BINA

Stress granules (SGs) are cytoplasmic assemblies formed under various stress conditions as a consequence of translation arrest. SGs contain RNA-binding proteins, ribosomal subunits and messenger RNAs (mRNAs). It is well known that mRNAs contribute to SG formation; however, the connection between SG assembly and nuclear processes that involve mRNAs is not well established. Here, we examine the effects of inhibiting mRNA transcription, splicing and export on the assembly of SGs and the related cytoplasmic P body (PB). We demonstrate that inhibition of mRNA transcription, splicing and export reduces the formation of canonical SGs in a eukaryotic initiation factor 2α phosphorylation-independent manner, and alters PB size and quantity. We find that the splicing inhibitor madrasin promotes the assembly of stress-like granules. We show that the addition of synthetic mRNAs directly to the cytoplasm …

Computational spectrometry is an emerging field that uses photodetection in conjunction with numerical algorithms for spectroscopic measurements. Compact single photodetectors made from layered materials are particularly attractive since they eliminate the need for bulky mechanical and optical components used in traditional spectrometers and can easily be engineered as heterostructures to optimize device performance. However, such photodetectors are typically nonlinear devices, which adds complexity to extracting optical spectra from their response. Here, we train an artificial neural network to recover the full nonlinear spectral photoresponse of a single GeSe-InSe p-n heterojunction device. The device has a spectral range of 400 to 1100 nm, a small footprint of ~25 × 25 square micrometers, and a mean reconstruction error of 2 × 10−4 for the power spectrum at 0.35 nanometers. Using our device, we …

Carbonaceous materials are the most common catalyst supports in proton exchange membrane fuel cell (PEMFCs), yet their corrosion is one of the limiting factors in achieving high durability. Herein, we doped carbon supports with boron (B) to increase the corrosion-resistance of the support. Two types of B-doped carbons were synthesized and studied as platinum support materials. They varied in their morphologies, surface areas, and the types of boron species. The durability of Pt/B-doped carbon catalysts was investigated using the US-DOE catalysts’ supports accelerated stress test (AST) and a mass-spectrometer connected to the fuel cell effluent stream to quantify the mass of corroded carbon support in operando. The addition of boron to the carbon increased the stability of Pt catalysts in long-term usage of PEMFC. After 4,000 AST cycles, more than 50% of initial current density was preserved for the boron …

The Kirkwood-Dirac quasiprobability distribution emerges from the quantum correlation function of two observables measured at distinct times and is therefore relevant for fundamental physics and quantum technologies. These quasiprobabilities follow all but one of Kolmogorov axioms for joint probability distributions: they can take non-positive values. Their experimental reconstruction becomes challenging when expectation values of incompatible observables are involved. Previous strategies aimed to reconstruct them using weak measurements or combining strong measurements. Here, we use a more direct approach, an interferometric scheme aided by an auxiliary system, to reconstruct the Kirkwood-Dirac quasiprobability distribution. We experimentally demonstrate the interferometric scheme in an electron-nuclear spin system associated with a nitrogen-vacancy center in diamond. By measuring the characteristic function, we reconstruct the quasiprobability distribution of the work and analyze the behavior of the first and second moments of work. Our results clarify the physical meaning of the work quasiprobability distribution in the context of quantum thermodynamics. Finally, having measured the real and imaginary parts of the Kirkwood-Dirac quasiprobability of work, we are also able to study the uncertainty of measuring the Hamiltonian of the system at two times, via the Robertson-Schr{\"o}dinger uncertainty relation, for different initial states.

In the current work, we analyzed the origin of difference in stabilities among the germacrene A and hedycaryol-derived carbocations. This study focused on twelve hydrocarbons derived from germacrene A and twelve from hedycaryol, which can be divided into three groups: four molecules containing 6-6 bicyclic rings, four 5-7 bicyclic compounds with the carbocation being on the seven-membered ring and the remaining four 5-7 bicyclic compounds with the carbocation on the five-membered ring. The variations in energy within the groups of carbocations (ie, 6-6 and two kinds of 5-7 bicyclic carbocations) can be ascribed to intramolecular repulsion interactions, as seen from non-covalent interactions plots. Despite the structural similarities between germacrene A and hedycaryol cations, they possess a somewhat different stability trend. These differences are attributed to C+··· OH intramolecular interactions present in some hedycaryol cations, which are absent in the carbocations derived from germecrene A.

The COVID-19 pandemic highlighted the necessity of fast, sensitive, and efficient methods to test large populations for respiratory viruses. The “gold standard” molecular assays for detecting respiratory viruses, such as quantitative polymerase chain reaction (qPCR) and reverse transcription qPCR (RT-qPCR), rely on invasive swab samples and require time-consuming and labor-intensive extraction processes. Moreover, the turnaround time for RT-qPCR-based assays is too lengthy for rapid screening. Extraction-free saliva-based methods provide a non-invasive sampling process with a fast turnaround time and are suitable for high-throughput applications. However, when used with a standard RT-qPCR system, the absence of extraction significantly reduces the assays’ sensitivity. Here, using a novel optical modulation biosensing (OMB) platform, we developed a rapid and highly sensitive extraction-free saliva …

X-ray imaging is a prevalent technique for non-invasively visualizing the interior of the human body and opaque instruments. In most commercial x-ray modalities, an image is formed by measuring the x-rays that pass through the object of interest. However, despite the potential of scattered radiation to provide additional information about the object, it is often disregarded due to its inherent tendency to cause blurring. Consequently, conventional imaging modalities do not measure or utilize these valuable data. In contrast, we propose and experimentally demonstrate a high-resolution technique for x-ray computed tomography (CT) that measures scattered radiation by exploiting computational ghost imaging (CGI). We show that our method can provide sub-200 {\mu}m resolution, exceeding the capabilities of most existing x-ray imaging modalities. Our research reveals a promising technique for incorporating scattered radiation data in CT scans to improve image resolution and minimize radiation exposure for patients. The findings of our study suggest that our technique could represent a significant advancement in the fields of medical and industrial imaging, with the potential to enhance the accuracy and safety of diagnostic imaging procedures.

Enhancing the reproducibility and comprehension of adaptive immune receptor repertoire sequencing (AIRR-seq) data analysis is critical for scientific progress. This study presents guidelines for reproducible AIRR-seq data analysis, and a collection of ready-to-use pipelines with comprehensive documentation. To this end, ten common pipelines were implemented using ViaFoundry, a user-friendly interface for pipeline management and automation. This is accompanied by versioned containers, documentation and archiving capabilities. The automation of pre-processing analysis steps and the ability to modify pipeline parameters according to specific research needs are emphasized. AIRR-seq data analysis is highly sensitive to varying parameters and setups; using the guidelines presented here, the ability to reproduce previously published results is demonstrated. This work promotes transparency …

We demonstrate the pioneering use of a quantum interferometer with x-rays, highlighting its effectiveness in precisely measuring the phase accumulated in opaque media. Our work uncovers novel opportunities for measuring sub-Angstrom optical-path differences.

Electrocatalysts play a critical role in energy technologies, but the development of active, efficient, and durable catalysts is impeded by the lack of methodologies to deconvolute the complex interplay between various aspects influencing the activity of the catalysts, e.g., the number of active sites, turnover frequency, and the reaction pathways. Fourier-transformed alternating current voltammetry (FTacV) is an emerging tool for the analysis of electroactive species and has been successfully applied to a variety of reactions such as the oxygen reduction reaction, oxygen evolution reaction, carbon dioxide reduction reaction, hydrogen evolution reaction, and hydrogen oxidation reaction. The harmonics generated from FTacV measurements neatly detect underlaying processes not visible by other, more commonly employed techniques for analysis of electrocatalysts, such as the rotating disc electrode and dc voltammetry …

Insertion of hydrophobic nanoparticles into phospholipid bilayers is limited to small particles that can incorporate into a hydrophobic membrane core between two lipid leaflets. Incorporation of nanoparticles above this size limit requires the development of challenging surface engineering methodologies. In principle, increasing the long-chain lipid component in the lipid mixture should facilitate incorporation of larger nanoparticles. Here, we explore the effect of incorporating very long phospholipids (C24:1) into small unilamellar vesicles on the membrane insertion efficiency of hydrophobic nanoparticles that are 5–11 nm in diameter. To this end, we improve an existing vesicle preparation protocol and utilized cryogenic electron microscopy imaging to examine the mode of interaction and evaluate the insertion efficiency of membrane-inserted nanoparticles. We also perform classical coarse-grained molecular …

The Kirkwood-Dirac quasiprobability distribution emerges from the quantum correlation function of two observables measured at distinct times and is therefore relevant for fundamental physics and quantum technologies. These quasiprobabilities follow all but one of Kolmogorov axioms for joint probability distributions: they can take non-positive values. Their experimental reconstruction becomes challenging when expectation values of incompatible observables are involved. Previous strategies aimed to reconstruct them using weak measurements or combining strong measurements. Here, we use a more direct approach, an interferometric scheme aided by an auxiliary system, to reconstruct the Kirkwood-Dirac quasiprobability distribution. We experimentally demonstrate the interferometric scheme in an electron-nuclear spin system associated with a nitrogen-vacancy center in diamond. By measuring the characteristic function, we reconstruct the quasiprobability distribution of the work and analyze the behavior of the first and second moments of work. Our results clarify the physical meaning of the work quasiprobability distribution in the context of quantum thermodynamics. Finally, having measured the real and imaginary parts of the Kirkwood-Dirac quasiprobability of work, we are also able to study the uncertainty of measuring the Hamiltonian of the system at two times, via the Robertson-Schr{\"o}dinger uncertainty relation, for different initial states.

Chiral induction of chiral crystals attracts significant attention due to its implications for developing chiral materials and understanding mechanisms of symmetry breaking enantioselective crystallization of naturally chiral inorganic crystals and their potential use in chiral discrimination, which are, however, largely unexplored. Here, we investigate the chiral induction during the crystallization of naturally chiral Ag2CO3 crystals using arginine amino acid as the chiral inducer. The chiral nature of Ag2CO3 was evaluated using various techniques. Chiral crystals exhibited chiral selective binding toward different amino acid enantiomers. The significant selectivity in adsorption was confirmed by circular dichroism, high-performance liquid chromatography, and isothermal titration calorimetry. Understanding chiral induction in crystal growth may open avenues for the controlled assembly of chiral materials and the development …

Nanoparticles are widely used in construction. Here, nano-SiO2 is employed, in a way that prevents agglomeration of the nanoparticles, as pozzolanic material to improve Portland cement hydration and to improve the properties of the concrete. To explore the effect of nano-SiO2 and core-shell PS@SiO2 on cement properties, spherical polystyrene particles were prepared by dispersion polymerization of styrene in polar solvents and characterized by FTIR and E-SEM. The core shells PS@SiO2 were synthesized by Stöber method. The results showed an amorphous nano-SiO2 layer can be deposited uniformly on polystyrene particles. This core/shell structure was reducing the aggregation of nano-SiO2 effectively. It was shown that PS@SiO2 particles improved the concrete performances compared to blended cement with nano-SiO2 due to the agglomeration affect. Highlights •Core/shell PS@SiO2 nanoparticles …

We demonstrate resolution enhancement of a standard hard x-ray imaging system from 500 μm to approximately 20 μm by extending the concept of ghost imaging to multipixel ghost imaging, enabling mega-pixel scale imaging in a short timeframe.

Terpene Synthases (TPS) catalyze the formation of multicyclic, complex terpenes and terpenoids from linear substrates. Molecular docking is an important research tool that can further our understanding of TPS multistep mechanisms and guide enzyme design. Standard docking programs are not well suited to tackle the unique challenges of TPS, like the many chemical steps which form multiple stereo-centers, the weak dispersion interactions between the isoprenoid chain and the hydrophobic region of the active site, description of carbocation intermediates, and finding mechanistically meaningful sets of docked poses. To address these and other unique challenges, we developed the multistate, multiscale docking program EnzyDock and used it to study many TPS and other enzymes. In this review we discuss the unique challenges of TPS, the special features of EnzyDock developed to address these challenges …

Nuclear forward scattering (NFS) is a synchrotron-based technique relying on the recoil-free nuclear resonance effect similar to Mössbauer spectroscopy. In this work, we introduce NFS for in situ and operando measurements during electrocatalytic reactions. The technique enables faster data acquisition and better discrimination of certain iron sites in comparison to Mössbauer spectroscopy. It is directly accessible at various synchrotrons to a broad community of researchers and is applicable to multiple metal isotopes. We demonstrate the power of this technique with the hydrogen evolution mechanism of an immobilized iron porphyrin supported on carbon. Such catalysts are often considered as model systems for iron–nitrogen-carbon (FeNC) catalysts. Using in situ and operando NFS in combination with theoretical predictions of spectroscopic data enables the identification of the intermediate that is formed prior …

A silicon mechanical-photonic wavelength converter, not based on absorption, has been recently proposed to address the need for all-silicon photodetectors in the infrared spectrum. Its implementation requires high-frequency modulation, from hundreds of kHz to 1 MHz, of a light beam over an area of a few hundred microns. Since the displacement amplitudes of tens of microns at these frequencies are unfeasible, a moving grate is proposed to locally modulate the light. The MEMS actuator, an array of 1 µm-wide 1 µm-spaced beams (100 × 100 µm2 area), achieved displacements of 70 nm at atmospheric pressure and 350 nm under low vacuum, with 10 Vpp actuation at 290 kHz (FOM displacement × frequency2 above previously reported works).

The term defect tolerance (DT) is used often to rationalize the exceptional optoelectronic properties of halide perovskites (HaPs) and their devices. Even though DT lacked direct experimental evidence, it became a “fact” in the field. DT in semiconductors implies that structural defects do not translate to electrical and optical effects (e.g., due to charge trapping), associated with such defects. We present pioneering direct experimental evidence for DT in Pb-HaPs by comparing the structural quality of 2-dimensional (2D), 2D-3D, and 3D Pb-iodide HaP crystals with their optoelectronic characteristics using high-sensitivity methods. Importantly, we get information from the materials’ bulk because we sample at least a few hundred nanometers, up to several micrometers, from the sample’s surface, which allows for assessing intrinsic bulk (and not only surface-) properties of HaPs. The results point to DT in 3D, 2D-3D, and 2D …

BackgroundThe exact mechanisms linking the gut microbiota and social behavior are still under investigation. We aimed to explore the role of the gut microbiota in shaping social behavior deficits using selectively bred mice possessing dominant (Dom) or submissive (Sub) behavior features. Sub mice exhibit asocial, depressive- and anxiety-like behaviors, as well as systemic inflammation, all of which are shaped by their impaired gut microbiota composition.MethodsAn age-dependent comparative analysis of the gut microbiota composition of Dom and Sub mice was performed using 16S rRNA sequencing, from early infancy to adulthood. Dom and Sub gastrointestinal (GI) tract anatomy, function, and immune profiling analyses were performed using histology, RT-PCR, flow cytometry, cytokine array, and dextran-FITC permeability assays. Short chain fatty acids (SCFA) levels in the colons of Dom and Sub mice were …

Recent advancements in thin-film lithium niobate (TFLN) photonics have led to a new generation of high-performance electro-optic devices, including modulators, frequency combs, and microwave-to-optical transducers. However, the broader adoption of TFLN-based devices that rely on all-optical nonlinearities have been limited by the sensitivity of quasi-phase matching (QPM), realized via ferroelectric poling, to fabrication tolerances. Here, we propose a scalable fabrication process aimed at improving the wavelength-accuracy of optical frequency mixers in TFLN. In contrast to the conventional pole-before-etch approach, we first define the waveguide in TFLN and then perform ferroelectric poling. This sequence allows for precise metrology before and after waveguide definition to fully capture the geometry imperfections. Systematic errors can also be calibrated by measuring a subset of devices to fine-tune the QPM design for remaining devices on the wafer. Using this method, we fabricated a large number of second harmonic generation devices aimed at generating 737 nm light, with 73% operating within 5 nm of the target wavelength. Furthermore, we also demonstrate thermo-optic tuning and trimming of the devices via cladding deposition, with the former bringing ~96% of tested devices to the target wavelength. Our technique enables the rapid growth of integrated quantum frequency converters, photon pair sources, and optical parametric amplifiers, thus facilitating the integration of TFLN-based nonlinear frequency mixers into more complex and functional photonic systems.