glycerol kinase (glpK) deletion strain. Quantitative RT-PCR analysis showed that GLI1 is expressed in all tissues, but is transiently upregulated during early post-germinative growth and leaf senescence. These data show that glycerol kinase is required for glycerol catabolism in Arabidopsis and that the accumulation of glycerol can enhance resistance to a variety of abiotic stresses associated with dehydration.
• Functional Annotation of the Arabidopsis Genome Using Controlled Vocabularies. Berardini, T. Z. (2004). 135(2) 745–755.
• Transforming a (β/α)8-Barrel Enzyme into a Split-Protein Sensor through Directed Evolution. Tafelmeyer, Petra; Johnsson, Nils; Johnsson, Kai (2004). 11(5) 681–689.
• K+ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions. Obrdlik, P.; El-Bakkoury, M.; Hamacher, T.; Cappellaro, C.; Vilarino, C.; Fleischer, C.; Ellerbrok, H.; Kamuzinzi, R.; Ledent, V.; Blaudez, D.; Sanders, D.; Revuelta, J. L.; Boles, E.; Andre, B.; Frommer, W. B. (2004). 101(33) 12242–12247.
• Oxidases, peroxidases and hydrogen peroxide: The suberin connection. Bernards, Mark A.; Summerhurst, D. Kristen; Razem, Fawzi A. (2004). 3(1-2) 113–126.
• ICE1: a regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Chinnusamy, Viswanathan; Ohta, Masaru; Kanrar, Siddhartha; Lee, Byeong-Ha; Hong, Xuhui; Agarwal, Manu; Zhu, Jian-Kang (2003). 17(8) 1043–1054.

  Cold temperatures trigger the expression of the CBF family of transcription factors, which in turn activate many downstream genes that confer chilling and freezing tolerance to plants. We report here the identification of ICE1 (inducer of CBF expression 1), an upstream transcription factor that regulates the transcription of CBF genes in the cold. An Arabidopsis ice1 mutant was isolated in a screen for mutations that impair cold-induced transcription of a CBF3 promoter-luciferase reporter gene. The ice1 mutation blocks the expression of CBF3 and decreases the expression of many genes downstream of CBFs, which leads to a significant reduction in plant chilling and freezing tolerance. ICE1 encodes a MYC-like bHLH transcriptional activator. ICE1 binds specifically to the MYC recognition sequences in the CBF3 promoter. ICE1 is expressed constitutively, and its overexpression in wild-type plants enhances the expression of the CBF regulon in the cold and improves freezing tolerance of the transgenic plants.
• Mechanisms of seed ageing under different storage conditions for Vigna radiata (L.) Wilczek: lipid peroxidation, sugar hydrolysis, Maillard reactions and their relationship to glass state transition. Murthy, U. M. N.; Kumar, P. P.; Sun, W. Q. (2003). 54(384) 1057–1067.
• The ploidy level of transgenic plants in Agrobacterium-mediated transformation of tomato cotyledons (Lycopersicon esculentum L.Mill.) is genotype and procedure dependent. Ellul, P.; Garcia-Sogo, B.; Pineda, B.; Ríos, G.; Roig, L.; Moreno, V. (2003). 106(2) 231–238.

  A protocol avoiding the feeder-layer cell system was optimized for Agrobacterium-mediated transformation of tomato cotyledonary explants. Over 500 transgenic plants from five tomato cultivars were regenerated in 15 independent experiments. Depending on both genotype and procedure, transformation frequencies ranged from 1.8% to 11.3%. The optimal transformation rate was obtained by inoculating explants with a bacterial suspension in exponential growth (D600 = 102–103 cells/ml) and transferring cotyledon explants to fresh selective regeneration medium every 3 weeks. The ploidy level of both tomato genotypes used as explant source and primary transformants, was studied by flow cytometry. The inbred lines and cultivars were diploid but a polysomatic pattern in the cotyledon explant was confirmed. The rate of tetraploid transgenic plants ranged from 24.5% to 80% and depended on both the genotype and the transformation procedure. Surprisingly, the percentages of transformed plants with higher ploidy levels were not related to the proportion of 4C and 8C nuclei in the cotyledonary tissue. For some genotypes the optimisation of the transformation rate resulted in an increase of tetraploid transgenic plants. Results obtained in this work indicate the convenience of checking the ploidy level of the primary transformants before performing basic studies or introducing tomato transgenic material in a breeding program.
• The Arabidopsis COG1 gene encodes a Dof domain transcription factor and negatively regulates phytochrome signaling. Park, Don Ha; Lim, Pyung Ok; Kim, Jeong Sik; Cho, Dae Shik; Hong, Sung Hyun; Nam, Hong Gil (2003). 34(2) 161–171.

  Light is a critical environmental factor that influences almost all developmental aspects of plants, including seed germination, seedling morphogenesis, and transition to reproductive growth. Plants have therefore developed an intricate network of mechanisms to perceive and process environmental light information. To further characterize the molecular basis of light-signaling processes in plants, we screened an activation tagging pool of Arabidopsis for altered photoresponses. A dominant mutation, cog1-D, attenuated various red (R) and far-red (FR) light-dependent photoresponses. The mutation was caused by overexpression of a gene encoding a member of the Dof family of transcription factors. The photoresponses in Arabidopsis were inversely correlated with the expression levels of COG1 mRNA. When the COG1 gene was overexpressed in transgenic plants, the plants exhibited hyposensitive responses to R and FR light in a manner inversely dependent on COG1 mRNA levels. On the other hand, transgenic lines expressing antisense COG1 were hypersensitive to R and FR light. Expression of the COG1 gene is light inducible and requires phytochrome A (phyA) for FR light-induced expression and phytochrome B (phyB) for R light-induced expression. Thus, the COG1 gene functions as a negative regulator in both the phyA- and phyB-signaling pathways. We suggest that these phytochromes positively regulate the expression of COG1, a negative regulator, as a mechanism for fine tuning the light-signaling pathway.
• Plant D–type cyclins and the control of G1 progression. Oakenfull, E. Ann; Riou-Khamlichi, Catherine; Murray, A. H. (N.-H. Chua; K. Roberts, eds.) (2002). 357(1422) 749–760.

  The basic pattern of controls that operate during the G1 phase of the plant cell cycle shows much closer similarity to animals than to the yeasts and other fungi. The activity of D–type cyclin (CycD) kinases is induced in response to stimulatory signals, and these phosphorylate the plant homologue of the retinoblastoma tumour susceptibility (Rb) protein. It is likely that Rb phosphorylation results in the activation of genes under the control of E2F transcription factors, including those required for S phase entry. As the initial triggers of the cascade, attention has focused on the CycDs, and a family of 10 genes is present in Arabidopsis , divided into three major and three minor groups. Analysis to date suggests that these groups are functionally distinct.
• Study of Soybean Seed Coat Components and Their Relationship to Water Absorption. Mullin, W. John; Xu, Weili (2001). 49(11) 5331–5335.
• Polyesters in Higher Plants. Kolattukudy, Pappachan E. T. Scheper, W. Babel, H. W. Blanch, C. L. Cooney, I. Endo, S. O. Enfors, K. E. L. Eriksson, A. Fiechter, M. Hoare, B. Mattiasson, H. J. Rehm, P. L. Rogers, H. Sahm, K. Schügerl, G. Stephanopoulos, G. T. Tsao, K. Venkat, J. Villadsen, U. von Stockar, C. Wandrey, W. Babel, A. Steinbüchel (eds.) (2001). (Vol. 71) 1–49.
• Influence of the Testa on Seed Dormancy, Germination, and Longevity in Arabidopsis. Debeaujon, Isabelle; Léon-Kloosterziel, Karen M.; Koornneef, Maarten (2000). 122(2) 403–414.
• Construction of a novel conjugative plasmid harboring a GFP reporter gene and its introduction into animal cells by transfection and trans-kingdom conjugation. Yoshida, K.; Takegami, T.; Katoh, A.; Nishikawa, M.; Nishida, T. (1997). (37) 157–158.

  We have established a novel method of gene introduction into eukaryotic cells by trans-kingdom conjugation between Escherichia coli/Agrobacterium tumefaciens bacteria and yeasts. To expand this to animal cells, we have constructed a novel conjugative plasmid, pBASGreen which contains SV40-ori/promoter, pUC-ori, IncQ type oriT/mob, Apr and Neor genes with GFP (green fluorescent protein) gene as a reporter. The introduction into COS1 and NIH3T3 animal cultured cells by conventional transfection was easily detected by fluorescence of the GFP gene product under a fluorescent microscope and the transfectants were effectively selected by the Neor marker. By the action of oriT/mob in the presence of tra genes on a helper plasmid, pBASGreen was directly mobilizable from E. coli into animal cells by trans-kingdom conjugation.
• The ABSCISIC ACID-INSENSITIVE3, FUSCA3, and LEAFY COTYLEDON1 loci act in concert to control multiple aspects of Arabidopsis seed development. Parcy, F; Valon, C; Kohara, A; Miséra, S; Giraudat, J (1997). 9(8) 1265–1277.
• Changes in malondialdehyde content and in superoxide dismutase, catalase and glutathione reductase activities in sunflower seeds as related to deterioration during accelerated aging. Bailly, Christophe; Benamar, Abdelilah; Corbineau, Francoise; Come, Daniel (1996). 97(1) 104–110.
• A Novel cis-Acting Element in an Arabidopsis Gene Is Involved in Responsiveness to Drought, Low-Temperature, or High-Salt Stress. Yamaguchi-Shinozaki, K. (1994). 6(2) 251–264.
• Effects of applied auxin, gibberellin and cytokinin on the activity of peroxidases in the peduncles of rose flowers. Zieslin, Naftaly; Ben-Zaken, Rachel (1992). 11(1) 53–57.
• Chemistry, Biochemistry, and Function of Suberin and Associated Waxes. Kolattukudy, P. E.; Espelie, K. E. T. E. Timell, J. W. Rowe (eds.) (1989). 304–367.
• Role of peroxidase in the development of water-impermeable seed coats in Sida spinosa L. Egley, G. H.; Paul, R. N.; Vaughn, K. C.; Duke, S. O. (1983). 157(3) 224–232.
• Gas permeability of plant cuticles: Oxygen permeability. Lendzian, Klaus J. (1982). 155(4) 310–315.
• Transfection and transformation of Agrobacterium tumefaciens. Holsters, M.; de Waele, D.; Depicker, A.; Messens, E.; van Montagu, M.; Schell, J. (1978). 163(2) 181–187.
• Spectrophotometric and kinetics investigation of the Berthelot reaction for the determination of ammonia. Patton, Charles J.; Crouch, S. R. (1977). 49(3) 464–469.
• NADH-dependent coupled enzyme assay for urease and other ammonia-producing systems. Kaltwasser, Heinrich; Schlegel, Hans Günter (1966). 16(1) 132–138.