Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei.

Topographical cues on cells can, through contact guidance, alter cellular plasticity and accelerate the regeneration of cultured tissue. Here we show how changes in the nuclear and cellular morphologies of human mesenchymal stromal cells induced by micropillar patterns via contact guidance influence the conformation of the cells' chromatin and their osteogenic differentiation in vitro and in vivo. The micropillars impacted nuclear architecture, lamin A/C multimerization and 3D chromatin conformation, and the ensuing transcriptional reprogramming enhanced the cells' responsiveness to osteogenic differentiation factors and decreased their plasticity and off-target differentiation. In mice with critical-size cranial defects, implants with micropillar patterns inducing nuclear constriction altered the cells' chromatin conformation and enhanced bone regeneration without the need for exogenous signalling molecules. Our findings suggest that medical device topographies could be designed to facilitate bone regeneration via chromatin reprogramming.

A soil-inspired dynamically responsive chemical system for microbial modulation.

Interactions between the microbiota and their colonized environments mediate critical pathways from biogeochemical cycles to homeostasis in human health. Here we report a soil-inspired chemical system that consists of nanostructured minerals, starch granules and liquid metals. Fabricated via a bottom-up synthesis, the soil-inspired chemical system can enable chemical redistribution and modulation of microbial communities. We characterize the composite, confirming its structural similarity to the soil, with three-dimensional X-ray fluorescence and ptychographic tomography and electron microscopy imaging. We also demonstrate that post-synthetic modifications formed by laser irradiation led to chemical heterogeneities from the atomic to the macroscopic level. The soil-inspired material possesses chemical, optical and mechanical responsiveness to yield write-erase functions in electrical performance. The composite can also enhance microbial culture/biofilm growth and biofuel production in vitro. Finally, we show that the soil-inspired system enriches gut bacteria diversity, rectifies tetracycline-induced gut microbiome dysbiosis and ameliorates dextran sulfate sodium-induced rodent colitis symptoms within in vivo rodent models.

Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).

Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.

Development of Fe3O4 core-TiO2 shell nanocomposites and nanoconjugates as a foundation for neuroblastoma radiosensitization.

BACKGROUND: Neuroblastoma is the most common extracranial solid malignancy in childhood which, despite the current progress in radiotherapy and chemotherapy protocols, still has a high mortality rate in high risk tumors. Nanomedicine offers exciting and unexploited opportunities to overcome the shortcomings of conventional medicine. The photocatalytic properties of Fe3O4 core-TiO2 shell nanocomposites and their potential for cell specific targeting suggest that nanoconstructs produced using Fe3O4 core-TiO2 shell nanocomposites could be used to enhance radiation effects in neuroblastoma. In this study, we evaluated bare, metaiodobenzylguanidine (MIBG) and 3,4-Dihydroxyphenylacetic acid (DOPAC) coated Fe3O4@TiO2 as potential radiosensitizers for neuroblastoma in vitro. RESULTS: The uptake of bare and MIBG coated nanocomposites modestly sensitized neuroblastoma cells to ionizing radiation. Conversely, cells exposed to DOPAC coated nanocomposites exhibited a five-fold enhanced sensitivity to radiation, increased numbers of radiation induced DNA double-strand breaks, and apoptotic cell death. The addition of a peptide mimic of the epidermal growth factor (EGF) to nanoconjugates coated with MIBG altered their intracellular distribution. Cryo X-ray fluorescence microscopy tomography of frozen hydrated cells treated with these nanoconjugates revealed cytoplasmic as well as nuclear distribution of the nanoconstructs. CONCLUSIONS: The intracellular distribution pattern of different nanoconjugates used in this study was different for different nanoconjugate surface molecules. Cells exposed to DOPAC covered nanoconjugates showed the smallest nanoconjugate uptake, with the most prominent pattern of large intracellular aggregates. Interestingly, cells treated with this nanoconjugate also showed the most pronounced radiosensitization effect in combination with the external beam x-ray irradiation. Further studies are necessary to evaluate mechanistic basis for this increased radiosensitization effect. Preliminary studies with the nanoparticles carrying an EGF mimicking peptide showed that this approach to targeting could perhaps be combined with a different approach to radiosensitization - use of nanoconjugates in combination with the radioactive iodine. Much additional work will be necessary in order to evaluate possible benefits of targeted nanoconjugates carrying radionuclides. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12645-021-00081-z.

Metal ion fluxes controlling amphibian fertilization.

Mammalian oocytes undergo major changes in zinc content and localization to be fertilized, the most striking being the rapid exocytosis of over 10 billion zinc ions in what are known as zinc sparks. Here, we report that fertilization of amphibian Xenopus laevis eggs also initiates a zinc spark that progresses across the cell surface in coordination with dynamic calcium waves. This zinc exocytosis is accompanied by a newly recognized loss of intracellular manganese. Synchrotron-based X-ray fluorescence and analytical electron microscopy reveal that zinc and manganese are sequestered in a system of cortical granules that are abundant at the animal pole. Through electron-nuclear double-resonance studies, we rule out Mn2+ complexation with phosphate or nitrogenous ligands in intact eggs, but the data are consistent with a carboxylate coordination environment. Our observations suggest that zinc and manganese fluxes are a conserved feature of fertilization in vertebrates and that they function as part of a physiological block to polyspermy.

Synthesis, Characterization, and Simulation of Four-Armed Megamolecules.

This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a para-nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.

Nanoscale chromatin imaging and analysis platform bridges 4D chromatin organization with molecular function.

Extending across multiple length scales, dynamic chromatin structure is linked to transcription through the regulation of genome organization. However, no individual technique can fully elucidate this structure and its relation to molecular function at all length and time scales at both a single-cell level and a population level. Here, we present a multitechnique nanoscale chromatin imaging and analysis (nano-ChIA) platform that consolidates electron tomography of the primary chromatin fiber, optical super-resolution imaging of transcription processes, and label-free nano-sensing of chromatin packing and its dynamics in live cells. Using nano-ChIA, we observed that chromatin is localized into spatially separable packing domains, with an average diameter of around 200 nanometers, sub-megabase genomic size, and an internal fractal structure. The chromatin packing behavior of these domains exhibits a complex bidirectional relationship with active gene transcription. Furthermore, we found that properties of PDs are correlated among progenitor and progeny cells across cell division.

Migration of Quaternary Ammonium Cations from Exfoliated Clay/Low-Density Polyethylene Nanocomposites into Food Simulants.

Clay/polymer nanocomposites (CPNs) are polymers incorporating refined clay particles that are frequently functionalized with quaternary ammonium cations (QACs) as dispersion aids. There is interest in commercializing CPNs for food contact applications because they have improved strength and barrier properties, but there are few studies on the potential for QACs in CPNs to transfer to foods under conditions of intended use. In this study, we manufactured low-density poly(ethylene) (LDPE)-based CPNs and assessed whether QACs can migrate into several food simulants under accelerated storage conditions. QACs were found to migrate to a fatty food simulant (ethanol) at levels of ∼1.1 µg mg-1 CPN mass after 10 days at 40 °C, constituting about 4% total migration (proportion of the initial QAC content in the CPN that migrated to the simulant). QAC migration into ethanol was ∼16× higher from LDPE containing approximately the same concentration of QACs but no clay, suggesting that most QACs in the CPN are tightly bound to clay particles and are immobile. Negligible QACs were found to migrate into aqueous, alcoholic, or acidic simulants from CPNs, and the amount of migrated QACs was also found to scale with the temperature and the initial clay concentration. The migration data were compared to a theoretical diffusion model, and it was found that the diffusion constant for QACs in the CPN was several orders of magnitude slower than predicted, which we attributed to the potential for QACs to migrate as dimers or other aggregates rather than as individual ions. Nevertheless, the use of the migration model resulted in a conservative estimate of the mass transfer of QAC from the CPN test specimens.

Particle-Attachment-Mediated and Matrix/Lattice-Guided Enamel Apatite Crystal Growth.

Tooth enamel is a hard yet resilient biomaterial that derives its unique mechanical properties from decussating bundles of apatite crystals. To understand enamel crystal nucleation and growth at a nanoscale level and to minimize preparation artifacts, the developing mouse enamel matrix was imaged in situ using graphene liquid cells and atomic resolution scanning transmission electron and cryo-fracture electron microscopy. We report that 1-2 nm diameter mineral precipitates aggregated to form larger 5 nm particle assemblies within ameloblast secretory vesicles or annular organic matrix subunits. Further evidence for the fusion of 1-2 nm mineral precipitates into 5 nm mineral aggregates via particle attachment was provided by matrix-mediated calcium phosphate crystal growth studies. As a next step, aggregated particles organized into rows of 3-10 subunits and developed lattice suprastructures with 0.34 nm gridline spacings corresponding to the (002) planes of apatite crystals. Mineral lattice suprastructures superseded closely matched organic matrix patterns, suggestive of a combination of organic/inorganic templates guiding apatite crystal growth. Upon assembly of 2-5 nm subunits into crystal ribbons, lattice fringes indicative of the presence of larger ordered crystallites were observed surrounding elongating crystal ribbons, presumably guiding the c-axis growth of composite apatite crystals. Cryo-fracture micrographs revealed reticular networks of an organic matrix on the surface of elongating enamel crystal ribbons, suggesting that protein coats facilitate c-axis apatite crystal growth. Together, these data demonstrate (i) the involvement of particle attachment in enamel crystal nucleation, (ii) a combination of matrix- and lattice-guided crystal growth, and (iii) fusion of individual crystals via a mechanism similar to Ostwald ripening.

Culture of and experiments with sea urchin embryo primary mesenchyme cells.

Skeletogenesis in the sea urchin embryo gives rise to a pair of intricate endoskeletal spicules. Deposition of these skeletal elements in the early larva is the outcome of a morphogenetic program that begins with maternal inputs in the early zygote and results in the specification of the large micromere-primary mesenchyme cell (PMC) lineage. PMCs are of considerable interest as a model system, not only to dissect the mechanism of specific developmental processes, but also to investigate their evolution and the unrivaled level of control over the formation of a graded, mechanically robust, yet single crystalline biomineral. The ability to study gene regulatory circuits, cellular behavior, signaling pathways, and molecular players involved in biomineralization is significantly boosted by the high level of autonomy of PMCs. In fact, in the presence of horse serum, micromeres differentiate into PMCs and produce spicules in vitro, separated from the embryonic milieu. PMC culture eliminates indirect effects that can complicate the interpretation of experiments in vivo, offers superior spatiotemporal control, enables PMC-specific readouts, and is compatible with most imaging and characterization techniques. In this chapter, we provide an updated protocol, based on the pioneering work by Okazaki and Wilt, for the isolation of micromeres and subsequent culture of PMCs, as well as protocols for fixation and staining for fluorescent microscopy, preparation of cell cultures for electron microscopy, and the isolation of RNA.

ß-Cyclodextrin Polymers on Microcrystalline Cellulose as a Granular Media for Organic Micropollutant Removal from Water.

Organic contaminants at low concentrations, known as micropollutants, are a growing threat to water resources. Implementing novel adsorbents capable of removing micropollutants during packed-bed adsorption is desirable for rapid water purification and other efficient separations. We previously developed porous polymers based on cyclodextrins that demonstrated rapid uptake and high affinity for dozens of micropollutants (MPs) in batch experiments. However, these polymers are typically produced as powders with irregular particle size distributions in the range of tens of micrometers. In this powdered form, cyclodextrin polymers cannot be implemented in packed-bed adsorption processes because the variable particle sizes yield insufficient porosity packing and consequently generate high back-pressure. Here we demonstrate a facile approach to remove micropollutants from water in a continuous manner by polymerizing cyclodextrin polymer networks onto cellulose microcrystals to provide a core/shell structure. Batch adsorption experiments demonstrate rapid pollutant uptake and high accessibility of the cyclodextrins on the adsorbent. Similarly, column experiments demonstrate rapid uptake of a model pollutant with minimal back-pressure, demonstrating potential for use in packed-bed adsorption processes. Furthermore, the pollutant-saturated columns were regenerated using methanol and reused three times with almost no change in performance. Column experiments conducted with a mixture of 15 micropollutants at environmentally relevant concentrations demonstrated that removal was determined by the affinity of each micropollutant for cyclodextrin polymers. The cyclodextrin polymer grafted onto cellulose microcrystals is more resistant to both anaerobic and aerobic biodegradation as compared to cyclodextrins and unmodified cellulose crystals, presumably due to the aromatic cross-linkers, demonstrating persistence. Collectively, the findings from this study demonstrate a general strategy to incorporate novel cyclodextrin adsorbents onto cellulose substrates to enable rapid and efficient removal of micropollutants during packed-bed adsorption as well as their promising long-term stability and regeneration capabilities.

The effects of chemical fixation on the cellular nanostructure.

Chemical fixation is nearly indispensable in the biological sciences, especially in circumstances where cryo-fixation is not applicable. While universally employed for the preservation of cell organization, chemical fixatives often introduce artifacts that can confound identification of true structures. Since biological research is increasingly probing ever-finer details of the cellular architecture, it is critical to understand the nanoscale transformation of the cellular organization due to fixation both systematically and quantitatively. In this work, we employed Partial Wave Spectroscopic (PWS) Microscopy, a nanoscale sensitive and label-free live cell spectroscopic-imaging technique, to analyze the effects of the fixation process through three commonly used fixation protocols for cells in vitro. In each method investigated, we detected dramatic difference in both nuclear and cytoplasmic nanoarchitecture between live and fixed states. But significantly, despite the alterations in cellular nanoscale organizations after chemical fixation, the population differences in chromatin structure (e.g. induced by a specific chemotherapeutic agent) remains. In conclusion, we demonstrated that the nanoscale cellular arrangement observed in fixed cells was fundamentally divorced from that in live cells, thus the quantitative analysis is only meaningful on the population level. This finding highlights the importance of live cell imaging techniques with nanoscale sensitivity or cryo-fixation in the interrogation of cellular structure, to complement more traditional chemical fixation methods.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Zinc sparks induce physiochemical changes in the egg zona pellucida that prevent polyspermy.

During fertilization or chemically-induced egg activation, the mouse egg releases billions of zinc atoms in brief bursts known as 'zinc sparks.' The zona pellucida (ZP), a glycoprotein matrix surrounding the egg, is the first structure zinc ions encounter as they diffuse away from the plasma membrane. Following fertilization, the ZP undergoes changes described as 'hardening', which prevent multiple sperm from fertilizing the egg and thereby establish a block to polyspermy. A major event in zona hardening is cleavage of ZP2 proteins by ovastacin; however, the overall physiochemical changes contributing to zona hardening are not well understood. Using X-ray fluorescence microscopy, transmission and scanning electron microscopy, and biological function assays, we tested the hypothesis that zinc release contributes to ZP hardening. We found that the zinc content in the ZP increases by 300% following activation and that zinc exposure modulates the architecture of the ZP matrix. Importantly, zinc-induced structural changes of the ZP have a direct biological consequence; namely, they reduce the ability of sperm to bind to the ZP. These results provide a paradigm-shifting model in which fertilization-induced zinc sparks contribute to the polyspermy block by altering conformations of the ZP matrix. This adds a previously unrecognized factor, namely zinc, to the process of ZP hardening.

Environmental release of core-shell semiconductor nanocrystals from free-standing polymer nanocomposite films.

Concomitant with the development of polymer nanocomposite (PNC) technologies across numerous industries is an expanding awareness of the uncertainty with which engineered nanoparticles embedded within these materials may be released into the external environment, particularly liquid media. Recently there has been an interest in evaluating potential exposure to nanoscale fillers from PNCs, but existing studies often rely upon uncharacterized, poor quality, or proprietary materials, creating a barrier to making general mechanistic conclusions about release phenomena. In this study we employed semiconductor nanoparticles (quantum dots, QDs) as model nanofillers to quantify potential release into liquid media under specific environmental conditions. QDs of two sizes were incorporated into low-density polyethylene by melt compounding and the mixtures were extruded as free-standing fluorescent films. These films were subjected to tests under conditions intended to accelerate potential release of embedded particles or dissolved residuals into liquid environments. Using inductively-coupled plasma mass spectrometry and laser scanning confocal microscopy, it was found that the acidity of the external medium, exposure time, and small differences in particle size (on the order of a few nm) all play pivotal roles in release kinetics. Particle dissolution was found to play a major if not dominant role in the release process. This paper also presents the first evidence that internally embedded nanoparticles contribute to the mass transfer, an observation made possible via the use of a model system that was deliberately designed to probe the complex relationships between nanoparticle-enabled plastics and the environment.

Nuclear Condensation during Mouse Erythropoiesis Requires Caspase-3-Mediated Nuclear Opening.

Mammalian erythropoiesis involves chromatin condensation that is initiated in the early stage of terminal differentiation. The mechanisms of chromatin condensation during erythropoiesis are unclear. Here, we show that the mouse erythroblast forms large, transient, and recurrent nuclear openings that coincide with the condensation process. The opening lacks nuclear lamina, nuclear pore complexes, and nuclear membrane, but it is distinct from nuclear envelope changes that occur during apoptosis and mitosis. A fraction of the major histones are released from the nuclear opening and degraded in the cytoplasm. We demonstrate that caspase-3 is required for the nuclear opening formation throughout terminal erythropoiesis. Loss of caspase-3 or ectopic expression of a caspase-3 non-cleavable lamin B mutant blocks nuclear opening formation, histone release, chromatin condensation, and terminal erythroid differentiation. We conclude that caspase-3-mediated nuclear opening formation accompanied by histone release from the opening is a critical step toward chromatin condensation during erythropoiesis in mice.

Enhancing DNA-Mediated Assemblies of Supramolecular Cage Dimers through Tuning Core Flexibility and DNA Length--A Combined Experimental-Modeling Study.

Two complementary small-molecule-DNA hybrid (SMDH) building blocks have been combined to form well-defined supramolecular cage dimers at DNA concentrations as high as 102 µM. This was made possible by combining a flexible small-molecule core and three DNA arms of moderate lengths (<20 base pairs). These results were successfully modeled by coarse-grained molecular dynamics simulations, which also revealed that the formation of ill-defined networks in the case of longer DNA arms can be significantly biased by the presence of deep kinetic traps. Notably, melting point studies revealed that cooperative melting behavior can be used as a means to distinguish the relative propensities for dimer versus network formation from complementary flexible three-DNA-arm SMDH (fSMDH3) components: sharp, enhanced melting transitions were observed for assemblies that result mostly in cage dimers, while no cooperative melting behavior was observed for assemblies that form ill-defined networks.

Nano-Biomechanical Study of Spatio-Temporal Cytoskeleton Rearrangements that Determine Subcellular Mechanical Properties and Endothelial Permeability.

The endothelial cell (EC) lining of the pulmonary vascular system forms a semipermeable barrier between blood and the interstitium and regulates various critical biochemical functions. Collectively, it represents a prototypical biomechanical system, where the complex hierarchical architecture, from the molecular scale to the cellular and tissue level, has an intimate and intricate relationship with its biological functions. We investigated the mechanical properties of human pulmonary artery endothelial cells (ECs) using atomic force microscopy (AFM). Concurrently, the wider distribution and finer details of the cytoskeletal nano-structure were examined using fluorescence microscopy (FM) and scanning transmission electron microscopy (STEM), respectively. These correlative measurements were conducted in response to the EC barrier-disrupting agent, thrombin, and barrier-enhancing agent, sphingosine 1-phosphate (S1P). Our new findings and analysis directly link the spatio-temporal complexities of cell re-modeling and cytoskeletal mechanical properties alteration. This work provides novel insights into the biomechanical function of the endothelial barrier and suggests similar opportunities for understanding the form-function relationship in other biomechanical subsystems.