Thraustochytrids: Evolution, Ultrastructure, Biotechnology, and Modeling.

The thraustochytrids are a group of marine protists known for their significant ecological roles as decomposers and parasites as well as for their potential biotechnological applications, yet their evolutionary and structural diversity remains poorly understood. Our review critically examines the phylogeny of this taxa, utilizing available up-to-date knowledge and their taxonomic classifications. Additionally, advanced imaging techniques, including electron microscopy, are employed to explore the ultrastructural characteristics of these organisms, revealing key features that contribute to their adaptive capabilities in varying marine environments.

Image-Based Quantitative Analysis of Epidermal Morphology in Wild Potato Leaves.

The epidermal leaf patterns of plants exhibit remarkable diversity in cell shapes, sizes, and arrangements, driven by environmental interactions that lead to significant adaptive changes even among closely related species. The Solanaceae family, known for its high diversity of adaptive epidermal structures, has traditionally been studied using qualitative phenotypic descriptions. To advance this, we developed a workflow combining multi-scale computer vision, image processing, and data analysis to extract digital descriptors for leaf epidermal cell morphology.

Catching the Big Fish in Big Data: A Meta-Analysis of Zebrafish Kidney scRNA-Seq Datasets Highlights Conserved Molecular Profiles of Macrophages and Neutrophils in Vertebrates.

The innate immune system (IIS) is an ancient and essential defense mechanism that protects animals against a wide range of pathogens and diseases. Although extensively studied in mammals, our understanding of the IIS in other taxa remains limited. The zebrafish () serves as a promising model organism for investigating IIS-related processes, yet the immunogenetics of fish are not fully elucidated.

Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of .

The innate immune system is the first line of defense in multicellular organisms. is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among . We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other from the GEO NCBI and the Single-Cell Expression Atlas.

Long-term cold, freezing and drought: overlapping and specific regulatory mechanisms and signal transduction in tea plant ( (L.) Kuntze).

Introduction: Low temperatures and drought are two main environmental constraints reducing the yield and geographical distribution of horticultural crops worldwide. Understanding the genetic crosstalk between stress responses has potential importance for crop improvement.

Methods: In this study, Illumina RNA-seq and Pac-Bio genome resequencing were used to annotate genes and analyze transcriptome dynamics in tea plants under long-term cold, freezing, and drought.

Particle-Based Imaging Tools Revealing Water Flows in Maize Nodal Vascular Plexus.

In plants, water flows are the major driving force behind growth and play a crucial role in the life cycle. To study hydrodynamics, methods based on tracking small particles inside water flows attend a special place. Thanks to these tools, it is possible to obtain information about the dynamics of the spatial distribution of the flux characteristics.

Transcriptomic Data Meta-Analysis Sheds Light on High Light Response in L.

The availability and intensity of sunlight are among the major factors of growth, development and metabolism in plants. However, excessive illumination disrupts the electronic balance of photosystems and leads to the accumulation of reactive oxygen species in chloroplasts, further mediating several regulatory mechanisms at the subcellular, genetic, and molecular levels. We carried out a comprehensive bioinformatic analysis that aimed to identify genetic systems and candidate transcription factors involved in the response to high light stress in L.

Isolation and transcriptome analysis of a biotechnologically promising Black Sea protist, .

Background: Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology.

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis.

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation.

Comparative transcriptome profiling of a resistant vs susceptible bread wheat ( L.) cultivar in response to water deficit and cold stress.

Bread wheat ( L.) is one of the most important agricultural plants wearing abiotic stresses, such as water deficit and cold, that cause its productivity reduction. Since resistance to abiotic factors is a multigenic trait, therefore modern genome-wide approaches can help to involve various genetic material in breeding.

Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [ (L.) Kuntze].

Cold and drought are two of the most severe threats affecting the growth and productivity of the tea plant, limiting its global spread. Both stresses cause osmotic changes in the cells of the tea plant by decreasing their water potential. To develop cultivars that are tolerant to both stresses, it is essential to understand the genetic responses of tea plant to these two stresses, particularly in terms of the genes involved.

Subcellular compartmentalization of the plant antioxidant system: an integrated overview.

The antioxidant system (AOS) maintains the optimal concentration of reactive oxygen species (ROS) in a cell and protects it against oxidative stress. In plants, the AOS consists of seven main classes of antioxidant enzymes, low-molecular antioxidants (e.g.

Stress-induced changes in the expression of antioxidant system genes for rice ( L.) and bread wheat ( L.).

Background: Plant cell metabolism inevitably forms reactive oxygen species (ROS), which can damage cells or lead to their death. The antioxidant system (AOS) evolved to eliminate a high concentration of ROS. For plants, this system consists of the seven classes of antioxidant enzymes and antioxidant compounds.

LSM-W: laser scanning microscopy worker for wheat leaf surface morphology.

Background: Microscopic images are widely used in plant biology as an essential source of information on morphometric characteristics of the cells and the topological characteristics of cellular tissue pattern due to modern computer vision algorithms. High-resolution 3D confocal images allow extracting quantitative characteristics describing the cell structure of leaf epidermis. For some issues in the study of cereal leaves development, it is required to apply the staining techniques with fluorescent dyes and to scan rather large fragments consisting of several frames.

The evolution of gene regulatory networks controlling Arabidopsis thaliana L. trichome development.

Background: The variation in structure and function of gene regulatory networks (GRNs) participating in organisms development is a key for understanding species-specific evolutionary strategies. Even the tiniest modification of developmental GRN might result in a substantial change of a complex morphogenetic pattern. Great variety of trichomes and their accessibility makes them a useful model for studying the molecular processes of cell fate determination, cell cycle control and cellular morphogenesis.

Quantitative characteristics of pubescence in wheat (Triticum aestivum L.) are associated with photosynthetic parameters under conditions of normal and limited water supply.

Density and length of leaf pubescence are important factors of diversity in the response to water deficiency among wheat genotypes. Many studies evidence an important protective value of leaf hairiness in plants, especially under the conditions of drought, thermal loads and increased solar radiation. However, the physiological and adaptive roles of such traits in cereals, including cultivated plants, have not been sufficiently studied to date.

Identification of nuclear genes controlling chlorophyll synthesis in barley by RNA-seq.

Background: Albinism in plants is characterized by lack of chlorophyll and results in photosynthesis impairment, abnormal plant development and premature death. These abnormalities are frequently encountered in interspecific crosses and tissue culture experiments. Analysis of albino mutant phenotypes with full or partial chlorophyll deficiency can shed light on genetic determinants and molecular mechanisms of albinism.

Regions of the bread wheat D genome associated with variation in key photosynthesis traits and shoot biomass under both well watered and water deficient conditions.

A quantitative trait locus (QTL) approach was taken to reveal the genetic basis in wheat of traits associated with photosynthesis during a period of exposure to water deficit stress. The performance, with respect to shoot biomass, gas exchange and chlorophyll fluorescence, leaf pigment content and the activity of various ascorbate-glutathione cycle enzymes and catalase, of a set of 80 wheat lines, each containing a single chromosomal segment introgressed from the bread wheat D genome progenitor Aegilops tauschii, was monitored in plants exposed to various water regimes. Four of the seven D genome chromosomes (1D, 2D, 5D, and 7D) carried clusters of both major (LOD >3.

Extraction of quantitative characteristics describing wheat leaf pubescence with a novel image-processing technique.

Leaf pubescence (hairiness) in wheat plays an important biological role in adaptation to the environment. However, this trait has always been methodologically difficult to phenotype. An important step forward has been taken with the use of computer technologies.