Formation of Amphiphilic Zwitterionic Thin Poly(SBMA-co-TFEMA) Brushes on Solid Surfaces for Marine Antifouling Applications.

Water molecules can bind to zwitterionic polymers, such as carboxybetaine and sulfobetaine, forming strong hydration layers along the polymer chains. Such hydration layers act as a barrier to impede the attachment of marine fouling organisms; therefore, zwitterionic polymer coatings have been of considerable interest as marine antifouling coatings. However, recent studies have shown that severe adsorption of marine sediments occurs on zwitterionic-polymer-coated surfaces, resulting in the degradation of their marine antifouling performance. Therefore, a novel approach for forming amphiphilic zwitterionic polymers using zwitterionic and hydrophobic monomers is being investigated to simultaneously inhibit both sediment adsorption and marine fouling. In this study, amphiphilic zwitterionic thin polymer brushes composed of sulfobetaine methacrylate (SBMA) and trifluoroethyl methacrylate (TFEMA) were synthesized on Si/SiO2 surfaces via surface-initiated atom transfer radical polymerization. For this, a facile metal-ion-mediated method was developed for immobilizing polymerization initiators on solid substrates to subsequently form poly(SBMA-co-TFEMA) brushes on the initiator-coated substrate surface. Poly(SBMA-co-TFEMA) brushes with various SBMA/TFEMA ratios were prepared to determine the composition at which both marine diatom adhesion and sediment adsorption can be prevented effectively. The results indicate that poly(SBMA-co-TFEMA) brushes prepared with an SBMA/TFEMA ratio of 3:7 effectively inhibit both sediment adsorption and marine diatom adhesion, thereby exhibiting balanced marine antifouling properties. Thus, the findings of this study provide important insights into the design of amphiphilic marine antifouling materials.

Structural Insights into the Penicillin-Binding Protein 4 (DacB) from Mycobacterium tuberculosis.

Mycobacterium tuberculosis, a major cause of mortality from a single infectious agent, possesses a remarkable mycobacterial cell envelope. Penicillin-Binding Proteins (PBPs) are a family of bacterial enzymes involved in the biosynthesis of peptidoglycan. PBP4 (DacB) from M. tuberculosis (MtbPBP4) has been known to function as a carboxypeptidase, and the role and significance of carboxypeptidases as targets for anti-tuberculosis drugs or antibiotics have been extensively investigated over the past decade. However, their precise involvement remains incompletely understood. In this study, we employed predictive modeling and analyzed the three-dimensional structure of MtbPBP4. Interestingly, MtbPBP4 displayed a distinct domain structure compared to its homologs. Docking studies with meropenem verified the presence of active site residues conserved in PBPs. These findings establish a structural foundation for comprehending the molecular function of MtbPBP4 and offer a platform for the exploration of novel antibiotics.

A Facile Method to Fabricate an Enclosed Paper-Based Analytical Device via Double-Sided Patterning for Ionic Contaminant Detection.

Microfluidic paper-based analytical devices (µPADs) have been developed for use in a variety of diagnosis and analysis fields. However, conventional µPADs with an open-channel system have limitations for application as analytical platforms mainly because of the evaporation and contamination of the sample solution. This study demonstrates the design and fabrication of an enclosed three-dimensional(3D)-µPAD and its application as a primary early analysis platform for ionic contaminants. To generate the hydrophobic PDMS barrier, double-sided patterning is carried out using a PDMS blade-coated stamp mold that is fabricated using 3D printing. The selective PDMS patterning can be achieved with controlled PDMS permeation of the cellulose substrate using 3D-designed stamp molds. We find the optimal conditions enabling the formation of enclosed channels, including round shape pattern and inter-pattern distance of 10 mm of stamp design, contact time of 0.5 min, and spacer height of 300 µm of double-sided patterning procedure. As a proof of concept, this enclosed 3D-µPAD is used for the simultaneous colorimetric detection of heavy metal ions in a concentration range of 0.1-2000 ppm, including nickel (Ni2+), copper (Cu2+), mercury (Hg2+), and radioactive isotope cesium-137 ions (Cs+). We confirm that qualitative analysis and image-based quantitative analysis with high reliability are possible through rapid color changes within 3 min. The limits of detection (LOD) for 0.55 ppm of Ni2+, 5.05 ppm of Cu2+, 0.188 ppm of Hg2+, and 0.016 ppm of Cs+ are observed, respectively. In addition, we confirm that the analysis is highly reliable in a wide range of ion concentrations with CV values below 3% for Ni2+ (0.56%), Cu2+ (0.45%), Hg2+ (1.35%), and Cs+ (2.18%). This method could be a promising technique to develop a 3D-µPAD with various applications as a primary early analysis device in the environmental and biological industries.

Focused Overview of Mycobacterium tuberculosis VapBC Toxin-Antitoxin Systems Regarding Their Structural and Functional Aspects: Including Insights on Biomimetic Peptides.

Tuberculosis, caused by Mycobacterium tuberculosis, is a lethal infectious disease of significant public health concern. The rise of multidrug-resistant and drug-tolerant strains has necessitated novel approaches to combat the disease. Toxin-antitoxin (TA) systems, key players in bacterial adaptive responses, are prevalent in prokaryotic genomes and have been linked to tuberculosis. The genome of M. tuberculosis strains harbors an unusually high number of TA systems, prompting questions about their biological roles. The VapBC family, a representative type II TA system, is characterized by the VapC toxin, featuring a PilT N-terminal domain with nuclease activity. Its counterpart, VapB, functions as an antitoxin, inhibiting VapC's activity. Additionally, we explore peptide mimics designed to replicate protein helical structures in this review. Investigating these synthetic peptides offers fresh insights into molecular interactions, potentially leading to therapeutic applications. These synthetic peptides show promise as versatile tools for modulating cellular processes and protein-protein interactions. We examine the rational design strategies employed to mimic helical motifs, their biophysical properties, and potential applications in drug development and bioengineering. This review aims to provide an in-depth understanding of TA systems by introducing known complex structures, with a focus on both structural aspects and functional and molecular details associated with each system.

Mycobacterium tuberculosis Rv0229c Shows Ribonuclease Activity and Reveals Its Corresponding Role as Toxin VapC51.

The VapBC system, which belongs to the type II toxin-antitoxin (TA) system, is the most abundant and widely studied system in Mycobacterium tuberculosis. The VapB antitoxin suppresses the activity of the VapC toxin through a stable protein-protein complex. However, under environmental stress, the balance between toxin and antitoxin is disrupted, leading to the release of free toxin and bacteriostatic state. This study introduces the Rv0229c, a putative VapC51 toxin, and aims to provide a better understanding of its discovered function. The structure of the Rv0229c shows a typical PIN-domain protein, exhibiting an ß1-α1-α2-ß2-α3-α4-ß3-α5-α6-ß4-α7-ß5 topology. The structure-based sequence alignment showed four electronegative residues in the active site of Rv0229c, which is composed of Asp8, Glu42, Asp95, and Asp113. By comparing the active site with existing VapC proteins, we have demonstrated the justification for naming it VapC51 at the molecular level. In an in vitro ribonuclease activity assay, Rv0229c showed ribonuclease activity dependent on the concentration of metal ions such as Mg2+ and Mn2+. In addition, magnesium was found to have a greater effect on VapC51 activity than manganese. Through these structural and experimental studies, we provide evidence for the functional role of Rv0229c as a VapC51 toxin. Overall, this study aims to enhance our understanding of the VapBC system in M. tuberculosis.

Domain swapping of the C-terminal helix promotes the dimerization of a novel ribonuclease protein from Mycobacterium tuberculosis.

Polyketide metabolism-associated proteins in Mycobacterium tuberculosis play an essential role in the survival of the bacterium, which makes them potential drug targets for the treatment of tuberculosis (TB). The novel ribonuclease protein Rv1546 is predicted to be a member of the steroidogenic acute regulatory protein-related lipid-transfer (START) domain superfamily, which comprises bacterial polyketide aromatase/cyclases (ARO/CYCs). Here, we determined the crystal structure of Rv1546 in a V-shaped dimer. The Rv1546 monomer consists of four α-helices and seven antiparallel ß-strands. Interestingly, in the dimeric state, Rv1546 forms a helix-grip fold, which is present in START domain proteins, via three-dimensional domain swapping. Structural analysis revealed that the conformational change of the C-terminal α-helix of Rv1546 might contribute to the unique dimer structure. Site-directed mutagenesis followed by in vitro ribonuclease activity assays was performed to identify catalytic sites of the protein. This experiment suggested that surface residues R63, K84, K88, and R113 are important in the ribonuclease function of Rv1546. In summary, this study presents the structural and functional characterization of Rv1546 and supplies new perspectives for exploiting Rv1546 as a novel drug target for TB treatment.

Surface-facilitated formation of polydopamine and its implications in melanogenesis.

This manuscript examines influences of differently functionalized surfaces on the formation of solution-dispersed polydopamine (pDA). Glass vials functionalized with different functional groups provided a set of conditions with which the relationship between the area of active surface and the rate of pDA formation could be systematically studied. The results suggest that charged and polar surfaces accelerate pDA formation in solution, with the effect of -NH2 surfaces being exceptionally strong. In the vials, pDA formed as both forms of dispersions in solution and films at solid-liquid interface. Further analyses confirmed that both forms of pDA formed with -NH2 surfaces were chemically similar to conventional pDA synthesized without help of functional surfaces. Among short peptide-based amyloid fibers with defined surface functional groups, and those displaying lysines (-NH2) greatly accelerated the formation of pDA, consistent with the results of -NH2-functionalized vials. The results suggest that pDA formation may be facilitated by surface functional groups of solid-liquid interfaces, and have implications for the overlooked roles of amyloid fibers in biological melanogenesis.

Reprogramming of T cell-derived small extracellular vesicles using IL2 surface engineering induces potent anti-cancer effects through miRNA delivery.

T cell-derived small extracellular vesicles (sEVs) exhibit anti-cancer effects. However, their anti-cancer potential should be reinforced to enhance clinical applicability. Herein, we generated interleukin-2-tethered sEVs (IL2-sEVs) from engineered Jurkat T cells expressing IL2 at the plasma membrane via a flexible linker to induce an autocrine effect. IL2-sEVs increased the anti-cancer ability of CD8+ T cells without affecting regulatory T (Treg ) cells and down-regulated cellular and exosomal PD-L1 expression in melanoma cells, causing their increased sensitivity to CD8+ T cell-mediated cytotoxicity. Its effect on CD8+ T and melanoma cells was mediated by several IL2-sEV-resident microRNAs (miRNAs), whose expressions were upregulated by the autocrine effects of IL2. Among the miRNAs, miR-181a-3p and miR-223-3p notably reduced the PD-L1 protein levels in melanoma cells. Interestingly, miR-181a-3p increased the activity of CD8+ T cells while suppressing Treg cell activity. IL2-sEVs inhibited tumour progression in melanoma-bearing immunocompetent mice, but not in immunodeficient mice. The combination of IL2-sEVs and existing anti-cancer drugs significantly improved anti-cancer efficacy by decreasing PD-L1 expression in vivo. Thus, IL2-sEVs are potential cancer immunotherapeutic agents that regulate both immune and cancer cells by reprogramming miRNA levels.

Surface Coating with Naphthalene Trisulfonate/Hafnium(IV) Complexes: Versatility and Post-Functionalization.

Naphthalene trisulfonate is found to have versatile surface coating capability when combined with hafnium(IV) ions, thereby forming complexes. Solid substrates such as titanium/titanium dioxide, glass, and nylon immersed in a solution of naphthalene trisulfonate and HfIV produces naphthalene trisulfonate/HfIV complex coating. The coating is not produced when the HfIV ions are absent or when naphthalene monosulfonate replaces naphthalene trisulfonate; this indicates the significance of HfIV ions and multiple sulfonates in this coating system. The versatile surface coating property of naphthalene trisulfonate/HfIV complexes is attributed to the coexistence of hydrophobic aromatic and hydrophilic side groups in naphthalene trisulfonate. Additionally, HfIV ion-mediated cross-linking reactions between naphthalene trisulfonate molecules induce molecular assembly, facilitating versatile surface coating. Post-functionalization of the coating is accomplished through additional HfIV-mediated coordinate bond formation; alginate and λ-carrageenan are successfully grafted onto the coating for nonbiofouling applications.

The Fabrication of Cesium Lead Bromide-Coated Cellulose Nanocomposites and Their Effect on the Detection of Nitrogen Gas.

In this work, we fabricate cesium lead bromide nanofibers (CsPbBr3 NFs) via the attachment of cesium lead bromide nanocrystals (CsPbBr3 NCs) on the surface of electrospun cellulose nanofibers (CNFs) and employ them in a sensor to effectively detect gaseous nitrogen. The CsPbBr3 NFs are produced initially by producing CsPbBr3 NCs through hot injection and dispersing on hexane, followed by dipping CNFs and ultrasonicate for 1 h. Morphological characterization through visual, SEM and TEM image, and crystalline structure analysis by XRD and FT-IR analysis of CsPbBr3 NFs and NCs show similar spectra except for PL due to unavoidable damage during the ultrasonication. Gaseous nitrogen is subsequently detected using the photoluminescence (PL) property of CsPbBr3 NFs, in which the PL intensity dramatically decreases under various flow rate. Therefore, we believe that the proposed CsPbBr3 NFs show significant promise for use in detection sensors in various industrial field and decrease the potential of fatal damage to workers due to suffocation.

The Haemophilus influenzae HipBA toxin-antitoxin system adopts an unusual three-com-ponent regulatory mechanism.

Type II toxin-antitoxin (TA) systems encode two proteins: a toxin that inhibits cell growth and an antitoxin that neutralizes the toxin by direct inter-molecular protein-protein inter-actions. The bacterial HipBA TA system is implicated in persister formation. The Haemophilus influenzae HipBA TA system consists of a HipB antitoxin and a HipA toxin, the latter of which is split into two fragments, and here we investigate this novel three-com-ponent regulatory HipBA system. Structural and functional analysis revealed that HipAN corresponds to the N-ter-minal part of HipA from other bacteria and toxic HipAC is inactivated by HipAN, not HipB. This study will be helpful in understanding the detailed regulatory mechanism of the HipBAN+C system, as well as why it is constructed as a three-com-ponent system.

Novel antitumor therapeutic strategy using CD4+ T cell-derived extracellular vesicles.

Extracellular vesicles (EVs) mediate cell-cell crosstalk by carrying bioactive molecules derived from cells. Recently, immune cell-derived EVs have been reported to regulate key biological functions such as tumor progression. CD4+ T cells orchestrate overall immunity; however, the biological role of their EVs is unclear. This study reveals that EVs derived from CD4+ T cells increase the antitumor response of CD8+ T cells by enhancing their proliferation and activity without affecting regulatory T cells (Tregs). Moreover, EVs derived from interleukin-2 (IL2)-stimulated CD4+ T cells induce a more enhanced antitumor response of CD8+ T cells compared with that of IL2-unstimulated CD4+ T cell-derived EVs. Mechanistically, miR-25-3p, miR-155-5p, miR-215-5p, and miR-375 within CD4+ T cell-derived EVs are responsible for the induction of CD8+ T cell-mediated antitumor responses. In a melanoma mouse model, the EVs potently suppress tumor growth through CD8+ T cell activation. This study demonstrates that the EVs, in addition to IL2, are important mediators between CD4+ and CD8+ T cells. Furthermore, unlike IL2, clinically used as an antitumor agent, CD4+ T cell-derived EVs stimulate CD8+ T cells without activating Tregs. Therefore, CD4+ T cell-derived EVs may provide a novel direction for cancer immunotherapy by inducing a CD8+ T cell-mediated antitumor response.

Effect of Molecular Weights on Metal-Mediated Grafting of Sulfobetaine Polymers onto Solid Surfaces for Non-Biofouling Applications.

The grafting of zwitterionic molecules onto solid surfaces is an important tool for decreasing the unwanted adsorption of biomolecules, such as proteins, bacteria, and cells. This has been achieved through various approaches, such as zwitterionic monolayer/multilayer formation, surface-initiated polymerization of zwitterionic monomers, and grafting of presynthesized zwitterionic polymers. Recently, a coordination-driven approach to grafting zwitterionic polymers onto solid surfaces has been discovered to be an effective method because of its versatility and robustness. However, the bacterial adhesion resistance of zwitterionic polymer grafting has been explored using only one molecular weight, and the non-biofouling performance against other fouling organisms has remained unexamined. In this study, the characteristics of coordination-driven surface zwitteration are systematically investigated. Sulfobetaine (SB) polymers with three different molecular weights are synthesized and employed for surface grafting. Polydopamine is used as a surface primer, and SB polymers are grafted onto the surfaces via the formation of metal-mediated coordinate bonds. The effect of molecular weight on the grafting efficiency and non-biofouling performance is investigated via protein adsorption and marine diatom adhesion assays. The SB polymer with a high molecular weight is found to be crucial for achieving strong resistance to protein adsorption and marine fouling.

Effect of N-Methylation on Dopamine Surface Chemistry.

Dopamine (DA) surface chemistry has received significant attention because of its applicability in a wide range of research fields and the ability to graft functional molecules onto numerous solid surfaces. Various DA derivatives have been newly synthesized to identify key factors affecting the coating efficiency and to advance the coating system development. The oxidation of catechol into quinone followed by internal cyclization via the nucleophilic attack of primary amine is crucial for DA-based surface coating. Thus, it is expected that the amine group's nucleophilicity control directly affects the coating efficiency. However, it has not been systematically investigated, and most studies have been conducted with the focus on the transformation of amines into amides, despite such approaches decreasing the coating efficiency; the nitrogen in amides is less nucleophilic than that in free amines. In this study, we investigated the effect of N-alkylation on dopamine surface chemistry. N,N-Dimethyldopamine (DMDA) was newly synthesized, and the coating efficiency was systematically compared with DA and N-methyldopamine (MDA). DA N-monomethylation improved the coating rate by increasing the nitrogen nucleophilicity, whereas N,N-dimethylation dramatically decreased the DA surface coating property. In addition, MDA remained capable of universal surface coating and secondary reactions using the surface catechols. This study provides opportunities for developing coating materials with advanced functions and an improved coating rate.

Structural and functional analysis of the D-alanyl carrier protein ligase DltA from Staphylococcus aureus Mu50.

D-Alanylation of the teichoic acids of the Gram-positive bacterial cell wall plays crucial roles in bacterial physiology and virulence. Deprivation of D-alanine from the teichoic acids of Staphylococcus aureus impairs biofilm and colony formation, induces autolysis and ultimately renders methicillin-resistant S. aureus highly susceptible to antimicrobial agents and host defense peptides. Hence, the D-alanylation pathway has emerged as a promising antibacterial target against drug-resistant S. aureus. D-Alanylation of teichoic acids is mediated via the action of four proteins encoded by the dlt operon, DltABCD, all four of which are essential for the process. In order to develop novel antimicrobial agents against S. aureus, the D-alanyl carrier protein ligase DltA, which is the first protein in the D-alanylation pathway, was focused on. Here, the crystal structure of DltA from the methicillin-resistant S. aureus strain Mu50 is presented, which reveals the unique molecular details of the catalytic center and the role of the P-loop. Kinetic analysis shows that the enantioselectivity of S. aureus DltA is much higher than that of DltA from other species. In the presence of DltC, the enzymatic activity of DltA is increased by an order of magnitude, suggesting a new exploitable binding pocket. This discovery may pave the way for a new generation of treatments for drug-resistant S. aureus.

Role of PemI in the Staphylococcus aureus PemIK toxin-antitoxin complex: PemI controls PemK by acting as a PemK loop mimic.

Staphylococcus aureus is a notorious and globally distributed pathogenic bacterium. New strategies to develop novel antibiotics based on intrinsic bacterial toxin-antitoxin (TA) systems have been recently reported. Because TA systems are present only in bacteria and not in humans, these distinctive systems are attractive targets for developing antibiotics with new modes of action. S. aureus PemIK is a type II TA system, comprising the toxin protein PemK and the labile antitoxin protein PemI. Here, we determined the crystal structures of both PemK and the PemIK complex, in which PemK is neutralized by PemI. Our biochemical approaches, including fluorescence quenching and polarization assays, identified Glu20, Arg25, Thr48, Thr49, and Arg84 of PemK as being important for RNase function. Our study indicates that the active site and RNA-binding residues of PemK are covered by PemI, leading to unique conformational changes in PemK accompanied by repositioning of the loop between ß1 and ß2. These changes can interfere with RNA binding by PemK. Overall, PemK adopts particular open and closed forms for precise neutralization by PemI. This structural and functional information on PemIK will contribute to the discovery and development of novel antibiotics in the form of peptides or small molecules inhibiting direct binding between PemI and PemK.

Coordination-Driven Surface Zwitteration for Antibacterial and Antifog Applications.

The enhancement of surface wettability by hydrophilic polymer coatings has been of great interest because it has been used to address several technical challenges such as biofouling and surface fogging. Among the hydrophilic polymers, zwitterionic polymers have been extensively utilized to coat solid surfaces due to their excellent capability to bind water molecules, thereby forming dense hydration layers on the solid surfaces. For these zwitterionic polymers to function appropriately on the solid surfaces, techniques for fixing polymers onto the solid surface with high efficiency are required. Herein, we report a new approach to graft zwitterionic polymers onto solid substrates. The approach is based on the mussel-inspired surface chemistry and metal coordination. It consists of polydopamine coating and the coordination-driven grafting of the zwitterionic polymers. Polydopamine coating enables the versatile surface immobilization of catechols. Zwitterionic polymers are then easily fixed onto the catechol-immobilized surface by metal-mediated crosslinking reactions. Using this approach, nanometer-thick zwitterionic polymer layers that are highly resistant to bacterial adhesion and fog generation could be successfully fabricated on solid substrates in a substrate-independent manner.

High-throughput formation and image-based analysis of basal-in mammary organoids in 384-well plates.

This manuscript describes a new method for forming basal-in MCF10A organoids using commercial 384-well ultra-low attachment (ULA) microplates and the development of associated live-cell imaging and automated analysis protocols. The use of a commercial 384-well ULA platform makes this method more broadly accessible than previously reported hanging drop systems and enables in-incubator automated imaging. Therefore, time points can be captured on a more frequent basis to improve tracking of early organoid formation and growth. However, one major challenge of live-cell imaging in multi-well plates is the rapid accumulation of large numbers of images. In this paper, an automated MATLAB script to handle the increased image load is developed. This analysis protocol utilizes morphological image processing to identify cellular structures within each image and quantify their circularity and size. Using this script, time-lapse images of aggregating and non-aggregating culture conditions are analyzed to profile early changes in size and circularity. Moreover, this high-throughput platform is applied to widely screen concentration combinations of Matrigel and epidermal growth factor (EGF) or heparin-binding EGF-like growth factor (HB-EGF) for their impact on organoid formation. These results can serve as a practical resource, guiding future research with basal-in MCF10A organoids.

Au@Zr-based metal-organic framework composite as an immunosensing platform for determination of hepatitis B virus surface antigen.

An ultrasensitive electrochemical immunosensor has been prepared using an immunofunctionalized zirconium (Zr)-based metal-organic framework (MOF) with gold (Au) decoration Au@UiO-66(NH2) composite-coated glassy carbon electrode (GCE) for the determination of infectious hepatitis B surface antigen (HBsAg). We fabricated GCE with specific composite via immune-functionalization using anti-HBsAg with Au nanoparticles embedded in UiO-66(NH2). The electrochemical sensing performance of the immunofunctionalized Au@UiO-66(NH2)/GCE with HBsAg was characterized by cyclic voltammetry and differential pulse voltammetry. Under optimized conditions, there was a linear dynamic relationship in the buffer system between the electrical signal and HBsAg levels over the range 1.13 fg mL-1-100 ng mL-1 (R2 = 0.999) with a detection limit of 1.13 fg mL-1. The total analysis time was 15 min per sample. Further validations were performed with HBsAg-spiked human serum samples, and similar detection limits as in the buffer system were observed with reduced signal intensities at lower concentrations of HBsAg (1, 10, and 100 fg mL-1) and minimal interference. The HBsAg electrochemical immunosensing assay had good selectivity and excellent reproducibility, thereby indicating its significant potential in the super-fast diagnosis of hepatitis B.

A Structural Approach into Drug Discovery Based on Autophagy.

Autophagy is a lysosome-dependent intracellular degradation machinery that plays an essential role in the regulation of cellular homeostasis. As many studies have revealed that autophagy is related to cancer, neurodegenerative diseases, metabolic diseases, and so on, and it is considered as a promising drug target. Recent advances in structural determination and computational technologies provide important structural information on essential autophagy-related proteins. Combined with high-throughput screening methods, structure-activity relationship studies have led to the discovery of molecules that modulate autophagy. In this review, we summarize the recent structural studies on autophagy-related proteins and the discovery of modulators, indicating that targeting autophagy can be utilized as an effective strategy for novel drug development.