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Berlin Brandenburg

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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 03 November 2015, Vol.112(44), pp.13633-8
    Description: Holocentric chromosomes lack a primary constriction, in contrast to monocentrics. They form kinetochores distributed along almost the entire poleward surface of the chromatids, to which spindle fibers attach. No centromere-specific DNA sequence has been found for any holocentric organism studied so far. It was proposed that centromeric repeats, typical for many monocentric species, could not occur in holocentrics, most likely because of differences in the centromere organization. Here we show that the holokinetic centromeres of the Cyperaceae Rhynchospora pubera are highly enriched by a centromeric histone H3 variant-interacting centromere-specific satellite family designated "Tyba" and by centromeric retrotransposons (i.e., CRRh) occurring as genome-wide interspersed arrays. Centromeric arrays vary in length from 3 to 16 kb and are intermingled with gene-coding sequences and transposable elements. We show that holocentromeres of metaphase chromosomes are composed of multiple centromeric units rather than possessing a diffuse organization, thus favoring the polycentric model. A cell-cycle-dependent shuffling of multiple centromeric units results in the formation of functional (poly)centromeres during mitosis. The genome-wide distribution of centromeric repeat arrays interspersing the euchromatin provides a previously unidentified type of centromeric chromatin organization among eukaryotes. Thus, different types of holocentromeres exist in different species, namely with and without centromeric repetitive sequences.
    Keywords: Centromere ; Chromosome ; Evolution ; Holokinetic ; Satellite DNA ; Centromere ; Genome, Plant ; Tandem Repeat Sequences ; Cyperaceae -- Genetics ; Euchromatin -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: The Plant journal : for cell and molecular biology, October 2012, Vol.72(1), pp.31-42
    Description: Unlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shade-avoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.
    Keywords: Body Patterning ; Arabidopsis -- Genetics ; Arabidopsis Proteins -- Genetics ; Homeodomain Proteins -- Genetics ; Transcription Factors -- Genetics
    ISSN: 09607412
    E-ISSN: 1365-313X
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  • 3
    Language: English
    In: Molecular ecology, December 2018, Vol.27(23), pp.4901-4915
    Description: Plant responses to insect egg depositions are known to shape subsequent defensive responses to larvae hatching from the eggs. Elm (Ulmus minor) leaves, on which elm leaf beetles laid their eggs, mount a more efficient defence against larvae hatching from the eggs. However, the molecular mechanisms of this egg-mediated, improved defence are insufficiently understood and have so far only been studied in annual plants. We analysed the dynamics of transcriptomic changes in larval feeding-damaged elm leaves with and without prior egg deposition using de novo assembled RNA-seq data. Compared to egg-free leaves, egg deposition-treated leaves showed earlier and/or faster transcriptional regulations, as well as slightly enhanced differential transcriptional regulation after the onset of larval feeding. These early responding transcripts were overrepresented in gene ontology terms associated with post-translational protein modification, signalling and stress (defence) responses. We found evidence of transcriptional memory in initially egg deposition-induced transcripts whose differential expression was reset prior to larval hatching, but was more rapidly induced again by subsequent larval feeding. This potential memory effect of prior egg deposition, as well as the earlier/faster and enhanced feeding-induced differential regulation of transcripts in egg deposition-treated leaves, may contribute to the egg-mediated reinforcing effect on the elm's defence against larvae. Hence, our study shows that a plant's experience of a stress-indicating environmental cue (here: insect eggs) can push the dynamics of the plant's transcriptomic response to subsequent stress (here: larval feeding). Such experience-mediated acceleration of a stress-induced plant response may result in improved stress resistance.
    Keywords: Ulmus Minor ; RNA Sequencing ; Defence ; Herbivory ; Insect Oviposition ; Priming ; Coleoptera ; Herbivory ; Oviposition ; Transcriptome ; Ulmus -- Genetics
    ISSN: 09621083
    E-ISSN: 1365-294X
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  • 4
    Language: English
    In: PLoS ONE, 01 January 2017, Vol.12(6), p.e0178402
    Description: Cistanthe longiscapa is an endemic annual herb and characteristic element of the Chilean Atacama Desert. Principal threats are the destruction of its seed deposits by human activities and reduced germination rates due to the decreasing occurrence of precipitation events. To enable population...
    Keywords: Sciences (General)
    E-ISSN: 1932-6203
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  • 5
    In: Journal of Integrative Plant Biology, June 2014, Vol.56(6), pp.518-526
    Description: To purchase or authenticate to the full-text of this article, please visit this link: http://onlinelibrary.wiley.com/doi/10.1111/jipb.12185/abstract Byline: Ronny Brandt, Marc Cabedo, Yakun Xie, Stephan Wenkel Abstract The Arabidopsis (Arabidopsis thaliana L.) genome encodes for four distinct classes of homeodomain leucine-zipper (HD-ZIP) transcription factors (HD-ZIPI to HD-ZIPIV), which are all organized in multi-gene families. HD-ZIP transcription factors act as sequence-specific DNA-binding proteins that are able to control the expression level of target genes. While HD-ZIPI and HD-ZIPII proteins are mainly associated with environmental responses, HD-ZIPIII and HD-ZIPIV are primarily known to act as patterning factors. Recent studies have challenged this view. It appears that several of the different HD-ZIP families interact genetically to align both morphogenesis and environmental responses, most likely by modulating phytohormone-signaling networks. Article Note: Available online on Feb. 15, 2014 at www.wileyonlinelibrary.com/journal/jipb
    Keywords: Transcription Factors ; Homeodomain ; Leucine Zipper ; Auxin ; Light Signaling ; Water Stress ; Abscisic Acid ; Leaf Development ; Revoluta ; Kanadi ; Micro
    ISSN: 1672-9072
    E-ISSN: 1744-7909
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  • 6
    Language: English
    In: Chemosphere, July 2015, Vol.131, pp.149-156
    Description: Cobalt (Co ) inhibits vegetative growth of gradually from 1 μM to 100 μM. Fronds accumulated up to 21 mg Co g dry weight at 10 μM external Co indicating hyperaccumulation. Interestingly, accumulation of Co did not decrease the iron (Fe) content in fronds, highlighting as a suitable system for studying effects of Co undisturbed by Fe deficiency symptoms unlike most other plants. Digital image analysis revealed the size distribution of fronds after Co treatment and also a reduction in pigmentation of newly formed daughter fronds unlike the mother fronds during the 7-day treatment. Neither chlorophyll nor photosystem II fluorescence changed significantly during the initial 4 d, indicating effective photosynthesis. During the later phase of the 7-day treatment, however, chlorophyll content and photosynthetic efficiency decreased in the Co -treated daughter fronds, indicating that Co inhibits the biosynthesis of chlorophyll rather than leading to the destruction of pre-existing pigment molecules. In addition, during the first 4 d of Co treatment starch accumulated in the fronds and led to the transition of chloroplasts to chloro-amyloplasts and amylo-chloroplasts, while starch levels strongly decreased thereafter.
    Keywords: Chloroplast ; Cobalt ; Lemnaceae ; Lemna Minor ; Phytotoxicity ; Starch Accumulation ; Chemistry ; Ecology
    ISSN: 0045-6535
    E-ISSN: 1879-1298
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  • 7
    Language: English
    In: Plant physiology, October 2015, Vol.169(2), pp.1240-53
    Description: An intricate network of antagonistically acting transcription factors mediates the formation of a flat leaf lamina of Arabidopsis (Arabidopsis thaliana) plants. In this context, members of the class III homeodomain leucine zipper (HD-ZIPIII) transcription factor family specify the adaxial domain (future upper side) of the leaf, while antagonistically acting KANADI transcription factors determine the abaxial domain (future lower side). Here, we used a messenger RNA sequencing approach to identify genes regulated by KANADI1 (KAN1) and subsequently performed a meta-analysis combining our data sets with published genome-wide data sets. Our analysis revealed that KAN1 acts upstream of several genes encoding auxin biosynthetic enzymes. When exposed to shade, we found three YUCCA genes, YUC2, YUC5, and YUC8, to be transcriptionally up-regulated, which correlates with an increase in the levels of free auxin. When ectopically expressed, KAN1 is able to transcriptionally repress these three YUC genes and thereby block shade-induced auxin biosynthesis. Consequently, KAN1 is able to strongly suppress shade-avoidance responses. Taken together, we hypothesize that HD-ZIPIII/KAN form the basis of a basic growth-promoting module. Hypocotyl extension in the shade and outgrowth of new leaves both involve auxin synthesis and signaling, which are under the direct control of HD-ZIPIII/KAN.
    Keywords: Gene Expression Regulation, Plant ; Arabidopsis -- Physiology ; Arabidopsis Proteins -- Genetics ; Cytochrome P-450 Enzyme System -- Metabolism ; Indoleacetic Acids -- Metabolism ; Transcription Factors -- Genetics
    ISSN: 00320889
    E-ISSN: 1532-2548
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  • 8
    Language: English
    In: Plant Systematics and Evolution, 2015, Vol.301(10), pp.2351-2375
    Description: Suaeda subg. Brezia (Chenopodiaceae/Amaranthaceae) comprises ~45 halophytic species distributed worldwide along coastlines and in saline inland habitats. Thirteen species are currently accepted from the Americas, but species delimitation is difficult due to the scarcity of distinguishing characters. Little is known yet about phylogenetic relationships and biogeography of American Brezia species. Here, we present molecular phylogenies based on DNA sequence data from the nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast rpl 32- trn L intergenic region. Our sampling comprised 157 accessions covering all 13 American Brezia species along with 38 accessions from 16 Eurasian taxa. Phylogenetic trees were generated using parsimony and Bayesian methods. Three monophyletic lineages were discerned in the ITS tree: the Suaeda maritima , S. prostrata and S. corniculata group. Most American species proved to belong to the S. corniculata group. Species boundaries were mostly not recovered or even contradicted by the ITS data, which could be a consequence of low sequence variation in terminal clades and/or reticulate evolution. The rpl 32- trn L phylogeny was poorly resolved, with the majority of American species being part of a polytomy with few supported internal nodes. Several incongruities were found between the nuclear and chloroplast tree, revealing at least four instances of hybridization and chloroplast capture between distant lineages. Chromosome counts showed that all American species are polyploid with hexaploidy prevailing. We discuss our results in terms of species relationships, hybridization, polyploidy and biogeography with emphasis on the colonization from NE Asia and Europe, and the subsequent spread and diversification in the Americas.
    Keywords: subg. ; Molecular phylogeny ; Hybrids ; Reticulate evolution ; Biogeography ; America
    ISSN: 0378-2697
    E-ISSN: 2199-6881
    E-ISSN: 16156110
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  • 9
    In: Journal Of Experimental Botany, 2016, Vol. 67(4), pp.1095-1107
    Description: Maize primary root tissues display extensive transcriptomic plasticity upon water deficit. The most significant adaptive changes in the elongation zone lead to reprogramming of metabolism and cell wall organization. Water deficit is the most important environmental constraint severely limiting global crop growth and productivity. This study investigated early transcriptome changes in maize ( Zea mays L.) primary root tissues in response to moderate water deficit conditions by RNA-Sequencing. Differential gene expression analyses revealed a high degree of plasticity of the water deficit response. The activity status of genes (active/inactive) was determined by a Bayesian hierarchical model. In total, 70% of expressed genes were constitutively active in all tissues. In contrast, 〈3% (50 genes) of water deficit-responsive genes (1915) were consistently regulated in all tissues, while 〉75% (1501 genes) were specifically regulated in a single root tissue. Water deficit-responsive genes were most numerous in the cortex of the mature root zone and in the elongation zone. The most prominent functional categories among differentially expressed genes in all tissues were ‘transcriptional regulation’ and ‘hormone metabolism’, indicating global reprogramming of cellular metabolism as an adaptation to water deficit. Additionally, the most significant transcriptomic changes in the root tip were associated with cell wall reorganization, leading to continued root growth despite water deficit conditions. This study provides insight into tissue-specific water deficit responses and will be a resource for future genetic analyses and breeding strategies to develop more drought-tolerant maize cultivars.
    Keywords: Drought ; Expression Pattern ; Low Water Potential ; Maize ; Primary Root ; Rna - Sequencing (Rna - Seq) ; Tissue Specificity ; Transcriptome ; Water Deficit.
    ISSN: 0022-0957
    E-ISSN: 1460-2431
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  • 10
    Language: English
    In: Methods in molecular biology (Clifton, N.J.), 2018, Vol.1723, pp.397-409
    Description: Spatiotemporal patterning throughout the plant body depends to a large degree on cell- and tissue-specific expression of genes. Subsequently, for a better understanding of cell and tissue differentiation processes during plant development it is important to conduct transcript analyses in individual cells or tissue types rather than in bulk tissues. Laser capture microdissection (LCM) provides a useful method for isolating specific cell types from complex tissue structures for downstream applications. Contrasting to mammalian cells, the texture of plant cells is more critical due to hard, cellulose-rich cell walls, large vacuoles, and air spaces which complicates tissue preparation and extraction of macromolecules, like DNA and RNA. In particular, developing barley seeds (i.e. grains) depict cell types with differences in osmomolarity (meristematic, differentiating and degenerating tissues) and contain high amounts of the main storage product starch. In this study, we report about methods allowing tissue-specific transcriptome profiling by RNA-seq of developing barley grain tissues from low-input RNA amounts. Details on tissue preparation, laser capture microdissection, RNA isolation, and linear mRNA amplification to produce high-quality samples for Illumina sequencing are provided. Particular emphasis was placed on the influence of the mRNA amplification step on the transcriptome data and the fidelity of deduced expression levels obtained by the developed methods. Analysis of RNA-seq data confirmed sample processing as a highly reliable and reproducible procedure that was also used for transcriptome analyses of different tissue types from barley plants.
    Keywords: Barley Seeds ; Cryosectioning ; Global Transcriptome Analysis ; Laser Capture Microdissection ; RNA-Seq ; Mrna Amplification ; Gene Expression Profiling ; High-Throughput Nucleotide Sequencing -- Methods ; Hordeum -- Genetics ; Laser Capture Microdissection -- Methods ; Plant Proteins -- Genetics ; RNA, Plant -- Genetics
    E-ISSN: 1940-6029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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