Shoot branching is a primary contributor to plant architecture, evolving independently in flowering plant sporophytes and moss gametophytes. Mechanistic understanding of branching is largely limited to flowering plants such as Arabidopsis, which have a recent evolutionary origin. We show that in gametophytic shoots of Physcomitrella, lateral branches arise by re-specification of epidermal cells into branch initials. A simple model co-ordinating the activity of leafy shoot tips can account for branching patterns, and three known and ancient hormonal regulators of sporophytic branching interact to generate the branching pattern- auxin, cytokinin and strigolactone. The mode of auxin transport required in branch patterning is a key divergence point from known sporophytic pathways. Although PIN-mediated basipetal auxin transport regulates branching patterns in flowering plants, this is not so in Physcomitrella, where bi-directional transport is required to generate realistic branching patterns. Experiments with callose synthesis inhibitors suggest plasmodesmal connectivity as a potential mechanism for transport.

• Klíčová slova
• Physcomitrella, apical dominance, branching, developmental biology, gametophyte, plant biology, stem cells,
• MeSH
• biologické modely MeSH
• biologický transport účinky léků   MeSH
• cytokininy biosyntéza   MeSH
• epidermis rostlin cytologie   růst a vývoj   MeSH
• geneticky modifikované rostliny MeSH
• kyseliny indoloctové metabolismus   farmakologie   MeSH
• laktony farmakologie   MeSH
• mechy účinky léků   růst a vývoj   MeSH
• morfogeneze účinky léků   MeSH
• mutace genetika   MeSH
• regulace genové exprese u rostlin účinky léků   MeSH
• regulátory růstu rostlin farmakologie   MeSH
• rostlinné proteiny metabolismus   MeSH
• rozvržení tělního plánu účinky léků   MeSH
• výhonky rostlin účinky léků   růst a vývoj   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cytokininy MeSH
• kyseliny indoloctové MeSH
• laktony MeSH
• regulátory růstu rostlin MeSH
• rostlinné proteiny MeSH

Due to their long lifespan, trees and bushes develop higher order of branches in a perennial manner. In contrast to a tall tree, with a clearly defined main stem and branching order, a bush is shorter and has a less apparent main stem and branching pattern. To address the developmental basis of these two forms, we studied several naturally occurring architectural variants in silver birch (Betula pendula). Using a candidate gene approach, we identified a bushy kanttarelli variant with a loss-of-function mutation in the BpMAX1 gene required for strigolactone (SL) biosynthesis. While kanttarelli is shorter than the wild type (WT), it has the same number of primary branches, whereas the number of secondary branches is increased, contributing to its bush-like phenotype. To confirm that the identified mutation was responsible for the phenotype, we phenocopied kanttarelli in transgenic BpMAX1::RNAi birch lines. SL profiling confirmed that both kanttarelli and the transgenic lines produced very limited amounts of SL. Interestingly, the auxin (IAA) distribution along the main stem differed between WT and BpMAX1::RNAi. In the WT, the auxin concentration formed a gradient, being higher in the uppermost internodes and decreasing toward the basal part of the stem, whereas in the transgenic line, this gradient was not observed. Through modeling, we showed that the different IAA distribution patterns may result from the difference in the number of higher-order branches and plant height. Future studies will determine whether the IAA gradient itself regulates aspects of plant architecture.

• Klíčová slova
• Betula pendula, auxin distribution, branching modeling, strigolactones, tree architecture,
• MeSH
• bříza MeSH
• kyseliny indoloctové * MeSH
• laktony MeSH
• regulace genové exprese u rostlin MeSH
• regulátory růstu rostlin * MeSH
• stromy MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• GR24 strigolactone MeSH Prohlížeč
• kyseliny indoloctové * MeSH
• laktony MeSH
• regulátory růstu rostlin * MeSH

Shoot branching from axillary buds (AXBs) is regulated by a network of inhibitory and promotive forces, which includes hormones. In perennials, the dwarfed stature of the embryonic shoot inside AXBs is indicative of gibberellin (GA) deficiency, suggesting that AXB activation and outgrowth require GA. Nonetheless, the role of GA in branching has remained obscure. We here carried out comprehensive GA transcript and metabolite analyses in hybrid aspen, a perennial branching model. The results indicate that GA has an inhibitory as well as promotive role in branching. The latter is executed in two phases. While the expression level of GA2ox is high in quiescent AXBs, decapitation rapidly downregulated it, implying increased GA signaling. In the second phase, GA3ox2-mediated de novo GA-biosynthesis is initiated between 12 and 24 h, prior to AXB elongation. Metabolite analyzes showed that GA1/4 levels were typically high in proliferating apices and low in the developmentally inactive, quiescent AXBs, whereas the reverse was true for GA3/6. To investigate if AXBs are differently affected by GA3, GA4, and GR24, an analog of the branch-inhibitor hormone strigolactone, they were fed into AXBs of single-node cuttings. GA3 and GA4 had similar effects on GA and SL pathway genes, but crucially GA3 induced AXB abscission whereas GA4 promoted outgrowth. Both GA3 and GA4 strongly upregulated GA2ox genes, which deactivate GA1/4 but not GA3/6. Thus, the observed production of GA3/6 in quiescent AXBs targets GA1/4 for GA2ox-mediated deactivation. AXB quiescence can therefore be maintained by GA3/6, in combination with strigolactone. Our discovery of the distinct tasks of GA3 and GA4 in AXB activation might explain why the role of GA in branching has been difficult to decipher. Together, the results support a novel paradigm in which GA3/6 maintains high levels of GA2ox expression and low levels of GA4 in quiescent AXBs, whereas activation and outgrowth require increased GA1/4 signaling through the rapid reduction of GA deactivation and subsequent GA biosynthesis.

• Klíčová slova
• GA2-oxidases, GA20-oxidases, GA3-oxidases, GID1, axillary branching, gibberellin, hormones, strigolactone,
• Publikační typ
• časopisecké články MeSH

The mammary gland consists of numerous tissue compartments, including mammary epithelium, an array of stromal cells, and the extracellular matrix (ECM). Bidirectional interactions between the epithelium and its surrounding stroma are essential for proper mammary gland development and homeostasis, whereas their deregulation leads to developmental abnormalities and cancer. To study the relationships between the epithelium and the stroma, development of models that could recapitulate essential aspects of these interacting systems in vitro has become necessary. Here we describe a three-dimensional (3D) co-culture assay and show that the addition of fibroblasts to mammary organoid cultures promotes the epithelium to undergo branching morphogenesis, thus allowing the role of the stromal microenvironment to be examined in this essential developmental process.

• Klíčová slova
• 3D culture, Branching morphogenesis, Extracellular matrix, Fibroblasts, Mammary epithelium, Matrigel, Organoids, Organotypic assay, Paracrine signaling,
• MeSH
• buněčné mikroprostředí fyziologie   MeSH
• buňky stromatu cytologie   MeSH
• epitel fyziologie   MeSH
• epitelové buňky cytologie   MeSH
• extracelulární matrix fyziologie   MeSH
• fibroblasty cytologie   MeSH
• kokultivační techniky metody   MeSH
• kultivované buňky MeSH
• mléčné žlázy zvířat cytologie   MeSH
• morfogeneze fyziologie   MeSH
• myši MeSH
• signální transdukce fyziologie   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

In most temperate fruit trees, fruits are located on one-year old shoots. In Prunus species, flowers and fruits are born in axillary position along those shoots. The axillary bud fate and branching patterns are thus key components of the cultivar potential fruit production. The objective of this study was to analyze the branching and bearing behaviors of 1-year-old shoots of apricot cultivars and clones genetically closely related. Shoot structures were analyzed in terms of axillary bud fates using hidden semi-Markov chains and compared depending on the genotype, year and shoot length. The shoots were composed of three successive zones containing latent buds (basal zone), central flower buds (median zone) and vegetative buds (distal zone), respectively. The last two zones contained few associated flower buds. The zones length (in number of metamers) and occurrence strongly depended on shoot development in the two successive years. With decrease in the number of metamers per shoot, the last two zones become shorter or may not develop. While the number of metamers of the basal and distal zones and the number of associated flower buds correlated to the number of metamers of the shoot, the number of metamers of the median zone and the transition probability from the median to the distal zone were cultivar specific.

• MeSH
• biologické modely * MeSH
• genotyp MeSH
• květy fyziologie   MeSH
• Markovovy řetězce MeSH
• meruňka obecná genetika   fyziologie   MeSH
• neparametrická statistika MeSH
• ovoce fyziologie   MeSH
• výhonky rostlin fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Mammary gland is composed of branched epithelial structure embedded within a complex stroma formed by several stromal cell types, including fibroblasts, and extracellular matrix (ECM). Development of mammary gland is tightly regulated by bidirectional epithelial-stromal interactions that include paracrine signaling, ECM remodeling and mechanosensing. Importantly, these interactions play crucial role in mammary gland homeostasis and when deregulated they contribute to tumorigenesis. Therefore, understanding the mechanisms underlying epithelial-stromal interactions is critical for elucidating regulation of normal mammary gland development and homeostasis and revealing novel strategies for breast cancer therapy. To this end, several three-dimensional (3D) cell culture models have been developed to study these interactions in vitro. In this chapter, a novel 3D organoid-fibrosphere coculture model of mammary gland is described with the capacity for studying not only the qualitative and quantitative aspects of interactions between mammary fibroblasts and epithelial organoids but also their radius and directionality.

• Klíčová slova
• 3D culture, Branching morphogenesis, Collagen, Extracellular matrix, Fibroblasts, Mammary gland, Matrigel, Organoids, Paracrine signaling, Spheroid,
• MeSH
• buněčná diferenciace MeSH
• buněčné sféroidy cytologie   MeSH
• buňky stromatu cytologie   MeSH
• epitelové buňky cytologie   MeSH
• fibroblasty cytologie   MeSH
• kokultivační techniky metody   MeSH
• kultivované buňky MeSH
• mléčné žlázy zvířat cytologie   MeSH
• myši MeSH
• organoidy cytologie   MeSH
• parakrinní signalizace MeSH
• proliferace buněk MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

In order to investigate the effect of terminal chain branching in the skin permeation enhancers, seven alcohols and seven acids with the chain length of 8-12 carbons and terminal methyl or ethyl branching were prepared. Their transdermal permeation-enhancing activities were evaluated in vitro using theophylline as a model permeant and porcine skin, and compared to those of the linear standards. Terminal methyl branching increased the enhancing activity only in 12C acid, no effect was seen in the shorter ones. Terminal ethyl however produced a significant increase in activity. In the alcohols, the branching was likely to change the mode of action, due to a different relationship between the activity and the chain length.

• MeSH
• biologické modely MeSH
• kůže metabolismus   MeSH
• mastné alkoholy chemie   farmakokinetika   MeSH
• mastné kyseliny chemie   farmakokinetika   MeSH
• permeabilita MeSH
• prasata MeSH
• theofylin farmakokinetika   MeSH
• vztahy mezi strukturou a aktivitou MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• mastné alkoholy MeSH
• mastné kyseliny MeSH
• theofylin MeSH

Angiogenesis is the process of new blood vessels growing from existing vasculature. Visualizing them as a three-dimensional (3D) model is a challenging, yet relevant, task as it would be of great help to researchers, pathologists, and medical doctors. A branching analysis on the 3D model would further facilitate research and diagnostic purposes. In this paper, a pipeline of vision algorithms is elaborated to visualize and analyze blood vessels in 3D from formalin-fixed paraffin-embedded (FFPE) granulation tissue sections with two different staining methods. First, a U-net neural network is used to segment blood vessels from the tissues. Second, image registration is used to align the consecutive images. Coarse registration using an image-intensity optimization technique, followed by finetuning using a neural network based on Spatial Transformers, results in an excellent alignment of images. Lastly, the corresponding segmented masks depicting the blood vessels are aligned and interpolated using the results of the image registration, resulting in a visualized 3D model. Additionally, a skeletonization algorithm is used to analyze the branching characteristics of the 3D vascular model. In summary, computer vision and deep learning is used to reconstruct, visualize and analyze a 3D vascular model from a set of parallel tissue samples. Our technique opens innovative perspectives in the pathophysiological understanding of vascular morphogenesis under different pathophysiological conditions and its potential diagnostic role.

• Klíčová slova
• 3D visualization, angiogenesis, artificial intelligence, biobanking, digital pathology, image registration and segmentation, neural networks,
• MeSH
• algoritmy MeSH
• kardiovaskulární fyziologické jevy MeSH
• morfogeneze MeSH
• neuronové sítě * MeSH
• počítačové zpracování obrazu MeSH
• zobrazování trojrozměrné * metody   MeSH
• Publikační typ
• časopisecké články MeSH

Data-driven cell tracking and segmentation methods in biomedical imaging require diverse and information-rich training data. In cases where the number of training samples is limited, synthetic computer-generated data sets can be used to improve these methods. This requires the synthesis of cell shapes as well as corresponding microscopy images using generative models. To synthesize realistic living cell shapes, the shape representation used by the generative model should be able to accurately represent fine details and changes in topology, which are common in cells. These requirements are not met by 3D voxel masks, which are restricted in resolution, and polygon meshes, which do not easily model processes like cell growth and mitosis. In this work, we propose to represent living cell shapes as level sets of signed distance functions (SDFs) which are estimated by neural networks. We optimize a fully-connected neural network to provide an implicit representation of the SDF value at any point in a 3D+time domain, conditioned on a learned latent code that is disentangled from the rotation of the cell shape. We demonstrate the effectiveness of this approach on cells that exhibit rapid deformations (Platynereis dumerilii), cells that grow and divide (C. elegans), and cells that have growing and branching filopodial protrusions (A549 human lung carcinoma cells). A quantitative evaluation using shape features and Dice similarity coefficients of real and synthetic cell shapes shows that our model can generate topologically plausible complex cell shapes in 3D+time with high similarity to real living cell shapes. Finally, we show how microscopy images of living cells that correspond to our generated cell shapes can be synthesized using an image-to-image model.

• Klíčová slova
• Cell shape modeling, Generative model, Implicit neural representation, Neural network,
• MeSH
• Caenorhabditis elegans * MeSH
• lidé MeSH
• mitóza MeSH
• nádory plic * MeSH
• neuronové sítě MeSH
• počítačové zpracování obrazu metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

The paper deals with modeling the liver perfusion intended to improve quantitative analysis of the tissue scans provided by the contrast-enhanced computed tomography (CT). For this purpose, we developed a model of dynamic transport of the contrast fluid through the hierarchies of the perfusion trees. Conceptually, computed time-space distributions of the so-called tissue density can be compared with the measured data obtained from CT; such a modeling feedback can be used for model parameter identification. The blood flow is characterized at several scales for which different models are used. Flows in upper hierarchies represented by larger branching vessels are described using simple 1D models based on the Bernoulli equation extended by correction terms to respect the local pressure losses. To describe flows in smaller vessels and in the tissue parenchyma, we propose a 3D continuum model of porous medium defined in terms of hierarchically matched compartments characterized by hydraulic permeabilities. The 1D models corresponding to the portal and hepatic veins are coupled with the 3D model through point sources, or sinks. The contrast fluid saturation is governed by transport equations adapted for the 1D and 3D flow models. The complex perfusion model has been implemented using the finite element and finite volume methods. We report numerical examples computed for anatomically relevant geometries of the liver organ and of the principal vascular trees. The simulated tissue density corresponding to the CT examination output reflects a pathology modeled as a localized permeability deficiency.

• Klíčová slova
• Bernoulli equation, Darcy flow, Dynamic contrast-enhanced computed tomography, Liver perfusion, Porous media, Transport equation,
• MeSH
• analýza metodou konečných prvků MeSH
• biologické modely MeSH
• jaterní oběh * fyziologie   MeSH
• játra krevní zásobení   diagnostické zobrazování   MeSH
• kontrastní látky farmakokinetika   MeSH
• lidé MeSH
• matematické pojmy MeSH
• počítačová rentgenová tomografie statistika a číselné údaje   MeSH
• počítačová simulace MeSH
• poréznost MeSH
• vylepšení rentgenového snímku metody   MeSH
• zobrazování trojrozměrné statistika a číselné údaje   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• kontrastní látky MeSH