Helical metaphase chromatid coiling is conserved

The higher-order metaphase chromosome organization has been under controversial discussion already for 140 years. Classical light and electron microscopy proposed chromatids to be composed of helically organized chromatin fibers, so-called chromonemata. More recently also non-helical models were suggested. We studied the chromosome organization in barley by interdisciplinary cutting-edge approaches, such as chromosome sorting, chromosome conformation capture, oligonucleotide-fluorescence in situ hybridization, base analog incorporation, super-resolution microscopy, and polymer simulation to elucidate the arrangement of chromatids of large mitotic metaphase chromosomes. Our data provide cumulative evidence for the presence of a helically arranged 400 nm chromatin fiber representing the chromonema within the chromatid arms. The number of turns is positively correlated with the arm length. Turn size and chromatin density decrease towards the telomeres. Due to the specialized functions of centromeres and nucleolus-organizing regions, the helical organization is interrupted at these regions, which display several thinners and straight chromatin fibers. Based on our findings and re-analyzing previously published data from other plant and non-plant species we conclude that the helical turning of metaphase chromatid arms is a conserved feature of large eukaryotic chromosomes.

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

The three-dimensional architecture of the genome affects genomic functions. Multiple genome architectures at different length scales, including chromatin loops, domains, compartments, and regions associated with nuclear lamina and nucleoli, have been discovered. However, how these structures are arranged in the same cell and how they are correlated with each other in different cell types in mammalian tissue are largely unknown. Here, we developed Multiplexed Imaging of Nucleome Architectures that measures multiscale chromatin folding, copy numbers of numerous RNA species, and associations of numerous genomic regions with nuclear lamina, nucleoli and surface of chromosomes in the same, single cells. We applied this method in mouse fetal liver, and identified de novo cell-type-specific chromatin architectures associated with gene expression, as well as chromatin organization principles independent of cell type. Polymer simulation showed that both intra-chromosomal phase-separating interactions and extra-chromosomal interactions are necessary to establish the observed organization. Our experiments and modeling provide a multiscale and multi-faceted picture of chromatin folding and nucleome architectures in mammalian tissue and illustrate physical principles for maintaining chromatin organization.

The influence of temperature and density on the microscopic structure and dynamics of long polymer chains: Molecular dynamics and dissipative particle dynamics modeling

Long polymer chains that mainly exhibit thermoplastic properties are recognized to demonstrate excellent thermal and mechanical features at the molecular level. For the purpose of facilitating its study, we present the results of a coarse-grained Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) simulations under the Canonical ensemble (NVT) conditions. For each simulation method, the structure, static and dynamic properties were analyzed, with particular emphasis on the influence of density and temperature on the equilibrium of the polymer. We find, after correcting the Soft Repulsive Potential (SRP) parameters used in DPD method, that both simulation methods describe the polymer physics with the same accuracy. This proves that the DPD method can simplify the polymer simulation and can reproduce with the same precision the equilibrium obtained in the MD simulation.

Identification of Shear Properties for Woven Fiber Reinforced Polymer Simulation

Finite element simulation of composite materials is still challenging as anisotropy of the material brings difficulty in accurately identifying shear properties for modeling. In this study, ±45° tensile tests, Iosipescu shear tests, rail shear tests and Arcan shear tests are conducted to obtain the engineering shear stress-strain curve of woven fiber reinforced polymer. Digital image correlation method is adopted to obtain the strain field of the specimens. It is indicated that Iosipescu shear tests introduce a strain field close to pure shear state while the other three test types introduce relatively large tensile strain or compressive strain. Shear properties obtained from Iosipescu tests are used to calibrate an extensively used composite material model, Matzenmiller-Lubliner-Taylor (MLT) model. The calibrated MLT model is then verified by simulating Arcan tests with different loading angles. The simulations indicate that MLT model gives reliable predictions on Arcan tests with smaller loading angles, while it overestimates the force-displacement responses at larger loading angles.