Marian Bemer

Marian Bemer
Wageningen University & Research | WUR · Department of Molecular Biology

PhD

About

62
Publications
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Publications

Publications (62)
Article
The timing of flowering and the inflorescence architecture are critical for the reproductive success of tomato (Solanum lycopersicum), but the gene regulatory networks underlying these traits have not been fully explored. Here we show that the tomato FRUITFULL-like (FUL-like) genes FUL2 and MADS-BOX PROTEIN 20 (MBP20) promote the vegetative-to-repr...
Preprint
Full-text available
Establishing the body plan of a multicellular organism relies on precisely orchestrated cell divisions coupled with pattern formation. In animals, cell proliferation and embryonic patterning are regulated by Polycomb group (PcG) proteins that form various multisubunit complexes (Grossniklaus and Paro, 2014). The evolutionary conserved Polycomb Repr...
Article
Full-text available
Post-embryonic development and longevity of flowering plants are, for a large part, determined by the activity and maturation state of stem cell niches formed in the axils of leaves, the so-called axillary meristems (AMs)1,2. The genes that are associated with AM maturation and underlie the differences between monocarpic (reproduce once and die) an...
Article
Full-text available
Establishing the body plan of a multicellular organism relies on precisely orchestrated cell divisions coupled with pattern formation. In animals, cell proliferation and embryonic patterning are regulated by Polycomb group (PcG) proteins that form various multisubunit complexes (Grossniklaus and Paro, 2014). The evolutionary conserved Polycomb Repr...
Article
Full-text available
Efficient seed dispersal in flowering plants is enabled by the development of fruits, which can be either dehiscent or indehiscent. Dehiscent fruits open at maturity to shatter the seeds, while indehiscent fruits do not open and the seeds are dispersed in various ways. The diversity in fruit morphology and seed shattering mechanisms is enormous wit...
Data
Time-line of developing Cynorkis fastigiata and Epipactis helleborine fruits, embedded in LR White and stained with toluidine blue. (A–F) C. fastigiata. (G–I). E. helleborine. Scale bars (A,C–F,I) = 0.2 mm, (B) = 0.1 mm, (G,H,J) = 0.5 mm, (K,L) = 1 mm. F, fertile valve; S, sterile valve.
Data
Growth of E. pusilla fruits by cell division and cell elongation. (A) Graph showing the number of cells in different growth stages. Cell number was determined in cross sections of fruits at different growth stages from at least 6 sterile and 6 fertile valves per growth stage. A trend line was drawn through the different data points. The error bars...
Data
ML tree of the SPATULA/ALCATRAZ genes in seed plants. Branch colors denote the following taxa: Persian green, Gymnosperms; Blue, Basal angiosperms; Middle washed yellow, Monocots; Green, Basal eudicots; Purple, Core eudicots; Red, Brassicaceae. Bootstrap values are placed above the nodes.
Data
ML tree of the REPLUMLESS/POUNDFOOLISH genes in seed plants. Branch colors denote the following taxa: Persian green, Gymnosperms; Blue, Basal angiosperms; Middle washed yellow, Monocots; Green, Basal eudicots; Purple, Core eudicots; Red, Brassicaceae. Bootstrap values are placed above the nodes.
Data
3D X-ray macroscopic reconstruction of a 3 WAP E. pusilla fruit. Umbilical cords (funiculi) can be detected between the vascular bundles of the fertile valves and the placenta regions. (No scale bar can be included for a 3D movie). WAP, week after pollination.
Data
Number of cell layers of Erycina pusilla, Epipactis helleborine, and Cynorkis fastigiata fruits during development. DAP, days after pollination; WAP, weeks after pollination; Cf, Cynorkis fastigiata; Eh, Epipactis helleborine.
Data
Accession numbers of RPL/PNF sequences used in the alignments and phylogenetic analyses. The Orchidaceae subfamilies are provided in parentheses.
Data
Alignment of the bHLH domain of SPATULA/ALCATRAZ proteins based on Pabon-Mora et al. (2014) extended with orchid gene lineages. The bHLH was drawn based on Toledo-Ortiz et al. (2003) and corresponds with positions K359-Q410. Within the bHLH domain, black arrows indicate positions E13, R16, L27, K39, L56, which are conserved in all bHLH plant and an...
Data
Alignment of the bHLH domain of HECATE3/INDEHISCENT proteins based on Pabon-Mora et al. (2014) extended with orchid gene lineages. The bHLH was drawn based on Toledo-Ortiz et al. (2003) and corresponds with positions N462-L515. Left black dashed box: N-flank of the bHLH domain: HEC domain (Kay et al., 2013) including domain 17 (Pires and Dolan, 201...
Data
Difference in MADS-box gene expression between developmental stages of the fruit of E. pusilla as calculated using a variance analysis of measures using a Tukey multi-comparisons test. P-value style: GP: >0.05 (ns), < 0.05 (*), < 0.01 (**), < 0.001 (***), < 0.0001 (****). No value, No expression; DAP, days after pollination, WAP, weeks after pollin...
Data
Accession numbers of IND/HEC3 sequences used in the alignments and phylogenetic analyses. The Orchidaceae subfamilies are provided in parentheses.
Data
Development of E. pusilla fruits from unfertilized ovary to mature fruit with ripe seeds. (A) Ovary. (B) Fruit 1 DAP. (C) Fruit 5 DAP. (D) Fruit 1 WAP. (E) Fruit 2 WAP. (F) Fruit 3 WAP. (G) Fruit 4 WAP. (H) Dehisced fruit 16 WAP. (I) Ripe seeds of dehisced fruit. DAP, days after pollination; WAP, weeks after pollination; Fl, flower; Cr, carpel; Fr,...
Data
Time-line of developing E. pusilla fruit cross sections of one of the fertile valves. (A) 2 WAP. (B) 5 WAP. (C) 8 WAP. (D) 11 WAP. Dashed circles indicate the left pollen tube bundle located in the fertile valve. Scale bar (A) = 0.2 mm, (B–D) = 0.5 mm.
Data
Results of the yeast-two hybrid assay. Thirteen E. pusilla MADS-box proteins and one Arabidopsis protein (AtFUL) were screened against each other. After mating, the diploid yeast were grown for 5 days on SD medium lacking Leu, Trp, and His, supplemented with 5 mM 3-amino-1,2,4 triazole. Growth indicates an interaction between bait and prey.
Data
Alignment of the BELL-domain and the Homeo-domain of REPLUMLESS/POUNDFOOLISH (PNF) proteins based on Pabon-Mora et al. (2014) extended with orchid gene lineages. The BELL domain (Smith et al., 2002) and the conserved Homeodomain, based on Mukherjee et al. (2009) were drawn.
Data
ML tree of the HECATE3/INDEHISCENT genes in seed plants. Branch colors denote the following taxa: Persian green, Gymnosperms; Blue, Basal angiosperms; Middle washed yellow, Monocots; Green, Basal eudicots; Purple, Core eudicots; Red, Brassicaceae. Bootstrap values are placed above the nodes.
Data
AttB-primers used for the creation of inserts for Gateway cloning.
Data
Transcript primer sequences and amplicon characteristics used for quantitative real-time PCR validation of the expression profiles of different transcripts, following MIQE guidelines (Bustin et al., 2009). The sequences listed here were downloaded from NCBI GenBank (www.ncbi.nlm.nih.gov), Orchidstra (orchidstra2.abrc.sinica.edu.tw) and our own frui...
Data
Accession numbers of SPT/ALC bHLH transcription factor sequences used in the alignment. The Orchidaceae subfamilies are provided in parentheses.
Article
The family of small auxin up-regulated RNA (SAUR) genes is a family of auxin-responsive genes with ~60–140 members in most higher plant species. Despite the early discovery of their auxin responsiveness, their function and mode of action remained unknown for a long time. In recent years, the importance of SAUR genes in the regulation of dynamic and...
Article
Full-text available
Monocarpic plants have a single reproductive cycle in their lives, where life span is determined by the coordinated arrest of all meristems, or global proliferative arrest (GPA). The molecular bases for GPA and the signaling mechanisms involved are poorly understood, other than systemic cues from developing seeds of unknown nature. Here we uncover...
Chapter
Our understanding of the epigenetic mechanisms that regulate gene expression has been largely increased in recent years by the development and refinement of different techniques. This has revealed that gene transcription is highly influenced by epigenetic mechanisms, i.e., those that do not involve changes in the genome sequence, but rather in nucl...
Chapter
Gene regulation by transcription factors involves complex protein interaction networks, which include chromatin remodeling and modifying proteins as an integral part. Decoding these protein interactions is crucial for our understanding of chromatin-mediated gene regulation. Here, we describe a method for the immunoprecipitation of in planta nuclear...
Book
This volume provides a comprehensive collection of protocols that can be used to study plant chromatin structure and composition. Chapters divided into three sections detail the profiling of chromatin features in relation to epigenetic regulation, investigate the interaction between chromatin modifications and gene regulation, and explore the 3D sp...
Article
Full-text available
MADS-domain transcription factors are well known for their roles in plant development and regulate sets of downstream genes that have been uncovered by high-throughput analyses. A considerable number of these targets are predicted to function in hormone responses or responses to environmental stimuli, suggesting that there is a close link between d...
Article
Specific and dynamic gene expression strongly depends on transcription factor (TF) activity and most plant TFs function in a combinatorial fashion. They can bind to DNA and control the expression of the corresponding gene in an additive fashion or cooperate by physical interactions, forming larger protein complexes. The importance of protein-protei...
Article
Full-text available
Embryonic development requires a correct balancing of maternal and paternal genetic information. This balance is mediated by genomic imprinting, an epigenetic mechanism that leads to parent-of-origin-dependent gene expression. The parental conflict (or kinship) theory proposes that imprinting can evolve due to a conflict between maternal and patern...
Article
Full-text available
Genomic imprinting results in monoallelic gene expression in a parent-of-origin-dependent manner and is regulated by the differential epigenetic marking of the parental alleles. In plants, genomic imprinting has been primarily described for genes expressed in the endosperm, a tissue nourishing the developing embryo that does not contribute to the n...
Article
Full-text available
Tomato (Solanum lycopersicum) contains two close homologs of the Arabidopsis thaliana MADS domain transcription factor FRUITFULL (FUL), FUL1 (previously called TDR4) and FUL2 (previously MBP7). Both proteins interact with the ripening regulator RIPENING INHIBITOR (RIN) and are expressed during fruit ripening. To elucidate their function in tomato,...
Article
Polycomb group (PcG) complexes play important roles in phase transitions and cell fate determination in plants and animals, by epigenetically repressing sets of genes that promote either proliferation or differentiation. The continuous differentiation of new organs in plants, such as leaves or flowers, requires a highly dynamic PcG function, which...
Chapter
Angiosperms exhibit an enormous diversity in inflorescence architecture and flower morphology. Despite this diversity, the genetic networks controlling the development of both structures are largely conserved. The majority of the regulators involved in flower initiation and development are members of the large family of MADS box transcription facto...
Article
Full-text available
Members of the plant type I MADS domain subfamily have been reported to be involved in reproductive development in Arabidopsis (Arabidopsis thaliana). However, from the 61 type I genes in the Arabidopsis genome, only PHERES1, AGAMOUS-LIKE80 (AGL80), DIANA, AGL62, and AGL23 have been functionally characterized, which revealed important roles for the...
Article
Full-text available
The MADS-box transcription factor family has expanded considerably in plants via gene and genome duplications and can be subdivided into type I and MIKC-type genes. The two gene classes show a different evolutionary history. Whereas the MIKC-type genes originated during ancient genome duplications, as well as during more recent events, the type I l...
Article
MADS box genes in plants consist of MIKC-type and type I genes. While MIKC-type genes have been studied extensively, the functions of type I genes are still poorly understood. Evidence suggests that type I MADS box genes are involved in embryo sac and seed development. We investigated two independent T-DNA insertion alleles of the Arabidopsis thali...