Physical modeling of nucleosome clustering in euchromatin resulting from interactions between epigenetic reader proteins.

Euchromatin is an accessible phase of genetic material containing genes that encode proteins with increased expression levels. The structure of euchromatin in vitro has been described as a 30-nm fiber formed from ordered nucleosome arrays. However, recent advances in microscopy have revealed an in vivo euchromatin architecture that is much more disordered, characterized by variable-length linker DNA and sporadic nucleosome clusters. In this work, we develop a theoretical model to elucidate factors contributing to the disordered in vivo architecture of euchromatin. We begin by developing a 1D model of nucleosome positioning that captures the interactions between bound epigenetic reader proteins to predict the distribution of DNA linker lengths between adjacent nucleosomes. We then use the predicted linker lengths to construct 3D chromatin configurations consistent with the physical properties of DNA within the nucleosome array, and we evaluate the distribution of nucleosome cluster sizes in those configurations. Our model reproduces experimental cluster-size distributions, which are dramatically influenced by the local pattern of epigenetic marks and the concentration of reader proteins. Based on our model, we attribute the disordered arrangement of euchromatin to the heterogeneous binding of reader proteins and subsequent short-range interactions between bound reader proteins on adjacent nucleosomes. By replicating experimental results with our physics-based model, we propose a mechanism for euchromatin organization in the nucleus that impacts gene regulation and the maintenance of epigenetic marks.

Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations.

We examine the relationship between the size of domains of epigenetic marks and the stability of those domains using our theoretical model that captures the physical mechanisms governing the maintenance of epigenetic modifications. We focus our study on histone H3 lysine-9 trimethylation, one of the most common and consequential epigenetic marks with roles in chromatin compaction and gene repression. Our model combines the effects of methyl spreading by methyltransferases and chromatin segregation into heterochromatin and euchromatin because of preferential heterochromatin protein 1 (HP1) binding. Our model indicates that, although large methylated domains are passed successfully from one chromatin generation to the next, small alterations to the methylation sequence are not maintained during chromatin replication. Using our predictive model, we investigate the size required for an epigenetic domain to persist over chromatin generations while surrounded by a much larger domain of opposite methylation and compaction state. We find that there is a critical size threshold in the hundreds-of-nucleosomes scale above which an epigenetic domain will be reliably maintained over generations. The precise size of the threshold differs for heterochromatic and euchromatic domains. Our results are consistent with natural alterations to the epigenetic sequence occurring during embryonic development and due to age-related epigenetic drift.

Critical process parameters in manufacturing of liposomal formulations of amphotericin B.

Identifying the critical process parameters (CPPs) of a complex drug product manufacture and the associated impact on critical quality attributes (CQAs) is essential to the development and quality control of both new and generic drugs. AmBisome, a liposomal amphotericin B (AMB) macrolide antibiotic widely adopted as an important antifungal drug product, was used as a model complex drug product in the current study. This study investigated how multi-step production approaches and related manufacturing conditions may affect essential physico-chemical and toxicological properties of the final drug product. A key challenge in the manufacture and analysis of liposomal AMB was the drug substance's propensity to aggregate, with associated poor solubility in water and organic solvents. This study identified three key CPPs in a four step manufacturing process: (i) proper acidification during formation of the drug-lipid complexes (Step 1), (ii) liposome heat curing following liposomal particle sizing (Step 3), and (iii) flash-freezing at the initial stages of the lyophilization cycle (Step 4). Over-acidification led to rapid degradation of the drug, whereas under-acidification hampered full solubilization and formation of the soluble drug-lipid complexes. Extended heat treatment of the formed liposomes at 65 °C, just above the lipid phase transition temperature, brought dramatic changes in the aggregated state and/or packing of the drug in the liposomal bilayer, as followed by the complex changes in the UV/Vis spectra. Such thermal conditioning resulted in a five- to ten-fold reduction in the in-vitro toxicity of the drug product, bringing it close to the values for AmBisome used as control and measured by the RBC assay. Finally, flash-freezing conditions during lyophilization was critical to prevent aggregation and maintaining the 80-120 nm liposome size when reconstituted. Our research found that changes in the amphotericin's UV/Vis spectra were a sensitive CQA measure and provided a set of quantitative parameters for a facile non-destructive process monitoring in-situ, as well as for comparison of the quality of final formulations.

Numerical evaluation and experimental validation of cross-flow microfiltration device design.

This research presents a comprehensive analysis of the design and validation of a cross-flow microfiltration device for separation of microspheres based on size. Simulation results showed that pillar size, pillar shape, incorporation of back-flow preventers, and rounding of pillar layouts affected flow patterns in a cross-flow microfiltration device. Simulation results suggest that larger pillar sizes reduce filtration capacity by decreasing the density of microfiltration gaps in the device. Therefore, 10 µm rather than 20 µm diameter pillars were incorporated in the device. Fluid flow was not greatly affected when comparing circular, octagonal, and hexagonal pillars. However, side-channel fluid velocities decreased when using triangular and square pillars. The lengths of back-flow prevention walls were optimized to completely prevent back flow without inhibiting filtration ability. A trade-off was observed in the designs of the pillar layouts; while rounding the pillars layout in the channels bends eliminated stagnation areas, the design also decreased side-channel fluid velocity compared to the right-angle layout. Experimental separation efficiency was tested using polydimethylsiloxane (PDMS) and silicon microfluidic devices with microspheres simulating white and red blood cells. Efficiencies for separation of small microspheres to the side channels ranged from 73 to 75%. The silicon devices retained the large microspheres in the main channel with efficiencies between 95 and 100%, but these efficiencies were lower with PDMS devices and were affected by sphere concentration. Additionally, PDMS devices resulted in greater agglomeration of spheres when compared to silicon devices. PDMS devices, however, were easier and less expensive to fabricate.