DyCeModel: a tool for 1D simulation for distribution of plant hormones controlling tissue patterning.

To study the mechanisms of growth and development, it is necessary to analyze the dynamics of the tissue patterning regulators in time and space and to take into account their effect on the cellular dynamics within a tissue. Plant hormones are the main regulators of the cell dynamics in plant tissues; they form gradients and maxima and control molecular processes in a concentration-dependent manner. Here, we present DyCeModel, a software tool implemented in MATLAB for one-dimensional simulation of tissue with a dynamic cellular ensemble, where changes in hormone (or other active substance) concentration in the cells are described by ordinary differential equations (ODEs). We applied DyCeModel to simulate cell dynamics in plant meristems with different cellular structures and demonstrated that DyCeModel helps to identify the relationships between hormone concentration and cellular behaviors. The tool visualizes the simulation progress and presents a video obtained during the calculation. Importantly, the tool is capable of automatically adjusting the parameters by fitting the distribution of the substance concentrations predicted in the model to experimental data taken from the microscopic images. Noteworthy, DyCeModel makes it possible to build models for distinct types of plant meristems with the same ODEs, recruiting specific input characteristics for each meristem. We demonstrate the tool's efficiency by simulation of the effect of auxin and cytokinin distributions on tissue patterning in two types of Arabidopsis thaliana stem cell niches: the root and shoot apical meristems. The resulting models represent a promising framework for further study of the role of hormone-controlled gene regulatory networks in cell dynamics.

PlantLayout pipeline to model tissue patterning.

To study the mechanisms underlying developmental pattern formation in a tissue, one needs to analyze the dynamics of the regulators in time and space across the tissue of a specific architecture. This problem is essential for the developmental regulators (morphogens) that distribute over the tissues anisotropically, forming there maxima and gradients and guiding cellular processes in a dose-dependent manner. Here we present the PlantLayout pipeline for MATLAB software, which facilitates the computational studies of tissue patterning. With its help, one can build a structural model of a two-dimensional tissue, embed it into a mathematical model in ODEs, perform numerical simulations, and visualize the obtained results - everything on the same platform. As a result, one can study the concentration dynamics of developmental regulators over the cell layout reconstructed from the real tissue. PlantLayout allows studying the dynamics and the output of gene networks guided by the developmental regulator in specific cells. The gene networks could be different for different cell types. One of the obstacles that PlantLayout removes semi-automatically is the determination of the cell wall orientation which is relevant when cells in the tissue have a polarity. Additionally, PlantLayout allows automatically extracting other quantitative and qualitative features of the cells and the cell walls, which might help in the modeling of a developmental pattern, such as the length and the width of the cell walls, the set of the neighboring cells, cell volume and cell perimeter. We demonstrate PlantLayout performance on the model of phytohormone auxin distribution over the plant root tip.

Auxin regulates functional gene groups in a fold-change-specific manner in Arabidopsis thaliana roots.

Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a diverse variety of processes such as cell wall biogenesis, transition through the cell cycle, or metabolism of a wide range of chemical substances. The coordination principles for such a complex orchestration are poorly understood at the systems level. Here, we perform an RNA-seq experiment to study the transcriptional response to auxin treatment  within gene groups of different biological processes, molecular functions, or cell components in a quantitative fold-change-specific manner. We find for Arabidopsis thaliana roots treated with auxin for 6 h that (i) there are functional groups within which genes respond to auxin with a surprisingly similar fold changes and that (ii) these fold changes vary from one group to another. These findings make it tempting to conjecture the existence of some transcriptional logic orchestrating the coordinated expression of genes within functional groups in a fold-change-specific manner. To obtain some initial insight about this coordinated expression, we performed a motif enrichment analysis and found cis-regulatory elements TBX1-3, SBX, REG, and TCP/site2 as the candidates conferring fold-change-specific responses to auxin in Arabidopsis thaliana.

A detailed expression map of the PIN1 auxin transporter in Arabidopsis thaliana root.

BACKGROUND: Theauxin efflux carrier PIN1 is a key mediator of polar auxin transport in developing plant tissues. This is why factors that are supposed to be involved in auxin distribution are frequently tested in the regulation of PIN1 expression. As a result, diverse aspects of PIN1 expression are dispersed across dozens of papers entirely devoted to other specific topics related to the auxin pathway. Integration of these puzzle pieces about PIN1 expression revealed that, along with a recurring pattern, some features of PIN1 expression varied from article to article. To determine if this uncertainty is related to the specific foci of articles or has a basis in the variability of PIN1 gene activity, we performed a comprehensive 3D analysis of PIN1 expression patterns in Arabidopsis thaliana roots. RESULTS: We provide here a detailed map of PIN1 expression in the primary root, in the lateral root primordia and at the root-shoot junction. The variability in PIN1 expression pattern observed in individual roots may occur due to differences in auxin distribution between plants. To simulate this effect, we analysed PIN1 expression in the roots from wild type seedlings treated with different IAA concentrations and pin mutants. Most changes in PIN1 expression after exogenous IAA treatment and in pin mutants were also recorded in wild type but with lower frequency and intensity. Comparative studies of exogenous auxin effects on PIN1pro:GUS and PIN1pro:PIN1-GFP plants indicated that a positive auxin effect is explicit at the level of PIN1 promoter activity, whereas the inhibitory effect relates to post-transcriptional regulation. CONCLUSIONS: Our results suggest that the PIN1 expression pattern in the root meristem accurately reflects changes in auxin content. This explains the variability of PIN1 expression in the individual roots and makes PIN1 a good marker for studying root meristem activity.

Combined in silico/in vivo analysis of mechanisms providing for root apical meristem self-organization and maintenance.

BACKGROUND AND AIMS: The root apical meristem (RAM) is the plant stem cell niche which provides for the formation and continuous development of the root. Auxin is the main regulator of RAM functioning, and auxin maxima coincide with the sites of RAM initiation and maintenance. Auxin gradients are formed due to local auxin biosynthesis and polar auxin transport. The PIN family of auxin transporters plays a critical role in polar auxin transport, and two mechanisms of auxin maximum formation in the RAM based on PIN-mediated auxin transport have been proposed to date: the reverse fountain and the reflected flow mechanisms. METHODS: The two mechanisms are combined here in in silico studies of auxin distribution in intact roots and roots cut into two pieces in the proximal meristem region. In parallel, corresponding experiments were performed in vivo using DR5::GFP Arabidopsis plants. KEY RESULTS: The reverse fountain and the reflected flow mechanism naturally cooperate for RAM patterning and maintenance in intact root. Regeneration of the RAM in decapitated roots is provided by the reflected flow mechanism. In the excised root tips local auxin biosynthesis either alone or in cooperation with the reverse fountain enables RAM maintenance. CONCLUSIONS: The efficiency of a dual-mechanism model in guiding biological experiments on RAM regeneration and maintenance is demonstrated. The model also allows estimation of the concentrations of auxin and PINs in root cells during development and under various treatments. The dual-mechanism model proposed here can be a powerful tool for the study of several different aspects of auxin function in root.

[Genetics of plant development: integrating data from different observations and experiments in databases].

Genetics of plant development as a scientific discipline integrates experimental evidence from such different fields of biology as embryology, plant anatomy, molecular biology, and genetics, and studies their relationships with ontogeny. To date, traditional publication of scientific studies in form of articles is supplemented by presenting the results of extensive genome-scale experiments in genomics, transcriptomics, proteomics, and phenomics in databases. The information burst, cased both by genome-scale studies and growth in the number of publications, requires the development of general standards of annotating data from different sources for their integration and comparison. In this review, we present classification and analysis of existing databases, in which the user can find various kinds of information essential for studying developmental genetics of plants, and discuss problems of data integration both within the informational resources and among them.

[Mathematical model of auxin distribution in the plant root].

Regulation of plant growth and development by auxin is mediated by the hormone controlled distribution and dose-dependent mechanisms of its action. A mathematical model is proposed, which described the distribution of auxin in the cells extending along the central axis of the Arabidopsis thaliana root. This model reproduces qualitatively both auxin distribution in cells of the root central axis under the normal conditions and under the conditions of decreased active transport and the recovery of auxin distribution and related meristem restoration during root regeneration after ablation of its tip. Different types of distribution of the auxin concentration over the vertical root axis are described, possible variants of root growth and lateral roots formation are proposed, and biological interpretation is given to different regimes of model behavior.

[The use of modified polystyrene plates in solid-phase immunoenzyme analysis for the diagnosis of infections]. / Ispol'zovanie modifitsirovannykh polistirolovykh planshetov v tverdofaznom immunofermentnom analize dlia diagnostiki nekotorykh infektsii.

The practical aspects of the theory of the adsorption of bioligands on the plastic surface have been considered and discussed. The possibility of standardizing polystyrene plates, as well as obtaining plates with the predetermined level of adsorption activity with respect to given antigens (antibodies), has been shown with the use of the patented technology for the modification of polystyrene plates. The data on the adsorption of antigens used as an experimental model (human and rabbit immunoglobulin fractions) are presented, and an increase in adsorption activity has been shown with the use of modified plates. For practical confirmation, some examples of using these plates in actual assay systems intended for the evaluation of HBsAg carriership and antibodies to HIV are given. A considerable increase (2- to 10-fold) of the signal from positive samples has been shown to occur, the signal from negative samples remaining practically unchanged.

[The use of the method of the complete advisability function for evaluating the quality and standardization of the plates in solid-phase EIA]. / Ispol'zovanie metoda polnoi funktsii zhelatel'nosti dlia otsenki kachestva i standartizatsii planshetov v tverdofaznon IFA.

An attempt to use the method of the complete advisability function for the evaluation of the quality of plates and their standardization in the enzyme-linked immunosorbent assay (ELISA) has been made. Correlations have been empirically established, thus making it possible to calculate the optimum proportions of different ELISA factors: the dose of the antigen (antibody) and the time of sorption, which ensures the best ELISA results with a given type of plates.

[A biopsy forceps with a needle for a flexible endoscope]. / Shchiptsy biopsiinye s igloi k gibkim éndoskopam.

Biopsy forceps with a suture needle were developed. They will enable to increase considerably the efficacy and accuracy of diagnostic procedures in early cancer and precancerous conditions, and the differentiation of malignant and benign affections of internal organs as well.