Competitive Chemical Reaction Kinetic Model of Nucleosome Assembly Using the Histone Variant H2A.Z and H2A In Vitro.

Nucleosomes not only serve as the basic building blocks for eukaryotic chromatin but also regulate many biological processes, such as DNA replication, repair, and recombination. To modulate gene expression in vivo, the histone variant H2A.Z can be dynamically incorporated into the nucleosome. However, the assembly dynamics of H2A.Z-containing nucleosomes remain elusive. Here, we demonstrate that our previous chemical kinetic model for nucleosome assembly can be extended to H2A.Z-containing nucleosome assembly processes. The efficiency of H2A.Z-containing nucleosome assembly, like that of canonical nucleosome assembly, was also positively correlated with the total histone octamer concentration, reaction rate constant, and reaction time. We expanded the kinetic model to represent the competitive dynamics of H2A and H2A.Z in nucleosome assembly, thus providing a novel method through which to assess the competitive ability of histones to assemble nucleosomes. Based on this model, we confirmed that histone H2A has a higher competitive ability to assemble nucleosomes in vitro than histone H2A.Z. Our competitive kinetic model and experimental results also confirmed that in vitro H2A.Z-containing nucleosome assembly is governed by chemical kinetic principles.

Alkaline ball-milled peanut-hull biosorbent effectively removes aqueous organic dyes.

Advanced biosorbents increasingly attract attention for their application in environment remediation. Here, a facile one-step approach to alkaline ball milling was used to synthesize a porous peanut hull biosorbent without heating. The alkaline ball-milled peanut-hull (ABP) biosorbent was characterized for its ability to remove Congo red (CR), titan yellow (TY), and methyl violet (MV) from aqueous solutions. ABP processed abundant O-containing functional groups and developed porosity, resulting in maximum sorption capacities of 4864.4 (CR), 455.9 (TY), and 126.1 (MV) mg g-1. Freundlich isotherm and PSO kinetic models best fit the anionic dye's (CR and TY) adsorption by ABP, indicating multiple mechanisms might control the adsorption process. Freundlich and PFO kinetics models best described cationic MV adsorption by ABP, suggesting the adsorption of cationic dye could also be governed by multi-mechanisms but less heterogeneous than that of anionic dye. The results suggest that alkaline ball-milling is promising approach to converting biomass into advanced biosorbents for organic dyes, especially anionic ones.

Characteristics and aqueous dye removal ability of novel biosorbents derived from acidic and alkaline one-step ball milling of hickory wood.

New classes of biosorbents are needed for various environment remediation applications. Thus, a facile and benign approach to synthesize porous biosorbents was developed using acidic or alkaline one-step ball milling of hickory wood biomass (AcBH and AlBH, respectively) without any external heat treatment, and their properties were compared. AcBH and AlBH were richer in O-containing functional groups, had enhanced porous structure and greater ability to remove crystal violet (CV, 476.4 mg g-1) and Congo red (CR, 221.8 mg g-1) dyes from aqueous solution, respectively, relative to hickory wood ball milled at neutral pH. Freundlich isotherm and pseudo second order kinetic models best fitted CR and CV adsorption onto biosorbents, indicating a mainly surface complexation adsorption mechanism. Further, both sorbents exhibited excellent stability and dye adsorption reusability. These results demonstrate that acidic and alkaline one-step ball milling is a facile and efficient approach for converting wood biomass into environmentally friendly biosorbents.

Preparation of biosorbent for the removal of organic dyes from aqueous solution via one-step alkaline ball milling of hickory wood.

Biosorbent has attracted considerable attention recently for use in environment remediation and pollution control. Here, a simple and efficient method of one-step alkaline ball milling was designed to prepare porous hickory biosorbent without any thermal treatments. The products were characterized for their ability to remove methyl violet (MV) and titan yellow (TY) organic dyes from aqueous solutions. The one-step alkaline ball milled hickory (OABMH) biosorbent exhibited mesoporous microstructure, homogeneous morphology, and a diversity of oxygen-containing functional groups. Furthermore, OABMH could sorb 212.2 mg g-1 MV and 5.6 mg g-1 TY polar dyes, respectively, mainly through the surface complexation mechanism. Freundlich adsorption isotherm and intraparticle diffusion kinetic models best described MV adsorption by OABMH biosorbents. The results indicate that one-step alkaline ball milling technique is an efficient and economical approach for converting biomass into advanced biosorbents for environment remediation and water treatment.

Nucleosome Assembly and Disassembly in vitro Are Governed by Chemical Kinetic Principles.

As the elementary unit of eukaryotic chromatin, nucleosomes in vivo are highly dynamic in many biological processes, such as DNA replication, repair, recombination, or transcription, to allow the necessary factors to gain access to their substrate. The dynamic mechanism of nucleosome assembly and disassembly has not been well described thus far. We proposed a chemical kinetic model of nucleosome assembly and disassembly in vitro. In the model, the efficiency of nucleosome assembly was positively correlated with the total concentration of histone octamer, reaction rate constant and reaction time. All the corollaries of the model were well verified for the Widom 601 sequence and the six artificially synthesized DNA sequences, named CS1-CS6, by using the salt dialysis method in vitro. The reaction rate constant in the model may be used as a new parameter to evaluate the nucleosome reconstitution ability with DNAs. Nucleosome disassembly experiments for the Widom 601 sequence detected by Förster resonance energy transfer (FRET) and fluorescence thermal shift (FTS) assays demonstrated that nucleosome disassembly is the inverse process of assembly and can be described as three distinct stages: opening phase of the (H2A-H2B) dimer/(H3-H4)2 tetramer interface, release phase of the H2A-H2B dimers from (H3-H4)2 tetramer/DNA and removal phase of the (H3-H4)2 tetramer from DNA. Our kinetic model of nucleosome assembly and disassembly allows to confirm that nucleosome assembly and disassembly in vitro are governed by chemical kinetic principles.