Understanding and Improving the Activity of Flavin-Dependent Halogenases via Random and Targeted Mutagenesis.

Flavin-dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes have been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications.

Functional genomics in inborn errors of immunity.

Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.

Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree).

Whole-genome duplication (WGD; i.e., polyploidy) and chromosomal rearrangement (i.e., genome shuffling) significantly influence genome structure and organization. Many polyploids show extensive genome shuffling relative to their pre-WGD ancestors. No reference genome is currently available for Platanaceae (Proteales), one of the sister groups to the core eudicots. Moreover, Platanus × acerifolia (London planetree; Platanaceae) is a widely used street tree. Given the pivotal phylogenetic position of Platanus and its 2-y flowering transition, understanding its flowering-time regulatory mechanism has significant evolutionary implications; however, the impact of Platanus genome evolution on flowering-time genes remains unknown. Here, we assembled a high-quality, chromosome-level reference genome for P. × acerifolia using a phylogeny-based subgenome phasing method. Comparative genomic analyses revealed that P. × acerifolia (2n = 42) is an ancient hexaploid with three subgenomes resulting from two sequential WGD events; Platanus does not seem to share any WGD with other Proteales or with core eudicots. Each P. × acerifolia subgenome is highly similar in structure and content to the reconstructed pre-WGD ancestral eudicot genome without chromosomal rearrangements. The P. × acerifolia genome exhibits karyotypic stasis and gene sub-/neo-functionalization and lacks subgenome dominance. The copy number of flowering-time genes in P. × acerifolia has undergone an expansion compared to other noncore eudicots, mainly via the WGD events. Sub-/neo-functionalization of duplicated genes provided the genetic basis underlying the unique flowering-time regulation in P. × acerifolia. The P. × acerifolia reference genome will greatly expand understanding of the evolution of genome organization, genetic diversity, and flowering-time regulation in angiosperms.

Diamond surface functionalization via visible light-driven C-H activation for nanoscale quantum sensing.

Nitrogen-vacancy (NV) centers in diamond are a promising platform for nanoscale NMR sensing. Despite significant progress toward using NV centers to detect and localize nuclear spins down to the single spin level, NV-based spectroscopy of individual, intact, arbitrary target molecules remains elusive. Such sensing requires that target molecules are immobilized within nanometers of NV centers with long spin coherence. The inert nature of diamond typically requires harsh functionalization techniques such as thermal annealing or plasma processing, limiting the scope of functional groups that can be attached to the surface. Solution-phase chemical methods can be readily generalized to install diverse functional groups, but they have not been widely explored for single-crystal diamond surfaces. Moreover, realizing shallow NV centers with long spin coherence times requires highly ordered single-crystal surfaces, and solution-phase functionalization has not yet been shown with such demanding conditions. In this work, we report a versatile strategy to directly functionalize C-H bonds on single-crystal diamond surfaces under ambient conditions using visible light, forming C-F, C-Cl, C-S, and C-N bonds at the surface. This method is compatible with NV centers within 10 nm of the surface with spin coherence times comparable to the state of the art. As a proof-of-principle demonstration, we use shallow ensembles of NV centers to detect nuclear spins from surface-bound functional groups. Our approach to surface functionalization opens the door to deploying NV centers as a tool for chemical sensing and single-molecule spectroscopy.

Bimodal brush-functionalized nanoparticles selective to receptor surface density.

Nanoparticles or drug carriers which can selectively bind to cells expressing receptors above a certain threshold surface density are very promising for targeting cells overexpressing specific receptors under pathological conditions. Simulations and theoretical studies have suggested that such selectivity can be enhanced by functionalizing nanoparticles with a bimodal polymer monolayer (BM) containing shorter ligated chains and longer inert protective chains. However, a systematic study of the effect of these parameters under tightly controlled conditions is still missing. Here, we develop well-defined and highly specific platforms mimicking particle-cell interface using surface chemistry to provide a experimental proof of such selectivity. Using surface plasmon resonance and atomic force microscopy, we report the selective adsorption of BM-functionalized nanoparticles, and especially, a significant enhanced selective behavior by using a BM with longer protective chains. Furthermore, a model is also developed to describe the repulsive contribution of the protective brush to nanoparticle adsorption. This model is combined with super-selectivity theory to support experimental findings and shows that the observed selectivity is due to the steric energy barrier which requires a high number of ligand-receptor bonds to allow nanoparticle adsorption. Finally, the results show how the relative length and molar ratio of two chains can be tuned to target a threshold surface density of receptors and thus lay the foundation for the rational design of BM-functionalized nanoparticles for selective targeting.

Molecular surface programming of rectifying junctions between InAs colloidal quantum dot solids.

Heavy-metal-free III-V colloidal quantum dots (CQDs) show promise in optoelectronics: Recent advancements in the synthesis of large-diameter indium arsenide (InAs) CQDs provide access to short-wave infrared (IR) wavelengths for three-dimensional ranging and imaging. In early studies, however, we were unable to achieve a rectifying photodiode using CQDs and molybdenum oxide/polymer hole transport layers, as the shallow valence bandedge (5.0 eV) was misaligned with the ionization potentials of the widely used transport layers. This occurred when increasing CQD diameter to decrease the bandgap below 1.1 eV. Here, we develop a rectifying junction among InAs CQD layers, where we use molecular surface modifiers to tune the energy levels of InAs CQDs electrostatically. Previously developed bifunctional dithiol ligands, established for II-VI and IV-VI CQDs, exhibit slow reaction kinetics with III-V surfaces, causing the exchange to fail. We study carboxylate and thiolate binding groups, united with electron-donating free end groups, that shift upward the valence bandedge of InAs CQDs, producing valence band energies as shallow as 4.8 eV. Photophysical studies combined with density functional theory show that carboxylate-based passivants participate in strong bidentate bridging with both In and As on the CQD surface. The tuned CQD layer incorporated into a photodiode structure achieves improved performance with EQE (external quantum efficiency) of 35% (>1 µm) and dark current density < 400 nA cm-2, a >25% increase in EQE and >90% reduced dark current density compared to the reference device. This work represents an advance over previous III-V CQD short-wavelength IR photodetectors (EQE < 5%, dark current > 10,000 nA cm-2).

Extracellular Vesicle Surface Display Enhances the Therapeutic Efficacy and Safety Profile of Cancer Immunotherapy.

Immunotherapy has emerged as a mainstay in cancer therapy, yet its efficacy is constrained by the risk of immune-related adverse events. In this study, we present a nanoparticle-based delivery system that enhances the therapeutic efficacy of immunomodulatory ligands while concurrently limiting systemic toxicity. We demonstrate that extracellular vesicles (EVs), lipid bilayer enclosed particles released by cells, can be efficiently engineered via iEDDA-mediated conjugation to display multiple immunomodulatory ligands on their surface. Display of immunomodulatory ligands on the EV surface conferred substantial enhancements in signaling efficacy, particularly for tumor necrosis factor receptor superfamily (TNFRSF) agonists, where EV surface display served as an alternative FcγR-independent approach to induce ligand multimerization and efficient receptor crosslinking. EVs displaying a complementary combination of immunotherapeutic ligands were able to shift the tumor immune milieu towards an anti-tumorigenic phenotype and significantly suppress tumor burden and increase survival in multiple models of metastatic cancer to a greater extent than an equivalent dose of free ligands. In summary, we present an EV-based delivery platform for cancer immunotherapeutic ligands that facilitates superior anti-tumor responses at significantly lower doses with less side-effects than is possible with conventional delivery approaches.

Biocompatible surface functionalization architecture for a diamond quantum sensor.

Quantum metrology enables some of the most precise measurements. In the life sciences, diamond-based quantum sensing has led to a new class of biophysical sensors and diagnostic devices that are being investigated as a platform for cancer screening and ultrasensitive immunoassays. However, a broader application in the life sciences based on nanoscale NMR spectroscopy has been hampered by the need to interface highly sensitive quantum bit (qubit) sensors with their biological targets. Here, we demonstrate an approach that combines quantum engineering with single-molecule biophysics to immobilize individual proteins and DNA molecules on the surface of a bulk diamond crystal that hosts coherent nitrogen vacancy qubit sensors. Our thin (sub-5 nm) functionalization architecture provides precise control over the biomolecule adsorption density and results in near-surface qubit coherence approaching 100 µs. The developed architecture remains chemically stable under physiological conditions for over 5 d, making our technique compatible with most biophysical and biomedical applications.

Probing the Impact of Surface Functionalization Module on the Performance of Mitoxantrone Prodrug Nanoassemblies: Improving the Effectiveness and Safety.

Prodrug nanoassemblies are emerging as a novel drug delivery system for chemotherapy, comprising four fundamental modules: a drug module, a modification module, a response module, and a surface functionalization module. Among these modules, surface functionalization is an essential process to enhance the biocompatibility and stability of the nanoassemblies. Here, we selected mitoxantrone (MTO) as the drug module and DSPE-PEG2K as surface functionalization module to develop MTO prodrug nanoassemblies. We systematically evaluated the effect of surface functionalization module ratios (10%, 20%, 40%, and 60% of prodrug, WDSPE-mPEG2000/Wprodrug) on the prodrug nanoassemblies. The results indicated that 40% NPs significantly improved the self-assembly stability and cellular uptake of prodrug nanoassemblies. Compared with MTO solution, 40% NPs showed better tumor specificity and pharmacokinetics, resulting in potent antitumor activity with a good safety profile. These findings highlighted the pivotal role of the surface functionalization module in regulating the performance of mitoxantrone prodrug nanoassemblies for cancer treatment.

Electron-Phonon Interaction Mediated Gigantic Enhancement of Thermoelectric Power Factor Induced by Topological Phase Transition.

We propose an effective strategy to significantly enhance the thermoelectric power factor (PF) of a series of 2D semimetals and semiconductors by driving them toward a topological phase transition (TPT). Employing first-principles calculations with an explicit consideration of electron-phonon interactions, we analyze the electronic transport properties of germanene across the TPT by applying hydrogenation and biaxial strain. We reveal that the nontrivial semimetal phase, hydrogenated germanene with 8% biaxial strain, achieves a considerable 4-fold PF enhancement, attributed to the highly asymmetric electronic structure and semimetallic nature of the nontrivial phase. We extend the strategy to another two representative 2D materials (stanene and HgSe) and observe a similar trend, with a marked 7-fold and 5-fold increase in PF, respectively. The wide selection of functional groups, universal applicability of biaxial strain, and broad spectrum of 2D semimetals and semiconductors render our approach highly promising for designing novel 2D materials with superior thermoelectric performance.

Synthesis and Raman Detection of 5-Amino-2-mercaptobenzimidazole Self-Assembled Monolayers in Nanoparticle-on-a-Mirror Plasmonic Cavity Driven by Dielectric Waveguides.

Functionalization of metallic surfaces by molecular monolayers is a key process in fields such as nanophotonics or biotechnology. To strongly enhance light-matter interaction in such monolayers, nanoparticle-on-a-mirror (NPoM) cavities can be formed by placing metal nanoparticles on such chemically functionalized metallic monolayers. In this work, we present a novel functionalization process of gold surfaces using 5-amino-2-mercaptobenzimidazole (5-A-2MBI) molecules, which can be used for upconversion from THz to visible frequencies. The synthesized surfaces and NPoM cavities are characterized by Raman spectroscopy, atomic force microscopy (AFM), and advancing-receding contact angle measurements. Moreover, we show that NPoM cavities can be efficiently integrated on a silicon-based photonic chip performing pump injection and Raman-signal extraction via silicon nitride waveguides. Our results open the way for the use of 5-A-2MBI monolayers in different applications, showing that NPoM cavities can be effectively integrated with photonic waveguides, enabling on-chip enhanced Raman spectroscopy or detection of infrared and THz radiation.

Natural Compounds as Pharmaceuticals: The Key Role of Cytochromes P450 Reactivity.

The design of drugs from natural products is a re-emerging area due to the need for bioactive compounds. The exploitation of natural products and their derivatives obtained by biocatalysis is in line with the higher attention given today to new sustainable technologies that better preserve the environment (green chemistry). The research field of cytochromes P450 (CYPs) is continuously providing new enzymes and mutants that produce metabolites suitable for late-stage functionalization for new potential drugs. This review provides an overview of the exploitation of CYPs as biocatalysts in drug synthesis. Additionally, recent progress in protein and metabolic engineering is provided to show how these enzymes offer a toolbox that can be combined with other biocatalytic or chemical processes to build new platforms for the green production of new drugs.

Zebrafish: unraveling genetic complexity through duplicated genes.

The zebrafish is an invaluable model organism for genetic, developmental, and disease research. Although its high conservation with humans is often cited as justification for its use, the zebrafish harbors oft-ignored genetic characteristics that may provide unique insights into gene structure and function. Zebrafish, along with other teleost fish, underwent an additional round of whole genome duplication after their split from tetrapods-resulting in an abundance of duplicated genes when compared to other vertebrates. These duplicated genes have evolved in distinct ways over the ensuing 350 million years. Thus, each gene within a duplicated gene pair has nuanced differences that create a unique identity. By investigating both members of the gene pair together, we can elucidate the mechanisms that underly protein structure and function and drive the complex interplay within biological systems, such as signal transduction cascades, genetic regulatory networks, and evolution of tissue and organ function. It is crucial to leverage such studies to explore these molecular dynamics, which could have far-reaching implications for both basic science and therapeutic development. Here, we will review the role of gene duplications and the existing models for gene divergence and retention following these events. We will also highlight examples within each of these models where studies comparing duplicated genes in the zebrafish have yielded key insights into protein structure, function, and regulation.

Organosilicon-Based Carbon Dots and Their Versatile Applications.

Carbon dots (CDs) are a newly discovered type of fluorescent material that has gained significant attention due to their exceptional optical properties, biocompatibility, and other remarkable characteristics. However, single CDs have some drawbacks such as self-quenching, low quantum yield (QY), and poor stability. To address these issues, researchers have turned to organosilicon, which is known for its green, economical, and abundant properties. Organosilicon is widely used in various fields including optics, electronics, and biology. By utilizing organosilicon as a synthetic precursor, the biocompatibility, QY, and resistance to self-quenching of CDs can be improved. Meanwhile, the combination of organosilicon with CDs enables the functionalization of CDs, which significantly expands their original application scenarios. This paper comprehensively analyzes organosilicon in two main categories: precursors for CD synthesis and matrix materials for compounding with CDs. The role of organosilicon in these categories is thoroughly reviewed. In addition, the paper presents various applications of organosilicon compounded CDs, including detection and sensing, anti-counterfeiting, optoelectronic applications, and biological applications. Finally, the paper briefly discusses current development challenges and future directions in the field.

Construction of Mineralization Nanostructures in Polymers for Mechanical Enhancement and Functionalization.

Mineralization capable of growing inorganic nanostructures efficiently, orderly, and spontaneously shows great potential for application in the construction of high-performance organic-inorganic composites. As a thermodynamically spontaneous solid-phase crystallization reaction involving dual organic and inorganic components, mineralization allows for the self-assembly of sophisticated and exclusive nanostructures within a polymer matrix. It results in a diversity of functions such as enhanced strength, toughness, electrical conductivity, selective permeability, and biocompatibility. While there are previous reviews discussing the progress of mineralization reactions, many of them overlook the significant benefits of interfacial regulation and functionalization that come from the incorporation of mineralized structures into polymers. Focusing on different means of assembly of mineralized nanostructures in polymer, the work analyzes their design principles and implementation strategies. Then, their different advantages and disadvantages are analyzed by combining nanostructures with organic substrates as well as involving the basis of different functionalizations. It is anticipated to provide insights and guidance for the future development of mineralized polymer composites and their application designs.

Precise Construction of Nitrogen-Enriched Porous Ionic Polymers as Highly Efficient Sulfur Dioxide Adsorbent.

Porous ionic polymers with unique features have exhibited high performance in various applications. However, the fabrication of functional porous ionic polymers with custom functionality and porosity for efficient removal of low-concentration SO2 remains challenging. Herein, a novel nitrogen-enriched porous ionic polymer NH2Py-PIP is prepared featuring high-content nitrogen sites (15.9 wt.%), adequate ionic sites (1.22 mmol g-1), and a hierarchical porous structure. The proposed construction pathway relies on a tailored nitrogen-functionalized cross-linker NH2Py, which effectively introduces abundant functional sites and improves the porosity of porous ionic polymers. NH2Py-PIP with a well-engineered SO2-affinity environment achieves excellent SO2/CO2 selectivity (1165) and high SO2 adsorption capacity (1.13 mmol g-1 at 0.002 bar), as well as enables highly efficient and reversible dynamic separation performance. Modeling studies further elucidate that the nitrogen sites and bromide anions collaboratively promote preferential adsorption of SO2. The unique design in this work provides new insights into constructing functional porous ionic polymers for high-efficiency separations.

Emerging Advances around Nanofluidic Transport and Mass Separation under Confinement in Atomically Thin Nanoporous Graphene.

Membrane separation stands as an environmentally friendly, high permeance and selectivity, low energy demand process that deserves scientific investigation and industrialization. To address intensive demand, seeking appropriate membrane materials to surpass trade-off between permeability and selectivity and improve stability is on the schedule. 2D materials offer transformational opportunities and a revolutionary platform for researching membrane separation process. Especially, the atomically thin graphene with controllable porosity and structure, as well as unique properties, is widely considered as a candidate for membrane materials aiming to provide extreme stability, exponentially large selectivity combined with high permeability. Currently, it has shown promising opportunities to develop separation membranes to tackle bottlenecks of traditional membranes, and it has been of great interest for tremendously versatile applications such as separation, energy harvesting, and sensing. In this review, starting from transport mechanisms of separation, the material selection bank is narrowed down to nanoporous graphene. The study presents an enlightening overview of very recent developments in the preparation of atomically thin nanoporous graphene and correlates surface properties of such 2D nanoporous materials to their performance in critical separation applications. Finally, challenges related to modulation and manufacturing as well as potential avenues for performance improvements are also pointed out.

Thiol-Ene Click Reaction in Constructing Liquid Separation Membranes for Water Treatment.

In the evolving landscape of water treatment, membrane technology has ascended to an instrumental role, underscored by its unmatched efficacy and ubiquity. Diverse synthesis and modification techniques are employed to fabricate state-of-the-art liquid separation membranes. Click reactions, distinguished by their rapid kinetics, minimal byproduct generation, and simple reaction condition, emerge as a potent paradigm for devising eco-functional materials. While the metal-free thiol-ene click reaction is acknowledged as a viable approach for membrane material innovation, a systematic elucidation of its applicability in liquid separation membrane development remains conspicuously absent. This review elucidates the pre-functionalization strategies of substrate materials tailored for thiol-ene reactions, notably highlighting thiolation and introducing unsaturated moieties. The consequential implications of thiol-ene reactions on membrane properties-including trade-off effect, surface wettability, and antifouling property-are discussed. The application of thiol-ene reaction in fabricating various liquid separation membranes for different water treatment processes, including wastewater treatment, oil/water separation, and ion separation, are reviewed. Finally, the prospects of thiol-ene reaction in designing novel liquid separation membrane, including pre-functionalization, products prediction, and solute-solute separation membrane, are proposed. This review endeavors to furnish invaluable insights, paving the way for expanding the horizons of thiol-ene reaction application in liquid separation membrane fabrication.

Pulmonary siRNA Delivery with Sophisticated Amphiphilic Poly(Spermine Acrylamides) for the Treatment of Lung Fibrosis.

RNA interference (RNAi) is an efficient strategy to post-transcriptionally silence gene expression. While all siRNA drugs on the market target the liver, the lung offers a variety of currently undruggable targets, which can potentially be treated with RNA therapeutics. To achieve this goal, the synthesis of poly(spermine acrylamides) (P(SpAA) is reported herein. Polymers are prepared via polymerization of N-acryloxysuccinimide (NAS) and afterward this active ester is converted into spermine-based pendant groups. Copolymerizations with decylacrylamide are employed to increase the hydrophobicity of the polymers. After deprotection, polymers show excellent siRNA encapsulation to obtain perfectly sized polyplexes at very low polymer/RNA ratios. In vitro 2D and 3D cell culture, ex vivo and in vivo experiments reveal superior properties of amphiphilic spermine-copolymers with respect to delivery of siRNA to lung cells in comparison to commonly used lipid-based transfection agents. In line with the in vitro results, siRNA delivery to human lung explants confirm more efficient gene silencing of protease-activated receptor 2 (PAR2), a G protein-coupled receptor involved in fibrosis. This study reveals the importance of the balance between efficient polyplex formation, cellular uptake, gene knockdown, and toxicity for efficient siRNA delivery in vitro, in vivo, and in fibrotic human lung tissue ex vivo.

Surface Bio-engineered Polymeric Nanoparticles.

Surface bio-engineering of polymeric nanoparticles (PNPs) has emerged as a cornerstone in contemporary biomedical research, presenting a transformative avenue that can revolutionize diagnostics, therapies, and drug delivery systems. The approach involves integrating bioactive elements on the surfaces of PNPs, aiming to provide them with functionalities to enable precise, targeted, and favorable interactions with biological components within cellular environments. However, the full potential of surface bio-engineered PNPs in biomedicine is hampered by obstacles, including precise control over surface modifications, stability in biological environments, and lasting targeted interactions with cells or tissues. Concerns like scalability, reproducibility, and long-term safety also impede translation to clinical practice. In this review, these challenges in the context of recent breakthroughs in developing surface-biofunctionalized PNPs for various applications, from biosensing and bioimaging to targeted delivery of therapeutics are discussed. Particular attention is given to bonding mechanisms that underlie the attachment of bioactive moieties to PNP surfaces. The stability and efficacy of surface-bioengineered PNPs are critically reviewed in disease detection, diagnostics, and treatment, both in vitro and in vivo settings. Insights into existing challenges and limitations impeding progress are provided, and a forward-looking discussion on the field's future is presented. The paper concludes with recommendations to accelerate the clinical translation of surface bio-engineered PNPs.