@article{2-s2.0-85209720046,

title = {Ultra-weak photon emission from DNA},

author = { M.A. Pietruszka and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85209720046&doi=10.1038%2fs41598-024-80469-0&partnerID=40&md5=d59293aecac092516e5e60b8823a4999},

doi = {10.1038/s41598-024-80469-0},

year  = {2024},

date = {2024-01-01},

journal = {Scientific Reports},

volume = {14},

number = {1},

publisher = {Nature Research},

abstract = {It is conventionally believed that macromolecules found in living cells, including DNA, RNA, and proteins, do not exhibit inherent light emission. However, recent studies have challenged this concept by demonstrating spontaneous light emission from nucleic acids under certain conditions and physiological temperatures. By noninvasive monitoring of barley genomic DNA and advanced statistical physics analyses, temperature-induced dynamic entropy fluctuations and fractal dimension oscillations were identified at a key organizational threshold. The study revealed evidence for non-equilibrium phase transitions, a noticeable photovoltaic current jump at zero bias voltage, and a proportional increase (scaling) of the photoinduced current corresponding to increasing amounts of DNA. In addition, we estimated DNA’s energy production rate at criticality and introduced an interferometer using coherent light emissions from the DNA-water interface. These findings suggest that DNA is a major source of ultraweak photon emission in biological systems. © The Author(s) 2024.},

note = {0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85180430930,

title = {Uncovering the mechanism of mitochondrial translation initiation in plants},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85180430930&doi=10.1016%2fj.tplants.2023.11.011&partnerID=40&md5=3f2fe1c873c5f896a2688c07358ad75b},

doi = {10.1016/j.tplants.2023.11.011},

year  = {2024},

date = {2024-01-01},

journal = {Trends in Plant Science},

volume = {29},

number = {3},

pages = {269-271},

publisher = {Elsevier Ltd},

abstract = {Mitochondrial translation differs significantly from that conducted in bacteria and plastids. Recent research conducted by Tran and colleagues has unveiled the plant-specific mechanisms of mitochondrial translation initiation. The authors identified two Arabidopsis thaliana (arabidopsis) mTRAN proteins that may bind to the 5′ untranslated region (UTR) of mitochondrial mRNAs by recognising newly discovered A/U-rich motifs. © 2023 Elsevier Ltd},

note = {0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85184750118,

title = {Proton-polarized states in DNA},

author = { M.A. Pietruszka and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85184750118&doi=10.1016%2fj.biosystems.2024.105125&partnerID=40&md5=81a9bceaf6e4ca6743ada0e70392fa58},

doi = {10.1016/j.biosystems.2024.105125},

year  = {2024},

date = {2024-01-01},

journal = {BioSystems},

volume = {237},

publisher = {Elsevier Ireland Ltd},

abstract = {We observed signatures of a phase transition in the double-stranded DNA fragment of known length and sequences using a non-invasive semiconductor-electrolyte interface technique and statistical physics methods. Observations revealed a coherence peak in the electromotive force and a significant decline in calculated dynamic entropy at a critical temperature and pH. This behavior may arise from the dynamic interaction of proton (H+) pairs with opposite momentum and spin, carrying a charge q=2+ under critical conditions. © 2024},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85193320146,

title = {An update on strigolactone signaling in plants},

author = { M. Korek and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85193320146&doi=10.1016%2fB978-0-443-13521-7.00004-X&partnerID=40&md5=e11fbfce38427018fbc19d0d0c81486c},

doi = {10.1016/B978-0-443-13521-7.00004-X},

year  = {2024},

date = {2024-01-01},

journal = {Strigolactones: Synthesis, Application and Role in Plants},

pages = {53-73},

publisher = {Elsevier},

abstract = {Strigolactone signaling pathway is based on an F-box–mediated cascade reaction. The critical step in starting the signal transduction is perception of strigolactone molecule by receptor DWARF 14 (D14). The binding of hormone molecule by D14 results in conformational change of the receptor, which is required for interaction with other components of the strigolactone signaling pathway. At the same time, a conservative catalytic motif (Ser96; His246; Asp217) of D14 leads to the hydrolysis of strigolactone molecule. Thus, D14 acts as a dual-functional receptor, responsible for strigolactone perception and strigolactone molecule degradation. Further, the signal relay leads to the formation of SKP-CULLIN-F-BOX (SCF) complex and repressor degradation via 26S proteasome. Mutation in genes encoding the core components of strigolactone signaling pathway results in semidwarfism and greater number of lateral shoots and roots of plants. Additionally, the mutant’s phenotype cannot be rescued by strigolactone treatment. Our knowledge about the genes encoding transcription factors (TFs), which regulate the plant’s response to strigolactones, remains elusive. The role of only a few strigolactone-dependent TFs was experimentally confirmed, including BRANCHED1 (BRC1) protein. The BRC1 is well known to act locally in buds and regulates the shoot branching by inhibiting the axillary bud outgrowth. However, to describe how strigolactones regulate other aspects of plant development and plant response to stresses, it is necessary to characterize the new TFs which are involved in strigolactone signal transduction. This remains the biggest challenge that will allow us to understand how strigolactones act. © 2024 Elsevier Inc. All rights reserved.},

note = {0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85196116815,

title = {Strigolactone insensitivity affects differential shoot and root transcriptome in barley},

author = { M. Korek and R.G. Uhrig and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85196116815&doi=10.1007%2fs13353-024-00885-w&partnerID=40&md5=586fef8a6403e7c5a50a9dd765a1a909},

doi = {10.1007/s13353-024-00885-w},

year  = {2024},

date = {2024-01-01},

journal = {Journal of Applied Genetics},

publisher = {Springer Science and Business Media Deutschland GmbH},

abstract = {Strigolactones (SLs) are plant hormones that play a crucial role in regulating various aspects of plant architecture, such as shoot and root branching. However, the knowledge of SL-responsive genes and transcription factors (TFs) that control the shaping of plant architecture remains elusive. Here, transcriptomic analysis was conducted using the SL-insensitive barley mutant hvd14.d (carried mutation in SL receptor DWARF14; HvD14) and its wild-type (WT) to unravel the differences in gene expression separately in root and shoot tissues. This approach enabled us to select more than six thousand SL-dependent genes that were exclusive to each studied organ or not tissue-specific. The data obtained, along with in silico analyses, found several TFs that exhibited changed expression between the analyzed genotypes and that recognized binding sites in promoters of other identified differentially expressed genes (DEGs). In total, 28 TFs that recognize motifs over-represented in DEG promoters were identified. Moreover, nearly half of the identified TFs were connected in a single network of known and predicted interactions, highlighting the complexity and multidimensionality of SL-related signalling in barley. Finally, the SL control on the expression of one of the identified TFs in HvD14- and dose-dependent manners was proved. Obtained results bring us closer to understanding the signalling pathways regulating SL-dependent plant development. © The Author(s) 2024.},

note = {0},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85171857887,

title = {Multi-omics insights into the positive role of strigolactone perception in barley drought response},

author = { A. Daszkowska-Golec and D. Mehta and R.G. Uhrig and A.J. Brąszewska-Zalewska and O. Novák and I.M. Fontana and M. Melzer and T. Płociniczak and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85171857887&doi=10.1186%2fs12870-023-04450-1&partnerID=40&md5=b4cdbd82982d8b64f033dd023c188683},

doi = {10.1186/s12870-023-04450-1},

issn = {14712229},

year  = {2023},

date = {2023-01-01},

journal = {BMC Plant Biology},

volume = {23},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Drought is a major environmental stress that affects crop productivity worldwide. Although previous research demonstrated links between strigolactones (SLs) and drought, here we used barley (Hordeum vulgare) SL-insensitive mutant hvd14 (dwarf14) to scrutinize the SL-dependent mechanisms associated with water deficit response. Results: We have employed a combination of transcriptomics, proteomics, phytohormonomics analyses, and physiological data to unravel differences between wild-type and hvd14 plants under drought. Our research revealed that drought sensitivity of hvd14 is related to weaker induction of abscisic acid-responsive genes/proteins, lower jasmonic acid content, higher reactive oxygen species content, and lower wax biosynthetic and deposition mechanisms than wild-type plants. In addition, we identified a set of transcription factors (TFs) that are exclusively drought-induced in the wild-type barley. Conclusions: Critically, we resolved a comprehensive series of interactions between the drought-induced barley transcriptome and proteome responses, allowing us to understand the profound effects of SLs in alleviating water-limiting conditions. Several new avenues have opened for developing barley more resilient to drought through the information provided. Moreover, our study contributes to a better understanding of the complex interplay between genes, proteins, and hormones in response to drought, and underscores the importance of a multidisciplinary approach to studying plant stress response mechanisms. © 2023, BioMed Central Ltd., part of Springer Nature.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85161838968,

title = {Strigolactones and abscisic acid interactions affect plant development and response to abiotic stresses},

author = { M. Korek and M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85161838968&doi=10.1186%2fs12870-023-04332-6&partnerID=40&md5=1a5f72610116f85ec8dcc72df1cf9c86},

doi = {10.1186/s12870-023-04332-6},

issn = {14712229},

year  = {2023},

date = {2023-01-01},

journal = {BMC Plant Biology},

volume = {23},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Strigolactones (SL) are the youngest group of plant hormones responsible for shaping plant architecture, especially the branching of shoots. However, recent studies provided new insights into the functioning of SL, confirming their participation in regulating the plant response to various types of abiotic stresses, including water deficit, soil salinity and osmotic stress. On the other hand, abscisic acid (ABA), commonly referred as a stress hormone, is the molecule that crucially controls the plant response to adverse environmental conditions. Since the SL and ABA share a common precursor in their biosynthetic pathways, the interaction between both phytohormones has been largely studied in the literature. Under optimal growth conditions, the balance between ABA and SL content is maintained to ensure proper plant development. At the same time, the water deficit tends to inhibit SL accumulation in the roots, which serves as a sensing mechanism for drought, and empowers the ABA production, which is necessary for plant defense responses. The SL-ABA cross-talk at the signaling level, especially regarding the closing of the stomata under drought conditions, still remains poorly understood. Enhanced SL content in shoots is likely to stimulate the plant sensitivity to ABA, thus reducing the stomatal conductance and improving the plant survival rate. Besides, it was proposed that SL might promote the closing of stomata in an ABA-independent way. Here, we summarize the current knowledge regarding the SL and ABA interactions by providing new insights into the function, perception and regulation of both phytohormones during abiotic stress response of plants, as well as revealing the gaps in the current knowledge of SL-ABA cross-talk. © 2023, The Author(s).},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85133330498,

title = {Characterization of Catechol-1,2-Dioxygenase (Acdo1p) From Blastobotrys raffinosifermentans and Investigation of Its Role in the Catabolism of Aromatic Compounds},

author = { A.K. Meier and S. Worch and A. Hartmann and M. Marzec and H.P. Mock and R. Bode and G. Kunze and F. Matthes},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85133330498&doi=10.3389%2ffmicb.2022.872298&partnerID=40&md5=4a4b0297a7dcede44b52c8be2aa81cdb},

doi = {10.3389/fmicb.2022.872298},

issn = {1664302X},

year  = {2022},

date = {2022-01-01},

journal = {Frontiers in Microbiology},

volume = {13},

publisher = {Frontiers Media S.A.},

abstract = {Gallic acid, protocatechuic acid, catechol, and pyrogallol are only a few examples of industrially relevant aromatics. Today much attention is paid to the development of new microbial factories for the environmentally friendly biosynthesis of industrially relevant chemicals with renewable resources or organic pollutants as the starting material. The non–conventional yeast, Blastobotrys raffinosifermentans, possesses attractive properties for industrial bio-production processes such as thermo- and osmotolerance. An additional advantage is its broad substrate spectrum, with tannins at the forefront. The present study is dedicated to the characterization of catechol-1,2-dioxygenase (Acdo1p) and the analysis of its function in B. raffinosifermentans tannic acid catabolism. Acdo1p is a dimeric protein with higher affinity for catechol (KM = 0.004 ± 0.001 mM; kcat = 15.6 ± 0.4 s–1) than to pyrogallol (KM = 0.1 ± 0.02 mM; kcat = 10.6 ± 0.4 s–1). It is an intradiol dioxygenase and its reaction product with catechol as the substrate is cis,cis-muconic acid. B. raffinosifermentans G1212/YIC102-AYNI1-ACDO1-6H, which expresses the ACDO1 gene under the control of the strong nitrate-inducible AYNI1 promoter, achieved a maximum catechol-1,2-dioxygenase activity of 280.6 U/L and 26.9 U/g of dry cell weight in yeast grown in minimal medium with nitrate as the nitrogen source and 1.5% glucose as the carbon source. In the same medium with glucose as the carbon source, catechol-1,2-dioxygenase activity was not detected for the control strain G1212/YIC102 with ACDO1 expression under the regulation of its respective endogenous promoter. Gene expression analysis showed that ACDO1 is induced by gallic acid and protocatechuic acid. In contrast to the wild-type strain, the B. raffinosifermentans strain with a deletion of the ACDO1 gene was unable to grow on medium supplemented with gallic acid or protocatechuic acid as the sole carbon source. In summary, we propose that due to its substrate specificity, its thermal stability, and its ability to undergo long-term storage without significant loss of activity, B. raffinosifermentans catechol-1,2-dioxygenase (Acdo1p) is a promising enzyme candidate for industrial applications. Copyright © 2022 Meier, Worch, Hartmann, Marzec, Mock, Bode, Kunze and Matthes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85123698276,

title = {MicroRNA: a new signal in plant-to-plant communication},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85123698276&doi=10.1016%2fj.tplants.2022.01.005&partnerID=40&md5=494d22019ad5517a9dba0dd30adb3737},

doi = {10.1016/j.tplants.2022.01.005},

issn = {13601385},

year  = {2022},

date = {2022-01-01},

journal = {Trends in Plant Science},

volume = {27},

number = {5},

pages = {418-419},

publisher = {Elsevier Ltd},

abstract = {Plants can communicate inter- and intraspecifically using signals transmitted via root exudate and volatiles released into the atmosphere. A recent study by Betti et al. discovered that miRNA is one of the signals used during plant communication. MiRNAs are secreted by plants and change the gene expression in neighbouring plants. © 2022 Elsevier Ltd},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121239796,

title = {Size does matter: piRNA and miRNA targeting},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121239796&doi=10.1016%2fj.tibs.2021.12.001&partnerID=40&md5=7c3aea734baaf61b351bb9096f8e9960},

doi = {10.1016/j.tibs.2021.12.001},

issn = {09680004},

year  = {2022},

date = {2022-01-01},

journal = {Trends in Biochemical Sciences},

volume = {47},

number = {4},

pages = {287-288},

publisher = {Elsevier Ltd},

abstract = {Piwi-interacting RNAs (piRNAs) guide PIWI proteins to bind and cleave RNAs. Originally, piRNAs were described as a system for transposable element repression. Recently, Anzelon, Choudhury, Hughes et al. uncovered the structural basis for piRNA targeting, whereby they are recognized in a manner distinct from targeting by miRNAs. © 2021 Elsevier Ltd},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85121336640,

title = {Whole exome sequencing-based identification of a novel gene involved in root hair development in barley (Hordeum vulgare l.)},

author = { K. Gajek and A. Janiak and U. Korotko and B. Chmielewska and M. Marzec and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85121336640&doi=10.3390%2fijms222413411&partnerID=40&md5=0d73d429a527fcb38849ebab9bd1fe43},

doi = {10.3390/ijms222413411},

issn = {16616596},

year  = {2021},

date = {2021-01-01},

journal = {International Journal of Molecular Sciences},

volume = {22},

number = {24},

publisher = {MDPI},

abstract = {Root hairs play a crucial role in anchoring plants in soil, interaction with microorganisms and nutrient uptake from the rhizosphere. In contrast to Arabidopsis, there is a limited knowledge of root hair morphogenesis in monocots, including barley (Hordeum vulgare L.). We have isolated barley mutant rhp1.e with an abnormal root hair phenotype after chemical mutagenesis of spring cultivar ‘Sebastian’. The development of root hairs was initiated in the mutant but inhibited at the very early stage of tip growth. The length of root hairs reached only 3% of the length of parent cultivar. Using a whole exome sequencing (WES) approach, we identified G1674A mutation in the HORVU1Hr1G077230 gene, located on chromosome 1HL and encoding a cellulose synthase-like C1 protein (HvCSLC1) that might be involved in the xyloglucan (XyG) synthesis in root hairs. The identified mutation led to the retention of the second intron and premature termination of the HvCSLC1 protein. The mutation co-segregated with the abnormal root hair phenotype in the F2 progeny of rhp1.e mutant and its wild-type parent. Additionally, different substitutions in HORVU1Hr1G077230 were found in four other allelic mutants with the same root hair phenotype. Here, we discuss the putative role of HvCSLC1 protein in root hair tube elongation in barley. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85098859776,

title = {Changes in plastid biogenesis leading to the formation of albino regenerants in barley microspore culture},

author = { M. Gajecka and M. Marzec and B. Chmielewska and J. Jelonek and J. Zbieszczyk and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85098859776&doi=10.1186%2fs12870-020-02755-z&partnerID=40&md5=d815420ef3c84b515da6b97e036cb855},

doi = {10.1186/s12870-020-02755-z},

issn = {14712229},

year  = {2021},

date = {2021-01-01},

journal = {BMC Plant Biology},

volume = {21},

number = {1},

publisher = {BioMed Central Ltd},

abstract = {Background: Microspore embryogenesis is potentially the most effective method of obtaining doubled haploids (DH) which are utilized in breeding programs to accelerate production of new cultivars. However, the regeneration of albino plants significantly limits the exploitation of androgenesis for DH production in cereals. Despite many efforts, the precise mechanisms leading to development of albino regenerants have not yet been elucidated. The objective of this study was to reveal the genotype-dependent molecular differences in chloroplast differentiation that lead to the formation of green and albino regenerants in microspore culture of barley. Results: We performed a detailed analysis of plastid differentiation at successive stages of androgenesis in two barley cultivars, ‘Jersey’ and ‘Mercada’ that differed in their ability to produce green regenerants. We demonstrated the lack of transition from the NEP-dependent to PEP-dependent transcription in plastids of cv. ‘Mercada’ that produced mostly albino regenerants in microspore culture. The failed NEP-to-PEP transition was associated with the lack of activity of Sig2 gene encoding a sigma factor necessary for transcription of plastid rRNA genes. A very low level of 16S and 23S rRNA transcripts and impaired plastid translation machinery resulted in the inhibition of photomorphogenesis in regenerating embryos and albino regenerants. Furthermore, the plastids present in differentiating ‘Mercada’ embryos contained a low number of plastome copies whose replication was not always completed. Contrary to ‘Mercada’, cv. ‘Jersey’ that produced 90% green regenerants, showed the high activity of PEP polymerase, the highly increased expression of Sig2, plastid rRNAs and tRNAGlu, which indicated the NEP inhibition. The increased expression of GLKs genes encoding transcription factors required for induction of photomorphogenesis was also observed in ‘Jersey’ regenerants. Conclusions: Proplastids present in microspore-derived embryos of albino-producing genotypes did not pass the early checkpoints of their development that are required for induction of further light-dependent differentiation of chloroplasts. The failed activation of plastid-encoded RNA polymerase during differentiation of embryos was associated with the genotype-dependent inability to regenerate green plants in barley microspore culture. The better understanding of molecular mechanisms underlying formation of albino regenerants may be helpful in overcoming the problem of albinism in cereal androgenesis. © 2021, The Author(s).},

note = {5},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85101356095,

title = {Uncovering the Mechanical Code of DNA Using ‘Loop-seq’},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85101356095&doi=10.1016%2fj.tig.2021.02.004&partnerID=40&md5=c285161cf015bc084308af6e8d351dbb},

doi = {10.1016/j.tig.2021.02.004},

issn = {01689525},

year  = {2021},

date = {2021-01-01},

journal = {Trends in Genetics},

volume = {37},

number = {6},

pages = {494-495},

publisher = {Elsevier Ltd},

abstract = {DNA mechanical properties play a critical role in different biological processes. Basu and coworkers described a method that measures DNA mechanics on the genome scale. Access to a high-throughput tool for measuring DNA mechanics opens up new possibilities to investigate this phenomenon with respect to establishing the chromatin regulatory landscape. © 2021 Elsevier Ltd},

note = {1},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096082604,

title = {New insights into the function of mammalian Argonaute2},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096082604&doi=10.1371%2fJOURNAL.PGEN.1009058&partnerID=40&md5=92ecc097c376a5632a5be25409daaceb},

doi = {10.1371/JOURNAL.PGEN.1009058},

issn = {15537390},

year  = {2020},

date = {2020-01-01},

journal = {PLoS Genetics},

volume = {16},

number = {11},

publisher = {Public Library of Science},

abstract = {Uncovering the mechanisms that recognise a microRNA (miRNA) target is 1 of the biggest challenges because the Ago-miRNA complex is able to overcome different derogations of complementarity when binding targets. However, the recently solved crystallographic structure of Argonaute2 (Ago2) and a high-throughput analysis that used repurposed sequencing techniques has brought us closer to achieving this goal. Copyright: © 2020 Marek Marzec. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.},

note = {3},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85096048767,

title = {Diverse roles of max1 homologues in rice},

author = { M. Marzec and A. Situmorang and P.B. Brewer and A.J. Brąszewska-Zalewska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096048767&doi=10.3390%2fgenes11111348&partnerID=40&md5=3076172ff4c3df945998075a69bb0bf9},

doi = {10.3390/genes11111348},

issn = {20734425},

year  = {2020},

date = {2020-01-01},

journal = {Genes},

volume = {11},

number = {11},

pages = {1-33},

publisher = {MDPI AG},

abstract = {Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85088304268,

title = {Barley strigolactone signalling mutant hvd14.d reveals the role of strigolactones in abscisic acid-dependent response to drought},

author = { M. Marzec and A. Daszkowska-Golec and A. Collin and M. Melzer and K. Eggert and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85088304268&doi=10.1111%2fpce.13815&partnerID=40&md5=a17d98cfe41937b5140917b7f9836499},

doi = {10.1111/pce.13815},

issn = {01407791},

year  = {2020},

date = {2020-01-01},

journal = {Plant Cell and Environment},

volume = {43},

number = {9},

pages = {2239-2253},

publisher = {Blackwell Publishing Ltd},

abstract = {Strigolactones (SLs) are a group of plant hormones involved in many aspects of plant development and stress adaptation. Here, we investigated the drought response of a barley (Hordeum vulgare L.) mutant carrying a missense mutation in the gene encoding the SL-specific receptor HvD14. Our results clearly showed that hvd14.d mutant is hyper-sensitive to drought stress. This was illustrated by a lower leaf relative water content (RWC), impaired photosynthesis, disorganization of chloroplast structure, altered stomatal density and slower closure of stomata in response to drought in the mutant compared to the wild type parent cultivar Sebastian. Although the content of abscisic acid (ABA) and its derivatives remained unchanged in the mutant, significant differences in expression of genes related to ABA biosynthesis were observed. Moreover, hvd14.d was insensitive to ABA during seed germination. Analysis of Arabidopsis thaliana mutant atd14-1 also demonstrated that mutation in the SL receptor resulted in increased sensitivity to drought. Our results indicate that the drought-sensitive phenotype of barley SL mutant might be caused by a disturbed ABA metabolism and/or signalling pathways. These results together uncovered a link between SL signalling and ABA-dependent drought stress response in barley. © 2020 John Wiley & Sons Ltd.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85085917933,

title = {Prime Editing: Game Changer for Modifying Plant Genomes},

author = { M. Marzec and G. Hensel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85085917933&doi=10.1016%2fj.tplants.2020.05.008&partnerID=40&md5=009b17a07cbb9f664589f3c893fa9158},

doi = {10.1016/j.tplants.2020.05.008},

issn = {13601385},

year  = {2020},

date = {2020-01-01},

journal = {Trends in Plant Science},

volume = {25},

number = {8},

pages = {722-724},

publisher = {Elsevier Ltd},

abstract = {Prime editing, developed by Anzalone et al., brings genome editing to a new level, because this approach allows introduction of all mutation types, including insertions, deletions, and all putative 12 types of base-to-base conversions. Previously tested in human cells, this technique has been adapted for use in plants by Lin et al. © 2020 Elsevier Ltd},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85078293343,

title = {Prime Editing: A New Way for Genome Editing},

author = { M. Marzec and A.J. Brąszewska-Zalewska and G. Hensel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85078293343&doi=10.1016%2fj.tcb.2020.01.004&partnerID=40&md5=d0dadda1407e926632f5e2d681e92a0b},

doi = {10.1016/j.tcb.2020.01.004},

issn = {09628924},

year  = {2020},

date = {2020-01-01},

journal = {Trends in Cell Biology},

volume = {30},

number = {4},

pages = {257-259},

publisher = {Elsevier Ltd},

abstract = {Precise and efficient use of genome editing tools are hampered by the introduction of DNA double-strand breaks, donor DNA templates, or homology-directed repair. A recent study expands the genome editing toolbox with the introduction of prime editing, which overcomes previous challenges and introduces insertions, deletions, and all putative 12 types of base-to-base conversions in human cells. © 2020 Elsevier Ltd},

note = {24},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85075546169,

title = {Plastid differentiation during microgametogenesis determines green plant regeneration in barley microspore culture},

author = { M. Gajecka and M. Marzec and B. Chmielewska and J. Jelonek and J. Zbieszczyk and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85075546169&doi=10.1016%2fj.plantsci.2019.110321&partnerID=40&md5=e6fa2af008d23476f81f00614719a9af},

doi = {10.1016/j.plantsci.2019.110321},

issn = {01689452},

year  = {2020},

date = {2020-01-01},

journal = {Plant Science},

volume = {291},

publisher = {Elsevier Ireland Ltd},

abstract = {Developing plants from in vitro culture of microspores or immature pollen grains (androgenesis) is a highly genotype-dependent process whose effectiveness in cereals is significantly reduced by occurrence of albino regenerants. Here, we examined a hypothesis that the molecular differentiation of plastids in barley microspores prior to in vitro culture affects the genotype ability to regenerate green plants in culture. At the mid-to-late uninucleate (ML) stage, routinely used to initiate microspore culture, the expression of most genes involved in plastid transcription, translation and starch synthesis was significantly higher in microspores of barley cv. ‘Mercada’ producing 90% albino regenerants, than in cv. ‘Jersey’ that developed 90% green regenerants. The ML microspores of cv. ‘Mercada’ contained a large proportion of amyloplasts filled with starch, while in cv. ‘Jersey’ there were only proplastids. Using additional spring barley genotypes that differed in their ability to regenerate green plants we confirmed the correlation between plastid differentiation prior to culture and albino regeneration in culture. The expression of GBSSI gene (Granule-bound starch synthaseI) in early-mid (EM) microspores was a good marker of a genotype potential to produce green regenerants during androgenesis. Initiating culture from EM microspores that significantly improved regeneration of green plants may overcome the problem of albinism. © 2019 The Author(s)},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85074062096,

title = {More precise, more universal and more specific – the next generation of RNA-guided endonucleases for genome editing},

author = { M. Marzec and G. Hensel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85074062096&doi=10.1111%2ffebs.15079&partnerID=40&md5=bc642d3e1742095d6744939dc8e01eb9},

doi = {10.1111/febs.15079},

issn = {1742464X},

year  = {2019},

date = {2019-01-01},

journal = {FEBS Journal},

volume = {286},

number = {23},

pages = {4657-4660},

publisher = {Blackwell Publishing Ltd},

abstract = {[No abstract available]},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85066150008,

title = {Binding or Hydrolysis? How Does the Strigolactone Receptor Work?},

author = { M. Marzec and P.B. Brewer},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85066150008&doi=10.1016%2fj.tplants.2019.05.001&partnerID=40&md5=56fa6f66b79456e833933b09c44590f1},

doi = {10.1016/j.tplants.2019.05.001},

issn = {13601385},

year  = {2019},

date = {2019-01-01},

journal = {Trends in Plant Science},

volume = {24},

number = {7},

pages = {571-574},

publisher = {Elsevier Ltd},

abstract = {The strigolactone (SL) receptor in plants is unusual in that it both binds and hydrolyses SL molecules. Landmark studies had proposed that a product of hydrolysis irreversibly binds the receptor and then activates signalling. However, recent breakthrough articles (Seto et al. Nat. Commun. 2019;10:191 and Shabek et al. Nature 2018;563:652–656) have revealed a new model based on inhibition of hydrolysis by protein conformation. © 2019 Elsevier Ltd},

note = {18},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85068482560,

title = {Arabidopsis NSE4 proteins act in somatic nuclei and meiosis to ensure plant viability and fertility},

author = { M. Zelkowski and K. Zelkowska and U. Conrad and S. Hesse and I. Lermontova and M. Marzec and A. Meister and A. Houben and V. Schubert},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85068482560&doi=10.3389%2ffpls.2019.00774&partnerID=40&md5=bfb04925376dbcf824caa3bcb856aee5},

doi = {10.3389/fpls.2019.00774},

issn = {1664462X},

year  = {2019},

date = {2019-01-01},

journal = {Frontiers in Plant Science},

volume = {10},

publisher = {Frontiers Media S.A.},

abstract = {The SMC 5/6 complex together with cohesin and condensin is a member of the structural maintenance of chromosome (SMC) protein family. In non-plant organisms SMC5/6 is engaged in DNA repair, meiotic synapsis, genome organization and stability. In plants, the function of SMC5/6 is still enigmatic. Therefore, we analyzed the crucial δ-kleisin component NSE4 of the SMC5/6 complex in the model plant Arabidopsis thaliana. Two functional conserved Nse4 paralogs (Nse4A and Nse4B) are present in A. thaliana, which may have evolved via gene subfunctionalization. Due to its high expression level, Nse4A seems to be the more essential gene, whereas Nse4B appears to be involved mainly in seed development. The morphological characterization of A. thaliana T-DNA mutants suggests that the NSE4 proteins are essential for plant growth and fertility. Detailed investigations in wild-type and the mutants based on live cell imaging of transgenic GFP lines, fluorescence in situ hybridization (FISH), immunolabeling and super-resolution microscopy suggest that NSE4A acts in several processes during plant development, such as mitosis, meiosis and chromatin organization of differentiated nuclei, and that NSE4A operates in a cell cycle-dependent manner. Differential response of NSE4A and NSE4B mutants after induced DNA double strand breaks (DSBs) suggests their involvement in DNA repair processes. © 2019 Zelkowski, Zelkowska, Conrad, Hesse, Lermontova, Marzec, Meister, Houben and Schubert.},

note = {16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85053198721,

title = {Targeted Base Editing Systems Are Available for Plants},

author = { M. Marzec and G. Hensel},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053198721&doi=10.1016%2fj.tplants.2018.08.011&partnerID=40&md5=ab52cfb4db2bfdf3c6f32ef0e6216be1},

doi = {10.1016/j.tplants.2018.08.011},

issn = {13601385},

year  = {2018},

date = {2018-01-01},

journal = {Trends in Plant Science},

volume = {23},

number = {11},

pages = {955-957},

publisher = {Elsevier Ltd},

abstract = {Use of RNA-guided endonucleases for targeted genome editing is one of the most important breakthrough discoveries of the 21st century. Recent studies have described modifications of this precise base editing technique that open up a new dimension to plant genome editing. © 2018 Elsevier Ltd},

note = {8},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85049165035,

title = {Regulation of root development and architecture by strigolactones under optimal and nutrient deficiency conditions},

author = { M. Marzec and M. Melzer},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85049165035&doi=10.3390%2fijms19071887&partnerID=40&md5=cba507a68fb7e3dd0781d3243322ccf4},

doi = {10.3390/ijms19071887},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {7},

publisher = {MDPI AG},

abstract = {Strigolactones (SLs) constitute a group of plant hormones which are involved in multiple aspects of plant growth and development. Beside their role in shoot and root development and plant architecture in general, SLs are also involved in plant responses to nutrient deficiency by promoting interactions with symbiotic organisms and via promotion of root elongation. Recent observations on the cross talk between SLs and other hormones demonstrate that the inhibition of adventitious root formation by ethylene is independent of SLs. Additionally, it was shown that root exposure to SLs leads to the accumulation of secondary metabolites, such as flavonols or antioxidants. These data suggest pleiotropic effects of SLs, that influence root development. The discovery that the commonly used synthetic SL analogue racGR24 might also mimic the function of other plant growth regulators, such as karrikins, has led us to consider the previously published publications under the new aspects. This review summarizes present knowledge about the function of SLs in shaping root systems under optimal and nutrient deficiency conditions. Results which appear inconsistent with the various aspects of root development are singled out. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {17},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85044129119,

title = {Key hormonal components regulate agronomically important traits in barley},

author = { M. Marzec and A.M. Alqudah},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044129119&doi=10.3390%2fijms19030795&partnerID=40&md5=d9a071d0f1bb101d2c09c50d46a7aa8f},

doi = {10.3390/ijms19030795},

issn = {16616596},

year  = {2018},

date = {2018-01-01},

journal = {International Journal of Molecular Sciences},

volume = {19},

number = {3},

publisher = {MDPI AG},

abstract = {The development and growth of plant organs is regulated by phytohormones, which constitute an important area of plant science. The last decade has seen a rapid increase in the unravelling of the pathways by which phytohormones exert their influence. Phytohormones function as signalling molecules that interact through a complex network to control development traits. They integrate metabolic and developmental events and regulate plant responses to biotic and abiotic stress factors. As such, they influence the yield and quality of crops. Recent studies on barley have emphasised the importance of phytohormones in promoting agronomically important traits such as tillering, plant height, leaf blade area and spike/spikelet development. Understanding the mechanisms of how phytohormones interact may help to modify barley architecture and thereby improve its adaptation and yield. To achieve this goal, extensive functional validation analyses are necessary to better understand the complex dynamics of phytohormone interactions and phytohormone networks that underlie the biological processes. The present review summarises the current knowledge on the crosstalk between phytohormones and their roles in barley development. Furthermore, an overview of how phytohormone modulation may help to improve barley plant architecture is also provided. © 2018 by the authors. Licensee MDPI, Basel, Switzerland.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85043326007,

title = {HorTILLUS—a rich and renewable source of induced mutations for forward/reverse genetics and pre-breeding programs in barley (Hordeumvulgare L.)},

author = { M.E. Szurman-Zubrzycka and J. Zbieszczyk and M. Marzec and J. Jelonek and B. Chmielewska and M.M. Kurowska and M. Krok and A. Daszkowska-Golec and J. Guzy-Wróbelska and D. Gruszka and M. Gajecka and P. Gajewska and M. Stolarek and P. Tylec and P. Sega and S. Lip and M. Kudełko and M. Lorek and M. Gorniak-Walas and A. Malolepszy and N. Podsiadlo and K.P. Szyrajew and A. Keisa and Z. Mbambo and E. Todorowska and M. Gaj and Z. Nita and W. Orlowska-Job and M. Maluszynski and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043326007&doi=10.3389%2ffpls.2018.00216&partnerID=40&md5=2be0ee225baa473124ed786053f7b1c1},

doi = {10.3389/fpls.2018.00216},

issn = {1664462X},

year  = {2018},

date = {2018-01-01},

journal = {Frontiers in Plant Science},

volume = {9},

publisher = {Frontiers Media S.A.},

abstract = {TILLING (Targeting Induced Local Lesions IN Genomes) is a strategy used for functional analysis of genes that combines the classical mutagenesis and a rapid, high-throughput identification of mutations within a gene of interest. TILLING has been initially developed as a discovery platform for functional genomics, but soon it has become a valuable tool in development of desired alleles for crop breeding, alternative to transgenic approach. Here we present the HorTILLUS (Hordeum—TILLING—University of Silesia) population created for spring barley cultivar “Sebastian” after double-treatment of seeds with two chemical mutagens: sodium azide (NaN3) and N-methyl-N-nitrosourea (MNU). The population comprises more than 9,600 M2 plants from which DNA was isolated, seeds harvested, vacuum-packed, and deposited in seed bank. M3 progeny of 3,481 M2 individuals was grown in the field and phenotyped. The screening for mutations was performed for 32 genes related to different aspects of plant growth and development. For each gene fragment, 3,072–6,912 M2 plants were used for mutation identification using LI-COR sequencer. In total, 382 mutations were found in 182.2Mb screened. The average mutation density in the HorTILLUS, estimated as 1 mutation per 477kb, is among the highest mutation densities reported for barley. The majority of mutations were G/C to A/T transitions, however about 8% transversions were also detected. Sixty-one percent of mutations found in coding regions were missense, 37.5% silent and 1.1% nonsense. In each gene, the missense mutations with a potential effect on protein function were identified. The HorTILLUS platform is the largest of the TILLING populations reported for barley and best characterized. The population proved to be a useful tool, both in functional genomic studies and in forward selection of barley mutants with required phenotypic changes. We are constantly renewing the HorTILLUS population, which makes it a permanent source of new mutations. We offer the usage of this valuable resource to the interested barley researchers on cooperative basis. © 2018 Szurman-Zubrzycka, Zbieszczyk, Marzec, Jelonek, Chmielewska, Kurowska, Krok, Daszkowska-Golec, Guzy-Wrobelska, Gruszka, Gajecka, Gajewska, Stolarek, Tylec, Sega, Lip, Kudełko, Lorek, Gorniak-Walas, Malolepszy, Podsiadlo, Szyrajew, Keisa, Mbambo, Todorowska, Gaj, Nita, Orlowska-Job, Maluszynski and Szarejko.},

note = {30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85028312195,

title = {Strigolactones and Gibberellins: A New Couple in the Phytohormone World?},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028312195&doi=10.1016%2fj.tplants.2017.08.001&partnerID=40&md5=2594411b61494a1c6afb61e317305505},

doi = {10.1016/j.tplants.2017.08.001},

issn = {13601385},

year  = {2017},

date = {2017-01-01},

journal = {Trends in Plant Science},

volume = {22},

number = {10},

pages = {813-815},

publisher = {Elsevier Ltd},

abstract = {Strigolactones (SLs) and gibberellins (GAs) are plant hormones that share some unique aspects of their perception and signalling pathways. Recent discoveries indicate that these two phytohormones may act together in processes of plant development and that SL biosynthesis is regulated by GAs. © 2017 Elsevier Ltd},

note = {25},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85029754063,

title = {Agdc1p - a gallic acid decarboxylase involved in the degradation of tannic acid in the yeast Blastobotrys (Arxula) adeninivorans},

author = { A.K. Meier and S. Worch and E. Böer and A. Hartmann and M. Mascher and M. Marzec and U. Scholz and J. Riechen and K. Baronian and F. Schauer and R. Bode and G. Kunze},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85029754063&doi=10.3389%2ffmicb.2017.01777&partnerID=40&md5=6df52c20ab57724a9556b357a26f2d3b},

doi = {10.3389/fmicb.2017.01777},

issn = {1664302X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Microbiology},

volume = {8},

number = {SEP},

publisher = {Frontiers Media S.A.},

abstract = {Tannins and hydroxylated aromatic acids, such as gallic acid (3;4;5-trihydroxybenzoic acid), are plant secondary metabolites which protect plants against herbivores and plant-associated microorganisms. Some microbes, such as the yeast Arxula adeninivorans are resistant to these antimicrobial substances and are able to use tannins and gallic acid as carbon sources. In this study, the Arxula gallic acid decarboxylase (Agdc1p) which degrades gallic acid to pyrogallol was characterized and its function in tannin catabolism analyzed. The enzyme has a higher affinity for gallic acid (Km -0.7 ± 0.2 mM; kcat -42.0 ± 8.2 s-1) than to protocatechuic acid (3;4-dihydroxybenzoic acid) (Km -3.2 ± 0.2 mM; kcat -44.0 ± 3.2 s-1). Other hydroxylated aromatic acids, such as 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, 2,3-dihydroxybenzoic acid, 2,4-dihydroxybenzoic acid and 2,5-dihydroxybenzoic acid are not gallic acid decarboxylase substrates. A. adeninivorans G1212/YRC102-AYNI1-AGDC1, which expresses the AGDC1 gene under the control of the strong nitrate inducible AYNI1 promoter achieved a maximum gallic acid decarboxylase activity of 1064.4 U/l and 97.5 U/g of dry cell weight in yeast grown in minimal medium with nitrate as nitrogen source and glucose as carbon source. In the same medium, gallic acid decarboxylase activity was not detected for the control strain G1212/YRC102 with AGDC1 expression under the control of the endogenous promoter. Gene expression analysis showed that AGDC1 is induced by gallic acid and protocatechuic acid. In contrast to G1212/YRC102-AYNI1-AGDC1 and G1212/YRC102, A. adeninivorans G1234 [δagdc1] is not able to grow on medium with gallic acid as carbon source but can grow in presence of protocatechuic acid. This confirms that Agdc1p plays an essential role in the tannic acid catabolism and could be useful in the production of catechol and cis, cis-muconic acid. However, the protocatechuic acid catabolism via Agdc1p to catechol seems to be not the only degradation pathway. © 2017 Meier, Worch, Böer, Hartmann, Mascher, Marzec, Scholz, Riechen, Baronian, Schauer, Bode and Kunze.},

note = {20},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85027728161,

title = {Enhancement of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) accumulation in Arxula adeninivorans by stabilization of production},

author = { M. Biernacki and M. Marzec and T. Roick and R. Pätz and K. Baronian and R. Bode and G. Kunze},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027728161&doi=10.1186%2fs12934-017-0751-4&partnerID=40&md5=54a2334326fb0d82e947e9ddf4ceec29},

doi = {10.1186/s12934-017-0751-4},

issn = {14752859},

year  = {2017},

date = {2017-01-01},

journal = {Microbial Cell Factories},

volume = {16},

number = {1},

publisher = {BioMed Central Ltd.},

abstract = {Background: In recent years the production of biobased biodegradable plastics has been of interest of researchers partly due to the accumulation of non-biodegradable plastics in the environment and to the opportunity for new applications. Commonly investigated are the polyhydroxyalkanoates (PHAs) poly(hydroxybutyrate) and poly(hydroxybutyrate-co-hydroxyvalerate) (PHB-V). The latter has the advantage of being tougher and less brittle. The production of these polymers in bacteria is well established but production in yeast may have some advantages, e.g. the ability to use a broad spectrum of industrial by-products as a carbon sources. Results: In this study we increased the synthesis of PHB-V in the non-conventional yeast Arxula adeninivorans by stabilization of polymer accumulation via genetic modification and optimization of culture conditions. An A. adeninivorans strain with overexpressed PHA pathway genes for β-ketothiolase, acetoacetyl-CoA reductase, PHAs synthase and the phasin gene was able to accumulate an unexpectedly high level of polymer. It was found that an optimized strain cultivated in a shaking incubator is able to produce up to 52.1% of the DCW of PHB-V (10.8gL-1) with 12.3%mol of PHV fraction. Although further optimization of cultivation conditions in a fed-batch bioreactor led to lower polymer content (15.3% of the DCW of PHB-V), the PHV fraction and total polymer level increased to 23.1%mol and 11.6gL-1 respectively. Additionally, analysis of the product revealed that the polymer has a very low average molecular mass and unexpected melting and glass transition temperatures. Conclusions: This study indicates a potential of use for the non-conventional yeast, A. adeninivorans, as an efficient producer of polyhydroxyalkanoates. © 2017 The Author(s).},

note = {9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-85021152716,

title = {Mutation in HvCBP20 (Cap binding protein 20) adapts barley to drought stress at phenotypic and transcriptomic levels},

author = { A. Daszkowska-Golec and A. Collin and M. Marzec and M. Słota and M.M. Kurowska and M. Gajecka and P. Gajewska and T. Płociniczak and K. Sitko and A. Pacak and Z. Szweykowska-Kulinska and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85021152716&doi=10.3389%2ffpls.2017.00942&partnerID=40&md5=769fb24d1f52b6fc895f399773d7ea69},

doi = {10.3389/fpls.2017.00942},

issn = {1664462X},

year  = {2017},

date = {2017-01-01},

journal = {Frontiers in Plant Science},

volume = {8},

publisher = {Frontiers Media S.A.},

abstract = {CBP20 (Cap-Binding Protein 20) encodes a small subunit of the cap-binding complex (CBC), which is involved in the conserved cell processes related to RNA metabolism in plants and, simultaneously, engaged in the signaling network of drought response, which is dependent on ABA. Here, we report the enhanced tolerance to drought stress of barley mutant in the HvCBP20 gene manifested at the morphological, physiological, and transcriptomic levels. Physiological analyses revealed differences between the hvcbp20.ab mutant and its WT in response to a water deficiency. The mutant exhibited a higher relative water content (RWC), a lower stomatal conductance and changed epidermal pattern compared to the WT after drought stress. Transcriptome analysis using the Agilent Barley Microarray integrated with observed phenotypic traits allowed to conclude that the hvcbp20.ab mutant exhibited better fitness to stress conditions by its much more efficient and earlier activation of stress-preventing mechanisms. The network hubs involved in the adjustment of hvcbp20.ab mutant to the drought conditions were proposed. These results enabled to make a significant progress in understanding the role of CBP20 in the drought stress response. © 2017 Daszkowska-Golec, Skubacz, Marzec, Slota, Kurowska, Gajecka, Gajewska, Płociniczak, Sitko, Pacak, Szweykowska-Kulinska and Szarejko.},

note = {19},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84994087005,

title = {Strigolactones as Part of the Plant Defence System},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84994087005&doi=10.1016%2fj.tplants.2016.08.010&partnerID=40&md5=2d9b269050e13497f2aca882ddd3802d},

doi = {10.1016/j.tplants.2016.08.010},

issn = {13601385},

year  = {2016},

date = {2016-01-01},

journal = {Trends in Plant Science},

volume = {21},

number = {11},

pages = {900-903},

publisher = {Elsevier Ltd},

abstract = {Strigolactones (SLs) are plant hormones, described as regulators of plant growth and development. Recently, it was proposed that these hormones might also be involved in the biotic stress response. However, SLs do not have a universal role in plant protection, instead only playing a part in resistance to specific pathogens. © 2016 Elsevier Ltd},

note = {33},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84973517421,

title = {Identification and functional analysis of the HvD14 gene involved in strigolactone signaling in Hordeum vulgare},

author = { M. Marzec and D. Gruszka and P. Tylec and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84973517421&doi=10.1111%2fppl.12460&partnerID=40&md5=8d2d51d9f2cfc4973f5f90cb22aa2d9d},

doi = {10.1111/ppl.12460},

issn = {00319317},

year  = {2016},

date = {2016-01-01},

journal = {Physiologia Plantarum},

volume = {158},

number = {3},

pages = {341-355},

publisher = {Blackwell Publishing Ltd},

abstract = {In this study, the barley HvD14 gene encoding α/β hydrolase, which is involved in strigolactone (SL) signaling, was identified. Bioinformatics analysis revealed that the identified gene is an orthologue of the D14, AtD14 and PhDAD2 genes that have been described in rice, Arabidopsis thaliana and petunia, respectively. Using TILLING strategy, an hvd14.d mutant that carried the G725A transition, located in the second exon, was identified. This mutation led to the substitution of a highly conserved glycine-193 to glutamic acid in the conserved fragment of the α/β hydrolase domain of the HvD14 protein. The plants that carry the hvd14.d allele were semi-dwarf and produced a higher number of tillers in comparison to the wild-type (WT) parent cultivar. Additionally, the root architecture of mutant plants was affected: the total length of the seminal roots was significantly reduced, and the density of the lateral roots was higher than in the WT. Plants with the hvd14.d allele were insensitive to treatment with GR24, which is the synthetic analogue of SL. Analysis of the indole-3-acetic acid (IAA) concentration in the lateral buds showed no differences between the WT and mutant plants. By contrast, the WT seedlings treated with GR24 developed a lower number of tillers, longer primary roots with a reduced number of lateral roots and had an increased concentration of IAA in lateral buds. This paper describes the first barley SL mutant and shows the potential functions of SLs in barley growth and development. © 2016 Scandinavian Plant Physiology Society},

note = {28},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84984644957,

title = {Perception and signaling of strigolactones},

author = { M. Marzec},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84984644957&doi=10.3389%2ffpls.2016.01260&partnerID=40&md5=d9730bbe394f4a39af3298fe0b2cac75},

doi = {10.3389/fpls.2016.01260},

issn = {1664462X},

year  = {2016},

date = {2016-01-01},

journal = {Frontiers in Plant Science},

volume = {7},

number = {AUG2016},

publisher = {Frontiers Research Foundation},

abstract = {Strigolactones (SLs), a recently discovered class of phytohormones, are important regulators of plant growth and development. While the biosynthetic pathway of these molecules is well documented, until recently there was not much known about the molecular mechanisms underlying SL perception and signal transduction in plants. Certain aspects of their perception and signaling, including the hormone-mediated interaction between receptor and F-box protein, degradation of suppressor proteins and activation of transcription factors, are also found in other phytohormones. However, some of SL signaling features seem to be specific for the SL signaling pathway. These include the enzymatic activity of the SL receptor and its destabilization caused by SLs. This review summarizes the current knowledge about SL signaling pathway in plants. © 2016 Marzec.},

note = {26},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84925871047,

title = {In Silico analysis of the genes encoding proteins that are involved in the biosynthesis of the RMS/MAX/D pathway revealed new roles of strigolactones in plants},

author = { M. Marzec and A. Muszyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84925871047&doi=10.3390%2fijms16046757&partnerID=40&md5=22c2180a53838f63abc2eba3fb10b199},

doi = {10.3390/ijms16046757},

issn = {16616596},

year  = {2015},

date = {2015-01-01},

journal = {International Journal of Molecular Sciences},

volume = {16},

number = {4},

pages = {6757-6782},

publisher = {MDPI AG},

abstract = {Strigolactones were described as a new group of phytohormones in 2008 and since then notable large number of their functions has been uncovered, including the regulation of plant growth and development, interactions with other organisms and a plant’s response to different abiotic stresses. In the last year, investigations of the strigolactone biosynthesis pathway in two model species, Arabidopsis thaliana and Oryza sativa, resulted in great progress in understanding the functions of four enzymes that are involved in this process. We performed in silico analyses, including the identification of the cis-regulatory elements in the promoters of genes encoding proteins of the strigolactone biosynthesis pathway and the identification of the miRNAs that are able to regulate their posttranscriptional level. We also searched the databases that contain the microarray data for the genes that were analyzed from both species in order to check their expression level under different growth conditions. The results that were obtained indicate that there are universal regulations of expression of all of the genes that are involved in the strigolactone biosynthesis in Arabidopsis and rice, but on the other hand each stage of strigolactone production may be additionally regulated independently. This work indicates the presence of crosstalk between strigolactones and almost all of the other phytohormones and suggests the role of strigolactones in the response to abiotic stresses, such as wounding, cold or flooding, as well as in the response to biotic stresses. © 2015 by the authors; licensee MDPI, Basel, Switzerland.},

note = {36},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84924363121,

title = {Arabinogalactan proteins are involved in root hair development in barley},

author = { M. Marzec and I. Szarejko and M. Melzer},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924363121&doi=10.1093%2fjxb%2feru475&partnerID=40&md5=0f52d4c10d6e7651432f41e6391a0fc3},

doi = {10.1093/jxb/eru475},

issn = {00220957},

year  = {2015},

date = {2015-01-01},

journal = {Journal of Experimental Botany},

volume = {66},

number = {5},

pages = {1245-1257},

publisher = {Oxford University Press},

abstract = {The arabinogalactan proteins (AGPs) are involved in a range of plant processes, including cell differentiation and expansion. Here, barley root hair mutants and their wild-type parent cultivars were used, as a model system, to reveal the role of AGPs in root hair development. The treatment of roots with different concentrations of βGlcY (a reagent which binds to all classes of AGPs) inhibited or totally suppressed the development of root hairs in all of the cultivars. Three groups of AGP (recognized by the monoclonal antibodies LM2; LM14; and MAC207) were diversely localized in trichoblasts and atrichoblasts of root hair-producing plants. The relevant epitopes were present in wild-type trichoblast cell walls and cytoplasm, whereas in wild-type atrichoblasts and in all epidermal cells of a root hairless mutant, they were only present in the cytoplasm. In all of cultivars the higher expression of LM2, LM14, and MAC207 was observed in trichoblasts at an early stage of development. Additionally, the LM2 epitope was detected on the surface of primordia and root hair tubes in plants able to generate root hairs. The major conclusion was that the AGPs recognized by LM2, LM14, and MAC207 are involved in the differentiation of barley root epidermal cells, thereby implying a requirement for these AGPs for root hair development in barley. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.},

note = {22},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84933059675,

title = {Root hair development in the grasses: What we already know and what we still need to know},

author = { M. Marzec and M. Melzer and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84933059675&doi=10.1104%2fpp.15.00158&partnerID=40&md5=ed92c1fed5ed952fe516759bd927acf1},

doi = {10.1104/pp.15.00158},

issn = {00320889},

year  = {2015},

date = {2015-01-01},

journal = {Plant Physiology},

volume = {168},

number = {2},

pages = {407-414},

publisher = {American Society of Plant Biologists},

abstract = {A priority in many crop improvement programs for a long time has been to enhance the tolerance level of plants to both abiotic and biotic stress. Recognition that the root system is the prime determinant of a plant’s ability to extract both water and minerals from the soil implies that its architecture is an important variable underlying a cultivar’s adaptation. The density and/or length of the root hairs (RHs) that are formed are thought to have a major bearing on the plant’s performance under stressful conditions. Any attempt to improve a crop’s root system will require a detailed understanding of the processes of RH differentiation. Recent progress in uncovering the molecular basis of root epidermis specialization has been recorded in the grasses. This review seeks to present the current view of RH differentiation in grass species. It combines what has been learned from molecular-based analyses, histological studies, and observation of the phenotypes of both laboratory- and field-grown plants. © 2015 American Society of Plant Biologists. All Rights Reserved.},

note = {30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84914146005,

title = {Induced variations in brassinosteroid genes define barley height and sturdiness, and expand the green revolution genetic toolkit},

author = { C. Dockter and D. Gruszka and I. Braumann and A. Druka and I. Druka and J. Franckowiak and S.P. Gough and A. Janeczko and M.M. Kurowska and J. Lundqvist and U. Lundqvist and M. Marzec and I. Matyszczak and A.H. Müller and J. Oklestkova and B. Schulz and S. Zakhrabekova and M. Hansson},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84914146005&doi=10.1104%2fpp.114.250738&partnerID=40&md5=f95e254bcf209d3c56eb585f06883b42},

doi = {10.1104/pp.114.250738},

issn = {00320889},

year  = {2014},

date = {2014-01-01},

journal = {Plant Physiology},

volume = {166},

number = {4},

pages = {1912-1927},

publisher = {American Society of Plant Biologists},

abstract = {Reduced plant height and culm robustness are quantitative characteristics important for assuring cereal crop yield and quality under adverse weather conditions. A very limited number of short-culm mutant alleles were introduced into commercial crop cultivars during the Green Revolution. We identified phenotypic traits, including sturdy culm, specific for deficiencies in brassinosteroid biosynthesis and signaling in semidwarf mutants of barley (Hordeum vulgare). This set of characteristic traits was explored to perform a phenotypic screen of near-isogenic short-culm mutant lines from the brachytic, breviaristatum, dense spike, erectoides, semibrachytic, semidwarf, and slender dwarf mutant groups. In silico mapping of brassinosteroid-related genes in the barley genome in combination with sequencing of barley mutant lines assigned more than 20 historic mutants to three brassinosteroid-biosynthesis genes (BRASSINOSTEROID-6-OXIDASE; CONSTITUTIVE PHOTOMORPHOGENIC DWARF; and DIMINUTO) and one brassinosteroid-signaling gene (BRASSINOSTEROIDINSENSITIVE1 [HvBRI1]). Analyses of F2 and M2 populations, allelic crosses, and modeling of nonsynonymous amino acid exchanges in protein crystal structures gave a further understanding of the control of barley plant architecture and sturdiness by brassinosteroidrelated genes. Alternatives to the widely used but highly temperature-sensitive uzu1.a allele of HvBRI1 represent potential genetic building blocks for breeding strategies with sturdy and climate-tolerant barley cultivars. © 2014 American Society of Plant Biologists. All rights reserved.},

note = {81},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84897584049,

title = {Increased symplasmic permeability in barley root epidermal cells correlates with defects in root hair development},

author = { M. Marzec and A. Muszyńska and M. Melzer and H. Sas-Nowosielska and E.U. Kurczyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897584049&doi=10.1111%2fplb.12066&partnerID=40&md5=8042210e45154415f0b6015e9f0d8c70},

doi = {10.1111/plb.12066},

issn = {14358603},

year  = {2014},

date = {2014-01-01},

journal = {Plant Biology},

volume = {16},

number = {2},

pages = {476-484},

abstract = {It is well known that the process of plant cell differentiation depends on the symplasmic isolation of cells. Before starting the differentiation programme, the individual cell or group of cells should restrict symplasmic communication with neighbouring cells. We tested the symplasmic communication between epidermal cells in the different root zones of parental barley plants Hordeum vulgare L., cv. 'Karat' with normal root hair development, and two root hairless mutants (rhl1.a and rhl1.b). The results clearly show that symplasmic communication was limited during root hair differentiation in the parental variety, whereas in both root hairless mutants epidermal cells were still symplasmically connected in the corresponding root zone. This paper is the first report on the role of symplasmic isolation in barley root cell differentiation, and additionally shows that a disturbance in the restriction of symplasmic communication is present in root hairless mutants. © 2013 German Botanical Society and The Royal Botanical Society of the Netherlands.},

note = {10},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84924104311,

title = {Importance of symplasmic communication in cell differentiation},

author = { M. Marzec and E.U. Kurczyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924104311&doi=10.4161%2fpsb.27931&partnerID=40&md5=29cf2dd4378aa903a74d02abd49488e5},

doi = {10.4161/psb.27931},

issn = {15592316},

year  = {2014},

date = {2014-01-01},

journal = {Plant Signaling and Behavior},

volume = {9},

number = {1},

publisher = {Landes Bioscience},

abstract = {Symplasmic communication via plasmodesmata (PD) is part of the system of information exchange between plant cells. Molecules that pass through the PD include ions, some hormones, minerals, amino acids, and sugars but also proteins, transcription factors, and different classes of RNA, and as such PD can participate in the coordination of plant growth and development. This review summarizes the current literature on this subject and the role of PD in signal exchange, the importance of symplasmic communication and symplasmic domains in plant cell differentiation, and highlights the future prospective in the exploration of PD functions in plants. Moreover, this review also describes the potential use of barley root epidermis and non-zygotic embryogenesis in study of symplasmic communication during cell differentiation. © 2014 Landes Bioscience.},

note = {4},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84899137346,

title = {Importance of symplasmic communication in cell differentiation},

author = { M. Marzec and E.U. Kurczyńska},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899137346&doi=10.4161%2fpsb.27931tt&partnerID=40&md5=08b24cce230ea4e888f311de5786eb5f},

doi = {10.4161/psb.27931tt},

issn = {15592316},

year  = {2014},

date = {2014-01-01},

journal = {Plant Signaling and Behavior},

volume = {9},

number = {JAN},

publisher = {Landes Bioscience},

abstract = {Symplasmic communication via plasmodesmata (PD) is part of the system of information exchange between plant cells. Molecules that pass through the PD include ions, some hormones, minerals, amino acids, and sugars but also proteins, transcription factors, and different classes of RNA, and as such PD can participate in the coordination of plant growth and development. This review summarizes the current literature on this subject and the role of PD in signal exchange, the importance of symplasmic communication and symplasmic domains in plant cell differentiation, and highlights the future prospective in the exploration of PD functions in plants. Moreover, this review also describes the potential use of barley root epidermis and non-zygotic embryogenesis in study of symplasmic communication during cell differentiation. 00811. © 2014 Landes Bioscience.},

note = {12},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84899135859,

title = {The evolutionary context of root epidermis cell patterning in grasses (Poaceae)},

author = { M. Marzec and M. Melzer and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899135859&doi=10.4161%2fpsb.27972&partnerID=40&md5=c183bf84da3de2967d7da0208f8bb62a},

doi = {10.4161/psb.27972},

issn = {15592316},

year  = {2014},

date = {2014-01-01},

journal = {Plant Signaling and Behavior},

volume = {9},

number = {FEB},

publisher = {Landes Bioscience},

abstract = {In the last century, the mechanism for establishing the root epidermal pattern in grasses was proposed as a differentiating trait that can be used in taxonomic studies and as a useful tool to indicate the relationships between genera. However, knowledge about root hair differentiation in monocots is still scarce. During the last few years, this process has been studied intensively, mainly based on genetics and histological studies. A histological analysis of the root epidermis pattern composed from root hairs (trichoblasts) and non-root hair cells (atrichoblasts), as well as observations of the mechanism of the establishment of this pattern allowed 2 different methods of epidermal cell specialization in monocots to be precisely described. Additionally, a recently published paper describing root hair development in barley shed new light on the evolutionary context of the mechanism of root epidermis cell specialization, which is discussed in the presented work. © 2014 Landes Bioscience.},

note = {16},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84891883727,

title = {Asymmetric growth of root epidermal cells is related to the differentiation of root hair cells in Hordeum vulgare (L.)},

author = { M. Marzec and M. Melzer and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84891883727&doi=10.1093%2fjxb%2fert300&partnerID=40&md5=dded9b3e5f4aeba968f86c75501bd51f},

doi = {10.1093/jxb/ert300},

issn = {00220957},

year  = {2013},

date = {2013-01-01},

journal = {Journal of Experimental Botany},

volume = {64},

number = {16},

pages = {5145-5155},

publisher = {Oxford University Press},

abstract = {The root epidermis of most vascular plants harbours two cell types, namely trichoblasts (capable of producing a root hair) and atrichoblasts. Here, in vivo analysis, confocal laser-scanning microscopy, transmission electron microscopy, histological analysis, and three-dimensional reconstruction were used to characterize the cell types present in the barley root epidermis and their distribution in the tissue. Both trichoblasts and atrichoblasts were present in the wildtype cultivars and could be distinguished from one another at an early stage. Trichoblast/atrichoblast differentiation depended on asymmetric cell expansion after a period of symmetrical cell division. After asymmetric growth, only the shorter epidermal cells could produce root hairs, whereas the longer cells became atrichoblasts. Moreover, the root epidermis did not develop root hairs at all if the epidermal cells did not differentiate into two asymmetric cell types. The root hairless phenotype of bald root barley (brb) and root hairless 1.b (rhl1.b) mutants was caused by a mutation in a gene related to the asymmetric expansion of the root epidermal cells. Additionally, the results showed that the mechanism of trichoblast/atrichoblast differentiation is not evolutionally conserved across the subfamilies of the Poaceae; in the Pooideae subfamily, both asymmetric division and asymmetric cell expansion have been observed. © The Author 2013. Published by Oxford University Press on behalf of the Society for Experimental Biology.},

note = {31},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84877338739,

title = {The role of strigolactones in nutrient-stress responses in plants},

author = { M. Marzec and A. Muszyńska and D. Gruszka},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84877338739&doi=10.3390%2fijms14059286&partnerID=40&md5=8e1929444590b73932f8aea3e37d5efa},

doi = {10.3390/ijms14059286},

issn = {16616596},

year  = {2013},

date = {2013-01-01},

journal = {International Journal of Molecular Sciences},

volume = {14},

number = {5},

pages = {9286-9304},

publisher = {MDPI AG},

abstract = {Strigolactones (SLs) are a new group of plant hormones, which have been intensively investigated during the last few years. The wide spectrum of SLs actions, including the regulation of shoot/root architecture, and the stimulation of the interactions between roots and fungi or bacteria, as well as the stimulation of germination of parasitic plants, indicates that this group of hormones may play an important role in the mechanisms that control soil exploration, and the root-mediated uptake of nutrients. Current studies have shown that SLs might be factors that have an influence on the plant response to a deficiency of macronutrients. Experimental data from the last four years have confirmed that the biosynthesis and exudation of SLs are increased under phosphorus and nitrogen deficiency. All these data suggest that SLs may regulate the complex response to nutrient stress, which include not only the modification of the plant developmental process, but also the cooperation with other organisms in order to minimize the effects of threats. In this paper the results of studies that indicate that SLs play an important role in the response to nutrient stress are reviewed and the consequences of the higher biosynthesis and exudation of SLs in response to phosphorus and nitrogen deficiency are discussed. © 2013 by the authors; licensee MDPI, Basel, Switzerland.},

note = {40},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-84862190811,

title = {The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair},

author = { D. Gruszka and M. Marzec and I. Szarejko},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862190811&doi=10.1186%2f1471-2229-12-88&partnerID=40&md5=26f2e976cd33d1e8a0173a75a410f71e},

doi = {10.1186/1471-2229-12-88},

issn = {14712229},

year  = {2012},

date = {2012-01-01},

journal = {BMC Plant Biology},

volume = {12},

abstract = {Background: The high level of conservation of genes that regulate DNA replication and repair indicates that they may serve as a source of information on the origin and evolution of the species and makes them a reliable system for the identification of cross-species homologs. Studies that had been conducted to date shed light on the processes of DNA replication and repair in bacteria, yeast and mammals. However, there is still much to be learned about the process of DNA damage repair in plants.Description: These studies, which were conducted mainly using bioinformatics tools, enabled the list of genes that participate in various pathways of DNA repair in Arabidopsis thaliana (L.) Heynh to be outlined; however, information regarding these mechanisms in crop plants is still very limited. A similar, functional approach is particularly difficult for a species whose complete genomic sequences are still unavailable. One of the solutions is to apply ESTs (Expressed Sequence Tags) as the basis for gene identification. For the construction of the barley EST DNA Replication and Repair Database (bEST-DRRD), presented here, the Arabidopsis nucleotide and protein sequences involved in DNA replication and repair were used to browse for and retrieve the deposited sequences, derived from four barley (Hordeum vulgare L.) sequence databases, including the " Barley Genome version 0.05" database (encompassing ca. 90% of barley coding sequences) and from two databases covering the complete genomes of two monocot models: Oryza sativa L. and Brachypodium distachyon L. in order to identify homologous genes. Sequences of the categorised Arabidopsis queries are used for browsing the repositories, which are located on the ViroBLAST platform. The bEST-DRRD is currently used in our project during the identification and validation of the barley genes involved in DNA repair.Conclusions: The presented database provides information about the Arabidopsis genes involved in DNA replication and repair, their expression patterns and models of protein interactions. It was designed and established to provide an open-access tool for the identification of monocot homologs of known Arabidopsis genes that are responsible for DNA-related processes. The barley genes identified in the project are currently being analysed to validate their function. © 2012 Gruszka et al.},

note = {6},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{2-s2.0-80053627631,

title = {TILLING - a shortcut in functional genomics},

author = { M.M. Kurowska and A. Daszkowska-Golec and D. Gruszka and M. Marzec and M. Szurman and I. Szarejko and M. Maluszynski},

url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80053627631&doi=10.1007%2fs13353-011-0061-1&partnerID=40&md5=59e48b59a6de3676dbabe53974f2599e},

doi = {10.1007/s13353-011-0061-1},

issn = {12341983},

year  = {2011},

date = {2011-01-01},

journal = {Journal of Applied Genetics},

volume = {52},

number = {4},

pages = {371-390},

abstract = {Recent advances in large-scale genome sequencing projects have opened up new possibilities for the application of conventional mutation techniques in not only forward but also reverse genetics strategies. TILLING (Targeting Induced Local Lesions IN Genomes) was developed a decade ago as an alternative to insertional mutagenesis. It takes advantage of classical mutagenesis, sequence availability and high-throughput screening for nucleotide polymorphisms in a targeted sequence. The main advantage of TILLING as a reverse genetics strategy is that it can be applied to any species, regardless of its genome size and ploidy level. The TILLING protocol provides a high frequency of point mutations distributed randomly in the genome. The great mutagenic potential of chemical agents to generate a high rate of nucleotide substitutions has been proven by the high density of mutations reported for TILLING populations in various plant species. For most of them, the analysis of several genes revealed 1 mutation/200-500 kb screened and much higher densities were observed for polyploid species, such as wheat. High-throughput TILLING permits the rapid and low-cost discovery of new alleles that are induced in plants. Several research centres have established a TILLING public service for various plant species. The recent trends in TILLING procedures rely on the diversification of bioinformatic tools, new methods of mutation detection, including mismatch-specific and sensitive endonucleases, but also various alternatives for LI-COR screening and single nucleotide polymorphism (SNP) discovery using next-generation sequencing technologies. The TILLING strategy has found numerous applications in functional genomics. Additionally, wide applications of this throughput method in basic and applied research have already been implemented through modifications of the original TILLING strategy, such as Ecotilling or Deletion TILLING. © 2011 The Author(s).},

note = {130},

keywords = {},

pubstate = {published},

tppubtype = {article}

}