A change in biophysical properties accompanies heterochromatin formation in mouse embryos.

The majority of our genome is composed of repeated DNA sequences that assemble into heterochromatin, a highly compacted structure that constrains their mutational potential. How heterochromatin forms during development and how its structure is maintained are not fully understood. Here, we show that mouse heterochromatin phase-separates after fertilization, during the earliest stages of mammalian embryogenesis. Using high-resolution quantitative imaging and molecular biology approaches, we show that pericentromeric heterochromatin displays properties consistent with a liquid-like state at the two-cell stage, which change at the four-cell stage, when chromocenters mature and heterochromatin becomes silent. Disrupting the condensates results in altered transcript levels of pericentromeric heterochromatin, suggesting a functional role for phase separation in heterochromatin function. Thus, our work shows that mouse heterochromatin forms membrane-less compartments with biophysical properties that change during development and provides new insights into the self-organization of chromatin domains during mammalian embryogenesis.

Profiling phagosome proteins identifies PD-L1 as a fungal-binding receptor.

Phagocytosis is the process by which myeloid phagocytes bind to and internalize potentially dangerous microorganisms1. During phagocytosis, innate immune receptors and associated signalling proteins are localized to the maturing phagosome compartment, forming an immune information processing hub brimming with microorganism-sensing features2-8. Here we developed proximity labelling of phagosomal contents (PhagoPL) to identify proteins localizing to phagosomes containing model yeast and bacteria. By comparing the protein composition of phagosomes containing evolutionarily and biochemically distinct microorganisms, we unexpectedly identified programmed death-ligand 1 (PD-L1) as a protein that specifically enriches in phagosomes containing yeast. We found that PD-L1 directly binds to yeast upon processing in phagosomes. By surface display library screening, we identified the ribosomal protein Rpl20b as a fungal protein ligand for PD-L1. Using an auxin-inducible depletion system, we found that detection of Rpl20b by macrophages cross-regulates production of distinct cytokines including interleukin-10 (IL-10) induced by the activation of other innate immune receptors. Thus, this study establishes PhagoPL as a useful approach to quantifying the collection of proteins enriched in phagosomes during host-microorganism interactions, exemplified by identifying PD-L1 as a receptor that binds to fungi.

ONECUT2 acts as a lineage plasticity driver in adenocarcinoma as well as neuroendocrine variants of prostate cancer.

Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.

Historic dog Furs Unravel the Origin and Artificial Selection of Modern Nordic Lapphund and Elkhound dog Breeds.

The origins and extreme morphological evolution of the modern dog breeds are poorly studied because the founder populations are extinct. Here, we analyse eight 100 to 200 years old dog fur samples obtained from traditional North Swedish clothing, to explore the origin and artificial selection of the modern Nordic Lapphund and Elkhound dog breeds. Population genomic analysis confirmed the Lapphund and Elkhound breeds to originate from the local dog population, and showed a distinct decrease in genetic diversity in agreement with intense breeding. We identified eleven genes under positive selection during the breed development. In particular, the MSRB3 gene, associated with breed-related ear morphology, was selected in all Lapphund and Elkhound breeds, and functional assays showed that a SNP mutation in the 3'UTR region suppresses its expression through miRNA regulation. Our findings demonstrate analysis of near-modern dog artifacts as an effective tool for interpreting the origin and artificial selection of the modern dog breeds.

USP3 plays a critical role in the induction of innate immune tolerance.

Microbial products, such as lipopolysaccharide (LPS), can elicit efficient innate immune responses against invading pathogens. However, priming with LPS can induce a form of innate immune memory, termed innate immune "tolerance", which blunts subsequent NF-κB signaling. Although epigenetic and transcriptional reprogramming has been shown to play a role in innate immune memory, the involvement of post-translational regulation remains unclear. Here, we report that ubiquitin-specific protease 3 (USP3) participates in establishing "tolerance" innate immune memory through non-transcriptional feedback. Upon NF-κB signaling activation, USP3 is stabilized and exits the nucleus. The cytoplasmic USP3 specifically removes the K63-linked polyubiquitin chains on MyD88, thus negatively regulating TLR/IL1ß-induced inflammatory signaling activation. Importantly, cytoplasmic translocation is a prerequisite step for USP3 to deubiquitinate MyD88. Additionally, LPS priming could induce cytoplasmic retention and faster and stronger cytoplasmic translocation of USP3, enabling it to quickly shut down NF-κB signaling upon the second LPS challenge. This work identifies a previously unrecognized post-translational feedback loop in the MyD88-USP3 axis, which is critical for inducing normal "tolerance" innate immune memory.

Assembly of the WHIP-TRIM14-PPP6C Mitochondrial Complex Promotes RIG-I-Mediated Antiviral Signaling.

Mitochondrial antiviral signaling platform protein (MAVS) acts as a central hub for RIG-I receptor proximal signal propagation. However, key components in the assembly of the MAVS mitochondrial platform that promote RIG-I mitochondrial localization and optimal activation are still largely undefined. Employing pooled RNAi and yeast two-hybrid screenings, we report that the mitochondrial adaptor protein tripartite motif (TRIM)14 provides a docking platform for the assembly of the mitochondrial signaling complex required for maximal activation of RIG-I-mediated signaling, consisting of WHIP and protein phosphatase PPP6C. Following viral infection, the ubiquitin-binding domain in WHIP bridges RIG-I with MAVS by binding to polyUb chains of RIG-I at lysine 164. The ATPase domain in WHIP contributes to stabilization of the RIG-I-dsRNA interaction. Moreover, phosphatase PPP6C is responsible for RIG-I dephosphorylation. Together, our findings define the WHIP-TRIM14-PPP6C mitochondrial signalosome required for RIG-I-mediated innate antiviral immunity.

ONECUT2 regulates RANKL-dependent enterocyte and microfold cell differentiation in the small intestine; a multi-omics study.

Microfold (M) cells reside in the intestinal epithelium of Peyer's patches (PP). Their unique ability to take up and transport antigens from the intestinal lumen to the underlying lymphoid tissue is key in the regulation of the gut-associated immune response. Here, we applied a multi-omics approach to investigate the molecular mechanisms that drive M cell differentiation in mouse small intestinal organoids. We generated a comprehensive profile of chromatin accessibility changes and transcription factor dynamics during in vitro M cell differentiation, allowing us to uncover numerous cell type-specific regulatory elements and associated transcription factors. By using single-cell RNA sequencing, we identified an enterocyte and M cell precursor population. We used our newly developed computational tool SCEPIA to link precursor cell-specific gene expression to transcription factor motif activity in cis-regulatory elements, uncovering high expression of and motif activity for the transcription factor ONECUT2. Subsequent in vitro and in vivo perturbation experiments revealed that ONECUT2 acts downstream of the RANK/RANKL signalling axis to support enterocyte differentiation, thereby restricting M cell lineage specification. This study sheds new light on the mechanism regulating cell fate balance in the PP, and it provides a powerful blueprint for investigation of cell fate switches in the intestinal epithelium.

High-Throughput Identification of Single Nanoparticles via Electrochemically Assisted High-Resolution Plasmonic Scattering Interferometric Microscopy.

The identification of nanoparticles within heterogeneous mixtures poses significant challenges due to the similarity in physical properties among different nanomaterials. Here, we present electrochemically assisted high-resolution plasmonic scattering interferometric microscopy (HR-PSIM). This technique allows for the high-throughput identification of nanoparticles by accurately measuring the refractive index of individual nanoparticles without interference from background signals. Through elimination of parabolic scattering interference and employing electrochemical modulation, HR-PSIM demonstrates high spatial resolution and stability against background noise, enabling the differentiation of nanoparticles with closely matched refractive indices, such as Au and Ag nanoparticles. The efficacy of this method is demonstrated through its application in real-time, label-free imaging of nanoparticle electrochemical activity, providing a platform for the precise and high-throughput characterization of nanomaterials. The robustness of our approach against electrochemical interference and its high spatial resolution mark a significant advancement in the field of nanomaterial analysis, promising wide-ranging applications in nanoparticle research and beyond.

Geometric Similarities and Topological Phases in Surface Magnon Polaritons.

Surface polaritons have proven to be uniquely capable of controlling light-matter interactions. Here we explore surface magnon polaritons in low-loss ferrimagnetic semiconductors, with a focus on their topological phases. We propose several surface magnon polariton devices, including microwave resonators that can strongly enhance magnetic fields and low-loss interconnects joining waveguides with vastly different impedances. Our work can facilitate the exploration of topological phases in polaritons and the development of topological microwave devices for quantum sensing and information processing.

Slow-Wave Hybrid Magnonics.

Cavity magnonics is an emerging research area focusing on the coupling between magnons and photons. Despite its great potential for coherent information processing, it has been long restricted by the narrow interaction bandwidth. In this Letter, we theoretically propose and experimentally demonstrate a novel approach to achieve broadband photon-magnon coupling by adopting slow waves on engineered microwave waveguides. To the best of our knowledge, this is the first time that slow wave is combined with hybrid magnonics. Its unique properties promise great potentials for both fundamental research and practical applications, for instance, by deepening our understanding of the light-matter interaction in the slow wave regime and providing high-efficiency spin wave transducers. The device concept can be extended to other systems such as optomagnonics and magnomechanics, opening up new directions for hybrid magnonics.

Human milk oligosaccharides and the association with microbiota in colostrum: a pilot study.

HMOs (Human milk oligosaccharide) has an impact on maternal and infant health. Colostrum samples of 70 breastfeeding women in China were collected and recorded clinical characteristics. The major oligosaccharides and microbiota were quantitated in colostrum. The concentration of fucosylated HMOs in primipara was higher than that of multipara (p = 0.030). The concentration of N-acetylated HMOs in vaginal delivery milk was less than that of cesarean (p = 0.038). Non-fucosylated HMOs of breastfeeding women were less than that of breast pump (p = 0.038). Meanwhile, the concentration of LNT was positively correlated with Lactobacillus (r = 0.250, p = 0.037). DS-LNT was negatively correlated with Staphylococcus (r = - 0.240, p = 0.045). There was a positive correlation of Streptococcus with LNFP II (r = 0.314, p = 0.011) and 3-SL (r = 0.322, p = 0.009). In addition, there was a negative correlation between 2'-FL and 3-FL (r = - 0.465, p = 0.001). There was a positive correlation between LNT and LNnT (r = 0.778, p = 0.001). Therefore, the concentration of HMOs is related to number of deliveries, delivery mode, lactation mode and perinatal antibiotic. The concentration of HMOs is related to Lactobacillus, Streptococcus and Streptococcus in colostrum. In addition, there are connections between different oligosaccharides in content. The study protocol was also registered in the ClinicalTrails.gov (ChiCTR2200064454) (Oct. 2022).

LNCHC directly binds and regulates YBX1 stability to ameliorate metabolic dysfunction-associated steatotic liver disease progression.

BACKGROUND AND AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) represents the foremost cause of chronic liver disease, yet its underlying mechanisms remain elusive. Our group previously discovered a novel long non-coding RNA (lncRNA) in rats, termed lncHC and its human counterpart, LNCHC. This study aimed to explore the role of LNCHC in the progression of MASLD. METHODS: RNA-binding proteins bound to LNCHC were searched by mass spectrometry. The target genes of LNCHC and Y-Box binding protein 1 (YBX1) were identified by RNA-seq. MASLD animal models were utilised to examine the roles of LNCHC, YBX1 and patatin-like phospholipase domain containing 3 (PNPLA3) in MASLD progression. RESULTS: Here, we identified LNCHC as a native restrainer during MASLD development. Notably, LNCHC directly binds YBX1 and prevents protein ubiquitination. Up-regulation of YBX1 then stabilises PNPLA3 mRNA to alleviate lipid accumulation in hepatocytes. Furthermore, both cell and animal studies demonstrate that LNCHC, YBX1 and PNPLA3 function to improve hepatocyte lipid accumulation and exacerbate metabolic dysfunction-associated steatohepatitis development. CONCLUSIONS: In summary, our findings unveil a novel LNCHC functionality in regulating YBX1 and PNPLA3 mRNA stability during MASLD development, providing new avenues in MASLD treatment.

Enantioselective Synthesis of P-Chirogenic 1,2,3-Triazolobenzophospholes.

An enantioselective synthesis of a new class of benzophosphole-based heterocycles bearing a fused triazole ring with enantioselectivities of ≤99% is reported. The key steps of the synthesis are based on an innovative stereospecific phosphinyl N â†’ O migration of aminophosphine-boranes into phosphinites, followed by an intramolecular cyclization. Five X-ray structures of P-chirogenic triazolobenzophospholes and a gold(I) complex were established, for assigning absolute configurations, the stereochemistry of the reactions, and the placement of the triazole substituent at the syn position of the P center.

Kyphoplasty is associated with reduced mortality risk for osteoporotic vertebral compression fractures: a systematic review and meta-analysis.

BACKGROUND: Vertebral augmentation, such as vertebroplasty (VP) or kyphoplasty (KP), has been utilized for decades to treat OVCFs; however, the precise impact of this procedure on reducing mortality risk remains a topic of controversy. This study aimed to explore the potential protective effects of vertebral augmentation on mortality in patients with osteoporotic vertebral compression fractures (OVCFs) using a large-scale meta-analysis. MATERIALS AND METHODS: Cochrane Library, Embase, MEDLINE, PubMed and Web of Science databases were employed for literature exploration until May 2023. The hazard ratios (HRs) and 95% confidence intervals (CIs) were utilized as a summary statistic via random-effect models. Statistical analysis was executed using Review Manager 5.3 software. RESULTS: After rigorous screening, a total of five studies with substantial sample sizes were included in the quantitative meta-analysis. The total number of participants included in the study was an 2,421,178, comprising of 42,934 cases of vertebral augmentation and 1,991,244 instances of non-operative management. The surgical intervention was found to be significantly associated with an 18% reduction in the risk of mortality (HR 0.82; 95% CI 0.78, 0.85). Subgroup analysis revealed a remarkable 71% reduction in mortality risk following surgical intervention during short-term follow-up (HR 0.29; 95% CI 0.26, 0.32). Furthermore, KP exhibited a superior and more credible decrease in the risk of mortality when compared to VP treatment. CONCLUSIONS: Based on a comprehensive analysis of large samples, vertebral augmentation has been shown to significantly reduce the mortality risk associated with OVCFs, particularly in the early stages following fractures. Furthermore, it has been demonstrated that KP is more reliable and effective than VP in terms of mitigating mortality risk.

Boronic functionalized aptamer macroarrays with dual-recognition and isothermal amplification of lipopolysaccharide detection.

A highly sensitive dual-recognition fluorescence amplification method is presented for lipopolysaccharide (LPS) detection based on boronic functionalized aptamer macroarrays with dual-recognition and isothermal amplification. The surface of the polystyrene microplate was firstly carboxylated, and then, 3-aminophenylboronic acid was conjugated to the carboxyl groups through EDC/NHS reaction, creating boronic acid groups as the capture moiety for LPS. A recognition DNA aptamer labeled with the fluorescent dye 6-FAM, which exhibits specificity towards LPS, was selected as the signal reporting moiety. By introducing primers and Klenow enzyme, the fluorescent-labeled aptamers are released from the microplate bottom, and double-stranded structures were formed via isothermal amplification. The addition of SYBR Green I, which strongly fluoresces upon binding to the double-stranded structures, enables signal amplification and detection. This detection method exhibits a linear range of 1-10,000 ng/mL and has a detection limit as low as 401.93 pg/mL. This analytical approach shows high selectivity and sensitivity and may serve as a universal platform in lipopolysaccharide detection.

Role of Polarization Interactions in the Formation of Dipole-Bound States.

Even though there is a critical dipole moment required to support a dipole-bound state (DBS), how molecular polarizability may influence the formation of DBSs is not well understood. Pyrrolide, indolide, and carbazolide provide an ideal set of anions to systematically examine the role of polarization interactions in the formation of DBSs. Here, we report an investigation of carbazolide using cryogenic photodetachment spectroscopy and high-resolution photoelectron spectroscopy (PES). A polarization-assisted DBS is observed at 20 cm-1 below the detachment threshold for carbazolide, even though the carbazolyl neutral core has a dipole moment (2.2 D) smaller than the empirical critical value (2.5 D) to support a dipole-bound state. Photodetachment spectroscopy reveals nine vibrational Feshbach resonances of the DBS, as well as three intense and broad shape resonances. The electron affinity of carbazolyl is measured accurately to be 2.5653 ± 0.0004 eV (20,691 ± 3 cm-1). The combination of photodetachment spectroscopy and resonant PES allows fundamental frequencies for 14 vibrational modes of carbazolyl to be measured. The three shape resonances are due to above-threshold excitation to the three low-lying electronic states (S1-S3) of carbazolide. Resonant PES of the shape resonances is dominated by autodetachment processes. Ultrafast relaxation from the S2 and S3 states to S1 is observed, resulting in constant kinetic energy features in the resonant PES. The current study provides decisive information about the role that polarization plays in the formation of DBSs, as well as rich spectroscopic information about the carbazolide anion and the carbazolyl radical.

High-Resolution, High-Throughput Plasmonic Imaging of Nanomaterials.

Label-free imaging of nanoscale targets with intrinsic properties is crucial for chemistry, physics, and life science to unveil the underlying mechanisms. Plasmonic imaging techniques are particularly attractive because they allow real-time imaging, providing insights into nanoscale detection and nanocatalysis. Here, we present a high-resolution plasmonic imaging method that is capable of imaging nanomaterials with high morphological fidelity and high throughput. We demonstrate that this approach allows for high-resolution plasmonic imaging of various nanomaterials ranging from nanoparticles and nanowires to two-dimensional nanomaterials and accurate tracking of the interfacial dynamics of nanoparticles. Given the experimental simplicity and capacity for label-free and real-time imaging of nanomaterials with high spatial resolution and high throughput, this approach can serve as a promising platform for characterizing nanomaterials at the single-particle level.

Plasmonic Probing of Deoxyribonucleic Acid Hybridization at the Single Base Pair Resolution.

Partial DNA duplex formation greatly impacts the quality of DNA hybridization and has been extensively studied due to its significance in many biological processes. However, traditional DNA sensing methods suffer from time-consuming amplification steps and hinder the acquisition of information about single-molecule behavior. In this work, we developed a plasmonic method to probe the hybridization process at a single base pair resolution and study the relationship between the complementarity of DNA analytes and DNA hybridization behaviors. We measured single-molecule hybridization events with Au NP-modified ssDNA probes in real time and found two hybridization adsorption events: stable and transient adsorption. The ratio of these two hybridization adsorption events was correlated with the length of the complementary sequences, distinguishing DNA analytes from different complementary sequences. By using dual incident angle excitation, we recognized different single-base complementary sequences. These results demonstrated that the plasmonic method can be applied to study partial DNA hybridization behavior and has the potential to be incorporated into the identification of similar DNA sequences, providing a sensitive and quantitative tool for DNA analysis.

Using Rayleigh Scattering to Correct the Inner Filter Effect of the Fluorescence Excitation-Emission Matrix.

Excitation-emission matrix (EEM) spectroscopy has been proven to be an effective tool for offline fluorescence analysis. However, the pretreatment of EEM data requires an additional ultraviolet-visible (UV-vis) absorption spectrum for inner filter effect (IFE) correction. This complicates the instrument structure and increases the test flow, thus hindering the practical application of EEM in environmental online monitoring. In this work, Rayleigh scattering in EEM, which is often masked, is leveraged to address this challenge as Rayleigh scattering light itself passes through the sample and experiences absorption. We establish a translation-corrected estimation by the Rayleigh scattering (TCERS) method to estimate absorbance, not only enabling the IFE self-correction of EEM but also providing orthogonal spectroscopy information. TCERS is hierarchically tested in real solutions, simulated turbid liquids, and various natural water samples. Results indicate that the predicted UV-vis absorption spectra have a cosine similarity of over 0.95 with the actual spectra. When using the predicted spectra to correct the IFE of EEM, only about 0.005/1.440 bits of information entropy are lost and the absolute errors in EEM are negligible. The proposed method has the potential to streamline the design of fluorescence spectrometers, making it possible to miniaturize, optimize, and popularize these instruments for various practical applications such as environmental monitoring.

piRNA-30473 contributes to tumorigenesis and poor prognosis by regulating m6A RNA methylation in DLBCL.

The initiation and progression of diffuse large B-cell lymphoma (DLBCL) is governed by genetic and epigenetic aberrations. As the most abundant eukaryotic messenger RNA (mRNA) modification, N6-methyladenosine (m6A) is known to influence various fundamental bioprocesses by regulating the target gene; however, the function of m6A modifications in DLBCL is unclear. PIWI-interacting RNAs (piRNAs) have been indicated to be epigenetic effectors in cancer. Here, we show that high expression of piRNA-30473 supports the aggressive phenotype of DLBCL, and piRNA-30473 depletion decreases proliferation and induces cell cycle arrest in DLBCL cells. In xenograft DLBCL models, piRNA-30473 inhibition reduces tumor growth. Moreover, piRNA-30473 is significantly associated with overall survival in a univariate analysis and is statistically significant after adjusting for the National Comprehensive Cancer Network-International Prognostic Index in the multivariate analysis. Additional studies demonstrate that piRNA-30473 exerts its oncogenic role through a mechanism involving the upregulation of WTAP, an m6A mRNA methylase, and thus enhances the global m6A level. Integrating transcriptome and m6A-sequencing analyses reveals that WTAP increases the expression of its critical target gene, hexokinase 2 (HK2), by enhancing the HK2 m6A level, thereby promoting the progression of DLBCL. Together, the piRNA-30473/WTAP/HK2 axis contributes to tumorigenesis by regulating m6A RNA methylation in DLBCL. Furthermore, by comprehensively analyzing our clinical data and data sets, we discover that the m6A regulatory genes piRNA-30473 and WTAP improve survival prediction in DLBCL patients. Our study highlights the functional importance of the m6A modification in DLBCL and might assist in the development of a prognostic stratification and therapeutic approach for DLBCL.