How Transcription Factor Clusters Shape the Transcriptional Landscape.

In eukaryotic cells, gene transcription typically occurs in discrete periods of promoter activity, interspersed with intervals of inactivity. This pattern deviates from simple stochastic events and warrants a closer examination of the molecular interactions that activate the promoter. Recent studies have identified transcription factor (TF) clusters as key precursors to transcriptional bursting. Often, these TF clusters form at chromatin segments that are physically distant from the promoter, making changes in chromatin conformation crucial for promoter-TF cluster interactions. In this review, I explore the formation and constituents of TF clusters, examining how the dynamic interplay between chromatin architecture and TF clustering influences transcriptional bursting. Additionally, I discuss techniques for visualizing TF clusters and provide an outlook on understanding the remaining gaps in this field.

Transcription factor clusters as information transfer agents.

Deciphering how genes interpret information from the concentration of transcription factors (TFs) within the cell nucleus remains a fundamental question in gene regulation. Recent advancements have unveiled the heterogeneous distribution of TF molecules in the nucleus, posing challenges to the precise decoding of concentration signals. To explore this phenomenon, we employ high-resolution single-cell imaging of a fluorescently tagged TF protein, Bicoid, in living fly embryos. We show that accumulation of Bicoid in submicron clusters preserves the spatial information of the maternal Bicoid gradient, and that cluster intensity, size, and frequency offer remarkably precise spatial cues. We further discover that various known gene targets of Bicoid activation colocalize with clusters and that for the target gene Hunchback, this colocalization is dependent on its enhancer binding affinity. Modeling information transfer through these clusters suggests that clustering offers a more rapid sensing mechanism for global nuclear concentrations than freely diffusing TF molecules detected by simple enhancers.

Outstanding heat loss via nano-octahedra above 20 nm in size: from wustite-rich nanoparticles to magnetite single-crystals.

Most studies on magnetic nanoparticle-based hyperthermia utilize iron oxide nanoparticles smaller than 20 nm, which are intended to have superparamagnetic behavior (SP-MNPs). However, the heating power of larger magnetic nanoparticles with non-fluctuating or fixed magnetic dipoles (F-MNPs) can be significantly greater than that of SP-MNPs if high enough fields (H > 15 mT) are used. But the synthesis of larger single nanocrystals of magnetite (Fe3O4) with a regular shape and narrow size distribution devoid of secondary phases remains a challenge. Iron oxide nanoparticles, grown over 25 nm, often present large shape and size polydispersities, twinning defects and a significant fraction of the wüstite-type (FeO) paramagnetic phase, resulting in degradation of magnetic properties. Herein, we introduce an improved procedure to synthesize monodisperse F-MNPs in the range of 25 to 50 nm with a distinct octahedral morphology and very crystalline magnetite phase. We unravel the subtle phase transformation that takes place during the synthesis by a thorough study in several non-optimized nanoparticles presenting a core-shell structure or composed of magnetite-type clusters embedded in a wüstite lattice. Optimized magnetite samples present a slight decrease in the saturation magnetization compared to bulk magnetite, which is successfully explained by the presence of Fe2+ vacancies. However, due to the high quality of these samples, AC magnetometry measurements have shown excellent specific absorption rates (>1000 W gFe3O4-1 at 40 mT and 300 kHz). Most importantly, the magnetic response and the hyperthermia performance of properly coated F-MNPs are kept basically unaltered in media with very different viscosities and ionic strength. Finally, using a physical model based on single magnetic domain approaches, we derive a novel connection between the octahedral shape and the high hyperthermia performance.

Multilayered inorganic-organic microdisks as ideal carriers for high magnetothermal actuation: assembling ferrimagnetic nanoparticles devoid of dipolar interactions.

The two major limitations for nanoparticle based magnetic hyperthermia in theranostics are the delivery of a sufficient number of magnetic nanoparticles (MNPs) with high heating power to specific target cells and the residence time of the MNPs at the target location. Ferromagnetic or Ferrimagnetic single domain nanoparticles (F-MNPs), with a permanent magnetic dipole, produce larger magnetic and thermal responses than superparamagnetic nanoparticles (SP-MNPs) but also agglomerate more. MNP agglomeration degrades their heating potential due to dipolar interaction effects and interferes with specific targeting. Additionally, MNPs bound to cells are often endocytosed by the cells or, in vivo, cleared out by the immune system via uptake in macrophages. Here, we present a versatile approach to engineer inorganic-polymeric microdisks, loaded with biomolecules, fluorophores and Fe3O4 F-MNPs that solves both challenges. These microdisks deliver the F-MNPs efficiently, while controlling any undesirable agglomeration and dipolar interaction, while also rendering the F-MNPs endocytosis resistant. We show that these micro-devices are suitable carriers to transport a flat assembly of F-MNPs to the cell membrane unchanged, preserving the magnetic response of the MNPs in any biological environment. The F-MNPs concentration per microdisk and degree of MNP interaction are tunable. We demonstrate that the local heat generated in microdisks is proportional to the surface density of F-MNPs when attached to the cell membrane. The key innovation in the production of these microdisks is the fabrication of a mushroom-shaped photolithographic template that enables easy assembly of the inorganic film, polymeric multilayers, and MNP cargo while permitting highly efficient lift-off of the completed microdisks. During the harvesting of the flat microdisks, the supporting mushroom-shaped templates are sacrificed. These resulting magnetic hybrid microdisks are tunable and efficient devices for magnetothermal actuation and hyperthermia.

Transient Magnetothermal Neuronal Silencing Using the Chloride Channel Anoctamin 1 (TMEM16A).

Determining the role and necessity of specific neurons in a network calls for precisely timed, reversible removal of these neurons from the circuit via remotely triggered transient silencing. Previously, we have shown that alternating magnetic field mediated heating of magnetic nanoparticles, bound to neurons, expressing temperature-sensitive cation channels TRPV1 remotely activates these neurons, evoking behavioral responses in mice. Here, we demonstrate how to apply magnetic nanoparticle heating to silence target neurons. Rat hippocampal neuronal cultures were transfected to express the temperature gated chloride channel, anoctamin 1 (TMEM16A). Spontaneous firing was suppressed within seconds of alternating magnetic field application to anoctamin 1 (TMEM16A) channel expressing, magnetic nanoparticle decorated neurons. Five seconds of magnetic field application leads to 12 s of silencing, with a latency of 2 s and an average suppression ratio of more than 80%. Immediately following the silencing period spontaneous activity resumed. The method provides a promising avenue for tether free, remote, transient neuronal silencing in vivo for both scientific and therapeutic applications.

Magnetothermal genetic deep brain stimulation of motor behaviors in awake, freely moving mice.

Establishing how neurocircuit activation causes particular behaviors requires modulating the activity of specific neurons. Here, we demonstrate that magnetothermal genetic stimulation provides tetherless deep brain activation sufficient to evoke motor behavior in awake mice. The approach uses alternating magnetic fields to heat superparamagnetic nanoparticles on the neuronal membrane. Neurons, heat-sensitized by expressing TRPV1 are activated with magnetic field application. Magnetothermal genetic stimulation in the motor cortex evoked ambulation, deep brain stimulation in the striatum caused rotation around the body-axis, and stimulation near the ridge between ventral and dorsal striatum caused freezing-of-gait. The duration of the behavior correlated tightly with field application. This approach provides genetically and spatially targetable, repeatable and temporarily precise activation of deep-brain circuits without the need for surgical implantation of any device.

Model Driven Optimization of Magnetic Anisotropy of Exchange-coupled Core-Shell Ferrite Nanoparticles for Maximal Hysteretic Loss.

This study provides a guide to maximizing hysteretic loss by matching the design and synthesis of superparamagnetic nanoparticles to the desired hyperthermia application. The maximal heat release from magnetic nanoparticles to the environment depends on intrinsic properties of magnetic nanoparticles (e.g. size, magnetization, and magnetic anisotropy), and extrinsic properties of the applied fields (e.g. frequency, field strength). Often, the biomedical hyperthermia application limits flexibility in setting of many parameters (e.g. nanoparticle size and mobility, field strength and frequency). We show that core-shell nanoparticles combining a soft (Mn ferrite) and a hard (Co ferrite) magnetic material form a system in which the effective magnetic anisotropy can be easily tuned independently of the nanoparticle size. A theoretical framework to include the crystal anisotropy contribution of the Co ferrite phase to the nanoparticles total anisotropy is developed. The experimental results confirm that this framework predicts the hysteretic heating loss correctly when including non-linear effects in an effective susceptibility. Hence, we provide a guide on how to characterize the magnetic anisotropy of core-shell magnetic nanoparticles, model the expected heat loss and therefore, synthesize tuned nanoparticles for a particular biomedical application.