Super-resolution imaging of T lymphocyte activation reveals chromatin decondensation and disrupted nuclear envelope.

T lymphocyte activation plays a pivotal role in adaptive immune response and alters the spatial organization of nuclear architecture that subsequently impacts transcription activities. Here, using stochastic optical reconstruction microscopy (STORM), we observe dramatic de-condensation of chromatin and the disruption of nuclear envelope at a nanoscale resolution upon T lymphocyte activation. Super-resolution imaging reveals that such alterations in nuclear architecture are accompanied by the release of nuclear DNA into the cytoplasm, correlating with the degree of chromatin decompaction within the nucleus. The authors show that under the influence of metabolism, T lymphocyte activation de-condenses chromatin, disrupts the nuclear envelope, and releases DNA into the cytoplasm. Taken together, this result provides a direct, molecular-scale insight into the alteration in nuclear architecture. It suggests the release of nuclear DNA into the cytoplasm as a general consequence of chromatin decompaction after lymphocyte activation.

Analysis of the gut microbiome associated to PVC biodegradation in yellow mealworms.

The potential of invertebrates in the biodegradation of plastic polymers such as polyvinyl chloride (PVC) is receiving increasing attention. The present study is aimed to identify the gut microbiome involved in this degradation in yellow mealworms, i.e., the larvae of Tenebrio molitor Linnaeus. The egested PVC polymer experienced a dramatic reduction in both number average molecular weight (Mn) and weight average molecular weight (Mw) of 99.3% and 99.6%, respectively, whereas FTIR analysis revealed chemical alterations. Mass spectrometry analysis identified two potential degradation products: phthalic acid, di(2-propylpentyl) ester and 2-Propenoic acid, tridecyl ester. Further, we used metagenomic sequencing to elucidate the response of the gut microbiome when transitioning from bran to PVC as a food source, identifying four microorganisms actively involved in PVC degradation. Additionally, metagenomic functional analysis of the gut microbiome identified 111 key gene modules that were significantly enriched. In summary, our findings suggest that yellow mealworms adapt to PVC degradation by modifying their gut microbiome both structurally and functionally.

Flattened chains dominate the adsorption dynamics of loosely adsorbed chains on modified planar substrates.

Herein, the adsorption of polystyrene (PS) on phenyl-modified SiO2-Si substrates was investigated. Different from those for PS adsorption on a neat SiO2-Si substrate, the growth rate (vads) in the linear regime and hads/Rg (hads, thickness of flattened and loosely adsorbed layers on the substrate; Rg, radius of gyration) declined with increasing molecular weight (Mw) of PS and the phenyl content on the modified substrates, while the thickness of the flattened layer (hflat) and its coverage increased with increasing phenyl content. The results indicated that the adsorption of loose chains was controlled by the adsorption of flattened chains, as it only occurred in the empty contact sites remaining after the adsorption of flattened chains. Before approaching quasi-equilibrium (t < tcross), the number of flattened chain contact sites increased due to an enthalpically favorable process and, correspondingly, their spatial positions dynamically changed, which perturbed the adsorption of loose chains. When the adsorption of flattened chains reached quasi-equilibrium (t > tcross), the adsorption of loose chains was determined by the empty contact sites. The coverage of flattened chains and time to reach quasi-equilibrium were increased with more phenyl groups on the substrate, enhancing π-π interfacial interactions and resulting in a decreased adsorption rate and fewer loosely adsorbed chains. Mw-dependent vads and hads/Rg differed on phenyl-modified substrates compared to the neat SiO2-Si substrate owing to fewer empty contact sites for loose chains. The study findings improve our understanding of the mechanism responsible for the formation and structure of the adsorbed layer on solid surfaces.

Exploring the Molecular Origin for the Long-Range Propagation of the Substrate Effect in Unentangled Poly(methyl methacrylate) Films.

The polymer/substrate interface plays a significant role in the dynamics of nanoconfined polymers because of its suppression on polymer mobility and its long-range propagation feature, while the molecular origin of the long-range substrate effect in unentangled polymer material is still ambiguous. Herein, we investigated the propagation distances of the substrate effect (h*) by a fluorinated tracer-labeled method of two unentangled polymer films supported on silicon substrates: linear and ring poly(methyl methacrylate) films with relatively low molecular weights. The results indicate that the value of h* has a molecular weight dependence of h*∝N (N is the degree of polymerization) in the unentangled polymer films, while h*∝N1/2 was presented as previously reported in the entangled films. A theoretical model, depending on the polymer/polymer intermolecular interaction, was proposed to describe the above long-range propagation behavior of the substrate effect and agrees with our experiment results very well. From the model, it revealed that the intermolecular friction determines the long-range propagation of the substrate effect in the unentangled system, but the intermolecular entanglement is the dominant role in entangled system. These results give us a deeper understanding of the long-range substrate effect.

Loosely Adsorbed Chains Expedite the Desorption of Flattened Polystyrene Chains on Flat Silicon Surface.

Herein, the desorption of the adsorbed chains (including two regions of flattened chains and loosely adsorbed chains) was examined by monitoring the chain exchange kinetics between the adsorbed chains and the top-free chains in a bilayer system by using fluorine-labeled polystyrene (PS). The results indicated that the exchange behavior of PS-flattened chains with the top-free chains is much slower than that of PS-loose chains and has a strong molecular weight (MW) dependence. Interestingly, in the presence of loosely adsorbed chains, the desorption of flattened chains was accelerated greatly and had weaker MW dependency. We attribute the MW-dependent desorption phenomena to the average number of contact sites between polymer adsorbed chains and the substrate, which rapidly increased with increasing MW. Likewise, the desorption of loosely adsorbed chains may provide extra conformational energy to accelerate the desorption of flattened chains.

The Amyloid Precursor Protein Modulates the Position and Length of the Axon Initial Segment.

The amyloid precursor protein (APP) is linked to the genetics and pathogenesis of Alzheimer's disease (AD). It is the parent protein of the ß-amyloid (Aß) peptide, the main constituent of the amyloid plaques found in an AD brain. The pathways from APP to Aß are intensively studied, yet the normal functions of APP itself have generated less interest. We report here that glutamate stimulation of neuronal activity leads to a rapid increase in App gene expression. In mouse and human neurons, elevated APP protein changes the structure of the axon initial segment (AIS) where action potentials are initiated. The AIS is shortened in length and shifts away from the cell body. The GCaMP8f Ca2+ reporter confirms the predicted decrease in neuronal activity. NMDA antagonists or knockdown of App block the glutamate effects. The actions of APP on the AIS are cell-autonomous; exogenous Aß, either fibrillar or oligomeric, has no effect. In culture, APPSwe (a familial AD mutation) induces larger AIS changes than wild type APP. Ankyrin G and ßIV-spectrin, scaffolding proteins of the AIS, both physically associate with APP, more so in AD brains. Finally, in humans with sporadic AD or in the R1.40 AD mouse model, both females and males, neurons have elevated levels of APP protein that invade the AIS. In vivo as in vitro, this increased APP is associated with a significant shortening of the AIS. The findings outline a new role for the APP and encourage a reconsideration of its relationship to AD.SIGNIFICANCE STATEMENT While the amyloid precursor protein (APP) has long been associated with Alzheimer's disease (AD), the normal functions of the full-length Type I membrane protein have been largely unexplored. We report here that the levels of APP protein increase with neuronal activity. In vivo and in vitro, modest amounts of excess APP alter the properties of the axon initial segment. The ß-amyloid peptide derived from APP is without effect. Consistent with the observed changes in the axon initial segment which would be expected to decrease action potential firing, we show that APP expression depresses neuronal activity. In mouse AD models and human sporadic AD, APP physically associates with the scaffolding proteins of the axon initial segment, suggesting a relationship with AD dementia.

Changes in nuclear pore numbers control nuclear import and stress response of mouse hearts.

Nuclear pores are essential for nuclear-cytoplasmic transport. Whether and how cells change nuclear pores to alter nuclear transport and cellular function is unknown. Here, we show that rat heart muscle cells (cardiomyocytes) undergo a 63% decrease in nuclear pore numbers during maturation, and this changes their responses to extracellular signals. The maturation-associated decline in nuclear pore numbers is associated with lower nuclear import of signaling proteins such as mitogen-activated protein kinase (MAPK). Experimental reduction of nuclear pore numbers decreased nuclear import of signaling proteins, resulting in decreased expression of immediate-early genes. In a mouse model of high blood pressure, reduction of nuclear pore numbers improved adverse heart remodeling and reduced progression to lethal heart failure. The decrease in nuclear pore numbers in cardiomyocyte maturation and resulting functional changes demonstrate how terminally differentiated cells permanently alter their handling of information flux across the nuclear envelope and, with that, their behavior.

Enhanced Glass Transition Temperature of Thin Polystyrene Films Having an Underneath Cross-Linked Layer.

Due to the importance of the interface in the segmental dynamics of supported macromolecule ultrathin films, the glass transition temperature (Tg) of polystyrene (PS) ultrathin films upon solid substrates modified with a cross-linked PS (CLPS) layer has been investigated. The results showed that the Tg of the thin PS films on a silica surface with a ∼5 nm cross-linked layer increased with reducing film thickness. Meanwhile, the increase in Tg of the thin PS films became more pronounced with increasing the cross-linking density of the layer. For example, a 20 nm thick PS film supported on CLPS with 1.8 kDa of cross-linking degree exhibited a ∼35 and ∼50 K increase in Tg compared to its bulk and that on neat SiO2 substrate, respectively. Such a large Tg elevation for the ultrathin PS films was attributed to the interfacial aggregation states in which chains diffused through nanolevel voids formed in the cross-linked layer to the SiO2-Si surface. In such a situation, the chains were topologically constrained in the cross-linked layer with less mobility. These results offer us the opportunity to tailor interfacial effects by changing the degree of cross-linking, which has great potential application in many polymer nanocomposites.

Ultrastructural visualization of chromatin in cancer pathogenesis using a simple small-molecule fluorescent probe.

Imaging chromatin organization at the molecular-scale resolution remains an important endeavor in basic and translational research. Stochastic optical reconstruction microscopy (STORM) is a powerful superresolution imaging technique to visualize nanoscale molecular organization down to the resolution of ~20 to 30 nm. Despite the substantial progress in imaging chromatin organization in cells and model systems, its routine application on assessing pathological tissue remains limited. It is, in part, hampered by the lack of simple labels that consistently generates high-quality STORM images on the highly processed clinical tissue. We developed a fast, simple, and robust small-molecule fluorescent probe-cyanine 5-conjugated Hoechst-for routine superresolution imaging of nanoscale nuclear architecture on clinical tissue. We demonstrated the biological and clinical significance of imaging superresolved chromatin structure in cancer development and its potential clinical utility for cancer risk stratification.

The role of the molecular weight of the adsorbed layer on a substrate in the suppressed dynamics of supported thin polystyrene films.

The adsorbed layer on a solid surface plays a crucial role in the dynamics of nanoconfinement polymer materials. However, the influence of the adsorbed layer is complex, and clarifying this influence on the dynamics of confined polymers remains a major challenge. In this paper, SiO2-Si substrates with various thicknesses and adsorbed layers of PS with various molecular weights were used to reveal the effect of the adsorbed layer on the corresponding segmental dynamics of the supported thin PS films. Strongly suppressed segmental dynamics of thin PS films were observed for the films supported on thicker adsorbed layers or prepared using higher molecular weight. Neutron reflectivity revealed that the overlap region thickness between the adsorbed layer and the top overlayer increased with increasing thickness and molecular weight of the adsorbed layer, both of which correlate well with the distance over which the polystyrene dynamics were depressed by the adsorbed layer. The results show that the influencing distance of the adsorbed layer is related to the overlap zone formed between the adsorption layer and the upper thin film. The effect of the adsorbed layer molecular weight can be ascribed to the fact that large loops and long tails in the adsorbed layer result in stronger interpenetrations and entanglements between polymer chains in the adsorbed layer and in the overlayer, causing a stronger substrate effect and suppression of the segment dynamics of the supported thin PS films.

Safety and efficacy of thalidomide in patients with transfusion-dependent ß-thalassemia: a randomized clinical trial.

Thalidomide induces γ-globin expression in erythroid progenitor cells, but its efficacy on patients with transfusion-dependent ß-thalassemia (TDT) remains unclear. In this phase 2, multi-center, randomized, double-blind clinical trial, we aimed to determine the safety and efficacy of thalidomide in TDT patients. A hundred patients of 14 years or older were randomly assigned to receive placebo or thalidomide for 12 weeks, followed by an extension phase of at least 36 weeks. The primary endpoint was the change of hemoglobin (Hb) level in the patients. The secondary endpoints included the red blood cell (RBC) units transfused and adverse effects. In the placebo-controlled period, Hb concentrations in patients treated with thalidomide achieved a median elevation of 14.0 (range, 2.5 to 37.5) g/L, whereas Hb in patients treated with placebo did not significantly change. Within the 12 weeks, the mean RBC transfusion volume for patients treated with thalidomide and placebo was 5.4 ± 5.0 U and 10.3 ± 6.4 U, respectively (P < 0.001). Adverse events of drowsiness, dizziness, fatigue, pyrexia, sore throat, and rash were more common with thalidomide than placebo. In the extension phase, treatment with thalidomide for 24 weeks resulted in a sustainable increase in Hb concentrations which reached 104.9 ± 19.0 g/L, without blood transfusion. Significant increase in Hb concentration and reduction in RBC transfusions were associated with non ß0/ß0 and HBS1L-MYB (rs9399137 C/T, C/C; rs4895441 A/G, G/G) genotypes. These results demonstrated that thalidomide is effective in patients with TDT.

Enhanced super-resolution microscopy by extreme value based emitter recovery.

Super-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we investigate and validate an efficient approach, referred to as extreme value-based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we validated the accuracy of EVER in improving the fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.

Probing Chromatin Compaction and Its Epigenetic States in situ With Single-Molecule Localization-Based Super-Resolution Microscopy.

Chromatin organization play a vital role in gene regulation and genome maintenance in normal biological processes and in response to environmental insults. Disruption of chromatin organization imposes a significant effect on many cellular processes and is often associated with a range of pathological processes such as aging and cancer. Extensive attention has been attracted to understand the structural and functional studies of chromatin architecture. Biochemical assays coupled with the state-of-the-art genomic technologies have been traditionally used to probe chromatin architecture. Recent advances in single molecule localization microscopy (SMLM) open up new opportunities to directly visualize higher-order chromatin architecture, its compaction status and its functional states at nanometer resolution in the intact cells or tissue. In this review, we will first discuss the recent technical advantages and challenges of using SMLM to image chromatin architecture. Next, we will focus on the recent applications of SMLM for structural and functional studies to probe chromatin architecture in key cellular processes. Finally, we will provide our perspectives on the recent development and potential applications of super-resolution imaging of chromatin architecture in improving our understanding in diseases.

Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies.

The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.

Optimized Stochastic Optical Reconstruction Microscopy for Imaging Chromatin Structure in Pathological Tissue.

Direct visualization of higher-order chromatin structure at the molecular scale is of great importance for understanding the impact of chromatin organization on gene expression in many biological processes. Understanding the changes in chromatin structure during pathological processes requires the use of in vivo models and clinical samples, and formalin-fixed, paraffin-embedded (FFPE) tissue is the most widespread form of preservation. Here we describe the details of PathSTORM, an optimized stochastic optical reconstruction microscopy (STORM) protocol for high-quality super-resolution imaging of densely packed higher-order chromatin organization in pathological tissue. We discuss detailed methods for fluorescence staining of DNA and histone proteins, as well as the key technical factors for obtaining high-quality STORM images in pathological tissue samples. © 2020 Wiley Periodicals LLC Basic Protocol 1: Fluorescence staining of chromatin in pathological tissue Basic Protocol 2: STORM data processing Support Protocol 1: Drift correction Support Protocol 2: Image reconstruction Support Protocol 3: Hematoxylin & eosin (H&E) staining.

Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis.

Genomic DNA is folded into a higher-order structure that regulates transcription and maintains genomic stability. Although progress has been made on understanding biochemical characteristics of epigenetic modifications in cancer, the in-situ higher-order folding of chromatin structure during malignant transformation remains largely unknown. Here, using optimized stochastic optical reconstruction microscopy (STORM) for pathological tissue (PathSTORM), we uncover a gradual decompaction and fragmentation of higher-order chromatin folding throughout all stages of carcinogenesis in multiple tumor types, and prior to tumor formation. Our integrated imaging, genomic, and transcriptomic analyses reveal functional consequences in enhanced transcription activities and impaired genomic stability. We also demonstrate the potential of imaging higher-order chromatin disruption to detect high-risk precursors that cannot be distinguished by conventional pathology. Taken together, our findings reveal gradual decompaction and fragmentation of higher-order chromatin structure as an enabling characteristic in early carcinogenesis to facilitate malignant transformation, which may improve cancer diagnosis, risk stratification, and prevention.

Glass transition temperature of single-chain polystyrene particles end-grafted to oxide-coated silicon.

A method based on the PeakForce QNM atomic force microscopic (AFM) adhesion measurement is employed to investigate the glassy dynamics of polystyrene (PS) single-chain particles end-grafted to SiO2-Si substrates with different diameters, D0, of 3.4 nm-8.8 nm and molar masses, Mn, of 8-123 kg/mol. As temperature was increased, the adhesion force, Fad, experienced by the AFM tip on pulling off the single chains after loading demonstrated a stepwise increase at an elevated temperature, which we identified to be Tg based on previous works. Our result shows that Tg of our grafted single chains increases with Mn in a manner consistent with the Fox-Flory equation, but the coefficient quantifying the Mn dependence of Tg is only (36 ± 6)% the value of bulk PS. In addition, the value of Tg in the Mn → ∞ limit is about 25 °C below the bulk Tg but more than 15 °C above that of (untethered) PS nanoparticles with D0 ≈ 100 nm suspended in a solution. Our findings are consistent with Tg of our single chains being dominated by simultaneous effects of the interfaces, which depress Tg, and end-grafting, which enhances Tg. The latter is believed to exert its influence on the glass transition dynamics by a mechanism reliant on chain connectivity and does not vary with chain length.

A guide to visualizing the spatial epigenome with super-resolution microscopy.

Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.

WindSTORM: Robust online image processing for high-throughput nanoscopy.

High-throughput nanoscopy becomes increasingly important for unraveling complex biological processes from a large heterogeneous cell population at a nanoscale resolution. High-density emitter localization combined with a large field of view and fast imaging frame rate is commonly used to achieve a high imaging throughput, but the image processing speed and the presence of heterogeneous background in the dense emitter scenario remain a bottleneck. Here, we present a simple non-iterative approach, referred to as WindSTORM, to achieve high-speed high-density emitter localization with robust performance for various image characteristics. We demonstrate that WindSTORM improves the computation speed by two orders of magnitude on CPU and three orders of magnitude upon GPU acceleration to realize online image processing, without compromising localization accuracy. Further, WindSTORM is highly robust to maximize the localization accuracy and minimize the image artifacts in the presence of nonuniform background. WindSTORM paves the way for next generation high-throughput nanoscopy.