Confined growth of Ag nanogap shells emitting stable Raman label signals for SERS liquid biopsy of pancreatic cancer.

To develop a reliable surface-enhanced Raman scattering (SERS) immunoassay as a new liquid biopsy modality, SERS nanoprobes emitting strong and stable signals are necessary. However, Ag nanoparticles used as SERS nanoprobes are prone to rapid fading of SERS signals by oxidation. This has driven the development of a new strategy for Ag-based SERS nanoprobes emitting stable and strong SERS signals over time. Herein, Ag nanogap shells entrapping Raman labels are created in the confined pores of mesoporous silica nanoparticles (AgNSM) through a rapid single-step reaction for SERS liquid biopsy. Each AgNSM nanoprobe possesses multiple nanogaps of 1.58 nm to entrap Raman labels, allowing superior long-term SERS signal stability and large enhancement of 1.5 × 106. AgNSM nanoprobes conjugated with an antibody specific for carbohydrate antigen (CA)19-9 are employed in the SERS sandwich immunoassay including antibody-conjugated magnetic nanoparticles for CA19-9 detection, showing a two orders of magnitude lower limit of detection (0.025 U mL-1) than an enzyme-linked immunosorbent assay (0.3 U mL-1). The AgNSM nanoprobe immunoassay accurately quantifies CA19-9 levels from clinical serum samples of early and advanced pancreatic cancer. AgNSM nanoprobes with stable SERS signals provide a new route to SERS liquid biopsy for effective detection of blood biomarkers.

Microbial succession during button mushroom (Agaricus bisporus) production evaluated via high-throughput sequencing.

Button mushrooms (Agaricus bisporus), are one of the most widely consumed mushrooms in the world. However, changes within its microbial community as it relates to the use of different raw materials and cultivation methods, as well as potential points of microbial contamination throughout the production process have not been investigated extensively. In the present study, button mushroom cultivation was investigated in each of the four stages (raw materials, composting (phase I, Ⅱ, and Ⅲ), casing, and harvesting), and samples (n = 186) from mushrooms and their related environments were collected from four distinct mushroom-growing farms (A-D) in Korea. Shifts within the bacterial consortium during mushroom production were characterized with 16 S rRNA amplicon sequencing. The succession of bacterial communities on each farm was dependent on the raw material incorporated, aeration, and the farm environment. The dominant phyla of the compost stack at the four farms were Pseudomonadota (56.7%) in farm A, Pseudomonadota (43.3%) in farm B, Bacteroidota (46.0%) in farm C, and Bacillota (62.8%) in farm D. During the Phase Ⅰ, highly heat-resistant microbes, such as those from the phylum Deinococcota (0.6-65.5%) and the families Bacillaceae (1.7-36.3%), Thermaceae (0.1-65.5%), and Limnochordaceae (0.3-30.5%) greatly proliferated. The microbial diversity within compost samples exhibited a marked decline as a result of the proliferation of thermophilic bacteria. In the spawning step, there were considerable increases in Xanthomonadaceae in the pasteurized composts of farms C and D - both of which employed an aeration system. In the harvesting phase, beta diversity correlated strongly between the casing soil layer and pre-harvest mushrooms, as well as between gloves and packaged mushrooms. The results suggest that gloves may be a major source of cross-contamination for packaged mushrooms, highlighting the need for enhanced hygienic practices during the harvesting phase to ensure product safety. These findings contribute to the current understanding of the influence of environmental and adjacent microbiomes on mushroom products to benefit the mushroom industry and relevant stakeholders by ensuring quality production.

Non-canonical transcriptional regulation of INHAT subunit SET/TAF-Iß by EZH2.

Enhancer of zeste homolog 2 (EZH2), with EED and SUZ12, forms the polycomb repressive complex 2 (PRC2), which catalyzes histone H3 lysine 27 (H3K27) methylation. Canonically, EZH2 is well known to repress transcription by mediating H3K27 tri-methylation (H3K27me3) at target gene promoters. In this study, we report that EZH2 non-canonically regulates transcription of SET/TAF-Iß, known as a subunit of inhibitor of acetyltransferases (INHAT) complex and as a proto-oncogene. Importantly, transcriptional regulation of SET/TAF-Iß by EZH2 was independent of PRC2 and its methyltransferase activity. Moreover, EZH2 and SET/TAF-Iß levels were positively correlated, and both genes were highly expressed in various cancers including colon cancer as indicated by the analysis of TCGA database. Taken together, our study suggests the non-canonical role of EZH2 as a transcriptional activator of SET/TAF-Iß independent of methyltransferase function in colon cancer.

SET7-mediated TIP60 methylation is essential for DNA double-strand break repair.

The repair of DNA double-strand breaks (DSBs) by homologous recombination (HR) is crucial for maintaining genomic integrity and is involved in numerous fundamental biological processes. Post-translational modifications by proteins play an important role in regulating DNA repair. Here, we report that the methyltransferase SET7 regulates HR-mediated DSB repair by methylating TIP60, a histone acetyltransferase and tumor suppressor involved in gene expression and protein stability. We show that SET7 targets TIP60 for methylation at K137, which facilitates DSB repair by promoting HR and determines cell viability against DNA damage. Interestingly, TIP60 demethylation is catalyzed by LSD1, which affects HR efficiency. Taken together, our findings reveal the importance of TIP60 methylation status by SET7 and LSD1 in the DSB repair pathway. [BMB Reports 2022; 55(11): 541-546].

Transition-Metal Dichalcogenide Artificial Antibodies with Multivalent Polymeric Recognition Phases for Rapid Detection and Inactivation of Pathogens.

Antibodies are recognition molecules that can bind to diverse targets ranging from pathogens to small analytes with high binding affinity and specificity, making them widely employed for sensing and therapy. However, antibodies have limitations of low stability, long production time, short shelf life, and high cost. Here, we report a facile approach for the design of luminescent artificial antibodies with nonbiological polymeric recognition phases for the sensitive detection, rapid identification, and effective inactivation of pathogenic bacteria. Transition-metal dichalcogenide (TMD) nanosheets with a neutral dextran phase at the interfaces selectively recognized S. aureus, whereas the nanosheets bearing a carboxymethylated dextran phase selectively recognized E. coli O157:H7 with high binding affinity. The bacterial binding sites recognized by the artificial antibodies were thoroughly identified by experiments and molecular dynamics simulations, revealing the significance of their multivalent interactions with the bacterial membrane components for selective recognition. The luminescent WS2 artificial antibodies could rapidly detect the bacteria at a single copy from human serum without any purification and amplification. Moreover, the MoSe2 artificial antibodies selectively killed the pathogenic bacteria in the wounds of infected mice under light irradiation, leading to effective wound healing. This work demonstrates the potential of TMD artificial antibodies as an alternative to antibodies for sensing and therapy.

Multivalent Nanosheet Antibody Mimics for Selective Microbial Recognition and Inactivation.

Antibodies are widely used as recognition elements in sensing and therapy, but they suffer from poor stability, long discovery time, and high cost. Herein, a facile approach to create antibody mimics with flexible recognition phases and luminescent rigid scaffolds for the selective recognition, detection, and inactivation of pathogenic bacteria is reported. Tripeptides with a nitriloacetate-Cu group are spontaneously assembled on transition metal dichalcogenide (TMD) nanosheets via coordination bonding, providing a diversity of TMD-tripeptide assembly (TPA) antibody mimics. TMD-TPA antibody mimics can selectively recognize various pathogenic bacteria with nanomolar affinities. The bacterial binding sites for TMD-TPA are identified by experiments and molecular dynamics simulations, revealing that the dynamic and multivalent interactions of artificial antibodies play a crucial role for their recognition selectivity and affinity. The artificial antibodies allow the rapid and selective detection of pathogenic bacteria at single copy in human serum and urine, and their effective inactivation for therapy of infected mice. This work demonstrates the potential of TMD-TPA antibody mimics as an alternative to natural antibodies for sensing and therapy.

Modulation of oligonucleotide-binding dynamics on WS2 nanosheet interfaces for detection of Alzheimer's disease biomarkers.

Non-covalent adsorption and desorption of oligonucleotides on two-dimensional nanosheets are widely employed to design nanobiosensors for the rapid optical detection of targets. A precise control over the weak interactions between nanosheet interfaces and oligonucleotides is crucial for a high-sensing performance. Herein, the interface of ultrathin WS2 nanosheets used as a fluorescence quencher was engineered by four different dextran polymers in an aqueous solution to control the adsorption kinetics and thermodynamics of the DNA probe. The WS2 nanosheets, functionalized by the carboxyl group-bearing dextran (CM-dex-WS2) or the trimethylammonium-modified dextran (TMA-dex-WS2), exhibited 3.6-fold faster adsorption rates of the fluorescein-labeled DNA probe (FAM-DNA), which led to the effective fluorescence quenching of FAM, compared to the nanosheets functionalized with pristine dextran (dex-WS2) or the hydrophobic phenoxy groups-bearing dextran (PhO-dex-WS2). Isothermal titration calorimetry measurements showed that the adsorption strength of FAM-DNA for CM-dex-WS2 was one order of magnitude greater than its hybridization energy for a target microRNA (miR-29a) that is well-known as an Alzheimer's disease (AD) biomarker, leading to the unfavorable desorption of the DNA probe from the surface. In contrast, TMA-dex-WS2 exhibited the proper adsorption strength of FAM-DNA, which was lower than its hybridization energy for miR-29a, leading to its favorable desorption from the nanosheet surface along with the noticeable restoration of the quenched fluorescence after its hybridization with miR-29a. Finally, the interface modulation of WS2 nanosheets allowed the selective and sensitive recognition of miR-29a against non-complementary RNA and single base-mismatched RNA in human serum via increases in target-specific fluorescence.

Ultrathin WO3 Nanosheets Converted from Metallic WS2 Sheets by Spontaneous Formation and Deposition of PdO Nanoclusters for Visible Light-Driven C-C Coupling Reactions.

It is not facile to obtain ultrathin two-dimensional (2D) WO3 nanosheets through the exfoliation of their bulk counterpart in solution due to strong covalent interaction between interlayers. In addition, they require additional functionalization with cocatalysts to expand their applicability in photocatalytic organic reactions owing to their insufficient conduction band edge position. Here, we report a chemical approach for the simultaneous production and functionalization of ultrathin 2D WO3 nanosheets through the direct conversion of metallic WS2 nanosheets, accomplished by the spontaneous formation and deposition of PdO nanoclusters on the nanosheet surface in H2O. When chemically exfoliated metallic WS2 nanosheets were simply mixed with K2PdCl4 in H2O under mild conditions (50 °C, 1 h), they were converted to semiconducting WO3 nanosheets on which PdO nanoclusters of a uniform size (∼3 nm) were spontaneously formed, leading to the production of PdO-functionalized ultrathin WO3 (PdO@WO3) nanohybrids. The conversion yield of WO3 nanosheets from metallic WS2 nanosheets increased with increasing coverage of PdO nanoclusters on the nanosheet surface. In addition, the conversion of WO3 nanosheets induced by PdO nanocluster formation was effective only in H2O but not in organic solvents, such as N-methylpyrrolidone and acetonitrile. A mechanical study suggests that the chemisorption of hydrated Pd precursors on the chalcogens of metallic WS2 nanosheets leads to their facile oxidation by water molecules, producing WO3 nanosheets covered with PdO nanoclusters. The as-prepared PdO@WO3 nanosheets exhibited excellent photocatalytic activity and recyclability in Suzuki cross-coupling reactions of various aryl halides under visible light irradiation.

Reaction Kinetics-Mediated Control over Silver Nanogap Shells as Surface-Enhanced Raman Scattering Nanoprobes for Detection of Alzheimer's Disease Biomarkers.

It is very challenging to accurately quantify the amounts of amyloid peptides Aß40 and Aß42, which are Alzheimer's disease (AD) biomarkers, in blood owing to their low levels. This has driven the development of sensitive and noninvasive sensing methods for the early diagnosis of AD. Here, an approach for the synthesis of Ag nanogap shells (AgNGSs) is reported as surface-enhanced Raman scattering (SERS) colloidal nanoprobes for the sensitive, selective, and multiplexed detection of Aß40 and Aß42 in blood. Raman label chemicals used for SERS signal generation modulate the reaction rate for AgNGSs production through the formation of an Ag-thiolate lamella structure, enabling the control of nanogaps at one nanometer resolution. The AgNGSs embedded with the Raman label chemicals emit their unique SERS signals with a huge intensity enhancement of up to 107 and long-term stability. The AgNGS nanoprobes, conjugated with an antibody specific to Aß40 or Aß42, are able to detect these AD biomarkers in a multiplexed manner in human serum based on the AgNGS SERS signals. Detection is possible for amounts as low as 0.25 pg mL-1 . The AgNGS nanoprobe-based sandwich assay has a detection dynamic range two orders of magnitude wider than that of a conventional enzyme-linked immunosorbent assay.

2D transition metal dichalcogenides with glucan multivalency for antibody-free pathogen recognition.

The ability to control the dimensions and properties of nanomaterials is fundamental to the creation of new functions and improvement of their performances in the applications of interest. Herein, we report a strategy based on glucan multivalent interactions for the simultaneous exfoliation and functionalization of two-dimensional transition metal dichalcogenides (TMDs) in an aqueous solution. The multivalent hydrogen bonding of dextran with bulk TMDs (WS2, WSe2, and MoSe2) in liquid exfoliation effectively produces TMD monolayers with binding multivalency for pathogenic bacteria. Density functional theory simulation reveals that the multivalent hydrogen bonding between dextran and TMD monolayers is very strong and thermodynamically favored (ΔEb = -0.52 eV). The resulting dextran/TMD hybrids (dex-TMDs) exhibit a stronger affinity (Kd = 11 nM) to Escherichia coli O157:H7 (E. coli) than E. coli-specific antibodies and aptamers. The dex-TMDs can effectively detect a single copy of E. coli based on their Raman signal.

Fluorescent 2D WS2 Nanosheets Bearing Chemical Affinity Elements for the Recognition of Glycated Hemoglobin.

It is required to exfoliate and functionalize 2D transition metal dichalcogenides (TMDs) in an aqueous solution for biological and medical applications. Herein, the approach for the simultaneous exfoliation and functionalization of 2D WS2 nanosheets using boronic acid-modified poly(vinyl alcohol) (B-PVA) in an aqueous solution is reported, and the B-PVA-functionalized WS2 nanosheets (B-PVA-WS2 ) are exploited as a fluorescent biosensor for the detection of glycated hemoglobin, HbA1c. The synthetic B-PVA polymer facilitates the exfoliation and functionalization of WS2 nanosheets from the bulk counterpart in the aqueous solution via a pulsed sonication process, resulting in fluorescent B-PVA-WS2 nanohybrids with a specific recognition of HbA1c. The fluorescence of the B-PVA-WS2 is quenched in the presence of HbA1c, whereas PVA-functionalized WS2 (PVA-WS2 ), not bearing boronic acid as a recognition moiety, shows no fluorescence changes upon the addition of the target. The B-PVA-WS2 is able to selectively detect HbA1c at the concentration as low as 3.3 × 10-8 m based on its specific fluorescence quenching.

ß-Lactoglobulin Peptide Fragments Conjugated with Caffeic Acid Displaying Dual Activities for Tyrosinase Inhibition and Antioxidant Effect.

The regulation of tyrosinase activity and reactive oxygen species is of great importance for the prevention of dermatological disorders in the fields of medicine and cosmetics. Herein, we report a strategy based on solid-phase peptide chemistry for the synthesis of ß-lactoglobulin peptide fragment/caffeic acid (CA) conjugates (CA-Peps) with dual activities of tyrosinase inhibition and antioxidation. The purity of the prepared conjugates, CA-MHIR, CA-HIRL, and CA-HIR, significantly increased to 99%, as acetonide-protected CA was employed in solid-phase coupling reactions on Rink amide resins. The tyrosinase inhibitory activities of all CA-Pep derivatives were higher than the activity of kojic acid, and CA-MHIR exhibited the highest tyrosinase inhibition activity (IC50 = 47.9 µM). Moreover, CA-Pep derivatives displayed significantly enhanced antioxidant activities in the peroxidation of linoleic acid as compared to the pristine peptide fragments. All CA-Pep derivatives showed no cytotoxicity against B16-F1 melanoma cells.