branching modeling
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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.
- 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
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.
The goal of the study was to design a model of cardiac ventricles with realistic geometry that enables simulation of the ventricular activation with normal conduction system functions, as well as with bundle branch blocks. In ventricles, electrical activation propagates from the His bundle to the left and right bundle branches and continues to the fascicles and branching fibers of the Purkinje system. The role of these parts of the conduction system is to lead the activation rapidly and synchronously to the left and right ventricle. The velocity of propagation in the conduction system is several times higher than in the surrounding ventricular myocardium. If the conduction system works normally, QRS duration representing the total activation time of the ventricles lies in the physiological range of about 80 to 120 ms but it is more than 120 ms in the case of bundle branch blocks. In our study, the realistic geometry of the ventricles was constructed on the base of a patient CT scan, defining epicardial and endocardial surfaces. The first part of the conduction system (fast-conducting bundle branches, fascicles in the left ventricle and initial parts of the Purkinje fibers) was modeled as polyline pathways isolated from the surrounding ventricular tissue. The remaining part of the Purkinje system was modeled as an endocardial layer with higher conduction velocity. The propagation of the electrical activation in the ventricular model was modeled using reaction-diffusion (RD) equations, except for the first part of the conduction system, where the activation times were evaluated algebraically with respect to predefined velocity of propagation and estimated distance between the His bundle and particular entry point to the layer with higher conduction velocity. Propagation of activation in cardiac ventricles was numerically solved in Comsol Multiphysics environment. Several configurations of the first part of the conduction system with different number of polyline pathways and entry points were proposed and tested to achieve realistic activation propagation. For the model with 9 starting points, realistic total activation time (TAT) of the whole ventricles of about 108 ms was obtained for the model with normal conduction system, and realistic TAT of 126 ms and 149 ms were obtained for the right and left bundle branch block (RBBB, LBBB), respectively. Very similar TAT was found also for the model with 7 starting points, but unrealistically long TAT was obtained in LBBB simulation for the model with only 5 starting points.
- MeSH
- anatomické modely MeSH
- biomedicínské technologie metody MeSH
- biomedicínský výzkum přístrojové vybavení trendy MeSH
- blokáda Tawarova raménka * diagnostické zobrazování patofyziologie MeSH
- lidé MeSH
- modely kardiovaskulární MeSH
- počítačová simulace klasifikace MeSH
- srdeční komory anatomie a histologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
In order to investigate the effect of branching and cyclization in the hydrophobic part of skin permeation enhancers, 17 novel branched-chain and cyclic 6-aminohexanoic acid esters were prepared. Their permeation enhancing activity was evaluated in vitro using human skin and theophylline as a model drug, and compared to that of the corresponding linear-chain analogues. The results showed that chain branching and cyclization has a negative influence on the enhancing activity of 6-aminohexanoates. For example, the enhancement ratios (ERs) of dodecan-1-yl, dodecan-2-yl, dodecan-4-yl, and cyclododecyl ester were 39.7, 29.3, 3.1, and 2.2, respectively. No significant change in the optimum length of the chain was observed. Dodecan-2-yl 6-aminohexanoate, the most active branched derivative, still maintains a remarkable enhancing activity (ER 29.3). Presumably, the relatively small degree of branching of these molecules does not prevent them from interacting with the lipid components of the stratum corneum. However, a higher degree of branching, cyclization of the chain, and presence of an aromatic ring resulted in a loss of activity. (c) 2005 Wiley-Liss, Inc.
- MeSH
- alkoholy chemie MeSH
- aminokapronáty MeSH
- estery farmakologie chemie MeSH
- financování vládou MeSH
- kožní absorpce účinky léků MeSH
- kyselina 6-aminokapronová farmakologie chemie MeSH
- lidé MeSH
- magnetická rezonanční spektroskopie MeSH
- techniky in vitro MeSH
- vysokoúčinná kapalinová chromatografie MeSH
- vztahy mezi strukturou a aktivitou MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
Maternal diabetes is associated with changes of the placental structure. These changes include great variability of vascularity manifested by strikingly hypovascular as well as hypervascular terminal villi. In this paper, normal placental terminal villi and pathological villi of type 1 diabetic placentas were compared concerning the structure of villous stroma, spatial arrangement of villous capillary bed and quantitative assessment of capillary branching pattern. Formalin fixed and paraffin embedded specimens of 14 normal and 17 Type 1 diabetic term placentas were used for picrosirius staining, vimentin and desmin immunohistochemistry and confocal microscopy. 3D models of villi and villous capillaries were constructed from stacks of confocal optical sections. Hypervascular as well as hypovascular villi of diabetic placenta displayed changed structure of villous stroma, i.e. the collagen envelope around capillaries looked thinner and the network of collagen fibers seemed less dense. The desmin immunocytochemistry has shown that stromal cells of hypervascular as well as hypovascular villi appeared nearly or completely void of desmin filaments. In comparison with normal villi, capillaries of hypovascular villi had a smaller diameter and displayed a markedly wavy course whereas in hypervascular villi numerous capillaries occurred in reduced stroma and often had a large diameter. The quantitative assessment of capillary branching has shown that villous capillaries are more branched in diabetic placentas. It is concluded that type 1 maternal diabetes enhances the surface area of the capillary wall by elongation, enlargement of diameter and higher branching of villous capillaries and disrupts the stromal structure of terminal villi.
- MeSH
- diabetes mellitus 1. typu patologie MeSH
- dospělí MeSH
- kapiláry patologie MeSH
- konfokální mikroskopie MeSH
- lidé MeSH
- mladý dospělý MeSH
- novorozenec MeSH
- placenta krevní zásobení patologie MeSH
- studie případů a kontrol MeSH
- těhotenství při diabetu patologie MeSH
- těhotenství MeSH
- zobrazování trojrozměrné MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- novorozenec MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Amoebae play an important ecological role as predators in microbial communities. They also serve as niche for bacterial replication, harbor endosymbiotic bacteria and have contributed to the evolution of major human pathogens. Despite their high diversity, marine amoebae and their association with bacteria are poorly understood. Here we describe the isolation and characterization of two novel marine amoebae together with their bacterial endosymbionts, tentatively named 'Candidatus Occultobacter vannellae' and 'Candidatus Nucleophilum amoebae'. While one amoeba strain is related to Vannella, a genus common in marine habitats, the other represents a novel lineage in the Amoebozoa. The endosymbionts showed only low similarity to known bacteria (85-88% 16S rRNA sequence similarity) but together with other uncultured marine bacteria form a sister clade to the Coxiellaceae. Using fluorescence in situ hybridization and transmission electron microscopy, identity and intracellular location of both symbionts were confirmed; one was replicating in host-derived vacuoles, whereas the other was located in the perinuclear space of its amoeba host. This study sheds for the first time light on a so far neglected group of protists and their bacterial symbionts. The newly isolated strains represent easily maintainable model systems and pave the way for further studies on marine associations between amoebae and bacterial symbionts.
- MeSH
- Amoeba klasifikace mikrobiologie MeSH
- buněčné jádro mikrobiologie MeSH
- cytoplazma mikrobiologie MeSH
- druhová specificita MeSH
- Gammaproteobacteria klasifikace izolace a purifikace fyziologie MeSH
- symbióza fyziologie MeSH
- vodní organismy klasifikace izolace a purifikace mikrobiologie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem 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.
- 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.
- 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
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.
