BINA

Pathogens such as bacteria and viruses cause disease in a range of hosts, from humans to plants. Bacterial biofilms, communities of bacteria, e.g., Staphylococcus aureusand Escherichia coli, attached to the surface, create a protective layer that enhances their survival in harsh environments and resistance to antibiotics and the host’s immune system. Biofilms are commonly associated with food spoilage and chronic infections, posing challenges for treatment and prevention. Tomato brown rugose fruit virus (ToBRFV), a newly discovered tobamovirus, infects tomato plants, causing unique symptoms on the fruit, posing a risk for tomato production. The present study focuses on the effectiveness of silane-phosphonium thin coatings on polymeric films, e.g., polypropylene. Phosphonium has significant antibacterial activity and is less susceptible to antibacterial resistance, making it a safer alternative with a reduced …

Ni-rich, Co-free layered oxide cathode materials are promising candidates for next-generation Li-ion batteries due to their high energy density. However, these cathode materials suffer from rapid capacity fading during electrochemical cycling. To overcome this shortcoming, so-called high-entropy (HE) materials, which are obtained by incorporating multiple dopants, have been suggested. Recent experimental work has shown that HE Ni-rich cathode materials can offer excellent capacity retention on cycling, although a thorough rationale for this has yet to be provided. Here, we present classical and first-principles calculations to elucidate the salient features of HE layered oxides as cathode materials in Li-ion batteries. We suggest that a combination of five prime factors may be responsible for the enhanced performance of HE Ni-rich layered oxide cathode materials over other Ni-rich cathodes: (1) low crystal lattice …

In pathogens, a unique class of metalloregulator proteins, called gene regulatory proteins, sense specific metal ions that initiate gene transcription of proteins that export metal ions from the cell, thereby preventing toxicity and cell death. CsoR is a metalloregulator protein found in various bacterial systems that “sense” Cu(I) ions with high affinity. Upon copper binding, CsoR dissociates from the DNA promoter region, resulting in initiation of gene transcription. Crystal structures of CsoR in the presence and absence of Cu(I) from various bacterial systems have been reported, suggesting either a dimeric or tetrameric structure of these helical proteins. However, structural information about the CsoR-DNA complex is missing. Here, we applied electron paramagnetic resonance (EPR) spectroscopy to follow the conformational and dynamical changes that Mycobacterium tuberculosis CsoR undergoes upon DNA binding in …

Machine-learning methods (ML) have shown great potential in the adaptive immune receptor repertoire (AIRR) field. However, there is a lack of large-scale ground-truth experimental AIRR data suitable for AIRR-ML-based disease diagnostics and therapeutics discovery. Simulated ground-truth AIRR data are required to complement the development and benchmarking of robust and interpretable AIRR-ML approaches where experimental data is inaccessible or insufficient as of yet. The challenge for simulated data to be useful is the ability to incorporate key features observed in experimental repertoires. These features, such as complex antigen or disease-associated immune information, cause AIRR-ML problems to be challenging. Here, we introduce LIgO, a modular software suite, which simulates AIRR data for the development and benchmarking of AIRR-based machine learning. LIgO incorporates different types of immune information both on the receptor and the repertoire level and preserves native-like generation probability distribution. Additionally, LIgO assists users in determining the computational feasibility of their simulations. We show two examples where LIgO simulation supports the development and validation of AIRR-ML methods: (1) how individuals carrying out-of-distribution immune information impacts receptor-level prediction performance and (2) how immune information co-occurring in the same AIRs have an impact on the performance of conventional receptor-level encoding and repertoire-level classification approaches. The LIgO software guides the advancement and assessment of interpretable AIRR-ML methods.

Nanocomposites are constructed from a matrix material combined with dispersed nanosized filler particles. Such a combination yields a powerful ability to tailor the desired mechanical, optical, electrical, thermodynamic, and antimicrobial material properties. Colloidal semiconductor nanocrystals (SCNCs) are exciting potential fillers, as they display size-, shape-, and composition-controlled properties and are easily embedded in diverse matrices. Here we present their role as quantum photoinitiators (QPIs) in acrylate-based polymer, where they act as a catalytic radical initiator and endow the system with mechanical, photocatalytic, and antimicrobial properties. By utilizing ZnO nanorods (NRs) as QPIs, we were able to increase the tensile strength and elongation at break of poly(ethylene glycol) diacrylate (PEGDA) hydrogels by up to 85%, unlike the use of the same ZnO NRs acting merely as fillers. Simultaneously …

Pathogens such as bacteria and viruses cause disease in a range of hosts, from humans to plants. Bacterial biofilms, communities of bacteria, e.g., Staphylococcus aureusand Escherichia coli, attached to the surface, create a protective layer that enhances their survival in harsh environments and resistance to antibiotics and the host’s immune system. Biofilms are commonly associated with food spoilage and chronic infections, posing challenges for treatment and prevention. Tomato brown rugose fruit virus (ToBRFV), a newly discovered tobamovirus, infects tomato plants, causing unique symptoms on the fruit, posing a risk for tomato production. The present study focuses on the effectiveness of silane-phosphonium thin coatings on polymeric films, e.g., polypropylene. Phosphonium has significant antibacterial activity and is less susceptible to antibacterial resistance, making it a safer alternative with a reduced …

RAG2-SCID is a primary immunodeficiency caused by mutations in Recombination-activating gene 2 (RAG2), a gene intimately involved in the process of lymphocyte maturation and function. ex-vivo manipulation of a patient’s own hematopoietic stem and progenitor cells (HSPCs) using CRISPR-Cas9/rAAV6 gene editing could provide a therapeutic alternative to the only current treatment, allogeneic hematopoietic stem cell transplantation (HSCT). Here we show an innovative RAG2 correction strategy that replaces the entire endogenous coding sequence (CDS) for the purpose of preserving the critical endogenous spatiotemporal gene regulation and locus architecture. Expression of the corrective transgene leads to successful development into CD3+TCRαβ+ and CD3+TCRγδ+ T cells and promotes the establishment of highly diverse TRB and TRG repertoires in an in-vitro T-cell differentiation platform. Thus, our …

Topological insulators are materials characterized by an insulating bulk and high mobility topologically protected surface states, making them promising candidates for future optoelectronic and quantum devices. Although their electronic properties have been extensively studied, their mid-infrared (MIR) properties and prospective photonic capabilities have not been fully uncovered. Here, we use a combination of far-field and near-field nanoscale imaging and spectroscopy to study chemical vapor deposition-grown Bi2Se3 nanobeams (NBs). We extract the MIR optical constants of Bi2Se3, revealing refractive index values as high as n ∼ 6.4, and demonstrate that the NBs support Mie resonances across the MIR. Local near-field reflection phase mapping reveals domains of various phase shifts, providing information on the local optical properties of the NBs. We experimentally measure up to 2π phase-shift across the …

The glass transition temperature is a key parameter of polymer coating layers that protect optical fibers, and it affects the proper function of the fibers in their service environment. Established protocols for glass transition temperature measurements are destructive, require samples of specific geometries, and may only be carried out offline. In this work, we report the nondestructive measurement of the glass transition temperature of an acrylate polymer coating layer over a working standard fiber. The method is based on forward stimulated Brillouin scattering. A large decrease in the modulus of the coating layer above the glass transition temperature manifests in the narrowing of the modal linewidths in the forward Brillouin scattering spectrum. The transition temperature agrees with the standard dynamic mechanical analysis of samples made of the same polymer. The protocol can be useful for coating materials …

When exposed to specific light wavelengths, carbon dots (CDs), which tend to be fluorescent, can emit colorful light. It provides them with a lot of adaptability for different applications including bioimaging, optoelectronics, and even environmental sensing. Poly(ethylenimine) (PEI) coated carbon dots (PEI-CDs) with a long emission wavelength were synthesized via the hydrothermal method. The resultant CDs show strong fluorescence with quantum yield up to 20.2%. The PEI-CDs exist with distinct pH-sensitive features with pH values in the range of 2–14. The optical characteristics of CDs are pH-responsive due to the presence of different amine groups on PEI, which is a functional polycationic polymer. One of the most widely employed nanoparticles for improving the fluorescence plasmonic characteristics of a nanocomposite is gold. Gold nanoparticles were coupled with PEI-CDs in this assay by using the EDC …

In many disordered systems, the diffusion of classical particles is described by a displacement distribution P(x, t) that displays exponential tails instead of Gaussian statistics expected for Brownian motion. However, the experimental demonstration of control of this behavior by increasing the disorder strength has remained challenging. In this work, we explore the Gaussian-to-exponential transition by using diffusion of poly(ethylene glycol) (PEG) in attractive nanoparticle–polymer mixtures and controlling the volume fraction of the nanoparticles. In this work, we find “knobs”, namely nanoparticle concentration and interaction, which enable the change in the shape of P(x,t) in a well-defined way. The Gaussian-to-exponential transition is consistent with a modified large deviation approach for a continuous time random walk and also with Monte Carlo simulations involving a microscopic model of polymer trapping via …

In this research we present a novel method to measure local optical dichroism in opaque crystal powder suspensions using the photoacoustic effect. Our method is based upon the laser speckle contrast technique, a novel technique to perform photoacoustic measurements that do not require contact with the sample. The main novelty of our work is the development of a simple statistical approach for measuring the chirality of crystal suspensions using the photoacoustic effect, which does not require arranging the crystals with a specific orientation on surfaces. A model chiral system was used to demonstrate our method, we have used Cobalt doped L-Histidine crystals that are photoacoustic active and established our ability to measure their optical dichroism in solution under completely random orientation.

A critical current challenge in the development of all-solid-state lithium batteries (ASSLBs) is reducing the cost of fabrication without compromising the performance. Here we report a sulfide ASSLB based on a high-energy, Co-free LiNiO2 cathode with a robust outside-in structure. This promising cathode is enabled by the high-pressure O2 synthesis and subsequent atomic layer deposition of a unique ultrathin LixAlyZnzOδ protective layer comprising a LixAlyZnzOδ surface coating region and an Al and Zn near-surface doping region. This high-quality artificial interphase enhances the structural stability and interfacial dynamics of the cathode as it mitigates the contact loss and continuous side reactions at the cathode/solid electrolyte interface. As a result, our ASSLBs exhibit a high areal capacity (4.65 mAh cm−2), a high specific cathode capacity (203 mAh g−1), superior cycling stability (92% capacity retention …