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Establishment of a Center of Plant Systems Biology and Biotechnology for the translation of fundamental research into sustainable bio-based technologies in Bulgaria

Deliverables

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Publications

Molecular mechanisms preventing senescence in response to prolonged darkness in a desiccation-tolerant plant

Author(s): Meriem Durgud, Saurabh Gupta, Ivan Ivanov, Amin Omidbakhshfard, Maria Benina, Saleh Alseekh, Nikola Staykov, Mareike Hauenstein, Paul Dijkwel, Stefan Hörtensteiner, Valentina Toneva, Yariv Brotman, Alisdair R. Fernie, Bernd Mueller-Roeber, Tsanko Gechev
Published in: Plant Physiology, 2018, Page(s) pp.00055.2018, ISSN 0032-0889
DOI: 10.1104/pp.18.00055

Jasmonate-responsive MYB factors spatially repress rutin biosynthesis in Fagopyrum tataricum

Author(s): Kaixuan Zhang, Maria D Logacheva, Yu Meng, Jianping Hu, Dongpu Wan, Long Li, Dagmar Janovská, Zhiyong Wang, Milen I Georgiev, Zhuo Yu, Fuyu Yang, Mingli Yan, Meiliang Zhou
Published in: Journal of Experimental Botany, Issue 69/8, 2018, Page(s) 1955-1966, ISSN 0022-0957
DOI: 10.1093/jxb/ery032

Targeting ncRNAs by plant secondary metabolites: The ncRNAs game in the balance towards malignancy inhibition

Author(s): Diana Gulei, Nikolay Mehterov, Seyed Mohammad Nabavi, Atanas Georgiev Atanasov, Ioana Berindan-Neagoe
Published in: Biotechnology Advances, 2017, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2017.11.003

Metabolomics 20 years on: what have we learned and what hurdles remain?

Author(s): Saleh Alseekh, Alisdair R. Fernie
Published in: The Plant Journal, Issue 94/6, 2018, Page(s) 933-942, ISSN 0960-7412
DOI: 10.1111/tpj.13950

The Integration of Metabolomics and Next-Generation Sequencing Data to Elucidate the Pathways of Natural Product Metabolism in Medicinal Plants

Author(s): Federico Scossa, Maria Benina, Saleh Alseekh, Youjun Zhang, Alisdair Fernie
Published in: Planta Medica, 2018, ISSN 0032-0943
DOI: 10.1055/a-0630-1899

Quantitative trait loci analysis identifies a prominent gene involved in the production of fatty-acid-derived flavor volatiles in tomato

Author(s): Karolina Garbowicz, Zhongyuan Liu, Saleh Alseekh, Denise Tieman, Mark Taylor, Anastasiya Kuhalskaya, Itai Ofner, Dani Zamir, Harry J. Klee, Alisdair R. Fernie, Yariv Brotman
Published in: Molecular Plant, 2018, ISSN 1674-2052
DOI: 10.1016/j.molp.2018.06.003

The NAC Transcription Factor SlNAP2 Regulates Leaf Senescence and Fruit Yield in Tomato

Author(s): Xuemin Ma, Youjun Zhang, Veronika Turečková, Gang-Ping Xue, Alisdair R. Fernie, Bernd Mueller-Roeber, Salma Balazadeh
Published in: Plant Physiology, Issue 177/3, 2018, Page(s) 1286-1302, ISSN 0032-0889
DOI: 10.1104/pp.18.00292

Defining the convergence of ethylene and auxin signaling in tomato

Author(s): Alisdair R. Fernie, Saleh Alseekh
Published in: New Phytologist, Issue 219/2, 2018, Page(s) 479-481, ISSN 0028-646X
DOI: 10.1111/nph.15251

Rewiring of the Fruit Metabolome in Tomato Breeding

Author(s): Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R. Fernie, Jie Luo, Sanwen Huang
Published in: Cell, Issue 172/1-2, 2018, Page(s) 249-261.e12, ISSN 0092-8674
DOI: 10.1016/j.cell.2017.12.019

Occurrence, biochemistry and biological effects of host-selective plant mycotoxins

Author(s): Veselin Petrov, Muhammad Kamran Qureshi, Jacques Hille, Tsanko Gechev
Published in: Food and Chemical Toxicology, Issue 112, 2018, Page(s) 251-264, ISSN 0278-6915
DOI: 10.1016/j.fct.2017.12.047

Nutrigenomics in cancer: Revisiting the effects of natural compounds

Author(s): Cornelia Braicu, Nikolay Mehterov, Boyan Vladimirov, Victoria Sarafian, Seyed Mohammad Nabavi, Atanas G. Atanasov, Ioana Berindan-Neagoe
Published in: Seminars in Cancer Biology, Issue 46, 2017, Page(s) 84-106, ISSN 1044-579X
DOI: 10.1016/j.semcancer.2017.06.011

Stoichiometric Correlation Analysis: Principles of Metabolic Functionality from Metabolomics Data

Author(s): Kevin Schwahn, Romina Beleggia, Nooshin Omranian, Zoran Nikoloski
Published in: Frontiers in Plant Science, Issue 8, 2017, ISSN 1664-462X
DOI: 10.3389/fpls.2017.02152

Genome-Wide Analysis of ROS Antioxidant Genes in Resurrection Species Suggest an Involvement of Distinct ROS Detoxification Systems during Desiccation

Author(s): Saurabh Gupta, Yanni Dong, Paul P. Dijkwel, Bernd Mueller-Roeber, Tsanko S. Gechev
Published in: International Journal of Molecular Sciences, Issue 20/12, 2019, Page(s) 3101, ISSN 1422-0067
DOI: 10.3390/ijms20123101

On the role of the tricarboxylic acid cycle in plant productivity

Author(s): Youjun Zhang, Alisdair R. Fernie
Published in: Journal of Integrative Plant Biology, Issue 60/12, 2018, Page(s) 1199-1216, ISSN 1672-9072
DOI: 10.1111/jipb.12690

Inhibition of TOR Represses Nutrient Consumption, Which Improves Greening after Extended Periods of Etiolation

Author(s): Yi Zhang, Youjun Zhang, Heather E. McFarlane, Toshihiro Obata, Andreas S. Richter, Mark Lohse, Bernhard Grimm, Staffan Persson, Alisdair R. Fernie, Patrick Giavalisco
Published in: Plant Physiology, Issue 178/1, 2018, Page(s) 101-117, ISSN 0032-0889
DOI: 10.1104/pp.18.00684

First report of Peanut stunt virus on beans in Bulgaria

Author(s): G. Pasev, V. Radeva-Ivanova, Y. Manoussopoulos, M. Turina, D. Kostova
Published in: New Disease Reports, Issue 38, 2018, Page(s) 9, ISSN 2044-0588
DOI: 10.5197/j.2044-0588.2018.038.009

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

Author(s): Adriano Nunes-Nesi, Saleh Alseekh, Franklin Magnum de Oliveira Silva, Nooshin Omranian, Gabriel Lichtenstein, Mohammad Mirnezhad, Roman R. Romero González, Julia Sabio y Garcia, Mariana Conte, Kirsten A. Leiss, Peter G. L. Klinkhamer, Zoran Nikoloski, Fernando Carrari, Alisdair R. Fernie
Published in: Metabolomics, Issue 15/4, 2019, ISSN 1573-3882
DOI: 10.1007/s11306-019-1503-8

Antidepressant-like effect of salidroside and curcumin on the immunoreactivity of rats subjected to a chronic mild stress model

Author(s): Liliya V. Vasileva, Kremena E. Saracheva, Mariya V. Ivanovska, Atanaska P. Petrova, Andrey S. Marchev, Milen I. Georgiev, Mariana A. Murdjeva, Damiyanka P. Getova
Published in: Food and Chemical Toxicology, Issue 121, 2018, Page(s) 604-611, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.09.065

Causes and solutions to “globesity”: The new fa(s)t alarming global epidemic

Author(s): Liliya V. Vasileva, Andrey S. Marchev, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 121, 2018, Page(s) 173-193, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.08.071

Data Reduction Approaches for Dissecting Transcriptional Effects on Metabolism

Author(s): Kevin Schwahn, Zoran Nikoloski
Published in: Frontiers in Plant Science, Issue 9, 2018, ISSN 1664-462X
DOI: 10.3389/fpls.2018.00538

Interorganelle Communication: Peroxisomal MALATE DEHYDROGENASE2 Connects Lipid Catabolism to Photosynthesis through Redox Coupling in Chlamydomonas

Author(s): Fantao Kong, Adrien Burlacot, Yuanxue Liang, Bertrand Légeret, Saleh Alseekh, Yariv Brotman, Alisdair R. Fernie, Anja Krieger-Liszkay, Fred Beisson, Gilles Peltier, Yonghua Li-Beisson
Published in: The Plant Cell, Issue 30/8, 2018, Page(s) 1824-1847, ISSN 1040-4651
DOI: 10.1105/tpc.18.00361

Passing the Baton: Substrate Channelling in Respiratory Metabolism

Author(s): Alisdair R. Fernie, Youjun Zhang, Lee J. Sweetlove
Published in: Research, Issue 2018, 2018, Page(s) 1-16, ISSN 2639-5274
DOI: 10.1155/2018/1539325

In vivo detection of protein cysteine sulfenylation in plastids

Author(s): Barbara De Smet, Patrick Willems, Alvaro D. Fernandez‐Fernandez, Saleh Alseekh, Alisdair R. Fernie, Joris Messens, Frank Van Breusegem
Published in: The Plant Journal, Issue 97/4, 2019, Page(s) 765-778, ISSN 0960-7412
DOI: 10.1111/tpj.14146

A Solanum neorickii introgression population providing a powerful complement to the extensively characterized Solanum pennellii population

Author(s): Yaacov Micha Brog, Sonia Osorio, Yoav Yichie, Saleh Alseekh, Elad Bensal, Andriy Kochevenko, Dani Zamir, Alisdair R. Fernie
Published in: The Plant Journal, Issue 97/2, 2019, Page(s) 391-403, ISSN 0960-7412
DOI: 10.1111/tpj.14095

Clinopodium vulgare L. (wild basil) extract and its active constituents modulate cyclooxygenase-2 expression in neutrophils

Author(s): Kristiana M. Amirova, Petya Dimitrova, Andrey S. Marchev, Ina Y. Aneva, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 124, 2019, Page(s) 1-9, ISSN 0278-6915
DOI: 10.1016/j.fct.2018.11.054

Crop metabolomics: from diagnostics to assisted breeding

Author(s): Saleh Alseekh, Luisa Bermudez, Luis Alejandro de Haro, Alisdair R. Fernie, Fernando Carrari
Published in: Metabolomics, Issue 14/11, 2018, ISSN 1573-3882
DOI: 10.1007/s11306-018-1446-5

Phytochemical composition and antioxidant activity of 63 Balkan pepper (Capsicum annuum L.) accessions

Author(s): Petko Denev, Velichka Todorova, Manol Ognyanov, Yordan Georgiev, Irina Yanakieva, Ivanka Tringovska, Stanislava Grozeva, Dimitrina Kostova
Published in: Journal of Food Measurement and Characterization, 2019, ISSN 2193-4126
DOI: 10.1007/s11694-019-00171-y

Immunoregulatory natural compounds in stress-induced depression: An alternative or an adjunct to conventional antidepressant therapy?

Author(s): Liliya V. Vasileva, Mariya V. Ivanovska, Marianna A. Murdjeva, Kremena E. Saracheva, Milen I. Georgiev
Published in: Food and Chemical Toxicology, Issue 127, 2019, Page(s) 81-88, ISSN 0278-6915
DOI: 10.1016/j.fct.2019.03.004

Arabidopsis RCD1 coordinates chloroplast and mitochondrial functions through interaction with ANAC transcription factors

Author(s): Alexey Shapiguzov, Julia P Vainonen, Kerri Hunter, Helena Tossavainen, Arjun Tiwari, Sari Järvi, Maarit Hellman, Fayezeh Aarabi, Saleh Alseekh, Brecht Wybouw, Katrien Van Der Kelen, Lauri Nikkanen, Julia Krasensky-Wrzaczek, Nina Sipari, Markku Keinänen, Esa Tyystjärvi, Eevi Rintamäki, Bert De Rybel, Jarkko Salojärvi, Frank Van Breusegem, Alisdair R Fernie, Mikael Brosché, Perttu Permi, Eva-M
Published in: eLife, Issue 8, 2019, ISSN 2050-084X
DOI: 10.7554/elife.43284

A novel seed plants gene regulates oxidative stress tolerance in Arabidopsis thaliana

Author(s): Neerakkal Sujeeth, Nikolay Mehterov, Saurabh Gupta, Muhammad K. Qureshi, Axel Fischer, Sebastian Proost, M. Amin Omidbakhshfard, Toshihiro Obata, Maria Benina, Nikola Staykov, Salma Balazadeh, Dirk Walther, Alisdair R. Fernie, Bernd Mueller-Roeber, Jacques Hille, Tsanko S. Gechev
Published in: Cellular and Molecular Life Sciences, 2019, ISSN 1420-682X
DOI: 10.1007/s00018-019-03202-5

COMPASS for rapid combinatorial optimization of biochemical pathways based on artificial transcription factors

Author(s): Gita Naseri, Jessica Behrend, Lisa Rieper, Bernd Mueller-Roeber
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
DOI: 10.1038/s41467-019-10224-x

Application of high-throughput phenotyping tool Tomato Analyzer to characterize Balkan Capsicum fruit diversity

Author(s): Amol N. Nankar, Ivanka Tringovska, Stanislava Grozeva, Velichka Todorova, Dimitrina Kostova
Published in: Scientia Horticulturae, Issue 260, 2020, Page(s) 108862, ISSN 0304-4238
DOI: 10.1016/j.scienta.2019.108862

Large‐scale metabolite quantitative trait locus analysis provides new insights for high‐quality maize improvement

Author(s): Kun Li, Weiwei Wen, Saleh Alseekh, Xiaohong Yang, Huan Guo, Wenqiang Li, Luxi Wang, Qingchun Pan, Wei Zhan, Jie Liu, Yanhua Li, Xiao Wu, Yariv Brotman, Lothar Willmitzer, Jiansheng Li, Alisdair R. Fernie, Jianbing Yan
Published in: The Plant Journal, 2019, ISSN 0960-7412
DOI: 10.1111/tpj.14317

Extensive Variations in Diurnal Growth Patterns and Metabolism Among Ulva spp. Strains

Author(s): Antoine Fort, Morgane Lebrault, Margot Allaire, Alberto A. Esteves-Ferreira, Marcus McHale, Francesca Lopez, Jose M. Fariñas-Franco, Saleh Alseekh, Alisdair R. Fernie, Ronan Sulpice
Published in: Plant Physiology, Issue 180/1, 2019, Page(s) 109-123, ISSN 0032-0889
DOI: 10.1104/pp.18.01513

Exploring the Diversity of Plant Metabolism

Author(s): Chuanying Fang, Alisdair R. Fernie, Jie Luo
Published in: Trends in Plant Science, Issue 24/1, 2019, Page(s) 83-98, ISSN 1360-1385
DOI: 10.1016/j.tplants.2018.09.006

MYB Transcription Repressors Regulate Plant Secondary Metabolism


Published in: ISSN 0735-2689
DOI: 10.1080/07352689.2019.1632542

Construction and applications of a B vitamin genetic resource for investigation of vitamin dependent metabolism in maize

Author(s): Masaharu Suzuki, Shan Wu, Manaki Mimura, Saleh Alseekh, Alisdair R. Fernie, Andrew D. Hanson, Donald R. McCarty
Published in: The Plant Journal, 2019, ISSN 0960-7412
DOI: 10.1111/tpj.14535

The Structure and Function of Major Plant Metabolite Modifications

Author(s): Shouchuang Wang, Saleh Alseekh, Alisdair R. Fernie, Jie Luo
Published in: Molecular Plant, Issue 12/7, 2019, Page(s) 899-919, ISSN 1674-2052
DOI: 10.1016/j.molp.2019.06.001

Comparative metabolite profiling of two switchgrass ecotypes reveals differences in drought stress responses and rhizosheath weight

Author(s): Tie-Yuan Liu, Mo-Xian Chen, Youjun Zhang, Fu-Yuan Zhu, Ying-Gao Liu, Yuan Tian, Alisdair R. Fernie, Nenghui Ye, Jianhua Zhang
Published in: Planta, Issue 250/4, 2019, Page(s) 1355-1369, ISSN 0032-0935
DOI: 10.1007/s00425-019-03228-w

Redox-Regulation of Photorespiration through Mitochondrial Thioredoxin o1

Author(s): Ole Reinholdt, Saskia Schwab, Youjun Zhang, Jean-Philippe Reichheld, Alisdair R. Fernie, Martin Hagemann, Stefan Timm
Published in: Plant Physiology, Issue 181/2, 2019, Page(s) 442-457, ISSN 0032-0889
DOI: 10.1104/pp.19.00559

Transposon-associated polymorphisms of stress-responsive gene promoters in natural variants of Arabidopsis thaliana

Author(s): Mladen Naydenov, Nadezhda Gospodinova, Elena Apostolova, Nikolaj Anachkov, Vesselin Baev, Mariyana Gozmanova, Ivan Minkov, Galina Yahubyan
Published in: Acta Biochimica Polonica, Issue 65/3, 2018, ISSN 0001-527X
DOI: 10.18388/abp.2017_1590

LoopRNA – Java Module for RNA Structure Annotation

Author(s): Georgi Minkov, Valentina Toneva, Zdravka Ivanova, Vesselin Baev
Published in: Comptes rendus de l’Acade'mie bulgare des Sciences, Issue Vol 71, No9, 2018, Page(s) 1215-1221, ISSN 1310-1331
DOI: 10.7546/crabs.2018.09.08

A new liquid chromatography-high resolution Orbitrap mass spectrometry-based strategy to characterize Glucuronide Oleanane-type Triterpenoid Carboxylic Acid 3, 28-O-Bidesmosides (GOTCAB) saponins.A case study of Gypsophila glomerata Pall ex M. B. (Caryophyllaceae)

Author(s): Reneta Gevrenova, Krum Bardarov, Sabine Bouguet-Bonnet, Yulian Voynikov, Vessela Balabanova, Dimitrina Zheleva-Dimitrova, Max Henry
Published in: Journal of Pharmaceutical and Biomedical Analysis, Issue 159, 2018, Page(s) 567-581, ISSN 0731-7085
DOI: 10.1016/j.jpba.2018.07.041

Evaluation of collection of pepper (Capsicum spp.) resources for resistance to Verticillium dahliae Kleb.

Author(s): Katya Vasileva, Velichka Todorova, Stojka Masheva
Published in: Bulgarian Journal of Agricultural Science, Issue 25 (No 5) 2019, 2019, Page(s) 1030-1038, ISSN 2534-983X

Genome draft of the Arabidopsis relative Pachycladon cheesemanii reveals novel strategies to tolerate New Zealand’s high ultraviolet B radiation environment

Author(s): Yanni Dong, Saurabh Gupta, Rixta Sievers, Jason J. Wargent, David Wheeler, Joanna Putterill, Richard Macknight, Tsanko Gechev, Bernd Mueller-Roeber, Paul P. Dijkwel
Published in: BMC Genomics, Issue 20/1, 2019, ISSN 1471-2164
DOI: 10.1186/s12864-019-6084-4

Full-length transcript-based proteogenomics of rice improves its genome and proteome annotation

Author(s): Mo-Xian Chen, Fu-Yuan Zhu, Bei Gao, Kai-Long Ma, Youjun Zhang, Alisdair R. Fernie, Xi Chen, Lei Dai, Neng-Hui Ye, Xue Zhang, Yuan Tian, Di Zhang, Shi Xiao, Jianhua Zhang, Ying-Gao Liu
Published in: Plant Physiology, 2019, Page(s) pp.00430.2019, ISSN 0032-0889
DOI: 10.1104/pp.19.00430

Rapid High-Yield Transient Expression of Swine Hepatitis E ORF2 Capsid Proteins in Nicotiana benthamiana Plants and Production of Chimeric Hepatitis E Virus-Like Particles Bearing the M2e Influenza Epitope

Author(s): Gergana G. Zahmanova, Milena Mazalovska, Katerina H. Takova, Valentina T. Toneva, Ivan N. Minkov, Eugenia S. Mardanova, Nikolai V. Ravin, George P. Lomonossoff
Published in: Plants, Issue 9/1, 2020, Page(s) 29, ISSN 2223-7747
DOI: 10.3390/plants9010029

Untargetted Metabolomic Exploration of the Mycobacterium tuberculosis Stress Response to Cinnamon Essential Oil

Author(s): Elwira Sieniawska, Rafał Sawicki, Joanna Golus, Milen I. Georgiev
Published in: Biomolecules, Issue 10/3, 2020, Page(s) 357, ISSN 2218-273X
DOI: 10.3390/biom10030357

A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress

Author(s): Mohammad Amin Omidbakhshfard, Neerakkal Sujeeth, Saurabh Gupta, Nooshin Omranian, Kieran J. Guinan, Yariv Brotman, Zoran Nikoloski, Alisdair R. Fernie, Bernd Mueller-Roeber, Tsanko S. Gechev
Published in: International Journal of Molecular Sciences, Issue 21/2, 2020, Page(s) 474, ISSN 1422-0067
DOI: 10.3390/ijms21020474

Tomato Phenotypic Diversity Determined by Combined Approaches of Conventional and High-Throughput Tomato Analyzer Phenotyping

Author(s): Amol N. Nankar, Ivanka Tringovska, Stanislava Grozeva, Daniela Ganeva, Dimitrina Kostova
Published in: Plants, Issue 9/2, 2020, Page(s) 197, ISSN 2223-7747
DOI: 10.3390/plants9020197

Molecular priming as an approach to induce tolerance against abiotic and oxidative stresses in crop plants

Author(s): Pavel Kerchev, Tom van der Meer, Neerakkal Sujeeth, Arno Verlee, Christian V. Stevens, Frank Van Breusegem, Tsanko Gechev
Published in: Biotechnology Advances, 2019, Page(s) 107503, ISSN 0734-9750
DOI: 10.1016/j.biotechadv.2019.107503

Guidelines for Sample Normalization to Minimize Batch Variation for Large-Scale Metabolic Profiling of Plant Natural Genetic Variance

Author(s): Saleh Alseekh, Si Wu, Yariv Brotman, Alisdair R. Fernie
Published in: Plant Metabolomics, Issue 1778, 2018, Page(s) 33-46
DOI: 10.1007/978-1-4939-7819-9_3