Families of the Alternative State — Transitions Actions Networks: Procedures and Algorithms

Author(s):  
A. S. Geyda

Исследуются системы, функционирующие таким образом, что в различных условиях это функционирование может быть представлено альтернативными сетями операций. Сети альтернируются в зависимости от условий функционирования. С использованием таких сетей исследуется новый вид свойств систем.

2019 ◽  
Vol 476 (20) ◽  
pp. 2981-3018 ◽  
Author(s):  
Petar H. Lambrev ◽  
Parveen Akhtar

Abstract The light reactions of photosynthesis are hosted and regulated by the chloroplast thylakoid membrane (TM) — the central structural component of the photosynthetic apparatus of plants and algae. The two-dimensional and three-dimensional arrangement of the lipid–protein assemblies, aka macroorganisation, and its dynamic responses to the fluctuating physiological environment, aka flexibility, are the subject of this review. An emphasis is given on the information obtainable by spectroscopic approaches, especially circular dichroism (CD). We briefly summarise the current knowledge of the composition and three-dimensional architecture of the granal TMs in plants and the supramolecular organisation of Photosystem II and light-harvesting complex II therein. We next acquaint the non-specialist reader with the fundamentals of CD spectroscopy, recent advances such as anisotropic CD, and applications for studying the structure and macroorganisation of photosynthetic complexes and membranes. Special attention is given to the structural and functional flexibility of light-harvesting complex II in vitro as revealed by CD and fluorescence spectroscopy. We give an account of the dynamic changes in membrane macroorganisation associated with the light-adaptation of the photosynthetic apparatus and the regulation of the excitation energy flow by state transitions and non-photochemical quenching.


2005 ◽  
Vol 432 (1) ◽  
pp. 181-187 ◽  
Author(s):  
E. Meyer-Hofmeister ◽  
B. F. Liu ◽  
F. Meyer

2020 ◽  
Vol 105 (3) ◽  
pp. 323-376
Author(s):  
Li-E Yang ◽  
Lu Lu ◽  
Kevin S. Burgess ◽  
Hong Wang ◽  
De-Zhu Li

Lamiids, a clade composed of approximately 15% of all flowering plants, contains more than 50,000 species dispersed across 49 families and eight orders (APG IV, 2016). This paper is the eighth in a series that analyzes pollen characters across angiosperms. We reconstructed a maximum likelihood tree based on the most recent phylogenetic studies for the Lamiids, comprising 150 terminal genera (including six outgroups) and covering all eight orders and 49 families within the clade. To illustrate pollen diversity across the Lamiids, pollen grains from 22 species (22 genera in 14 families) were imaged under light, scanning, and transmission electron microscopy. Eighteen pollen characters that were documented from previous publications, websites, and our new observations were coded and optimized onto the reconstructed phylogenetic tree using Fitch parsimony, maximum likelihood, and hierarchical Bayesian analysis. Pollen morphology of the Lamiids is highly diverse, particularly in shape class, pollen size, aperture number, endoaperture shape, supratectal element shape, and tectum sculpture. In addition, some genera show relatively high infrageneric pollen variation within the Lamiids: i.e., Coffea L., Jacquemontia Choisy, Justicia L., Pedicularis L., Psychotria L. nom. cons., Sesamum L., Stachytarpheta Vahl, and Veronica L. The plesiomorphic states for 16 pollen characters were inferred unambiguously, and 10 of them displayed consistent plesiomorphic states under all optimization methods. Seventy-one lineages at or above the family level are characterized by pollen character state transitions. We identified diagnostic character states for monophyletic clades and explored palynological evidence to shed light on unresolved relationships. For example, palynological evidence supports the monophyly of Garryales and Metteniusaceae, and sister relationships between Icacinaceae and Oncothecaceae, as well as between Vahliales and Solanales. The evolutionary patterns of pollen morphology found in this study reconfirm several previously postulated evolutionary trends, which include an increase in aperture number, a transition from equatorially arranged apertures to globally distributed ones, and an increase in exine ornamentation complexity. Furthermore, there is a significant correlation between pollen characters and a number of ecological factors, e.g., pollen size and pollination type, pollen ornamentation and pollination type, and shape class and plant growth form. Our results provide insight into the ecological, environmental, and evolutionary mechanisms driving pollen character state changes in the Lamiids.


Author(s):  
Catherine E. De Vries

This chapter introduces a benchmark theory of public opinion towards European integration. Rather than relying on generic labels like support or scepticism, the chapter suggests that public opinion towards the EU is both multidimensional and multilevel in nature. People’s attitudes towards Europe are essentially based on a comparison between the benefits of the status quo of membership and those associated with an alternative state, namely one’s country being outside the EU. This comparison is coined the ‘EU differential’. When comparing these benefits, people rely on both their evaluations of the outcomes (policy evaluations) and the system that produces them (regime evaluations). This chapter presents a fine-grained conceptualization of what it means to be an EU supporter or Eurosceptic; it also designs a careful empirical measurement strategy to capture variation, both cross-nationally and over time. The chapter cross-validates these measures against a variety of existing and newly developed data sources.


Nature Plants ◽  
2021 ◽  
Author(s):  
Xiaowei Pan ◽  
Ryutaro Tokutsu ◽  
Anjie Li ◽  
Kenji Takizawa ◽  
Chihong Song ◽  
...  

2021 ◽  
Author(s):  
Keiko U Torii

Abstract Background Stomata are adjustable pores on the surface of plant shoots for efficient gas exchange and water control. The presence of stomata is essential for plant growth and survival, and the evolution of stomata is considered as a key developmental innovation of the land plants, allowing colonization on land from aquatic environments some 450 million years ago. In the past two decades, molecular genetic studies using the model plant Arabidopsis thaliana identified key genes and signalling modules that regulate stomatal development: master-regulatory transcription factors that orchestrate cell-state transitions and peptide-receptor signal transduction pathways, which, together, enforce proper patterning of stomata within the epidermis. Studies in diverse plant species, ranging from bryophytes to angiosperm grasses, have begun to unravel the conservation and uniqueness of the core modules in stomatal development. Scope Here, I review the mechanisms of stomatal development in the context of epidermal tissue patterning. First, I introduce the core regulatory mechanisms of stomatal patterning and differentiation in the model species Arabidopsis thaliana. Subsequently, experimental evidence is presented supporting the idea that different cell types within the leaf epidermis, namely stomata, hydathodes pores, pavement cells, and trichomes, either share developmental origins or mutually influence each other’s gene regulatory circuits during development. Emphasis is taken on extrinsic and intrinsic signals regulating the balance between stomata and pavement cells, specifically by controlling the fate of Stomatal-Lineage Ground Cells (SLGCs) to remain within the stomatal-cell lineage or differentiate into pavement cells. Finally, I discuss the influence of inter-tissue-layer communication between the epidermis and underlying mesophyll/vascular tissues on stomatal differentiation. Understanding the dynamic behaviors of stomatal precursor cells and their differentiation in the broader context of tissue and organ development may help design plants tailored for optimal growth and productivity in specific agricultural applications and a changing environment.


Author(s):  
Kevin Y. Huang ◽  
Enrico Petretto

Single-cell transcriptomics analyses of the fibrotic lung uncovered two cell states critical to lung injury recovery in the alveolar epithelium- a reparative transitional cell state in the mouse and a disease-specific cell state (KRT5-/KRT17+) in human idiopathic pulmonary fibrosis (IPF). The murine transitional cell state lies between the differentiation from type 2 (AT2) to type 1 pneumocyte (AT1), and the human KRT5-/KRT17+ cell state may arise from the dysregulation of this differentiation process. We review major findings of single-cell transcriptomics analyses of the fibrotic lung and re-analyzed data from 7 single-cell RNA sequencing studies of human and murine models of IPF, focusing on the alveolar epithelium. Our comparative and cross-species single-cell transcriptomics analyses allowed us to further delineate the differentiation trajectories from AT2 to AT1 and AT2 to the KRT5-/KRT17+ cell state. We observed AT1 cells in human IPF retain the transcriptional signature of the murine transitional cell state. Using pseudotime analysis, we recapitulated the differentiation trajectories from AT2 to AT1 and from AT2 to KRT5-/KRT17+ cell state in multiple human IPF studies. We further delineated transcriptional programs underlying cell state transitions and determined the molecular phenotypes at terminal differentiation. We hypothesize that in addition to the reactivation of developmental programs (SOX4, SOX9), senescence (TP63, SOX4) and the Notch pathway (HES1) are predicted to steer intermediate progenitors to the KRT5-/KRT17+ cell state. Our analyses suggest that activation of SMAD3 later in the differentiation process may explain the fibrotic molecular phenotype typical of KRT5-/KRT17+ cells.


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