Bottom-up modeling of chromatin segregation due to epigenetic modifications

Predicting how epigenetic marks control the 3D organization of the genome is key to understanding how these marks regulate gene expression. We show that a physical model of a chromosome with experimentally measured local interactions segregates into euchromatin- and heterochromatin-like phases. The model reproduces many of the features of the large-scale organization of the chromosome as measured by Hi-C. Our work provides an estimate of the amount of epigenetic marking needed to segregate a gene into heterochromatin.

We use a chromosome-scale simulation to show that the preferential binding of heterochromatin protein 1 (HP1) to regions high in histone methylation (specifically H3K9me3) results in phase segregation and reproduces features of the observed Hi-C contact map. Specifically, we perform Monte Carlo simulations with one computational bead per nucleosome and an H3K9me3 pattern based on published ChIP-seq signals. We implement a binding model in which HP1 preferentially binds to trimethylated histone tails and then oligomerizes to bridge together nucleosomes. We observe a phase reminiscent of heterochromatin—dense and high in H3K9me3—and another reminiscent of euchromatin—less dense and lacking H3K9me3. This segregation results in a plaid contact probability map that matches the general shape and position of published Hi-C data. Analysis suggests that a roughly 20-kb segment of H3K9me3 enrichment is required to drive segregation into the heterochromatic phase.

Experimental and Numerical Analysis for the Mechanical Characterization of PETG Polymers Manufactured with FDM Technology under Pure Uniaxial Compression Stress States for Architectural Applications

This paper presents the numerical and experimental analysis performed on the polymeric material Polyethylene Terephthalate Glycol (PETG) manufactured with Fused Deposition Modeling Technology (FDM) technology, aiming at obtaining its mechanical characterization under uniaxial compression loads. Firstly, with the objective of evaluating the printing direction that poses a greater mechanical strength, eighteen test specimens were manufactured and analyzed according to the requirements of the ISO-604 standards. After that, a second experimental test analyzed the mechanical behavior of an innovative structural design manufactured in Z and X–Y directions under uniaxial compression loads according to the requirements of the Spanish CTE standard. The experimental results point to a mechanical linear behavior of PETG in X, Y and Z manufacturing directions up to strain levels close to the yield strength point. SEM micrographs show different structural failures linked to the specimen manufacturing directions. Test specimens manufactured along X present a brittle fracture caused by a delamination process. On the contrary, test specimens manufactured along X and Y directions show permanent plastic deformations, great flexibility and less strength under compression loads. Two numerical analyses were performed on the structural part using Young’s compression modulus obtained from the experimental tests and the load specifications required for the Spanish CTE standards. The comparison between numerical and experimental results presents a percentage of relative error of 2.80% (Z-axis), 3.98% (X-axis) and 3.46% (Y-axis), which allows characterizing PETG plastic material manufactured with FDM as an isotropic material in the numerical simulation software without modifying the material modeling equations in the data software. The research presented here is of great help to researchers working with polymers and FDM technology for companies that might need to numerically simulate new designs with the PETG polymer and FDM technology.

Analysis and Simulation of Polymer Injectivity Test in a High Temperature High Salinity Carbonate Reservoir

Polymer flooding has gained much interest within the oil industry in the past few decades as one of the most successful chemical enhanced oil recovery (CEOR) methods. The injectivity of polymer solutions in porous media is a key factor in polymer flooding projects. The main challenge that faces prediction of polymer injectivity in field applications is the inherent non-Newtonian behavior of polymer solutions. Polymer in situ rheology in porous media may exhibit complex behavior that encompasses shear thickening at high flow rates in addition to the typical shear thinning at low rates. This shear-dependent behavior is usually measured in lab core flood experiments. However, data from field applications are usually limited to the well bottom-hole pressure (BHP) as the sole source of information. In this paper, we analyze BHP data from field polymer injectivity test conducted in a Middle Eastern heterogeneous carbonate reservoir characterized by high-temperature and high-salinity (HTHS) conditions. The analysis involved incorporating available data to build a single-well model to simulate the injectivity test. Several generic sensitivities were tested to investigate the impact of stepwise variation in injection flow rate and polymer concentration. Polymer injection was reflected in a non-linear increase in pressure with injection, and longer transient behavior toward steady state. The results differ from water injection which have linear pressure response to rate variation, and quick stabilization of pressure after rate change. The best match of the polymer injection was obtained with complex rheology, that means the combined shear thickening at high rate near the well and moving through apparent Newtonian and shear thinning at low rate.

Helical chromonema coiling is conserved in eukaryotes

Efficient chromatin condensation is required to transport chromosomes during mitosis and meiosis, forming daughter cells. While it is well accepted that these processes follow fundamental rules, there has been a controversial debate for more than 140 years on whether the higher-order chromatin organization in chromosomes is evolutionarily conserved. Here, we summarize historical and recent investigations based on classical and modern methods. In particular, classical light microscopy observations based on living, fixed, and treated chromosomes covering a wide range of plant and animal species, and even in single-cell eukaryotes suggest that the chromatids of large chromosomes are formed by a coiled chromatin thread, named the chromonema. More recently, these findings were confirmed by electron and super-resolution microscopy, oligo-FISH, molecular interaction data, and polymer simulation. Altogether, we describe common and divergent features of coiled chromonemata in different species. We hypothesize that chromonema coiling in large chromosomes is a fundamental feature established early during the evolution of eukaryotes to handle increasing genome sizes.