2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions

Functional changes of cells upon developmental switches and in response to environmental cues are often reflected in nuclear phenotypes, showing distinctive chromatin states corresponding to transcriptional changes. Such characteristic nuclear shapes have been microscopically monitored and can be quantified after differential staining of euchromatin and heterochromatin domains. Here, we examined several nuclear parameters (size, DNA content, DNA density, chromatin compaction, relative heterochromatin fraction (RHF), and number of chromocenters) in relation to spatial distribution of genes and transposon elements (TEs), using standard 2D fluorescence microscopy. We provide nuclear profiles for different cell types and different accessions of Arabidopsis thaliana. A variable, yet significant, fraction of TEs was found outside chromocenters in all cell types, except for guard cells. The latter cell type features nuclei with the highest level of chromatin compaction, while their chromocenters seem to contain gene-rich regions. The highest number of parameter correlations was found in the accession Cvi, whereas Ler showed only few correlations. This may point at differences in phenotype robustness between accessions. The significantly high association of NOR chromocenters in accessions Ws and Cvi corresponds to their low RHF level.

Solvent quality and chromosome folding in Escherichia coli

SummaryAll cells must fold their genomes, including bacterial cells where the chromosome is compacted into a domain-organized meshwork called nucleoid. Polymer conformation depends highly on the quality of the solvent. Yet, the solvent quality for the DNA polymer inside cells remains unexplored. Here, we developed a method to assess this fundamental physicochemical property in live bacteria. By determining the DNA concentration and apparent average mesh size of the nucleoid, we provide evidence that the cytoplasm is a poor solvent for the chromosome in Escherichia coli. Monte Carlo simulations showed that such a poor solvent compacts the chromosome and promotes spontaneous formation of chromosomal domains connected by lower-density DNA regions. Cryo-electron tomography and fluorescence microscopy revealed that the (poly)ribosome density within the nucleoid is spatially heterogenous and correlates negatively with DNA density. These findings have broad implications to our understanding of chromosome folding and intracellular organization.

A high local DNA concentration for nucleating a DNA/Fe coordination shell on gold nanoparticles

A high localized DNA density on AuNP can facilitate the formation of DNA/Fe hybrids. The TEM images of AuNP@DNA/Fe nanoparticles (above) and aggregated AuNP@DNA nanoparticles (below).

DNA density-dependent uptake of DNA origami-based two-or three-dimensional nanostructures by immune cells

Using DNA nanostructures with almost identical molecular weight and structural flexibility, this work clearly showed that compactly packaged DNA nanostructures with high DNA density are suitable for the delivery to immune cells.

Effect of Metabolite Extract of Streptomyces hygroscopicus subsp. hygroscopicus on Plasmodium falciparum 3D7 in Vitro

Background: Malaria eradication has been complicated by the repeated emergence of antimalarial drug resistances. We aimed to determine whether a metabolite extract of Streptomyces hygrocopicus subsp. hygroscopicus could decrease the viability of Plasmodium falciparum 3D7 in vitro. Methods: S. hygroscopicus subsp. hygroscopicus isolates were inoculated and fermented on the ISP4 medium. The fermented S. hygroscopicus was mixed with ethylacetate 1:5 (v/v), and the solvent phase was evaporated. Several concentrations of isolated extract was added to the P. falciparum 3D7 culture containing trophozoite and schizont stages in 24 wells plates when the degree of parasite-infected erythrocytes reached 5%, then incubated for 8 hours. DNA parasite density was measured using flow cytometry, parasite degree and morphology were observed under microscopic by Giemsa-stained smears. Results: The metabolite extract affected the morphology of almost all of parasite asexual stages. Schizonts and trophozoites failed to grow and appeared damaged with pycnotic cores and loss of cytoplasmic content. At 8 hours there was a significant decrease in DNA parasite density in culture exposed to 2.6 mg/ml and 13 mg/ml (P = 0.002; P = 0.024) of the extract. The degree of parasite-infected erythrocytes was decreased from the beginning of exposure (0.02 mg/ml of the extract). There was a significant inverse correlation between the concentration of extract and the degree of parasite-infected erythrocytes as well as the density of DNA parasite (r = -0.772, P = 0.000; r =-0.753; P =0.000). Conclusion: Metabolite extract of S. hygroscopicus subsp. hygroscopicus causes morphological damage, decreases the degree of parasite-infected erythrocytes and the DNA density of P. falciparum 3D7 in vitro.

Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes

Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.