Search Results (690)

Figure 1
<p>Phylogenetic tree of the <span class="html-italic">GLN</span> gene family in <span class="html-italic">Arabidopsis thaliana</span>, <span class="html-italic">Oryza sativa</span>, and <span class="html-italic">Glycine max</span>. A phylogenetic tree was built by using MEGAX (1 × 10³ bootstrap replicates). Each species is represented by a distinct color in the phylogenetic tree to facilitate differentiation. Genes prefixed with “Os” prefix designates genes from <span class="html-italic">Oryza sativa</span>, “At” prefix indicates genes from <span class="html-italic">Arabidopsis thaliana</span>, and “Gm” corresponds to <span class="html-italic">Glycine max</span>.</p> Full article ">Figure 2
<p>Analysis and prediction of gene structure, conserved motifs and domains for <span class="html-italic">GmGLN</span> genes. (<b>A</b>) Gene structure of <span class="html-italic">GmGLN</span> genes—green boxes indicate 5′or 3′ UTR regions, yellow boxes indicate exons, and lines with black represent introns. (<b>B</b>) Conserved domains for <span class="html-italic">GmGLN</span> protein family. (<b>C</b>) Conserved motifs for <span class="html-italic">GmGLN</span> protein family.</p> Full article ">Figure 2 Cont.
<p>Analysis and prediction of gene structure, conserved motifs and domains for <span class="html-italic">GmGLN</span> genes. (<b>A</b>) Gene structure of <span class="html-italic">GmGLN</span> genes—green boxes indicate 5′or 3′ UTR regions, yellow boxes indicate exons, and lines with black represent introns. (<b>B</b>) Conserved domains for <span class="html-italic">GmGLN</span> protein family. (<b>C</b>) Conserved motifs for <span class="html-italic">GmGLN</span> protein family.</p> Full article ">Figure 2 Cont.
<p>Analysis and prediction of gene structure, conserved motifs and domains for <span class="html-italic">GmGLN</span> genes. (<b>A</b>) Gene structure of <span class="html-italic">GmGLN</span> genes—green boxes indicate 5′or 3′ UTR regions, yellow boxes indicate exons, and lines with black represent introns. (<b>B</b>) Conserved domains for <span class="html-italic">GmGLN</span> protein family. (<b>C</b>) Conserved motifs for <span class="html-italic">GmGLN</span> protein family.</p> Full article ">Figure 3
<p>Localization of <span class="html-italic">GmGLN</span> genes on chromosomes. A total of 109 <span class="html-italic">GmGLN</span> genes are distributed across chromosomes 1 through 20. Each vertical bar is annotated with the corresponding chromosome number at its apex. A scale indicating the chromosome length in megabases (Mb) is provided alongside.</p> Full article ">Figure 3 Cont.
<p>Localization of <span class="html-italic">GmGLN</span> genes on chromosomes. A total of 109 <span class="html-italic">GmGLN</span> genes are distributed across chromosomes 1 through 20. Each vertical bar is annotated with the corresponding chromosome number at its apex. A scale indicating the chromosome length in megabases (Mb) is provided alongside.</p> Full article ">Figure 4
<p>Analysis of gene ontology (GO) enrichment for the <span class="html-italic">GmGLN</span> gene family was stratified into three principal domains: biological process (BP), cellular component (CC), and molecular function (MF). GO terms with a <span class="html-italic">p</span>-value threshold of less than 5 × 10⁻² were considered to be statistically significant.</p> Full article ">Figure 5
<p>Heat map of the <span class="html-italic">GmGLN</span> gene family in different tissues for soybean. The heat map utilizes a color scale on its right side to represent the relative expression level, with a gradient ranging from light green to orange-red indicative of a progressive increase in expression.</p> Full article ">

Figure 1
<p>Graphical abstract of histone methylation-mediated transcriptional activation. Created in BioRender. Rai, N. (2024) <a href="https://BioRender.com/m31m407" target="_blank">https://BioRender.com/m31m407</a>, 2 December 2024.</p> Full article ">Figure 2
<p>A graphical representation of the multifaceted roles of H3K4 methylation in the pathogenic adaptation of human and plant pathogenic fungi. Created in BioRender. Rai, N. (2024) <a href="https://BioRender.com/q87f061" target="_blank">https://BioRender.com/q87f061</a>, 2 December 2024.</p> Full article ">

Figure 1
<p>Root scans of maize inbred seedlings under different treatments. CK: distilled water treatment; PEG: 15% PEG treatment; AP: 25 mg/L5-ALA + 15%PEG treatment.</p> Full article ">Figure 2
<p>Different lowercase letters represent the same inbred line with significant differences under different treatments (<span class="html-italic">p</span> &lt; 0.05). CK: distilled water treatment; PEG: 15% PEG treatment; AP: 25 mg/L5-ALA + 15%PEG treatment. (<b>a</b>) Root/shoot ratio; (<b>b</b>) Number of lateral roots; (<b>c</b>) Relative water content.</p> Full article ">Figure 3
<p>Different lowercase letters represent the same inbred line with significant difference under different treatments (<span class="html-italic">p</span> &lt; 0.05). CK: distilled water treatment; PEG: 15% PEG treatment; AP: 25 mg/L5-ALA + 15% PEG treatment. (<b>a</b>) Proline content; (<b>b</b>) Relative electric conductivity; (<b>c</b>) MDA content; (<b>d</b>) SOD activity; (<b>e</b>) POD activity; (<b>f</b>) CAT activity.</p> Full article ">Figure 4
<p>Heatmap of the expression quantity correlation between two samples. T-CK: Distilled water treatment TS141; T-PEG: 15% PEG processing TS141; T-AP: 25 mg/L 5-ALA + 15% PEG to treat TS141; Z-CK: Distillation water treatment Zheng58; Z-PEG: 15% PEG treatment Zheng58; Z-AP: 25 mg/L 5-ALA + 15% PEG treatment Zheng58; The number after the sample number indicates that the same treatment is repeated.</p> Full article ">Figure 5
<p>Upregulated and downregulated DEG numbers and Venn analysis between different treatments. (<b>a</b>) Downregulated distribution of DEG numbers in different treatment groups; (<b>b</b>) Venn analysis of expressed genes in different treatment groups; (<b>c</b>) Venn diagram analysis of upregulated DEG numbers in different treatment groups; (<b>d</b>) Venn analysis of downregulated DEG numbers in different treatment groups.</p> Full article ">Figure 6
<p>GO annotations of inbred lines TS141 and Zheng58 under different treatments. (<b>a</b>) GO annotations for inbred line TS141 under normal treatment and drought stress; (<b>b</b>) GO annotations for inbred line Zheng58 under normal treatment and drought stress; (<b>c</b>) GO annotation for inbred line TS141 under 5-ALA application; (<b>d</b>) GO annotation for inbred line Zheng58 under 5-ALA application.</p> Full article ">Figure 7
<p>KEGG metabolic pathway analysis of TS141 and Zheng58 under different treatments. (<b>a</b>) KEGG metabolic pathways of TS141 under normal treatment and drought stress; (<b>b</b>) KEGG metabolic pathways of Zheng58 under normal treatment and drought stress; (<b>c</b>) KEGG metabolic pathway of TS141 under external application of 5-ALA; (<b>d</b>) KEGG metabolic pathway of Zheng58 under 5-ALA application.</p> Full article ">Figure 8
<p>The expression patterns of 5 selected genes identified by RNA-seq was verified by qRT-PCR. (<b>a</b>) Heat map showing the expression changes (logy-fold change) in response to the Z-AP, T-CK, T-AP, Z-CK, T-PEG, and Z-PEG treatments for each candidate gene as measured by RNA-seq and qRT-PCR; (<b>b</b>) Scatter plot showing the changes in the expression (logy-fold change) of selected genes based on RNA-seq via qRT-PCR. Gene expression levels are indicated by colored bars.</p> Full article ">Figure 9
<p>Module construction based on WGCNA. (<b>a</b>) Gene network module; (<b>b</b>) Gene co-expression network heat map; (<b>c</b>) Gene phylogenetic tree and trait correlation heat map; (<b>d</b>) Heatmap of correlations between modules and traits. The closer the correlation is to the absolute value of 1, the more relevant the trait is to the gene of the module.</p> Full article ">Figure 10
<p>Functional analysis of genes in the blue and turquoise modules. (<b>a</b>) GO enrichment analysis in the yellow module; (<b>b</b>) KEGG enrichment analysis in the yellow module; (<b>c</b>) GO enrichment analysis in the turquoise module; (<b>d</b>) KEGG enrichment analysis in the turquoise module.</p> Full article ">Figure 11
<p>Co-expression regulatory network analysis of the blue module. Red represents hub genes. (<b>a</b>) Network interaction analysis of hub genes in the yellow module; (<b>b</b>) Network interaction analysis of hub genes in the turquoise module. The color gradients of the dots represent high or low soft thresholds of connectivity, with a redder dot color representing a higher soft threshold of connectivity.</p> Full article ">

Figure 1
<p>CONSORT flow diagram.</p> Full article ">

Figure 1
<p><b>Different mechanical and geometrical approaches in 2D vertex models.</b> (<b>a</b>) Schematic of a 2D vertex model showing key mechanical parameters: area elasticity <math display="inline"><semantics> <msub> <mi>K</mi> <mi>α</mi> </msub> </semantics></math>, area contractility <math display="inline"><semantics> <msub> <mo>Γ</mo> <mi>α</mi> </msub> </semantics></math>, and line tension at cell interfaces <math display="inline"><semantics> <msub> <mo>Λ</mo> <mrow> <mi>i</mi> <mi>j</mi> </mrow> </msub> </semantics></math>. (<b>b</b>) Lateral vertex model representing the planar cross-section of an epithelium. (<b>c</b>) Pseudo three-dimensional vertex model where the target apical cell size is determined by the position of the nucleus within each cell. The nucleus position is dependent on the stage of the cell cycle, influencing cell geometry. Although the model is 2D, it simulates 3D biological aspects by relating nuclear positioning to cell morphology.</p> Full article ">Figure 2
<p><b>Different geometrical and mechanical approaches in 3D vertex models.</b> (<b>a</b>) Representation of a scutoid, a geometrical shape that appears in epithelial tissue organisation when cells have different neighbours in the apical and basal surfaces. (<b>b</b>) Representation of apical tissue surface as a 2D manifold in a 3D space used to model folding epithelia. Also known as a 3D apical vertex model. (<b>c</b>) Three-dimensional Vertex models can be used as well to represent non-epithelial configurations of confluent biological tissues [<a href="#B6-biophysica-04-00039" class="html-bibr">6</a>,<a href="#B24-biophysica-04-00039" class="html-bibr">24</a>].</p> Full article ">Figure 3
<p><b>Finer discretisation of cell edges allows for more flexible and fluid polygonal representations.</b> (<b>a</b>) In the conventional vertex model, vertices are positioned at tricellular junctions or tissue boundaries. (<b>b</b>) Additional discretisation of cellular edges, as presented in [<a href="#B51-biophysica-04-00039" class="html-bibr">51</a>], enables the inclusion of extracellular spaces and local cortical tensions. (<b>c</b>) A further level of discretisation is achieved by assigning each cell its own set of vertices, as in <span class="html-italic">PolyHoop</span>, allowing for more detailed local cell–cell interactions [<a href="#B10-biophysica-04-00039" class="html-bibr">10</a>].</p> Full article ">Figure 4
<p><b>Heterogeneity and feedback.</b> Vertex and SPV models allow for distinct ascriptions of mechanical parameters for each cell. In practice, this allows for cell-type specific mechanical regimes here schematised with different colours. When setting the line-tension for heterotypic interfaces to be higher than that of homotypic interfaces (centre panels), cell types are able to sort, forming a straight interface. This is consistent with in vivo examples of boundaries of lineage segregation. More generally, cell-type-specific parameters can also be allowed to vary as a function of the local mechanical or signalling environment (right diagram). This allows for mechanochemical feedback among cells. In principle, feedback between signals, state, and mechanics allows the modelling of new emergent behaviours that go beyond the confines of homogeneous vertex models, or continuum descriptions of chemical cellular interactions.</p> Full article ">Figure 5
<p><b>Schematic description of the principles underlying approximate Bayesian computation</b>. Here, univariate summary statistics <math display="inline"><semantics> <msub> <mi>s</mi> <mi>i</mi> </msub> </semantics></math> are computed for both the simulated and real experimental data, and the distances between these dictate whether samples from the parameter distributions are accepted as likely originating from the true posterior. The sampling step is repeated until the desired number of samples is obtained using the successful parameters to generate the posterior distribution.</p> Full article ">

Figure 1
<p>Structural organization of the <span class="html-italic">Drosophila melanogaster</span> eggshell (the figure is based on Figure 1 from [<a href="#B2-ijms-25-12499" class="html-bibr">2</a>] with modifications).</p> Full article ">Figure 2
<p>CR and ThS staining of the eggshell of the wild-type flies and the flies homozygous for the <span class="html-italic">Cp36^dec2−1</span> chromosomal rearrangement. (<b>A</b>) Staining of the fruit fly eggs with CR in brightfield and polarized light. (<b>B</b>) Staining of fruit fly eggs with ThS under UV light and in brightfield. (<b>C</b>–<b>C</b>″) Staining of the micropyle (<b>C</b>), the pillars (<b>C′</b>), and the modified pillars of the dorsal appendages (<b>C</b>″) with ThS (green fluorescence under UV light). Scale bars, 200 µm (<b>A</b>,<b>B</b>); 20 µm (<b>C</b>–<b>C</b>″).</p> Full article ">Figure 3
<p>Immunodetection of the s36 protein in the fruit fly egg lysates and intact eggshells. (<b>A</b>) Immunoblotting of the s36 protein obtained from the egg lysates of the wild-type and mutant flies homozygous for the <span class="html-italic">Cp36^dec2−1</span> chromosomal rearrangement. The protein lysates were separated into soluble and insoluble fractions by low-speed centrifugation. The s36 protein was detected in the insoluble fraction in the Oregon-R eggs and in the soluble fraction of the mutant eggs homozygous for the <span class="html-italic">Cp36^dec2−1</span> chromosomal rearrangement. (<b>B</b>) Densitometric quantification of the data is shown in A. The relative intensities of the bands corresponding to S36 are presented as the mean ± SEM of three independent egg lysate samples. (<b>C</b>) Staining of the Oregon-R and the mutant eggs with the s36-specific antibodies. The s36-specific antibodies bind the eggshell of the Oregon-R flies (red fluorescence) but do not bind the eggshell of the mutant flies homozygous for the <span class="html-italic">Cp36^dec2−1</span> chromosomal rearrangement. (<b>D</b>–<b>F</b>) Staining of the micropyle, the pillars, and the dorsal appendages of the Oregon-R eggs with the s36-specific antibodies (red) and ThS (green). The s36-specific antibodies bind the micropyle (<b>D</b>), the pillars (<b>E</b>), and the modified pillars in the dorsal appendages (<b>F</b>) and colocalize with the amyloid-specific dye ThS. Scale bars, 200 µm (<b>C</b>); 20 µm (<b>D</b>–<b>F</b>).</p> Full article ">Figure 4
<p>Structure of the <span class="html-italic">CG33223</span> gene and its products in the <span class="html-italic">Drosophila melanogaster</span> strain BDSC #4842 (chromosome X) with the <span class="html-italic">Cp36^dec2−1</span> chromosomal rearrangement. The direction of transcription is indicated by a black arrow. The open reading frame is indicated in brown color. The exons are indicated as gray rectangles, and the intron is a black line. The boundaries of the deletion are indicated by a hatching and by a red cross. The polypeptide produced in wild-type flies is indicated in a greenish color. Also, a red cross indicates that the polypeptide is not formed against the background of deletion. The IDs of the <span class="html-italic">CG33223</span> products were obtained from the FlyBase database (<a href="https://flybase.org/" target="_blank">https://flybase.org/</a>, accessed on 10 May 2024).</p> Full article ">Figure 5
<p>Fibrils immunoprecipitated with antibodies against the s36 protein from the Oregon-R eggs. (<b>A</b>) An electron micrograph of fibrils stained with uranyl acetate. (<b>B</b>) CR staining of the s36 protein immunoprecipitated from the Oregon-R eggs. The left panel is brightfield (red), and the right panel is polarized light (apple-green). Scale bars, 100 nm (<b>A</b>); 20 µm (<b>B</b>).</p> Full article ">Figure 5 Cont.
<p>Fibrils immunoprecipitated with antibodies against the s36 protein from the Oregon-R eggs. (<b>A</b>) An electron micrograph of fibrils stained with uranyl acetate. (<b>B</b>) CR staining of the s36 protein immunoprecipitated from the Oregon-R eggs. The left panel is brightfield (red), and the right panel is polarized light (apple-green). Scale bars, 100 nm (<b>A</b>); 20 µm (<b>B</b>).</p> Full article ">Figure 6
<p>Distribution of potentially amyloidogenic region of the s36 protein across the phylogenetic tree of the genus <span class="html-italic">Drosophila</span>. Group representatives that have the s36 amyloidogenic sequence are in bold (only within the subgenus <span class="html-italic">Sophophora</span>). The number of representatives is indicated in brackets.</p> Full article ">

Figure 1
<p>Histological evaluation of the squirrel testis. In the immature phase (<b>a</b>), the seminiferous tubules lack lumens and have small diameters. Sertoli cells are located at the basis of the germinal epithelium, while a few spermatogonia occupy a more central position. During the pubertal phase (<b>b</b>), the lumen starts forming in some seminiferous tubules. The germinal epithelium contains Sertoli cells, primary spermatocytes, and spermatids, with Leydig cells seen in the peritubular interstice. In the spermatogenesis phase (<b>c</b>), the seminiferous tubules have large lumens, and elongated spermatids are visible.</p> Full article ">Figure 2
<p>Gene expression-normalized data. The figure shows NGF, NTRK1, and p75NTR qPCR expression data normalized to the reference gene <span class="html-italic">ACTB</span>. Gene expression is compared between the three reproductive stages: immature, pubertal, and spermatogenesis. The expression levels of the <span class="html-italic">NGF</span> gene are different in the pubertal group versus the immature and spermatogenesis groups (<span class="html-italic">p</span> &lt; 0.01). Different letters placed on the top of the boxes indicate statistically significant differences.</p> Full article ">Figure 3
<p>Western blotting of the squirrel testis. Western blotting on the top left is relative to the NGF antibody (kDa 34), the pan-NTRK antibody (kDa 130), and the p75NTR antibody (kDa 72). On the right, the western blot is for the ACTB reference protein. To the left of each western blotting image is shown the positive control (mouse brain) followed by the three sexual phenotypes: immature (lanes 1, 2, and 3), pubertal (lanes 4, 5, 6), and spermatogenesis (lanes 7, 8, 9, 10, and 11). Numbers below the lanes represent the Sample ID. To the right of each western blot, the weight in kDa of the respective antibodies is revealed in the running line outlined in the box.</p> Full article ">Figure 4
<p>Protein expression-normalized data. The graphs show the results derived by analyzing the western blot images. The expression of the three proteins NGF, p75NTR, and pan-TRK (pan-TRK antibody recognizes the active domains of the neurotrophins NGF, BDNF, and NT-3) is normalized for the value of the reference protein ACTB. Statistical analysis shows no significant differences in NGF, pan-NTRK, and p75NTR protein levels of the immature, pubertal, and spermatogenesis groups. Different letters placed on the top of the boxes indicate statistically significant differences.</p> Full article ">Figure 5
<p>NGF immunopositivity in grey squirrel testis morphotypes. (<b>a</b>–<b>c</b>) NGF protein is observed at the level of Leydig cells (arrows). The positivity appears more intense in the pubertal morphotype (<b>b</b>) and active spermatogenesis (<b>c</b>) compared to the immature morphotype (<b>a</b>).</p> Full article ">Figure 6
<p>Immunopositivity for NTRK1 in grey squirrel testis morphotypes. The receptor is shown in Leydig cells of the immature morphotype ((<b>a</b>), arrow); in basal germ cells (arrow) and in the perinuclear region of type I spermatocytes (asterisk and top panel) of the pubertal morphotype (<b>b</b>); and in spermatids and spermatozoa of the mature morphotype ((<b>c</b>), arrow).</p> Full article ">Figure 7
<p>Immunopositivity for p75NTR in the morphotypes of grey squirrel testes. p75NTR is not visible in the parenchyma of the immature morphotype (<b>a</b>) where the nerves located in the capsule (top panel) appear positive, providing validity to the immunohistochemical reaction. In the pubertal morphotype (<b>b</b>) a weak positivity of Sertoli cells is observed (arrows) which significantly increases in the mature morphotype ((<b>c</b>), arrow).</p> Full article ">Figure 8
<p>NGF protein plasma content. The graph depicts NGF levels assessed by the ELISA method in the plasma of immature, pubertal, and spermatogenesis stages. In the pubertal group, the level of NGF is higher than the two other groups (<span class="html-italic">p</span> ˂ 0.01). Different letters placed on the top of the boxes indicate statistically significant differences.</p> Full article ">

Figure 1
<p>Different growth habits of wheat during overwintering period.</p> Full article ">Figure 2
<p>A Core Regulatory Pathway Controlling Rice Tiller Angle Mediated by the <span class="html-italic">LA1</span>-Dependent Asymmetric Distribution of Auxin. Note: The red arrow denotes positive regulation, while the blue arrow denotes negative regulation. Loss of <span class="html-italic">LA1</span> function enhances PAT, leading to an uneven distribution of auxin, which induces asymmetric expression of auxin response factors <span class="html-italic">WOX6</span> and <span class="html-italic">WOX11</span>, reduces stem gravity, and results in an increased tiller angle. <span class="html-italic">HSFA2D</span>, an upstream positive regulator of <span class="html-italic">LA1</span>-dependent auxin asymmetrical distribution, reduces the expression of the <span class="html-italic">LA1</span> gene when its function is lost. <span class="html-italic">HOX1</span> and <span class="html-italic">HOX28</span> are positive regulators upstream of <span class="html-italic">HSFA2D</span>, regulating tillering angle by inhibiting the <span class="html-italic">HSFA2D-LA1</span> pathway and controlling the asymmetric distribution of auxin, thereby increasing the tillering angle. BRXL4, a <span class="html-italic">LA1</span>-interacting protein, affects the localization of LA1 and the tiller angle through physical interaction. Normally, a lower OsBRXL4/<span class="html-italic">LA1</span> ratio maintains a smaller tiller angle; however, an increase in OsBRXL4 leads to a gradual increase in the tillering angle due to decreased nuclear localization of <span class="html-italic">LA1</span>. The <span class="html-italic">LA3</span>-<span class="html-italic">LA2</span>-<span class="html-italic">OspPGM</span> complex acts on the same pathway upstream of <span class="html-italic">LA1</span> to mediate the asymmetric distribution of auxin and negatively regulate the tillering angle of rice. Loss of <span class="html-italic">OsPINb</span> function promotes PAT, resulting in an increased tiller angle, while overexpression of OsPIN2 leads to an increased tiller angle by inhibiting <span class="html-italic">LA1</span>. The OsmiR167a-<span class="html-italic">OsARF12/17/25</span> module regulates the tiller angle through auxin-mediated asymmetric distribution of <span class="html-italic">WOX6</span> and <span class="html-italic">WOX11</span>.</p> Full article ">

Figure 1
<p>Map of the <span class="html-italic">MtNF-YB10</span> gene. The gene does not contain introns. A part of the gene encoding B domain, conservative for NF-YB proteins, is shown in pale green. Targets 1, 2, and 3 are marked with dark green arrows, pointing to PAM. <a href="#plants-13-03226-f001" class="html-fig">Figure 1</a> was generated in Snapgene v6.2.1.</p> Full article ">Figure 2
<p>Alignment of sequences of edited and wildtype (wt) alleles identified from cloned PCR fragments from three T0 transgenic lines. Only aligned regions of interest are displayed; target without PAM is underlined. <a href="#plants-13-03226-f002" class="html-fig">Figure 2</a> was generated in Ugene v48.1.</p> Full article ">Figure 3
<p>Sequencing chromatogram of a PCR fragment obtained from the <span class="html-italic">MtNF-YB10</span> locus of a T1 <span class="html-italic">mtnf-yb10-25-2</span> plant. The blue two-headed arrow marks part of the sequence corresponding to the target site. Different line colours correspond to different nucleotide types written in the bottom. <a href="#plants-13-03226-f003" class="html-fig">Figure 3</a> was generated in Ugene v48.1.</p> Full article ">Figure 4
<p>Phenotypic comparison of 34-day-old wt and mutant <span class="html-italic">mtnf-yb10-25-2</span> progeny plants and seeds. (<b>a</b>,<b>b</b>) True leaves of wt (<b>a</b>) and mutant (<b>b</b>) plants; (<b>c</b>,<b>d</b>) cotyledons of wt (<b>c</b>) and mutant (<b>d</b>) plants; (<b>e</b>,<b>f</b>) general view of wt (<b>e</b>) and mutant (<b>f</b>) seeds. Scale bars are 1 mm for (<b>a</b>,<b>b</b>), 2 mm for (<b>c</b>,<b>d</b>), and 1 mm for (<b>e</b>,<b>f</b>).</p> Full article ">Figure 5
<p>Evaluation of seed size, germination rate, and root length of wt and mutant <span class="html-italic">mtnf-yb10-25-2</span> progeny plants. (<b>a</b>,<b>b</b>) Boxplots representing seed length (<b>a</b>) and width (<b>b</b>) for wildtype R108 and mutant <span class="html-italic">mtnf-yb10</span> plants. Data were obtained for 7–10 seeds for different genotypes. To assess the statistical significance of the observed differences, the Wilcoxon signed-rank test was used. (<b>c</b>) Mosaic plot representing the number of germinated and not germinated seeds for different genotypes. The germination rate differed significantly between genotypes (<span class="html-italic">p</span>-value = 0.008901, Fisher test). (<b>d</b>) Boxplot representing root length for wt R108 and mutant <span class="html-italic">mtnf-yb10</span> seedlings. Data were obtained for 16–22 seedlings for different genotypes. To assess the statistical significance of the observed differences, the Wilcoxon signed-rank test was used.</p> Full article ">Figure 6
<p>Evaluation of capacity for callus formation and SE for mutant <span class="html-italic">mtnf-yb10-25-2</span> progeny plants. (<b>a</b>,<b>b</b>) Boxplot representing callus weight (<b>a</b>) and number of somatic embryos (<b>b</b>) after in vitro cultivation of explants from wildtype R108 and mutant <span class="html-italic">mtnf-yb10</span> plants. Data were obtained from 24–27 explants for different genotypes; each explant was taken from the individual plant. To assess the statistical significance of the observed differences, the Wilcoxon signed-rank test was used. (<b>c</b>) Calli developed from explants taken from wildtype R108 and mutant <span class="html-italic">mtnf-yb10</span> plants on the 68th day of cultivation.</p> Full article ">Figure 7
<p>Analysis of T2 progeny of the <span class="html-italic">mtnf-yb10-25-2</span> plant. (<b>a</b>) PCR identification of <span class="html-italic">mtnf-yb10-25-2</span> progeny plants without insertion of the cassette with <span class="html-italic">Cas9</span> expression. 1,5—wt R108; 2,6—T2 plant without insertion of the cassette with Cas9 expression (<span class="html-italic">mtnf-yb10-25-2-6</span>); 3,4,7,8—two plants with insertion of the cassette with <span class="html-italic">Cas9</span> expression; 1,2,3,4—reference gene <span class="html-italic">MtH3L</span> fragments; 5,6,7,8—<span class="html-italic">SpCas9</span> fragments; 9—H₂O (K-); margins—1 Kb SibEnzyme ladder; (<b>b</b>) T2 plant <span class="html-italic">mtnf-yb10-25-2-6</span> without insertion of the <span class="html-italic">Cas9</span> gene at the flowering stage.</p> Full article ">

Figure 1
<p>Functional analysis of lncRNA MSTRG.20890.1 in dermal fibroblasts. (<b>A</b>) Screening of lncRNA MSTRG.20890.1 related to secondary hair follicle morphogenesis. (<b>B</b>) Expression of lncRNA in different treatment groups. (<b>C</b>) The apoptosis of dermal fibroblasts was detected after lncRNA MSTRG.20890.1 interference. (<b>D</b>) EDU was used to detect the proliferation of lncRNA MSTRG.20890.1-sh cell line. (<b>E</b>) CCK8 was used to detect the proliferation of lncRNA MSTRG.20890.1-sh cell line. (<b>F</b>) Expression of lncRNA MSTRG.20890.1 in skin samples at different embryonic periods. (<b>G</b>) Screening of lncRNA MSTRG.20890.1 interference vector. (<b>H</b>) Migration ability of lncRNA MSTRG.20890.1-sh cell line. (<b>I</b>) Cell cycle determination of lncRNA MSTRG.20890.1-sh cell line.</p> Full article ">Figure 2
<p>LncRNA MSTRG.20890.1 acts as a sponge for chi-miR-24-3p in cashmere goat. (<b>A</b>) Detection of lncRNA MSTRG.20890.1 expression in the nucleus and cytoplasm of dermal fibroblasts. (<b>B</b>) lncLocator software predicts the distribution of lncRNA MSTRG.20890.1 in cells. (<b>C</b>) Schematic diagram of wild/mutant lncRNA MSTRG.20890.1 luciferase reporter vector construction. (<b>D</b>) RNAhybrid (v2.1.2) software predicts the sequence of lncRNA MSTRG.20890.1 binding site to chi-miR-24-3p. (<b>E</b>) Relative expression of chi-miR-24-3p after transfection of dermal fibroblasts with lncRNA MSTRG.20890.1-sh. (<b>F</b>) Dual-luciferase reporter gene system to detect target binding of lncRNA MSTRG.20890.1 to chi-miR-24-3p.</p> Full article ">Figure 3
<p>Chi-miR-24-3p can reverse the effect of lncRNA MSTRG.20890.1 on the cell phenotype of dermal fibroblasts. (<b>A</b>) The expression of lncRNA MSTRG.20890.1 was detected in chi-miR-24-3p interference/overexpression cell lines. (<b>B</b>) The cell cycle of lncRNA MSTRG.20890.1-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>C</b>) The migration of lncRNA MSTRG.20890.1-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>D</b>) lncRNA MSTRG.20890.1-sh cell line was added with chi-miR-24-3p inhibitor to detect cell proliferation. (<b>E</b>) The apoptosis of lncRNA MSTRG.20890.1-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>F</b>) Expression of marker genes for cell proliferation/apoptosis.</p> Full article ">Figure 4
<p>Prediction and analysis of chi-miR-24-3p target gene. (<b>A</b>) Construction of chi-miR-24-3p-mRNA regulatory network. (<b>B</b>) Schematic diagram of wild-type/mutant-type ADAMTS3-3′UTR luciferase reporter vector construction. (<b>C</b>) Detection of <span class="html-italic">ADAMTS3</span> expression in chi-miR-24-3p interference/overexpression dermal fibroblast cell lines. (<b>D</b>) Targeted binding of chi-miR-24-3p toADAMTS3-3′UTR was detected. (<b>E</b>) GO enrichment analysis of chi-miR-24-3p target genes. (<b>F</b>) KEGG enrichment analysis of chi-miR-24-3p target genes.</p> Full article ">Figure 5
<p>Functional analysis of <span class="html-italic">ADAMTS3</span> in dermal fibroblasts. (<b>A</b>) Screening of <span class="html-italic">ADAMTS3</span> interference vector. (<b>B</b>) The apoptosis of dermal fibroblasts was detected after <span class="html-italic">ADAMTS3</span> interference. (<b>C</b>) Migration ability of ADAMTS3-sh cell line. (<b>D</b>) EDU was used to detect the proliferation of ADAMTS3-sh cell line. (<b>E</b>) Cell cycle determination of ADAMTS3-sh cell line.</p> Full article ">Figure 6
<p>Chi-miR-24-3p can reverse the effect of <span class="html-italic">ADAMTS3</span> on the cell phenotype of dermal fibroblasts. (<b>A</b>) The apoptosis of ADAMTS3-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>B</b>) The migration of ADAMTS3-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>C</b>) The cell cycle of ADAMTS3-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>D</b>) The proliferation of ADAMTS3-sh cell line was detected after adding chi-miR-24-3p inhibitor. (<b>E</b>) Expression of marker genes for cell proliferation/apoptosis.</p> Full article ">Figure 7
<p>Diagram of the lncRNA MSTRG.20890.1/chi-miR-24-3p/ADAMTS3 regulatory mechanism.</p> Full article ">

Figure 1
<p>Phylogenetic tree of MAP65 gene family in seven species. Phylogenetic analysis of MAP65s across <span class="html-italic">Phyllostachys edulis</span>, <span class="html-italic">Raddia guianensis</span>, <span class="html-italic">Dendrocalamus latiflorus</span>, <span class="html-italic">Guadua angustifolia</span>, <span class="html-italic">Oryza sativa</span>, <span class="html-italic">Populus trichocarpa</span>, and <span class="html-italic">Arabidopsis thaliana</span>. Roman numerals I, II, III, IV, and V denote distinct gene clusters (groups). Variations in symbol shapes and colors represent different species.</p> Full article ">Figure 2
<p>Conserved motifs and gene structure of PeMAP65s. The motif distribution of MAP65s (<b>left</b>). A total of 12 motifs are represented, each within differently colored boxes. Gene structures of <span class="html-italic">PeMAP65</span>s (<b>right</b>). The light green box represents the exon, the blue-green box represents the UTR, and the black line indicates the intron.</p> Full article ">Figure 3
<p><span class="html-italic">Cis</span>-acting elements predicted in the promoter of <span class="html-italic">PeMAP65</span>s. All <span class="html-italic">cis</span>-acting elements were categorized into three categories. The heatmap demonstrates the number of <span class="html-italic">cis</span>-acting elements with the higher number in blue and the lower number in yellow. On the right, the number in the differently colored boxes represents the count of <span class="html-italic">cis</span>-acting elements in each category.</p> Full article ">Figure 4
<p>Chromosomal location and synteny analysis of <span class="html-italic">PeMAP65</span>s. (<b>A</b>) The distribution of the <span class="html-italic">PeMAP65</span>s located on the chromosomes in <span class="html-italic">P. edulis</span>. The genetic distance of 13 chromosomes are represented by the scale in megabases (Mb) on the left. Black lines represent the location of the gene on each chromosome. (<b>B</b>) Collinearity analysis of the <span class="html-italic">PeMAP65</span> gene family. Each <span class="html-italic">PeMAP65</span> is marked with a short black line on the chromosome, and collinear gene pairs are represented by a black curve. (<b>C</b>) The <span class="html-italic">Ka</span> (non-synonymous substitution) and <span class="html-italic">Ks</span> (synonymous substitution) values of <span class="html-italic">MAP65</span>s were calculated. Pe, <span class="html-italic">P. edulis</span>, Rgu, <span class="html-italic">R. guianensis</span>, Dl, <span class="html-italic">D. latiflorus</span>, Gan, <span class="html-italic">G. angustifolia.</span> (<b>D</b>) Collinearity analysis of <span class="html-italic">MAP65</span>s between <span class="html-italic">P. edulis</span> and three other bamboo species and rice. The gray lines indicate collinear blocks within the <span class="html-italic">P. edulis</span> genome and other plant genomes, and the red curves indicate <span class="html-italic">MAP65</span>s with collinearity.</p> Full article ">Figure 5
<p>The expression patterns of <span class="html-italic">PeMAP65</span>s in 26 tissues. The heatmap represents the expression levels of <span class="html-italic">PeMAP65</span>s calculated by Log2FPKM.</p> Full article ">Figure 6
<p>The expression pattern of <span class="html-italic">PeMAP65</span>s in bamboo shoots with different degrees of lignification. (<b>A</b>) The heatmap represents the expression level (Log2FPKM) of <span class="html-italic">PeMAP65</span>s at the 13th internode of bamboo shoots with different heights. T, M, and L represent the top, middle, and lower portions of the 13th internode. (<b>B</b>) The relative expression levels of <span class="html-italic">PeMAP65</span>s in different internodes of moso bamboo shoots with a height of 2.5 m. S1 represents the 22nd internode. S2 and S3 represent the top and lower portions of the 18th internode. S4 and S6 represent the top, middle, and lower portions of the 13th internode. Data represent means (±SD) of three biological replicates. The different letters indicate significant differences, for which the relative expression level between two samples was greater than or equal to 2.</p> Full article ">Figure 7
<p>Co-expression networks of PeMAP65s. (<b>A</b>) Co-expression networks constructed by the database of co-expression networks with functional modules for moso bamboo. Red ellipses represent <span class="html-italic">PeMAP65</span>s, green ellipses represent the co-expressed genes with <span class="html-italic">PeMAP65</span>s, and gray lines represent the edges between these co-expressed genes. (<b>B</b>,<b>C</b>) KEGG functional enrichment on the genes co-expressed with <span class="html-italic">PeMAP65</span>s in two clusters based on the expression patterns of <span class="html-italic">PeMAP65</span>s in different lignified shoots.</p> Full article ">Figure 8
<p>The transcriptional level of <span class="html-italic">PeMAP65-18</span> was upregulated by PeMYB46. (<b>A</b>) A hierarchical gene regulatory network. At the top level, <span class="html-italic">MYB46</span> (blue) is shown as a direct target of <span class="html-italic">MAP65-18</span> (green). (<b>B</b>) The correlation heatmap of <span class="html-italic">PeMAP65</span>s with the genes related to SCW biosynthesis. The data represent the Pearson coefficient. (<b>C</b>) The relative expression level of <span class="html-italic">PeMYB46</span> in different internodes. The different letters indicated significant differences, which the relative expression level between two samples was greater than or equal to 2. (<b>D</b>) Schematic diagram of MYB binding sites on the <span class="html-italic">PeMAP65-18</span> promoter. (<b>E</b>) Y1H validation of the interaction between PeMYB46 and <span class="html-italic">PeMAP65-18</span> promoter. (<b>F</b>) Schematic diagrams of the effector (<span class="html-italic">PeMYB46</span>) and reporter (<span class="html-italic">PeMAP65-18</span>pro) constructs were used in the dual-luciferase reporter assay. (<b>G</b>) An image of luciferase activity. (<b>H</b>) Relative luciferase activity was measured. Error bars represent SD. Statistical analysis was performed using the <span class="html-italic">t</span> test (n = 7, ****, <span class="html-italic">p</span> &lt; 0.0001).</p> Full article ">Figure 9
<p>Subcellular localization of PeMAP65-18 in tobacco leaves. EV-GFP represents the empty vector containing <span class="html-italic">35S</span>::<span class="html-italic">GFP</span>. AtTUB6-mCherry used for microtubule localization marker. DMSO or oryzalin (100 μM) treatment for 30 min. Scale bars = 20 µm.</p> Full article ">

Figure 1
<p>Demolition of the Gordon district and construction of the Vörösmarty housing estate. The aerial photograph shows the original, archaic, organic urban fabric on the right. On the left, it has already been erased, and some of the uniform concrete block houses of the new housing estate are already standing. Source: fentrol.hu—Lechner Nonprofit Kft.</p> Full article ">Figure 2
<p>Aerial photograph of the city sports hall (<b>1</b>), county library (<b>2</b>), labour union headquarters (<b>3</b>), and their surroundings in 1973. The remains of the original urban fabric can be seen in the top left corner of the image; almost the entire area was similar before the construction of these buildings. One of Miskolc’s first prefabricated large-panel buildings can be seen in the upper right corner of the image (<b>4</b>). Source: fentrol.hu—Lechner Nonprofit Kft., numbers by author.</p> Full article ">Figure 3
<p>Right: city sports hall (1968–1970, István Horváth, József Szabó, László Thury); left: county library (1972, János Dézsi). Source: author’s photo, 2024.</p> Full article ">Figure 4
<p>Mezőkövesd, Hadas district—analysis by László Szőke. Captions: left column, top to bottom—current clusters of blocks, current blocks, current buildings; right column, up to down—current plots and streets, suggested corrections of plots, suggested corrections of streets. Source: <a href="https://ybldij.hu/dijazottak-2021-szoke-laszlo" target="_blank">https://ybldij.hu/dijazottak-2021-szoke-laszlo</a> (accessed on 18 October 2024).</p> Full article ">Figure 5
<p>Mezőkövesd, Hadas district, aerial photo, 2024. Source: Google Maps.</p> Full article ">Figure 6
<p>László Szőke: The deciphered development history of the central area of Sárospatak before and after the construction of the Perényi-Rákóczi castle. Source: <a href="https://ybldij.hu/dijazottak-2021-szoke-laszlo" target="_blank">https://ybldij.hu/dijazottak-2021-szoke-laszlo</a> (accessed on 18 October 2024).</p> Full article ">Figure 7
<p>Competition plan for the centre of Góra Kalwaria, Poland, simulating gradual, step-by-step development. The numbers indicate the stages of the process; the disturbing building is marked with an arrow on stage 0. Source: [<a href="#B18-heritage-07-00276" class="html-bibr">18</a>].</p> Full article ">Figure 8
<p>Tree and semilattice based on Alexander. The numbers indicate individual elements, the multi-digit strings indicate sets containing the elements with given numbers. Source: [<a href="#B30-heritage-07-00276" class="html-bibr">30</a>] (pp. 6–7).</p> Full article ">Figure 9
<p>Reconstruction of the medieval topography of Miskolc by Éva Gyulai. Texts translated to English by the Author. Source: [<a href="#B33-heritage-07-00276" class="html-bibr">33</a>] Figure 29.</p> Full article ">Figure 10
<p>Reindl Ferenc’s map of Miskolc from 1781. Source: [<a href="#B34-heritage-07-00276" class="html-bibr">34</a>] (pp. 34–35).</p> Full article ">Figure 11
<p>The centre of Miskolc on the map of the royal cadastral survey from 1892 to 1894. Source: [<a href="#B34-heritage-07-00276" class="html-bibr">34</a>] (p. 66).</p> Full article ">Figure 12
<p>The (Aa) tissue type of the Lovra catalogue. Source: [<a href="#B26-heritage-07-00276" class="html-bibr">26</a>] (p. 199).</p> Full article ">Figure 13
<p>The (Ac) tissue type of the Lovra catalogue. Source: [<a href="#B26-heritage-07-00276" class="html-bibr">26</a>] (p. 199).</p> Full article ">Figure 14
<p>The widening Palóczy street, forming the main square of the medieval New Town. Source: author’s photo, 2024.</p> Full article ">Figure 15
<p>The widening Rákóczi street. Source: author’s photo, 2024.</p> Full article ">Figure 16
<p>The widening of the main (Széchenyi) street at the Town Hall square. Source: author’s photo, 2024.</p> Full article ">Figure 17
<p>Back courtyard on Széchenyi street. Source: author’s photo, 2024.</p> Full article ">Figure 18
<p>The plot and the data flow of the algorithm that generates it. Inputs are on the left with wires extending from their right side, while the outputs of the cluster are on the right with wires extending from their left side. Parts that are only activated in later increments (e.g., the street wing) are highlighted in orange. Source: author’s work.</p> Full article ">Figure 19
<p>A plot series and the data flow of the algorithm that generates it. The larger boxes represent plot-clusters, and their contents are displayed in the previous figure. They inherit each other’s outputs as shown. Source: author’s work.</p> Full article ">Figure 20
<p>The data flow of the entire town. The larger boxes are clusters of plot series. To improve visibility, many wires are hidden, but the interconnectivity is still apparent. Source: author’s work.</p> Full article ">Figure 21
<p>Denser version of the keyboard tissue: L-shaped buildings. Source: author’s work.</p> Full article ">Figure 22
<p>Lovra-Ac tissue type generated by algorithm. Source: author’s work.</p> Full article ">Figure 23
<p>Ac-dense tissue type generated by algorithm. Source: author’s work.</p> Full article ">Figure 24
<p>Nine variations of the first increment. Scale on the image is in metres. Source: author’s work.</p> Full article ">Figure 25
<p>One variation of the first increment; 3D view. Source: author’s work.</p> Full article ">Figure 26
<p>Nine variations of the second increment. Scale on the image is in metres. Source: author’s work.</p> Full article ">Figure 27
<p>One variation of the second increment; 3D view. Source: author’s work.</p> Full article ">Figure 28
<p>Nine variations of the third increment. Scale on the image is in metres. Source: author’s work.</p> Full article ">Figure 29
<p>One variation of the third increment; 3D view. Source: author’s work.</p> Full article ">Figure 30
<p>Nine variations of the fourth increment. Scale on the image is in metres. Source: author’s work.</p> Full article ">Figure 31
<p>One variation of the fourth increment; 3D view. Source: author’s work.</p> Full article ">Figure 32
<p>Nine variations of the fifth increment. Scale on the image is in metres. Source: author’s work.</p> Full article ">Figure 33
<p>One variation of the fifth increment; 3D view. Source: author’s work.</p> Full article ">Figure 34
<p>The five increments in 3D side by side. Source: author’s work.</p> Full article ">Figure 35
<p>The city centre of Miskolc in 1953, looking to the south. In the background, Hangman’s hill can be seen. Source: Fortepan, Bernhardt Ágnes.</p> Full article ">Figure 36
<p>The area (Hangman’s hill) in 2023 on aerial photograph. Source: Google Maps.</p> Full article ">Figure 37
<p>Five possible steps of densification shown on the example of one single urban block, which is a cluster in Grasshopper. Source: author’s work.</p> Full article ">Figure 38
<p>First increment of the growth, top view. Blue: existing plots and buildings; black: new (generated) plots and buildings. Source: author’s work.</p> Full article ">Figure 39
<p>First increment of the growth; 3D view. Source: author’s work.</p> Full article ">Figure 40
<p>Second increment of the growth, top view. Blue: existing plots and buildings; black: new (generated) plots and buildings. Source: author’s work.</p> Full article ">Figure 41
<p>Second increment of the growth; 3D view. Source: author’s work.</p> Full article ">Figure 42
<p>Third increment of the growth, top view. Blue: existing plots and buildings; black: new (generated) plots and buildings. Source: author’s work.</p> Full article ">Figure 43
<p>Third increment of the growth; 3D view. Source: author’s work.</p> Full article ">Figure 44
<p>Fourth increment of the growth, top view. Blue: existing plots and buildings; black: new (generated) plots and buildings. Source: author’s work.</p> Full article ">Figure 45
<p>Fourth increment of the growth; 3D view. Source: author’s work.</p> Full article ">Figure 46
<p>Fifth increment of the growth, top view. Blue: existing plots and buildings; black: new (generated) plots and buildings. Source: author’s work.</p> Full article ">Figure 47
<p>Fifth increment of the growth; 3D view. Source: author’s work.</p> Full article ">

Figure 1
<p>The transversal section of an Arabidopsis mature silique showing the essential tissues required for efficient seed dispersal. SL: separation layer; LL: lignification layer; deh zone: dehiscence zone.</p> Full article ">Figure 2
<p>A schematic transversal section of an Arabidopsis mature silique focused on the expression domain(s) of the set of transcriptional regulators driving the specification of the dehiscence zone. Each color represents a functionally different tissue. LIGN: lignification layer; SEP: separation layer.</p> Full article ">Figure 3
<p>(<b>a</b>) A GRN proposed for the <span class="html-italic">A. thaliana</span> fruit dehiscence mechanism based on the literature. The network topology depicts the nodes considered in the model as well as the experimentally supported genetic interactions among them. Black edges with arrowheads are activating regulations and red edges with flat ends represent repressive regulations. Each node color represents a functionally different tissue. A dual color fill is for those active in more than one tissue. Green: valve (V); orange: valve margin (VM); yellow: separation layer (SL); blue: replum (R). (<b>b</b>) Attractors obtained with the network configuration in (<b>a</b>). Each column is the attractor that corresponds to a cell type, valve (V), valve margin (VM), or replum (R). Each network gene is represented by a table row. Red or 0 stands for a transcriptionally repressed gene or an absent protein; blue or 1 is for a transcriptionally active gene or a present protein.</p> Full article ">Figure 4
<p>(<b>a</b>) The localization of NTT-n2YPET in anthesis ovaries. The signal is clearly detected along a narrow stripe in the valve margin (<b>left</b>), that in a transversal section appears to be confined to the separation layer. (<b>b</b>) A BiFC assay showing fluorescence complementation mediated by the interaction of NTT and FIL. Controls for the BiFC experiment are shown in Supplementary File S4. (<b>c</b>,<b>d</b>) Transient assays of SHPpro:LUC (<b>c</b>) and FULpro:LUC (<b>d</b>) expression. SHP:LUC-35S::REN and FUL:LUC-35S::REN reporter constructs were transiently expressed in <span class="html-italic">Nicotiana benthamiana</span> leaves either alone or together with effectors 35S:NTT, 35S:FIL, or both. The expression of REN was used as an internal control. LUC activity was normalized with REN in each case and the relative activity of the reporter + effectors to the reporter alone was calculated (n = 6). Asterisks indicate significant differences according to a Student’s <span class="html-italic">t</span>-test (<span class="html-italic">p</span> &lt; 0.05) from the values obtained when the promoter::LUC-35S::REN reporters were infiltrated alone, while n.s. means no significant differences between the indicated data.</p> Full article ">Figure 5
<p>(<b>a</b>) A GRN proposed for the A. thaliana DZ including NTT and the set of novel interactions. Black edges with arrowheads are activating regulations and red edges with flat ends represent repressive regulations. Each node color represents a functionally different tissue. An octagonal bold line shape is for a novel NTT node. Dual color fill is for those active in more than one tissue. Green: valve (V); orange: valve margin (VM); yellow: separation layer (SL); blue: replum (R). (<b>b</b>) Recovered attractors corresponding to those expected for a dehiscent Arabidopsis fruit. Each column is the attractor that corresponds to a cell type, valve (V), lignification layer (LL), separation layer (SL), or replum (R). Each network gene is represented by a table row. Red or 0 stands for a transcriptionally repressed gene or absent protein; blue or 1 is for a transcriptionally active gene or a present protein.</p> Full article ">Figure 6
<p>Attractor robustness analysis. The attractors recovered after perturbing either the Boolean functions (<b>a</b>) or transition states (<b>b</b>) of the DZ GRN and similar random networks. The red line represents the result corresponding to the DZ network model. The blue line determines the significance level calculated from inducing the same type of perturbations to similar random networks. In panel (<b>a</b>), the bars represent the frequency with which random networks recovered a certain percentage of their original attractors. Panel (<b>b</b>) illustrates the normalized Hamming distance between the successor states of the original and the perturbed network obtained after perturbing the state transitions in random networks and the dynamic GRN dehiscence model.</p> Full article ">Figure 7
<p>Attractors recovered by loss- or gain-of-function mutant simulations of selected Arabidopsis DZ regulators. Each column is an attractor configuration: valve (V), lignification layer (LL), separation layer (SL), or replum (R). The rows represent the state of each node: the squares in blue indicate nodes that are in an “ON” state and those in red are in an “OFF” state. Columns labeled with an asterisk indicate attractors with differences from the four canonical configurations. (<b>a</b>) Simulation of <span class="html-italic">FUL</span> loss-of-function (<span class="html-italic">ful</span> mutant). (<b>b</b>) Simulation of FUL gain-of-function. (<b>c</b>) Simulation of <span class="html-italic">SHP1</span> and <span class="html-italic">SHP2</span> loss-of-function (<span class="html-italic">shp1 shp2</span> double mutant). (<b>d</b>) Simulation of SHP1 and SHP2 gain-of-function. (<b>e</b>) Simulation of NTT gain-of-function. (<b>f</b>) Simulation of <span class="html-italic">IND</span> loss-of-function (<span class="html-italic">ind</span> mutant). (<b>g</b>) Simulation of <span class="html-italic">ALC</span> loss-of-function (<span class="html-italic">alc</span> mutant). (<b>h</b>) Simulation of <span class="html-italic">SPT</span> loss-of-function (<span class="html-italic">spt</span> mutant). (<b>i</b>) Simulation of <span class="html-italic">RPL</span> loss-of-function (<span class="html-italic">rpl</span> mutant).</p> Full article ">