The Outer Western Carpathians are part of the Alpine-Himalayan orogenic belt, and they are formed mostly by the Upper Cretaceous and Paleogene deep-sea “flysch” sequences. Orava region (northern ...Slovakia), situated in the central part of the Magura Nappe, has an important position for the solution of the geological structure and development of the Magura Nappe. At the beginning of the research, determination of the sedimentary sequences of the Magura Nappe and the fundamental lithotypes and lithofacies was required. A total of 1164 paleocurrent measurements were measured and assigned to lithotypes and lithostratigraphic units obtained during the detailed sedimentological study. The main purpose of the research was the interpretation of the filling history and tectonic activity of the Magura Basin. The results of the detailed sedimentological study were integrated with published data from surrounding regions. Presented palinspastic maps propose a reconstruction of the filling history and tectonic activity in chronological order during the Upper Cretaceous to Oligocene. Maps focus in detail on the western part of the Magura Basin, but they display its surroundings as well. The sedimentary record reflects the activity and gradual shifting of the Western Carpathian accretionary wedge to the north, the uplift of source areas, and the changes in the sea level of the Magura Basin. The paleocurrent analyses joined with the sedimentological and petrographic research allowed to reconstruct the paleogeographic properties of the northern sources of detritic material (Hostýn, Fore-Magura and Silesian Ridges), of the southern source of the material (Western Carpathians accretionary wedge) and of intrabasinal sources as well (Szczawina and Southern-Magura Ridges). We propose a discussion about the character of filling history, defining and position of the source areas and about Hostýn Ridge defined here.
•Division of sedimentary sequences into fundamental lithofacies and lithotypes•Acquirement of 1164 new paleocurrent measurements assigned to lithotype and lithostratigraphic units•Integration of new and old paleogeographic data•Interpretation of the geological, structural and depositional history in the paleogeographic models•Proposition for discussion about the character of the basin and source areas
DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR ...of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
Core promoterome of barley embryo Pavlu, Simon; Nikumbh, Sarvesh; Kovacik, Martin ...
Computational and structural biotechnology journal,
12/2024, Letnik:
23
Journal Article
Recenzirano
Odprti dostop
Precise localization and dissection of gene promoters are key to understanding transcriptional gene regulation and to successful bioengineering applications. The core RNA polymerase II initiation ...machinery is highly conserved among eukaryotes, leading to a general expectation of equivalent underlying mechanisms. Still, less is known about promoters in the plant kingdom. In this study, we employed cap analysis of gene expression (CAGE) at three embryonic developmental stages in barley to accurately map, annotate, and quantify transcription initiation events. Unsupervised discovery of de novo sequence clusters grouped promoters based on characteristic initiator and position-specific core-promoter motifs. This grouping was complemented by the annotation of transcription factor binding site (TFBS) motifs. Integration with genome-wide epigenomic data sets and gene ontology (GO) enrichment analysis further delineated the chromatin environments and functional roles of genes associated with distinct promoter categories. The TATA-box presence governs all features explored, supporting the general model of two separate genomic regulatory environments. We describe the extent and implications of alternative transcription initiation events, including those that are specific to developmental stages, which can affect the protein sequence or the presence of regions that regulate translation. The generated promoterome dataset provides a valuable genomic resource for enhancing the functional annotation of the barley genome. It also offers insights into the transcriptional regulation of individual genes and presents opportunities for the informed manipulation of promoter architecture, with the aim of enhancing traits of agronomic importance.
Petrographic examination, heavy mineral analysis and detrital zircon U-Pb dating were performed on the Eocene siliciclastic rocks in the Rača Unit of the Outer Western Carpathians in order to reveal ...their origin and establish the development of the Magura Basin during the Eocene. The medium- to fine-grained sublitharenites and quartzarenites were mainly derived from extra-basinal sources, and the deposits predominantly contain minerals from metamorphic rocks. The terrigenous material was derived from low- to medium-grade metapelites and granitoids. The sedimentation was also controlled by a sediment supply from the mafic source. The basic and metabasic rocks contain pyrope-rich garnets and Cr-spinels. Palaeo-currents document that the sedimentary material was supplied from the South-East. The first detrital zircon U-Pb ages confirm zircon-producing events occurring in the Proterozoic from approximately 2200 to 590 Ma; but predominantly in the Paleozoic between 550 and 60 Ma. The palaeocurrent indicators, petrographic data, heavy mineral spectra and zircon geochronology strongly suggest that the Tisza Mega-Unit Variscan crystalline basement erosion with accompanying sedimentary cover supplied the Magura Basin from the South. The Mecsek Zone is also suggested to support the Villáni-Bihor and part of the Békes-Codru zones in supplying the Magura Basin during the Eocene to Oligocene. The Eocene transport of significant detrital material to the Magura Basin is also related to erosion of the Marmarosh Massif Proterozoic–Ordovician low- to medium-grade crystalline basement. Therefore, it is most likely that Magura Basin sedimentation was dominated by supply from the sub-ophiolitic Fore-Marmarosh Suture Zone of the Eastern Carpathians.
•First report of the U-Pb zircon dating of the Magura Nappe siliciclastic rocks•Corrosion and geochemistry of the heavy minerals to determine their provenance•Palaeogeography of the Magura Basin during the Bartonian–Early Priabonian
Wild barley is abundant, occupying large diversity of sites, ranging from the northern mesic Mediterranean meadows to the southern xeric deserts in Israel. This is also reflected in its wide ...phenotypic heterogeneity. We investigated the dynamics of DNA content changes in seed tissues in ten wild barley accessions that originated from an environmental gradient in Israel. The flow cytometric measurements were done from the time shortly after pollination up to the dry seeds. We show variation in mitotic cell cycle and endoreduplication dynamics in both diploid seed tissues (represented by seed maternal tissues and embryo) and in the triploid endosperm. We found that wild barley accessions collected at harsher xeric environmental conditions produce higher proportion of endoreduplicated nuclei in endosperm tissues. Also, a comparison of wild and cultivated barley strains revealed a higher endopolyploidy level in the endosperm of wild barley, that is accompanied by temporal changes in the timing of the major developmental phases. In summary, we present a new direction of research focusing on connecting spatiotemporal patterns of endoreduplication in barley seeds and possibly buffering for stress conditions.
Understanding the mechanisms regulating the development of cereal seeds is essential for plant breeding and increasing yield. However, the analysis of cereal seeds is challenging owing to the minute ...size, the liquid character of some tissues, and the tight inter-tissue connections. Here, we demonstrate a detailed protocol for dissection of the embryo, endosperm, and seed maternal tissues at early, middle, and late stages of barley seed development. The protocol is based on a manual tissue dissection using fine-pointed tools and a binocular microscope, followed by ploidy analysis-based purity control. Seed maternal tissues and embryos are diploid, while the endosperm is triploid tissue. This allows the monitoring of sample purity using flow cytometry. Additional measurements revealed the high quality of RNA isolated from such samples and their usability for high-sensitivity analysis. In conclusion, this protocol describes how to practically dissect pure tissues from developing grains of cultivated barley and potentially also other cereals.
Seeds are complex biological systems comprising three genetically distinct tissues: embryo, endosperm, and maternal tissues (including seed coats and pericarp) nested inside one another. Cereal ...grains represent a special type of seeds, with the largest part formed by the endosperm, a specialized triploid tissue ensuring embryo protection and nourishment. We investigated dynamic changes in DNA content in three of the major seed tissues from the time of pollination up to the dry seed. We show that the cell cycle is under strict developmental control in different seed compartments. After an initial wave of active cell division, cells switch to endocycle and most endoreduplication events are observed in the endosperm and seed maternal tissues. Using different barley cultivars, we show that there is natural variation in the kinetics of this process. During the terminal stages of seed development, specific and selective loss of endoreduplicated nuclei occurs in the endosperm. This is accompanied by reduced stability of the nuclear genome, progressive loss of cell viability, and finally programmed cell death. In summary, our study shows that endopolyploidization and cell death are linked phenomena that frame barley grain development.
Rabl organization is a type of interphase chromosome arrangement with centromeres and telomeres clustering at opposite nuclear poles. Here, we analyzed nuclear morphology and chromosome organization ...in cycling and endoreduplicated nuclei isolated from embryo and endosperm tissues of developing barley seeds. We show that endoreduplicated nuclei have an irregular shape, less sister chromatid cohesion at 5S rDNA loci, and a reduced amount of centromeric histone CENH3. While the chromosomes of the embryo and endosperm nuclei are initially organized in Rabl configuration, the centromeres and telomeres are intermingled within the nuclear space in the endoreduplicated nuclei with an increasing endoreduplication level. Such a loss of chromosome organization suggests that Rabl configuration is introduced and further reinforced by mitotic divisions in barley cell nuclei in a tissue- and seed age-dependent manner.
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