Defocus-integration interferometric scattering microscopy for speckle suppression and enhancing nanoparticle detection on a substrate.

Direct optical detection and imaging of single nanoparticles on a substrate in wide field underpin vast applications across different research fields. However, speckles originating from the unavoidable random surface undulations of the substrate ultimately limit the size of the decipherable nanoparticles by the current optical techniques, including the ultrasensitive interferometric scattering microscopy (iSCAT). Here, we report a defocus-integration iSCAT to suppress the speckle noise and to enhance the detection and imaging of single nanoparticles on an ultra-flat glass substrate and a silicon wafer.

B-Cell Receptor Repertoire: Recent Advances in Autoimmune Diseases.

In the field of contemporary medicine, autoimmune diseases (AIDs) are a prevalent and debilitating group of illnesses. However, they present extensive and profound challenges in terms of etiology, pathogenesis, and treatment. A major reason for this is the elusive pathophysiological mechanisms driving disease onset.

Aberrant H3K4me3 modification of immune response genes in CD4 T cells of patients with systemic lupus erythematosus.

Background: Increasing evidence has highlighted the significant role of histone modifications in pathogenesis of systemic lupus erythematosus (SLE). However, few studies have comprehensively analyzed trimethylation of histone H3 lysine 4 (H3K4me3) features at specific immune gene loci in SLE patients.

Methods: We conducted H3K4me3 chromatin immunoprecipitation sequencing (ChIP-seq) on CD4 T cells from SLE patients and healthy controls (HC).

Tunable all-optical microwave logic gates based on nonreciprocal topologically protected edge modes.

All-optical logic gates have been studied intensively owing to their potential to enable broadband, low-loss and high-speed communications. However, poor tunability has remained a key challenge in this field. In this work, we propose a Y-shaped structure composed of Yttrium Iron Garnet (YIG) layers that can serve as tunable all-optical logic gates, including, but not limited to, OR, AND and NOT gates, by applying external magnetic fields to magnetize the YIG layers.

3D genome organization and epigenetic regulation in autoimmune diseases.

Three-dimensional (3D) genomics is an emerging field of research that investigates the relationship between gene regulatory function and the spatial structure of chromatin. Chromatin folding can be studied using chromosome conformation capture (3C) technology and 3C-based derivative sequencing technologies, including chromosome conformation capture-on-chip (4C), chromosome conformation capture carbon copy (5C), and high-throughput chromosome conformation capture (Hi-C), which allow scientists to capture 3D conformations from a single site to the entire genome. A comprehensive analysis of the relationships between various regulatory components and gene function also requires the integration of multi-omics data such as genomics, transcriptomics, and epigenomics.

mA methyltransferase METTL3 programs CD4 T-cell activation and effector T-cell differentiation in systemic lupus erythematosus.

Background: Systemic lupus erythematosus (SLE) is an autoimmune disorder in which excessive CD4 T-cell activation and imbalanced effector T-cell differentiation play critical roles. Recent studies have implied a potential association between posttranscriptional N6-methyladenosine (mA) modification and CD4 T-cell-mediated humoral immunity. However, how this biological process contributes to lupus is not well understood.

Integrated analysis of ATAC-seq and RNA-seq reveals the transcriptional regulation network in SLE.

Background: CD4 T cells have a vital role in the pathogenesis of systemic lupus erythematosus (SLE), abnormal gene expression in CD4 T cells partly accounting for dysfunctional CD4T cells. However, the underying regulatory mechanisms of abnormal gene expression in CD4 T cells derived from SLE patients are not fully understood.

Methods: The peripheral blood CD4 T cells were acquired from 4 SLE patients and 4 matched healthy controls.

3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus.

Objectives: Three-dimensional (3D) genome alterations can dysregulate gene expression by rewiring physical interactions within chromosomes in a tissue-specific or cell-specific manner and lead to diseases. We aimed to elucidate the 3D genome structure and its role in gene expression networks dysregulated in systemic lupus erythematosus (SLE).

Methods: We performed Hi-C experiments using CD4 T cells from 7 patients with SLE and 5 age-matched and sex-matched healthy controls (HCs) combined with RNA sequencing analysis.

Optical Fingerprint of Flat Substrate Surface and Marker-Free Lateral Displacement Detection with Angstrom-Level Precision.

We report that flat substrates such as glass coverslips with surface roughness well below 0.5 nm feature notable speckle patterns when observed with high-sensitivity interference microscopy. We uncover that these speckle patterns unambiguously originate from the subnanometer surface undulations, and develop an intuitive model to illustrate how subnanometer nonresonant dielectric features could generate pronounced interference contrast in the far field.

Chromatin organizer SATB1 controls the cell identity of CD4 CD8 double-positive thymocytes by regulating the activity of super-enhancers.

CD4 and CD8 double-positive (DP) thymocytes play a crucial role in T cell development in the thymus. DP cells rearrange the T cell receptor gene Tcra to generate T cell receptors with TCRβ. DP cells differentiate into CD4 or CD8 single-positive (SP) thymocytes, regulatory T cells, or invariant nature kill T cells (iNKT) in response to TCR signaling.

Anomalous band center localization in the one-dimensional Anderson model with a disordered distribution of infinite variance.

We perform a detailed numerical study of the influence of distributions without a finite second moment on the Lyapunov exponent through the one-dimensional tight-binding Anderson model with diagonal disorder. Using the transfer matrix parametrization method and considering a specific distribution function, we calculate the Lyapunov exponent numerically and demonstrate its relation with the fractional lower order moments of the disorder probability density function. For the lower order of moments of disorder distribution with an infinite variance, we obtain the anomalous behavior near the band center.

Phase separation of Epstein-Barr virus EBNA2 protein reorganizes chromatin topology for epigenetic regulation.

Epstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by reorganizing chromatin and manipulating epigenetics. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation.

Slow wave and truly rainbow trapping in a one-way terahertz waveguide.

Slowing down or even trapping electromagnetic (EM) waves attract researchers' attention for its potential applications in energy storage, optical signal processing and nonlinearity enhancement. However, conventional trapping, in fact, is not truly trapping because of the existence of strong coupling effects and reflections. In this paper, a novel metal-semiconductor-semiconductor-metal (MSSM) heterostructure is presented, and novel truly rainbow trapping of terahertz waves is demonstrated based on a tapered MSSM structure.

The role of chromatin organizer Satb1 in shaping TCR repertoire in adult thymus.

T cells recognize the universe of foreign antigens with a diverse repertoire of T cell receptors generated by V(D)J recombination. Special AT-rich binding protein 1 (Satb1) is a chromatin organizer that plays an essential role in T cell development. Previous study has shown that Satb1 regulates the re-induction of recombinase Rag1 and Rag2 in CD4CD8 thymocytes, affecting the secondary rearrangement of the gene.

HiCoP, a simple and robust method for detecting interactions of regulatory regions.

Background: Chromatin physical interactions provide essential information for understanding the regulation of cis-elements like enhancers, promoters, and insulators in cell development and differentiation. The Hi-C assay is a technique detecting chromatin structures of the whole genome, but not sensitive to interactions of regulatory elements. Several methods, like HiChIP, DNase-C, and OCEAN-C, have been developed for enriching interactions of regulatory regions, but all of them have some shortcomings.

Localization behavior induced by asymmetric disorder for the one-dimensional Anderson model.

The behavior of the Lyapunov exponent under a small asymmetric disorder distribution is investigated for the one-dimensional Anderson model in the vicinity of the band center and for finite in-band energies. The special effect that could be found in systems with an asymmetric disorder distribution is shown to be small through a perturbation calculation. We obtain a quadratic formula for the Lyapunov exponent and show the enhancement of localization close to the band center induced by asymmetric disorder distribution.

Transcriptomic Analysis of mRNA-lncRNA-miRNA Interactions in Hepatocellular Carcinoma.

Fully elucidating the molecular mechanisms of non-coding RNAs (ncRNAs), including micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), underlying hepatocarcinogenesis is challenging. We characterized the expression profiles of ncRNAs and constructed a regulatory mRNA-lncRNA-miRNA (MLMI) network based on transcriptome sequencing (RNA-seq) of hepatocellular carcinoma (HCC, n = 9) patients. Of the identified miRNAs (n = 203) and lncRNAs (n = 1,090), we found 16 significantly differentially expressed (DE) miRNAs and three DE lncRNAs.

[The improvewment of DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing].

Objective: To optimize DNA library construction in non-crosslinked chromatin immunoprecipitation coupled with next-generation sequencing (Native ChIP-seq) to obtain high-quality Native ChIP-seq data.

Methods: Human nasopharyngeal carcinoma HONE1 cell lysate was digested with MNase for release of the nucleosomes, and the histone-DNA complexes were immunoprecipitated with specific antibodies. The protein component in the precipitate was digested with proteinase K followed by DNA purification; the DNA library was constructed for sequence analysis.

Actions of water extract from Cordyceps militaris in hyperuricemic mice induced by potassium oxonate combined with hypoxanthine.

Ethnopharmacological Relevance: Cordyceps militaris was recorded in the classic traditional Chinese medicine book with the main functions of "protecting liver and enhancing kidney functions", influencing serum uric acid levels.

Aim Of Study: The aim is to investigate the hypouricemic effects and possible mechanism of C. militaris in hyperuricemic mice.