The Dynamic Influence of Linker Histone Saturation within the Poly-Nucleosome Array.

Linker histones bind to nucleosomes and modify chromatin structure and dynamics as a means of epigenetic regulation. Biophysical studies have shown that chromatin fibers can adopt a plethora of conformations with varying levels of compaction. Linker histone condensation, and its specific binding disposition, has been associated with directly tuning this ensemble of states. However, the atomistic dynamics and quantification of this mechanism remains poorly understood. Here, we present molecular dynamics simulations of octa-nucleosome arrays, based on a cryo-EM structure of the 30-nm chromatin fiber, with and without the globular domains of the H1 linker histone to determine how they influence fiber structures and dynamics. Results show that when bound, linker histones inhibit DNA flexibility and stabilize repeating tetra-nucleosomal units, giving rise to increased chromatin compaction. Furthermore, upon the removal of H1, there is a significant destabilization of this compact structure as the fiber adopts less strained and untwisted states. Interestingly, linker DNA sampling in the octa-nucleosome is exaggerated compared to its mono-nucleosome counterparts, suggesting that chromatin architecture plays a significant role in DNA strain even in the absence of linker histones. Moreover, H1-bound states are shown to have increased stiffness within tetra-nucleosomes, but not between them. This increased stiffness leads to stronger long-range correlations within the fiber, which may result in the propagation of epigenetic signals over longer spatial ranges. These simulations highlight the effects of linker histone binding on the internal dynamics and global structure of poly-nucleosome arrays, while providing physical insight into a mechanism of chromatin compaction.

Elucidating the influence of linker histone variants on chromatosome dynamics and energetics.

Linker histones are epigenetic regulators that bind to nucleosomes and alter chromatin structures and dynamics. Biophysical studies have revealed two binding modes in the linker histone/nucleosome complex, the chromatosome, where the linker histone is either centered on or askew from the dyad axis. Each has been posited to have distinct effects on chromatin, however the molecular and thermodynamic mechanisms that drive them and their dependence on linker histone compositions remain poorly understood. We present molecular dynamics simulations of chromatosomes with the globular domain of two linker histone variants, generic H1 (genGH1) and H1.0 (GH1.0), to determine how their differences influence chromatosome structures, energetics and dynamics. Results show that both unbound linker histones adopt a single compact conformation. Upon binding, DNA flexibility is reduced, resulting in increased chromatosome compaction. While both variants enthalpically favor on-dyad binding, energetic benefits are significantly higher for GH1.0, suggesting that GH1.0 is more capable than genGH1 of overcoming the large entropic reduction required for on-dyad binding which helps rationalize experiments that have consistently demonstrated GH1.0 in on-dyad states but that show genGH1 in both locations. These simulations highlight the thermodynamic basis for different linker histone binding motifs, and details their physical and chemical effects on chromatosomes.

Efficacy of vitrectomy in improving the outcome of Bacillus cereus endophthalmitis.

PURPOSE: To evaluate the efficacy of vitrectomy with vancomycin for the treatment of experimental Bacillus cereus endophthalmitis. METHODS: Endophthalmitis was initiated in rabbits via intravitreal injection of 100 colony-forming unit B. cereus. Treatment groups included 25-gauge transconjunctival sutureless vitrectomy with intravitreal vancomycin (1 mg) or vancomycin alone. Groups were treated at 4, 5, or 6 hours after infection. At 48 hours (for 4-hour and 5-hour groups) or 36 hours (for the 6-hour group) after infection, eyes were analyzed by electroretinography, histology, and inflammatory cell counts. RESULTS: Treatment with vitrectomy/vancomycin at 4 hours resulted in significantly greater retinal function compared with that of vancomycin alone. Intraocular inflammation after treatment at 4 hours was minimal for both the treatment groups. Treatment with vitrectomy/vancomycin or vancomycin alone at 5 hours or 6 hours after infection resulted in similar levels of retinal function loss (i.e., >90%) and significant intraocular inflammation. CONCLUSION: These results demonstrate that vitrectomy may be of therapeutic benefit in the treatment of B. cereus endophthalmitis but only during the early stages of infection.