Global nuclear reorganization during heterochromatin replication in the giant-genome plant Nigella damascena L.

Among flowering plants, genome size varies remarkably, by >2200-fold, and this variation depends on the loss and gain of noncoding DNA sequences that form distinct heterochromatin complexes during interphase. In plants with giant genomes, most chromatin remains condensed during interphase, forming a dense network of heterochromatin threads called interphase chromonemata. Using super-resolution light and electron microscopy, we studied the ultrastructure of chromonemata during and after replication in root meristem nuclei of Nigella damascena L.

Towards the synthesis of spectral imaging and machine learning-based approaches for non-invasive phenotyping of plants.

High-throughput phenotyping is now central to the progress of plant sciences, accelerated breeding, and precision farming. The power of phenotyping comes from the automated, rapid, non-invasive collection of large datasets describing plant objects. In this context, the goal of extracting relevant information from different kinds of images is of paramount importance.

Influence of Nanoparticles and Metal Vapors on the Color of Laboratory and Atmospheric Discharges.

Currently, electrical discharges occurring at altitudes of tens to hundreds of kilometers from the Earth's surface attract considerable attention from researchers from all over the world. A significant number of (nano)particles coming from outer space burn up at these altitudes. As a result, vapors of various substances, including metals, are formed at different altitudes.

Modulation of behavioral and neurochemical responses of adult zebrafish by fluoxetine, eicosapentaenoic acid and lipopolysaccharide in the prolonged chronic unpredictable stress model.

Long-term recurrent stress is a common cause of neuropsychiatric disorders. Animal models are widely used to study the pathogenesis of stress-related psychiatric disorders. The zebrafish (Danio rerio) is emerging as a powerful tool to study chronic stress and its mechanisms.

Live-Cell Imaging and Analysis of Nuclear Body Mobility.

The cell nucleus contains different domains and nuclear bodies, whose position relative to each other inside the nucleus can vary depending on the physiological state of the cell. Changes in the three-dimensional organization are associated with the mobility of individual components of the nucleus. In this chapter, we present a protocol for live-cell imaging and analysis of nuclear body mobility.

The GAR domain integrates functions that are necessary for the proper localization of fibrillarin (FBL) inside eukaryotic cells.

Fibrillarin (FBL) is an essential nucleolar protein that participates in pre-rRNA methylation and processing. The methyltransferase domain of FBL is an example of an extremely well-conserved protein domain in which the amino acid sequence was not substantially modified during the evolution from to . An additional N-terminal glycine-arginine-rich (GAR) domain is present in the FBL of eukaryotes.

ANHIR: Automatic Non-Rigid Histological Image Registration Challenge.

Automatic Non-rigid Histological Image Registration (ANHIR) challenge was organized to compare the performance of image registration algorithms on several kinds of microscopy histology images in a fair and independent manner. We have assembled 8 datasets, containing 355 images with 18 different stains, resulting in 481 image pairs to be registered. Registration accuracy was evaluated using manually placed landmarks.

Complete Genome Sequence of " Syntrophocurvum alkaliphilum" Strain B(2M), Obtained from the Metagenome of a Salt-Tolerant Alkaliphilic Anaerobic Syntrophic Butyrate-Degrading Consortium.

A highly salt-tolerant and alkaliphilic syntrophic consortium that degrades butyrate under sulfate-reducing conditions was purified from a hypersaline soda lake in southwest Siberia. Here, we present the complete genome sequence of the syntrophic primary butyrate degrader in order to understand the molecular mechanisms of interaction between consortium members.

3-D Quantification of Filopodia in Motile Cancer Cells.

We present a 3D bioimage analysis workflow to quantitatively analyze single, actin-stained cells with filopodial protrusions of diverse structural and temporal attributes, such as number, length, thickness, level of branching, and lifetime, in time-lapse confocal microscopy image data. Our workflow makes use of convolutional neural networks trained using real as well as synthetic image data, to segment the cell volumes with highly heterogeneous fluorescence intensity levels and to detect individual filopodial protrusions, followed by a constrained nearest-neighbor tracking algorithm to obtain valuable information about the spatio-temporal evolution of individual filopodia. We validated the workflow using real and synthetic 3-D time-lapse sequences of lung adenocarcinoma cells of three morphologically distinct filopodial phenotypes and show that it achieves reliable segmentation and tracking performance, providing a robust, reproducible and less time-consuming alternative to manual analysis of the 3D+t image data.

Heterochromatin restricts the mobility of nuclear bodies.

Nuclear bodies are relatively immobile organelles. Here, we investigated the mechanisms underlying their movement using experimentally induced interphase prenucleolar bodies (iPNBs). Most iPNBs demonstrated constrained diffusion, exhibiting infrequent fusions with other iPNBs and nucleoli.

FiloGen: A Model-Based Generator of Synthetic 3-D Time-Lapse Sequences of Single Motile Cells With Growing and Branching Filopodia.

The existence of diverse image datasets accompanied by reference annotations is a crucial prerequisite for an objective benchmarking of bioimage analysis methods. Nevertheless, such a prerequisite is hard to satisfy for time lapse, multidimensional fluorescence microscopy image data, manual annotations of which are laborious and often impracticable. In this paper, we present a simulation system capable of generating 3-D time-lapse sequences of single motile cells with filopodial protrusions of user-controlled structural and temporal attributes, such as the number, thickness, length, level of branching, and lifetime of filopodia, accompanied by inherently generated reference annotations.

Non-Rigid Contour-Based Registration of Cell Nuclei in 2-D Live Cell Microscopy Images Using a Dynamic Elasticity Model.

The analysis of the pure motion of subnuclear structures without influence of the cell nucleus motion and deformation is essential in live cell imaging. In this paper, we propose a 2-D contour-based image registration approach for compensation of nucleus motion and deformation in fluorescence microscopy time-lapse sequences. The proposed approach extends our previous approach, which uses a static elasticity model to register cell images.

RNA-dependent disassembly of nuclear bodies.

Nuclear bodies are membraneless organelles that play important roles in genome functioning. A specific type of nuclear bodies known as interphase prenucleolar bodies (iPNBs) are formed in the nucleoplasm after hypotonic stress from partially disassembled nucleoli. iPNBs are then disassembled, and the nucleoli are reformed simultaneously.

Localized Movement and Levels of 53BP1 Protein Are Changed by γ-irradiation in PML Deficient Cells.

We studied epigenetics, distribution pattern, kinetics, and diffusion of proteins recruited to spontaneous and γ-radiation-induced DNA lesions. We showed that PML deficiency leads to an increased number of DNA lesions, which was accompanied by changes in histone signature. In PML wt cells, we observed two mobile fractions of 53BP1 protein with distinct diffusion in spontaneous lesions.

Advanced Image Acquisition and Analytical Techniques for Studies of Living Cells and Tissue Sections.

Studies on fixed samples or genome-wide analyses of nuclear processes are useful for generating snapshots of a cell population at a particular time point. However, these experimental approaches do not provide information at the single-cell level. Genome-wide studies cannot assess variability between individual cells that are cultured in vitro or originate from different pathological stages.

Cell Tracking Accuracy Measurement Based on Comparison of Acyclic Oriented Graphs.

Tracking motile cells in time-lapse series is challenging and is required in many biomedical applications. Cell tracks can be mathematically represented as acyclic oriented graphs. Their vertices describe the spatio-temporal locations of individual cells, whereas the edges represent temporal relationships between them.

Localized movement and morphology of UBF1-positive nucleolar regions are changed by γ-irradiation in G2 phase of the cell cycle.

The nucleolus is a well-organized site of ribosomal gene transcription. Moreover, many DNA repair pathway proteins, including ATM, ATR kinases, MRE11, PARP1 and Ku70/80, localize to the nucleolus (Moore et al., 2011 ).

HP1β-dependent recruitment of UBF1 to irradiated chromatin occurs simultaneously with CPDs.

Background: The repair of spontaneous and induced DNA lesions is a multistep process. Depending on the type of injury, damaged DNA is recognized by many proteins specifically involved in distinct DNA repair pathways.

Results: We analyzed the DNA-damage response after ultraviolet A (UVA) and γ irradiation of mouse embryonic fibroblasts and focused on upstream binding factor 1 (UBF1), a key protein in the regulation of ribosomal gene transcription.

Coilin is rapidly recruited to UVA-induced DNA lesions and γ-radiation affects localized movement of Cajal bodies.

Cajal bodies are important nuclear structures containing proteins that preferentially regulate RNA-related metabolism. We investigated the cell-type specific nuclear distribution of Cajal bodies and the level of coilin, a protein of Cajal bodies, in non-irradiated and irradiated human tumor cell lines and embryonic stem (ES) cells. Cajal bodies were localized in different nuclear compartments, including DAPI-poor regions, in the proximity of chromocenters, and adjacent to nucleoli.

Hybrid detectors improved time-lapse confocal microscopy of PML and 53BP1 nuclear body colocalization in DNA lesions.

We used hybrid detectors (HyDs) to monitor the trajectories and interactions of promyelocytic leukemia (GFP-PML) nuclear bodies (NBs) and mCherry-53BP1-positive DNA lesions. 53BP1 protein accumulates in NBs that occur spontaneously in the genome or in γ-irradiation-induced foci. When we induced local DNA damage by ultraviolet irradiation, we also observed accumulation of 53BP1 proteins into discrete bodies, instead of the expected dispersed pattern.

Comparative structural and functional analysis of two octaheme nitrite reductases from closely related Thioalkalivibrio species.

Unlabelled: Octaheme nitrite reductase from the haloalkaliphilic bacterium Thioalkalivibrio paradoxus was isolated and characterized. A comparative structural and functional analysis of two homologous octaheme nitrite reductases from closely related Thioalkalivibrio species was performed. It was shown that both enzymes have similar catalytic properties, owing to high structural similarity.

Performance of ELISA HBsAg Test Kits with Use of the Different Types of Panels Containing HBsAg.

Serological diagnostics of hepatitis B in clinical laboratories is mainly based on detection of HBs antigen (HBsAg) in human serum or plasma using commercial ELISA kits. In manufacturing and laboratory practice, sensitivity of ELISA kit is measured against either international or national reference standard. This approach is necessary, but limited as it does not take into account factors that influence on HBsAg detection kit potency at low HBsAg concentration and when HBsAg subtypes/variants are present in species.