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Cadherins are calcium dependent adhesion proteins that establish and maintain the intercellular mechanical contact by bridging the gap between adjacent cells. Desmoglein-2 (Dsg2) and desmocollin-2 (Dsc2) are tissue specific cadherin isoforms of the cell-cell contact in cardiac desmosomes. Mutations in the DSG2 -gene and in the DSC2 -gene are related to arrhythmogenic right ventricular cardiomyopathy (ARVC) a rare but severe heart muscle disease. Here, several possible homophilic and heterophilic binding interactions of wild-type Dsg2, wild-type Dsc2, as well as one Dsg2- and two Dsc2-variants, each associated with ARVC, are investigated. Using single molecule force spectroscopy (SMFS) with atomic force microscopy (AFM) and applying Jarzynski's equality the kinetics and thermodynamics of Dsg2/Dsc2 interaction can be determined. The free energy landscape of Dsg2/Dsc2 dimerization exposes a high activation energy barrier, which is in line with the proposed strand-swapping binding motif. Although the binding motif is not affected by any of the mutations, the binding kinetics of the interactions differ significantly from the wild-type. While wild-type cadherins exhibit an average complex lifetime of approx. 0.3 s interactions involving a variant consistently show - lifetimes that are substantially larger. The lifetimes of the wild-type interactions give rise to the picture of a dynamic adhesion interface consisting of continuously dissociating and (re)associating molecular bonds, while the delayed binding kinetics of interactions involving an ARVC-associated variant might be part of the pathogenesis. Our data provide a comprehensive and consistent thermodynamic and kinetic description of cardiac cadherin binding, allowing detailed insight into the molecular mechanisms of cell adhesion. [Display omitted] • Integrity of heart muscle tissue relies on weak molecular bonds between cadherins. • Single molecule force spectroscopy reveals cadherin binding kinetics. • Wild-type cadherin bonds exhibit characteristic fast (re-) binding kinetics. • Specific cardiomyopathy associated cadherin variants slow binding kinetics. • Impaired molecular dynamics could be a cardiomyopathy-specific pathomechanism. [ABSTRACT FROM AUTHOR]

Cancer remains a significant global health challenge, prompting exploration into alternative treatments such as those derived from natural compounds found in traditional medicine. Recent research has underscored the role of proteins like Focal Adhesion Kinase (FAK), Vascular Endothelial Growth Factor (VEGF), and Metastasis-Associated Protein 1 (MTA1) in driving cancer cell proliferation and survival. Here, we investigated the potential of a single molecule to modulate these key proteins involved in metastasis, offering a promising avenue for cancer therapy. Terminalia elliptica, commonly known as Asna, possesses a diverse range of medicinal properties, including antimicrobial, anti-inflammatory, anticancer, antidiabetic, antiaging, hepatoprotective, antioxidant, and neuroprotective activities. Our study aimed to explore the anticancer potential of Terminalia elliptica by identifying bioactive compounds capable of targeting FAK, VEGF, and MTA1 to impede cancer metastasis. Through in silico analysis, we conducted network analysis using Cytoscape to assess the significance of these bioactive compounds in the inhibition of signaling pathways driving metastasis. The utilization of these bioactives as potential candidates for targeted therapy of VEGF, FAK, and MTA1 regulated pathways was preliminarily assessed by Molecular Docking and MD Simulation. Our findings revealed that phytobioactives namely, Chebulinic Acid of Terminalia elliptica, exhibited notable binding affinity and interaction with FAK, and Chebulagic Acid with VEGF, and MTA1. This discovery holds promise as a novel therapeutic approach for combating cancer, offering potential benefits in cancer treatment and management. [ABSTRACT FROM AUTHOR]

Proteins play a vital role in different biological processes by forming complexes through precise folding with exclusive inter‐ and intra‐molecular interactions. Understanding the structural and regulatory mechanisms underlying protein complex formation provides insights into biophysical processes. Furthermore, the principle of protein assembly gives guidelines for new biomimetic materials with potential applications in medicine, energy, and nanotechnology. Atomic force microscopy (AFM) is a powerful tool for investigating protein assembly and interactions across spatial scales (single molecules to cells) and temporal scales (milliseconds to days). It has significantly contributed to understanding nanoscale architectures, inter‐ and intra‐molecular interactions, and regulatory elements that determine protein structures, assemblies, and functions. This review describes recent advancements in elucidating protein assemblies with in situ AFM. We discuss the structures, diffusions, interactions, and assembly dynamics of proteins captured by conventional and high‐speed AFM in near‐native environments and recent AFM developments in the multimodal high‐resolution imaging, bimodal imaging, live cell imaging, and machine‐learning‐enhanced data analysis. These approaches show the significance of broadening the horizons of AFM and enable unprecedented explorations of protein assembly for biomaterial design and biomedical research. [ABSTRACT FROM AUTHOR]

Metalated covalent organic frameworks (COFs) for 2D and 3D topologies are continuously being developed, whereas metalated COFs with 1D topologies are still in their infancy. Here, a novel 1D phenanthroline‐based COF containing 4,4‐(1,10‐phenanthroline‐2,9‐diyl)bis[benzaldehyde] (PBA) is reported (PAD‐COF). Subsequently, a metalated 1D COF, Co SAS/PAD‐COF, is constructed using the bidentate ligand properties of PBA and anchoring the single Co atoms in PAD‐COF through a post‐synthetic modification strategy. This complex significantly improved the photocatalytic performance of PAD‐COF, and the CO yield of the optimized Co SAS/PAD‐COF was stable at 3091 µmol g−1 h−1 with a selectivity of 93%, which is approximately 43.7 times that of the original PAD‐COF. Experimental and theoretical results demonstrate the excellent CO2 photoreduction activity of Co SAS/PAD‐COF owing to the synergistic effect of single Co catalytic sites and PAD‐COF. Among them, PAD‐COF, as the host, adsorbs CO2 molecules and loads single Co atoms. Meanwhile, Co atoms function as catalytic sites and promote the adsorption and activation of CO2, while reducing the reaction energy barrier formed by the *COOH intermediates. Therefore, this unique metalated 1D COF provides a fresh approach to photocatalytic CO2 reduction. [ABSTRACT FROM AUTHOR]

Single-molecule localization microscopy (SMLM) surpasses the diffraction limit by randomly switching fluorophores between fluorescent and dark states, precisely pinpointing the resulted isolated emission patterns, thereby reconstructing the super-resolution images based on the accumulated locations of thousands to millions of single molecules. This technique achieves a ten-fold improvement in resolution, unveiling the intricate details of molecular activities and structures in cells and tissues. Multicolor SMLM extends this capability by imaging distinct protein species labeled with various fluorescent probes, providing insights into structural intricacies and spatial relationships among different targets. This review explores recent advancements in multicolor SMLM, evaluates the strengths and limitations of each variant, and discusses the future prospects. [ABSTRACT FROM AUTHOR]

Background: Retention of apolipoprotein B (apoB)-containing lipoproteins within the arterial wall plays a major causal role in atherosclerotic cardiovascular disease (ASCVD). There is a single apoB molecule in all apoB-containing lipoproteins. Therefore, quantitation of apoB directly estimates the number of atherogenic particles in plasma. ApoB is the preferred measurement to refine the estimate of ASCVD risk. Low-density lipoprotein (LDL) particles are by far the most abundant apoB-containing particles. In patients with elevated lipoprotein(a) (Lp(a)), apoB may considerably underestimate risk because Mendelian randomization studies have shown that the atherogenicity of Lp(a) is approximately 7-fold greater than that of LDL on a per apoB particle basis. In subjects with increased Lp(a), the association between LDL-cholesterol and incident CHD (coronary heart disease) is increased, but the association between apoB and incident CHD is diminished or even lost. Thus, there is a need to understand the mechanisms of Lp(a), LDL-cholesterol and apoB-related CHD risk and to provide clinicians with a simple practical tool to address these complex and variable relationships. How can we understand a patient's overall lipid-driven atherogenic risk? What proportion of this risk does apoB capture? What proportion of this risk do Lp(a) particles carry? To answer these questions, we created a novel metric of atherogenic risk: risk-weighted apolipoprotein B. Methods: In nmol/L: Risk-weighted apoB = apoB - Lp(a) + Lp(a) x 7 = apoB + Lp(a) x 6. Proportion of risk captured by apoB = apoB divided by risk-weighted apoB. Proportion of risk carried by Lp(a) = Lp(a) × 7 divided by risk-weighted apoB. Results: Risk-weighted apoB agrees with risk estimation from large epidemiological studies and from several Mendelian randomization studies. Conclusions: ApoB considerably underestimates risk in individuals with high Lp(a) levels. The association between apoB and incident CHD is diminished or even lost. These phenomena can be overcome and explained by risk-weighted apoB. [ABSTRACT FROM AUTHOR]

Background: Polyhydroxyalkanoates (PHAs) are optimal potential materials for industrial and medical uses, characterized by exceptional sustainability, biodegradability, and biocompatibility. These are primarily from various bacteria and archaea. Bacterial strains with effective PHA formation capabilities and minimal production cost form the foundation for PHA production. Detailed genomic analysis of these PHA-generating bacteria is vital to understand their PHA production pathways and enhance their synthesis capability. Results: ZZQ-149, a halophilic, PHA-producing bacterium, was isolated from the sediment of China's Qinghai Lake. Here, we decoded the full genome of ZZQ-149 using Single Molecule Real Time (SMRT) technology based on PacBio RS II platform, coupled with Illumina sequencing platforms. Physiological, chemotaxonomic traits, and phylogenetic analysis based on 16 S rRNA gene and single copy core genes of ninety-nine Halomonas type strains identified ZZQ-149 as the type strain of Halomonas qinghailakensis. Furthermore, a low average nucleotide identity (ANI, < 95%) delineated the genetic differences between ZZQ-149 and other Halomonas species. The ZZQ-149 genome, with a DNA G + C content of 52%, comprises a chromosome (3, 798, 069 bps) and a plasmid (6, 107 bps). The latter encodes the toxin-antitoxin system, BrnT/BrnA. Through comprehensive genome sequencing and analysis, we identified multiple PHA-synthesizing enzymes and an unprecedented combination of eight PHA-synthesizing pathways in ZZQ-149. Conclusions: Being a halophilic, PHA-producing bacterium, ZZQ-149 exhibits potential as a high PHA producer for engineered bacteria via genome editing while ensuring low-cost PHA production through continuous, unsterilized fermentation. [ABSTRACT FROM AUTHOR]

Here we report the synthesis and luminescent properties of the modified polyhedral oligomeric silsesquioxane (POSS) that possesses two types of luminophores, cyanobenzene and N,N‐diethylaniline for inducing significant emission not only from each dye but also from molecular interactions on the POSS core. From the optical measurements in the diluted solution, we observed both locally‐excited emission and excimer emission originating from intramolecular interactions assisted by POSS. Moreover, highly‐efficient exciplex emission was observed from the thin film, indicating that the interaction between luminophores easily occurs in the solid state by accumulating two kinds of molecules in the single POSS molecule. Finally, we also found that the modified POSS showed a unique acid responsiveness which can be caused by protonation at two types of amino moieties. In this manuscript, it is shown that POSS is able to play various roles at the same time: recruiting excited molecules to form exciplexes, suppressing concentration quenching in the solid state, and imparting stimulus responsiveness to exciplexes. [ABSTRACT FROM AUTHOR]

ABSTRACT Venturello‐structured polyoxometalates (POMs) are effective homogeneous catalysts and confining POMs to size‐matched metal‐organic frameworks (MOFs) as heterogeneous catalyst is an effective way to improve their practical application. The appropriate pore and narrow window of pristine UiO‐67 can not only enclose POMs in single molecule but also limit their leaching and can provide a suitable platform for the oxidation of most sulfur‐containing organic compound. The composite (CTA)3PW4@UiO‐67 was prepared by a facile in situ synthesis method, characterized by a variety of means and tested for desulfurization of multicomponent simulated diesel. The results prove that the active component (CTA)3PW4 is effectively encapsulated, and the composite (CTA)3PW4@UiO‐67 show remarkable desulfurization activity and excellent reusability. In addition, the kinetics and possible mechanism of the reaction were investigated. This work opens up a new idea for the design of “host‐guest adapted” catalyst suitable for fuel desulfurization technology. [ABSTRACT FROM AUTHOR]

A synergetic interaction between two or more photochromic chromophores has a potential to achieve advanced photochemical properties beyond conventional photochromic molecules and to realize photochemical control of complex systems using only a single molecule. Herein, we report a hybrid photochromic molecule consisting of hexaarylbiimidazole (HABI) and terarylene that exhibits multi‐state photochromism. The biphotochrome hybrid shows four‐state photochromic reaction involving sequentially proceeding photoreactions. The UV or visible light irradiation to the biphotochrome leads to the C−N bond breaking reaction of the HABI in preference to the ring‐closing reaction of the 6π‐electron system in the terarylene unit, leading to two terarylene radical molecules. The photogenerated terarylene radical further exhibits the 6π‐electrocyclization reaction by UV irradiation. The delocalized π‐radical on the closed‐ring form of the terarylene is efficient to enhance the photosensitivity to the NIR−I and ‐II region. Furthermore, a recombination reaction of radicals between the open‐ and closed‐ring isomers of terarylene affords an unprecedented photochromic dimer as a structural isomer of the initial molecule. This is a consequence of the sequential hybrid photochromic system involving the HABI and terarylene units. [ABSTRACT FROM AUTHOR]

Optical microcavities, particularly whispering gallery mode (WGM) microcavities enhanced by plasmonic nanorods, are emerging as powerful platforms for single‐molecule sensing. However, the impact of optical forces from the plasmonic near field on analyte molecules is inadequately understood. Using a standard optoplasmonic WGM single‐molecule sensor to monitor two enzymes, both of which undergo an open‐to‐closed‐to‐open conformational transition, the work done on an enzyme by the WGM sensor as atoms of the enzyme move through the electric field gradient of the plasmonic hotspot during conformational change has been quantified. As the work done by the sensor on analyte enzymes can be modulated by varying WGM intensity, the WGM microcavity system can be used to apply free energy penalties to regulate enzyme activity at the single‐molecule level. The findings advance the understanding of optical forces in WGM single‐molecule sensing, potentially leading to the capability to precisely manipulate enzyme activity at the single‐molecule level through tailored optical modulation. [ABSTRACT FROM AUTHOR]

Dengue virus, an arbovirus of genus Flavivirus, is an infectious disease causing organisms in the tropical environment leading to numerous deaths every year. No therapeutic is available against the virus till date with only symptomatic relief available. Here, we have tried to design therapeutic compounds from scratch by fragment based method followed by pharmacophore based modelling to find suitable similar structure molecules and validated the same by MD simulation, followed by binding energy calculations and ADMET analysis. The receptor binding region of the dengue envelope protein was considered as the target for prevention of viral host cell entry and thus infection. This resulted in the final selection of kanamycin as a stable binding molecule against the Dengue virus envelope protein receptor binding domain. This study results in selection of a single molecule having high binding energy and prominent stable interactions as determined by post simulation analyses. This study aims to provide a direction for development of small molecule therapeutics against the dengue virus in order to control infection. This study may open a new avenue in the arena of structure based and fragment based therapeutic design to obtain novel molecules with therapeutic potential. [ABSTRACT FROM AUTHOR]

Alpha-synuclein (aSyn) aggregates in the central nervous system are the main pathological hallmark of Parkinson's disease (PD). ASyn aggregates have also been detected in many peripheral tissues, including the skin, thus providing a novel and accessible target tissue for the detection of PD pathology. Still, a wellestablished validated quantitative biomarker for early diagnosis of PD that also allows for tracking of disease progression remains lacking. The main goal of this research was to characterize aSyn aggregates in skin biopsies as a comparative and quantitative measure for PD pathology. Using direct stochastic optical reconstruction microscopy (dSTORM) and computational tools, we imaged total and phosphorylated-aSyn at the single molecule level in sweat glands and nerve bundles of skin biopsies from healthy controls (HCs) and PD patients. We developed a user-friendly analysis platform that offers a comprehensive toolkit for researchers that combines analysis algorithms and applies a series of cluster analysis algorithms (i.e., DBSCAN and FOCAL) onto dSTORM images. Using this platform, we found a significant decrease in the ratio of the numbers of neuronal marker molecules to phosphorylated-aSyn molecules, suggesting the existence of damaged nerve cells in fibers highly enriched with phosphorylatedaSyn molecules. Furthermore, our analysis found a higher number of aSyn aggregates in PD subjects than in HC subjects, with differences in aggregate size, density, and number of molecules per aggregate. On average, aSyn aggregate radii ranged between 40 and 200 nm and presented an average density of 0.001-0.1 molecules/nm2. Our dSTORM analysis thus highlights the potential of our platform for identifying quantitative characteristics of aSyn distribution in skin biopsies not previously described for PD patients while offering valuable insight into PD pathology by elucidating patient aSyn aggregation status. [ABSTRACT FROM AUTHOR]

Here, we employ polymer physics models of chromatin to investigate the 3D folding of a 2 Mb wide genomic region encompassing the human LTN1 gene, a crucial DNA locus involved in key cellular functions. Through extensive Molecular Dynamics simulations, we reconstruct in silico the ensemble of single-molecule LTN1 3D structures, which we benchmark against recent in situ Hi-C 2.0 data. The model-derived single molecules are then used to predict structural folding features at the single-cell level, providing testable predictions for super-resolution microscopy experiments. [ABSTRACT FROM AUTHOR]

Background: microRNAs (miRNAs) were recognized as a promising source of diagnostic biomarker. Herein, we aim to evaluate the performance of an ultrasensitive method for detecting serum miRNAs using single molecule arrays (Simoa). Methods: In this study, candidate miRNAs were trained and tested by RT-qPCR in a cohort of PTB patients. Besides that, ultrasensitive serum miRNA detection were developed using the Single Molecule Array (Simoa) platform. In this ultrasensitive sandwich assay, two target-specific LNA-modified oligonucleotide probes can be simply designed to be complementary to the half-sequence of the target miRNA respectively. We characterized its analytical performance and measured miRNAs in the serum of patients with pulmonary tuberculosis and healthy individuals. Results: We identified a five signature including three upregulated (miR-101, miR-196b, miR-29a) and two downregulated (miR-320b, miR-99b) miRNAs for distinguishing PTB patients from HCs, and validated in our 104 PTB patients. On the basis of Simoa technology, we developed a novel, fully automated digital analyser, which can be used to directly detect miRNAs in serum samples without pre-amplification. We successfully detected miRNAs at femtomolar concentrations (with limits of detection [LODs] ranging from 0.449 to 1.889 fM). Simoa-determined serum miR-29a and miR-99b concentrations in patients with PTB ((median 6.06 fM [range 0.00-75.22]), (median 2.53 fM [range 0.00-24.95]), respectively) were significantly higher than those in HCs ((median 2.42 fM [range 0.00-28.64]) (P < 0.05), (median 0.54 fM [range 0.00-9.12] (P < 0.0001), respectively). Serum levels of miR-320b were significantly reduced in patients with PTB (median 2.11 fM [range 0.00-39.30]) compared with those in the HCs (median 4.76 fM [range 0.00-25.10]) (P < 0.001). A combination of three miRNAs (miR-29a, miR-99b, and miR-320b) exhibited a good capacity to distinguish PTB from HCs, with an area under the curve (AUC) of 0.818 (sensitivity: 83.9%; specificity: 79.7%). Conclusions: This study benchmarks the role of Simoa as a promising tool for monitoring miRNAs in serum and offers considerable potential as a non-invasive platform for the early diagnosis of PTB. [ABSTRACT FROM AUTHOR]

Donor–acceptor (D–A) structure with charge transfer (CT) effect is widely utilized in the construction of organic luminescent materials. The adjustment of their CT effect and related luminescent property usually relies on the changes of molecular structure with different D or A moieties, which will lead to some uncertainties in structure‐property relationship. With the aim to explore the clear inherent luminescent mechanism for D–A molecule with CT effect, it is ideal that the regulation of intramolecular charge transfer in one same D–A molecule can be realized. Accordingly, three D–A type organic phosphorescence luminogens are designed and synthesized. Once being doped into different polymer matrixes, disparate charge transfer effects and related room temperature phosphorescence (RTP) properties can be achieved for a single molecule. Subsequent experiments confirm that different distributions of molecules with locally excited (LE) state and CT state are mainly responsible for their distinct RTP behaviors, exhibiting the well‐clarified structure‐property relationship of D–A type phosphorescence luminogens. Furthermore, the transition from CT to LE state can even be realized through chemical reaction, leading to the activated RTP effect for practical applications. [ABSTRACT FROM AUTHOR]

The kinesin-9 family comprises two subfamilies specific to ciliated eukaryotic cells, and has recently attracted considerable attention because of its importance in ciliary bending and formation. However, only scattered data are available on the motor properties of kinesin-9 family members; these properties have not been compared under identical experimental conditions using kinesin-9 motors from the same species. Here, we report the comprehensive motor properties of two kinesin-9 molecules of Tetrahymena thermophila, TtK9A (Kif9/Klp1 ortholog) and TtK9B1 (Kif6 ortholog), using microtubule-based in vitro assays, including single-motor and multi-motor assays and microtubule-stimulated ATPase assays. Both subfamilies exhibit microtubule plus-end-directed, extremely slow motor activity, both in single and multiple molecules. TtK9A shows lower processivity than TtK9B1. Our findings indicate that the considerable slow movement of kinesin-9 that corresponds to low ATP hydrolysis rates is a common feature of the ciliary kinesin-9 family. [ABSTRACT FROM AUTHOR]

We refresh the design of zero-mode waveguides (ZMWs) by introducing metamaterials that makes the zeroth order resonant mode existence. Of particular importance, the resulting electromagnetic field exhibits nearly constant distribution but not a trivial solution of Maxwell's equation, showing great advantage to equalize the excitation rate of molecules throughout the waveguides. A closed form expression for the wave impedance is derived which is verified by the finite-difference time-domain simulations. Benefitted from the cavity Purcell effect which is lacking in existing ZMWs, fluorescence amplification and lifetime reduction are simultaneously enhanced. A practical design where the excitation volume reduced down to sub-zeptoliter and the fluorescence lifetime shortened to picosecond scale is illustrated. This result makes single molecule real time (SMRT) sensing of biochemical reactions at biophysically relevant concentrations (~ μM) possible, combining off-the-shelf ultrafast lasers. [ABSTRACT FROM AUTHOR]

Imaging-based spatial transcriptomics technologies such as Multiplexed error-robust fluorescence in situ hybridization (MERFISH) can capture cellular processes in unparalleled detail. However, rigorous and robust analytical tools are needed to unlock their full potential for discovering subcellular biological patterns. We present Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), a computational toolkit for extracting molecular relationships from spatial transcriptomics data at single molecule resolution. InSTAnT employs specialized statistical tests and algorithms to detect gene pairs and modules exhibiting intriguing patterns of co-localization, both within individual cells and across the cellular landscape. We showcase the toolkit on five different datasets representing two different cell lines, two brain structures, two species, and three different technologies. We perform rigorous statistical assessment of discovered co-localization patterns, find supporting evidence from databases and RNA interactions, and identify associated subcellular domains. We uncover several cell type and region-specific gene co-localizations within the brain. Intra-cellular spatial patterns discovered by InSTAnT mirror diverse molecular relationships, including RNA interactions and shared sub-cellular localization or function, providing a rich compendium of testable hypotheses regarding molecular functions. Here, the authors introduce the Intracellular Spatial Transcriptomic Analysis Toolkit (InSTAnT), which allows researchers to study the information encoded in the physical proximity of individual transcripts by detecting persistent subcellular patterns. [ABSTRACT FROM AUTHOR]

Objective: To evaluate the safety of COVID-19 vaccines in patients with multiple sclerosis (MS) by assessing their impact on serum neurofilament light chain (sNfL) levels as a marker of neuroaxonal damage. Methods: Single-center observational longitudinal study including patients with MS who consecutively received their initial vaccination against SARS-CoV-2 at Hospital Universitario Ramo'n y Cajal, following the first national immunization program in Spain. Serum samples were collected at baseline and after receiving the second dose of the vaccine. sNfL levels were quantified using the single molecule array (SIMOA) technique. Adverse events, including clinical or radiological reactivation of the disease, were recorded. Results: Fifty-two patients were included (median age, 39.7 years [range, 22.5-63.3]; 71.2% female). After SARS-CoV-2 vaccination, no increased inflammatory activity, either determined by the presence of relapses and/or new MRI lesions and/or high sNfL levels, was detected. Accordingly, there was no difference between median sNfL levels before and after vaccination (5.39 vs. 5.76 pg/ml, p=0.6). Despite this, when looking at baseline patient characteristics before vaccination, younger age associated with disease activity after vaccination (OR 0.87, 95% CI: 0.77-0.98, p=0.022). Larger studies are needed to validate these results. Conclusion: COVID-19 vaccines did not cause reactivation of disease at a clinical, radiological or molecular level, thus suggesting that they are safe in MS patients. [ABSTRACT FROM AUTHOR]

Inferring the 3D structure and conformation of disordered biomolecules, e.g., single stranded nucleic acids (ssNAs), remains challenging due to their conformational heterogeneity in solution. Here, we use escape-time electrometry (ETe) to measure with sub elementary-charge precision the effective electrical charge in solution of short to medium chain length ssNAs in the range of 5–60 bases. We compare measurements of molecular effective charge with theoretically calculated values for simulated molecular conformations obtained from Molecular Dynamics simulations using a variety of forcefield descriptions. We demonstrate that the measured effective charge captures subtle differences in molecular structure in various nucleic acid homopolymers of identical length, and also that the experimental measurements can find agreement with computed values derived from coarse-grained molecular structure descriptions such as oxDNA, as well next generation ssNA force fields. We further show that comparing the measured effective charge with calculations for a rigid, charged rod—the simplest model of a nucleic acid—yields estimates of molecular structural dimensions such as linear charge spacings that capture molecular structural trends observed using high resolution structural analysis methods such as X-ray scattering. By sensitively probing the effective charge of a molecule, electrometry provides a powerful dimension supporting inferences of molecular structural and conformational properties, as well as the validation of biomolecular structural models. The overall approach holds promise for a high throughput, microscopy-based biomolecular analytical approach offering rapid screening and inference of molecular 3D conformation, and operating at the single molecule level in solution. [ABSTRACT FROM AUTHOR]

Introduction: Alemtuzumab is a highly effective pulsed immune reconstitution therapy for multiple sclerosis (MS). Aim: To evaluate serum neurofilament light chain (sNfL) and serum glial fibrillary acidic protein (sGFAP) in patients with relapsing-remitting MS who have been treated with Alemtuzumab over the course of 2 years. Methods: This prospective study involved MS patients treated with Alemtuzumab at a referral MS center. Both sNfL and sGFAP were analyzed at baseline and then again at 6, 12, and 24 months post-treatment using the single molecule array (SiMoA) technique. We also recruited matched healthy controls (HCs) for comparison. Results: The study included 46 patients (with a median age of 34.2 [Interquartile range (IQR), 28.7–42.3] years, 27 of which were women [58%]) and 76 HCs. No differences in demographic characteristics were observed between patients and HC. The median disease duration was 6.22 (IQR, 1.56–10.13) years. The median annualized relapse rate before treatment was 2 (IQR, 1–3). At baseline, sNfL and sGFAP levels were higher in MS patients (median of 18.8 [IQR, 10.7–52.7] pg/ml and 158.9 [IQR, 126.9–255.5] pg/ml, respectively) when compared to HC (6.11 [IQR, 2.03–8.54] pg/ml and 91.0 [72.6–109] pg/ml, respectively) (p<0.001 for both comparisons). The data indicates that 80% of patients had high (≥10 pg/ml) sNfL values at baseline. We observed a significant decrease in sNfL levels at 6 (65%, p = 0.02), 12 (70.8%, p<0.001), and 24 (78.1%, p<0.001) months. sNfL reached similar levels to HC only after 24 months of Alemtuzumab treatment. During the follow-up period, no changes were identified in the sGFAP values. Conclusion: Alemtuzumab leads to the normalization of sNfL values in MS patients after 2 years of treatment, with no apparent effect on sGFAP values. [ABSTRACT FROM AUTHOR]

Previously [A.O. Savostianov, I.Yu. Eremchev, T. Plakhotnik, and A.V. Naumov, Phys. Rev. B 110, 045430 (2024)], we have shown that the zero-phonon line broadening of single tetra-tert-butylterrylene molecules embedded in the matrix of amorphous polyisobutylene is a result of coupling with resonant vibrational modes arising due to the impurity effect on the host normal modes. However, the question remained whether this model would be compatible with the extensive single-molecule spectroscopy and photon echo data previously obtained for the same host/guest system. In the present work we demonstrate the high predictive power of the resonant mode model treated in the framework of the non-perturbative theory of electron–phonon coupling, and good agreement with all experimental data. Furthermore, for single-molecule data we find an unexpectedly large dispersion of the force constants for impurity molecules. To explain this dispersion, we propose a simple microscopic model that assumes fluctuations in the distance between the impurity molecule and its nearest surroundings. [ABSTRACT FROM AUTHOR]

The ability for cells to localize and activate peripheral membrane-binding proteins is critical for signal transduction. Ubiquitously important in these signaling processes are phosphatidylinositol phosphate (PIP) lipids, which are dynamically phosphorylated by PIP lipid kinases on intracellular membranes. Functioning primarily at the plasma membrane, phosphatidylinositol-4-phosphate 5-kinases (PIP5K) catalyzes the phosphorylation of PI(4)P to generate most of the PI(4,5)P2 lipids found in eukaryotic plasma membranes. Recently, we determined that PIP5K displays a positive feedback loop based on membrane-mediated dimerization and cooperative binding to its product, PI(4,5)P2. Here, we examine how two motifs contribute to PI(4,5)P2 recognition to control membrane association and catalysis of PIP5K. Using a combination of single molecule TIRF microscopy and kinetic analysis of PI(4)P lipid phosphorylation, we map the sequence of steps that allow PIP5K to cooperatively engage PI(4,5)P2. We find that the specificity loop regulates the rate of PIP5K membrane association and helps orient the kinase to more effectively bind PI(4,5)P2 lipids. After correctly orienting on the membrane, PIP5K transitions to binding PI(4,5)P2 lipids near the active site through a motif previously referred to as the substrate or PIP-binding motif (PIPBM). The PIPBM has broad specificity for anionic lipids and serves a role in regulating membrane association in vitro and in vivo. Overall, our data supports a two-step membrane-binding model where the specificity loop and PIPBM act in concert to help PIP5K orient and productively engage anionic lipids to drive the positive feedback during PI(4,5)P2 production. [ABSTRACT FROM AUTHOR]

Monoclonal antibodies (Mabs) are widely used in a variety of fields, including protein identification, life sciences, medicine, and natural product chemistry. This review focuses on Mabs against naturally occurring active compounds. The preparation of Mabs against various active compounds began in the 1980s, and now there are fewer than 50 types. Eastern blotting, which was developed as an antibody staining method for low-molecular-weight compounds, is useful for its ability to visually represent specific components. In this method, a mixture of lower-molecular-weight compounds, particularly glycosides, are separated by thin-layer chromatography (TLC). The compounds are then transferred to a membrane by heating, followed by treatment with potassium periodate (KIO4) to open the sugar moiety of the glycoside on the membrane to form an aldehyde group. Proteins are then added to form Schiff base bonds to enable adsorption on the membrane. A Mab is bound to the glycoside moiety on the membrane and reacts with a secondary antibody to produce color. Double Eastern blotting, which enables the simultaneous coloration of two glycosides, can be used to evaluate quality and estimate pharmacological effects. An example of staining by Eastern blotting and a component search based on the results will also be presented. A Mab-associated affinity column is a method for isolating antigen molecules in a single step. However, the usefulness of the wash fractions that are not bound to the affinity column is unknown. Therefore, we designated the wash fraction the "knockout extract". Comparing the nitric oxide (NO) production of a glycyrrhizin (GL)-knockout extract of licorice with a licorice extract revealed that the licorice extract is stronger. Therefore, the addition of GL to the GL-knockout extract of licorice increased NO production. This indicates that GL has synergic activity with the knockout extract. The GL-knockout extract of licorice inhibited high-glucose-induced epithelial–mesenchymal transition in NRK-52E cells, primarily by suppressing the Notch2 pathway. The real active constituent in licorice may be constituents other than GL, which is the causative agent of pseudohyperaldosteronism. This suggests that a GL-knockout extract of licorice may be useful for the treatment of diabetic nephritis. [ABSTRACT FROM AUTHOR]

Rapid detection of potentially toxic heavy metals like Hg(II) has attracted great attention in the last few decades due to the importance to maintain a safe and sustainable environment for human beings. Coordination chemistry and concepts therein, play an important role in the detection of Hg(II). Size, charge, and nature of the donor atom and the respective cation (metal ion), are crucial in selective interactions between the sensor and metal ions. The sensors designed for the purpose, coordinate to Hg(II) ion through various donor sites, coordination causes a change in the electron density in organic molecules and results in either visible color change or enhancing/quenching fluorescence intensity. Since Hg(II) is soft metal, with d10 electron system, so majority of the sensors have soft donor sites which prefer to coordinate with Hg(II). Oxygen is also present in some chelating ligands which is least preferred coordination site, due to its hard nature. There are several reports of replacing other ligating sites by sulfur for enhanced mercury sensing. In some cases, desulfurization is being detected as clear change in spectral behavior during the sensing process. Efforts are still in progress to design and introduce a sensor with utmost sensitivity and selectivity. In this review, we made an attempt to explain the coordination aspects of Hg(II) detectors, reasons for poor efficiency and possible suggestions to improve the selection criterion of various compounds. It will help researchers to know about important concepts in designing more sensitive and selective sensors for detection of Hg(II) in environmental and biological samples. [ABSTRACT FROM AUTHOR]

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Copyright of Journal of Beijing University of Technology is the property of Journal of Beijing University of Technology, Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Single molecules can be used as miniaturized functional electronic components, when contacted by macroscopic electrodes. Mechanosensitivity describes a change in conductance for a certain change in electrode separation and is a desirable feature for applications such as ultrasensitive stress sensors. We combine methods of artificial intelligence with high-level simulations based on electronic structure theory to construct optimized mechanosensitive molecules from predefined, modular molecular building blocks. In this way, we overcome time-consuming, inefficient trial-and-error cycles in molecular design. We unveil the black box machinery usually connected to methods of artificial intelligence by presenting all-important evolutionary processes. We identify the general features that characterize well-performing molecules and point out the crucial role of spacer groups for increased mechanosensitivity. Our genetic algorithm provides a powerful way to search chemical space and to identify the most promising molecular candidates. [ABSTRACT FROM AUTHOR]

In single-molecule free diffusion experiments, molecules spend most of the time outside a laser spot and generate bursts of photons when they diffuse through the focal spot. Only these bursts contain meaningful information and, therefore, are selected using physically reasonable criteria. The analysis of the bursts must take into account the precise way they were chosen. We present new methods that allow one to accurately determine the brightness and diffusivity of individual molecule species from the photon arrival times of selected bursts. We derive analytical expressions for the distribution of inter-photon times (with and without burst selection), the distribution of the number of photons in a burst, and the distribution of photons in a burst with recorded arrival times. The theory accurately treats the bias introduced due to the burst selection criteria. We use a Maximum Likelihood (ML) method to find the molecule's photon count rate and diffusion coefficient from three kinds of data, i.e., the bursts of photons with recorded arrival times (burstML), inter-photon times in bursts (iptML), and the numbers of photon counts in a burst (pcML). The performance of these new methods is tested on simulated photon trajectories and on an experimental system, the fluorophore Atto 488. [ABSTRACT FROM AUTHOR]

Polariton chemistry has emerged as an appealing branch of synthetic chemistry that promises mode selectivity and a cleaner approach to kinetic control. Of particular interest are the numerous experiments in which reactivity has been modified by virtue of performing the reaction inside infrared optical microcavities in the absence of optical pumping; this effort is known as "vibropolaritonic chemistry." The optimal conditions for these observations are (1) resonance between cavity and reactive modes at normal incidence (k = 0) and (2) a monotonic increase of the effect with the concentration of emitters in the sample. Importantly, vibropolaritonic chemistry has only been experimentally demonstrated in the so-called "collective" strong coupling regime, where there is a macroscopic number of molecules (rather than a single molecule) coupled to each photon mode of the microcavity. Strikingly, efforts to understand this phenomenon from a conceptual standpoint have encountered several roadblocks, and no single, unifying theory has surfaced thus far. This Perspective documents the most relevant approaches taken by theorists, laying out the contributions and unresolved challenges from each work. We expect this Perspective to not only serve as a primer for experimentalists and theorists alike but also inform future endeavors in the quest for the ultimate formalism of vibropolaritonic chemical kinetics. [ABSTRACT FROM AUTHOR]

[Display omitted] Notwithstanding the progress made, cargo molecules encapsulated within ferritin via oral administration in the gastric environment remains a persistent challenge. This study focuses on the strategic enhancement of ferritin stability in harsh gastric environment. By taking advantagie of computational-assisted design, we strategically introduced up to 96 disulfide bonds along three key inter-subunit interfaces to one single ferritin molecule with human H-chain ferritin and shrimp (Marsupenaeus japonicus) ferritin as starting materials, producing two kinds of robust ferritin nanocages with markedly enhanced acid and protease (pepsin and rennin) resistance. The crystal structure of ferritin nanocage confirmed our design at an atomic level. Encapsulation experiments demonstrated successful loading of bioactive cargo molecules (e.g., doxorubicin) into the engineered ferritin nanocages, with pronouncedly improved protection against leakage under acidic condition and the presence of pepsin and rennin as compared to their native counterparts. This study presents a potential approach for the design and engineering of protein nanocages for oral administration. [ABSTRACT FROM AUTHOR]

Diet can be considered as one of the pivotal factors in regulating gastrointestinal health, and polyphenols widely distributed in human daily diet. The polyphenols and their metabolites playing a series of beneficial effects in human gastrointestinal tract that can regulate of the gut microbiota, increase intestinal barrier function, repair gastrointestinal mucosa, reduce oxidative stress, inhibit the secretion of inflammatory factors and regulating immune function, and their absorption and biotransformation mainly depend on the activity of intestinal microflora. However, little is known about the two-way interaction between polyphenols and intestinal microbiota. The objective of this review is to highlight the structure optimization and effect of flavonoids on intestinal flora, and discusses the mechanisms of dietary flavonoids regulating intestinal flora. The multiple effects of single molecule of flavonoids, and inter-dependence between the gut microbiota and polyphenol metabolites. Moreover, the protective effects of polyphenols on intestinal barrier function, and effects of interaction between plant polyphenols and macromolecules on gastrointestinal health. This review provided valuable insight that may be useful for better understanding the mechanism of the gastrointestinal health effects of polyphenols, and provide a scientific basis for their application as functional food. HIGHLIGHTS: Possible mechanism of flavonoids regulating intestinal flora. Flavonoids optimize the structure and composition of gut microbiota. Polyphenol improve intestinal barrier function. Interaction between polyphenols and macromolecules improves gastrointestinal health The two-way interaction between flavonoids and intestinal microflora to improve bioavailability [ABSTRACT FROM AUTHOR]

Tethering of two biologically active molecules in a single unit is considered as a captivating solution for the extension of existing antibiotics. β-Lactams which display a vast array of biological properties due to various ring substitutions continue to attract the attention of synthetic chemists. The incorporation of the 'isoxazole' nucleus in its appendage is known to enhance the properties of β-lactam compounds. Its inclusion in the compounds offers decreased toxicity, increased efficacy, and improved pharmacokinetics spectrum. In the reported work, we highlight the efficient use of 1,3-dipolar cycloaddition reaction to synthesize novel isoxazole/dihydroisoxazole ring-linked β-lactam hybrids using 3-propargyloxy-β-lactams/3-allyl-β-lactams as synthons. The methodology devised has been found to be highly regioselective and generalized for the selected substrates to provide a variety of novel hybrid compounds under elementary reaction conditions. The synthesized compounds have been well characterized by various spectroscopic techniques and optimized reaction conditions for both types of hybrid compounds have been studied. [ABSTRACT FROM AUTHOR]

Single Molecule Localisation Microscopy (SMLM) is becoming a widely used technique in cell biology. After processing the images, the molecular localisations are typically stored in a table as xy (or xyz) coordinates, with additional information, such as number of photons, etc. This set of coordinates can be used to generate an image to visualise the molecular distribution, for example, a 2D or 3D histogram of localisations. Many different methods have been devised to analyse SMLM data, among which cluster analysis of the localisations is popular. However, it can be useful to first segment the data, to extract the localisations in a specific region of a cell or in individual cells, prior to downstream analysis. Here we describe a pipeline for annotating localisations in an SMLM dataset in which we compared membrane segmentation approaches, including Otsu thresholding and machine learning models, and subsequent cell segmentation. We used an SMLM dataset derived from dSTORM images of sectioned cell pellets, stained for the membrane proteins EGFR (epidermal growth factor receptor) and EREG (epiregulin) as a test dataset. We found that a Cellpose model retrained on our data performed the best in the membrane segmentation task, allowing us to perform downstream cluster analysis of membrane versus cell interior localisations. We anticipate this will be generally useful for SMLM analysis. LAY DESCRIPTION: A form of microscopy called single‐molecule localisation microscopy (SMLM) allows researchers to locate the positions of proteins with very high precision inside cells. The organisation of these proteins is typically important for their function. Once the imaging data is acquired, it is useful to segment (select areas) regions of the cells to find out how proteins are organised in these specific regions. Here we have developed an approach that can select localisations of proteins within the plasma membrane as well as localisations within the cell, for downstream analysis. We used this data to determine how clusters of molecules varied between the plasma membrane and the interior of the cell. This approach could be generally useful for segmenting SMLM datasets. [ABSTRACT FROM AUTHOR]

Non-equilibrium Green's function (NEGF) and density functional theory (DFT) calculations are used to explore the impact of doping on the electron transport properties in a single tetracene molecule linked to gold electrodes using isocyanide anchoring groups. Boron (B) and Nitrogen (N) atoms are used for doping and co-doping (BN) of the carbon atoms placed at the edge of the tetracene molecule. It was found that the chemical doping of tetracene molecules mainly impacts the rectification trends compared to non-doped molecules. Our findings indicate that B doping significantly improves the rectification ratio compared to other dopants because of a greater difference between the current values under positive and negative biases as a result of asymmetric I-V characteristics. These inferences have also been assessed in terms of MPSH and transmission spectra. In addition, novel characteristic of negative differential resistance (NDR) is attained in single dopant molecular junctions. [ABSTRACT FROM AUTHOR]

Theories of bulk coacervation of oppositely charged polyelectrolytes (PE) obscure single molecule level thermodynamic details, considered significant for coacervate equilibrium, whereas simulations account for only pairwise Coulomb interaction. Also, studies of effects of asymmetry on PE complexation are rare compared to symmetric PEs. We develop a theoretical model, accounting for all entropic and enthalpic contributions at the molecular level, and the mutual segmental screened Coulomb and excluded volume interactions between two asymmetric PEs, by constructing a Hamiltonian following Edwards and Muthukumar. Assuming maximal ion-pairing in the complex, the system free energy comprising configurational entropy of the polyions and free-ion entropy of the small ions is minimized. The effective charge and size of the complex, larger than sub-Gaussian globules as for symmetric chains, increase with asymmetry in polyion length and charge density. The thermodynamic drive for complexation is found to increase with ionizability of symmetric polyions and with a decrease in asymmetry in length for equally ionizable polyions. The crossover Coulomb strength demarcating the ion-pair enthalpy-driven (low strength) and counterion release entropy-driven (high strength) is marginally dependent on the charge density, because so is the degree of counterion condensation, and strongly dependent on the dielectric environment and salt. The key results match the trends in simulations. The framework may provide a direct way to calculate thermodynamic dependencies of complexation on experimental parameters such as electrostatic strength and salt, thus to better analyze and predict observed phenomena for different sets of polymer pairs. [ABSTRACT FROM AUTHOR]

Organic semiconductors (OSCs) are widely used in flexible display, renewable energy, and biosensors, owing to their unique solid-state physical and optoelectronic properties. Among the abundant crystal library of OSCs, asymmetric aryl anthracene derivatives have irreplaceable advantages due to the interplay between their distinct π-conjugated geometry and molecular stacking as well as efficient light emission and charge transport properties that can be simultaneously utilized. However, the poor crystal stacking patterns of most asymmetric molecules limit their utility as excellent OSCs. Thus, it is crucial to clarify the structural features that enable the extremely ordered stacking and favorable electronic structure of asymmetric anthracene derivatives to become high-performance OSCs. This contribution investigates the charge transport properties of a series of asymmetric aryl anthracene derivatives to reveal the modulation factors of the molecular stacking modes and to explore the structural factors, which are beneficial to charge transport. The analysis demonstrated that the vinyl-linker facilitated the injection of hole carriers, and the alkynyl-linker effectively reduces the reorganization energy. Importantly, the linear polarizability and permanent dipole moment of a single molecule play a vital regulation to molecular stacking modes and the transfer integral of the dimer. The "head-to-head stacking" motif shows a compact stacking pattern and the maximum 2D anisotropic mobility more than 10 cm2 V−1 s−1. These findings sharpen our understanding of the charge transport properties in asymmetric organic semiconductors and are essential for developing a diverse range of high-performance OSC materials. [ABSTRACT FROM AUTHOR]

The rigorous quantum mechanical description of the collective interaction of many molecules with the radiation field is usually considered numerically intractable, and approximation schemes must be employed. Standard spectroscopy usually contains some levels of perturbation theory, but under strong coupling conditions, other approximations are used. A common approximation is the 1-exciton model in which processes involving weak excitations are described using a basis comprising the ground state and singly excited states of the molecule cavity-mode system. In another frequently used approximation in numerical investigations, the electromagnetic field is described classically, and the quantum molecular subsystem is treated in the mean-field Hartree approximation with its wavefunction assumed to be a product of single molecules' wavefunctions. The former disregards states that take long time to populate and is, therefore, essentially a short time approximation. The latter is not limited in this way, but by its nature, disregards some intermolecular and molecule-field correlations. In this work, we directly compare results obtained from these approximations when applied to several prototype problems involving the optical response of molecules-in-optical cavities systems. In particular, we show that our recent model investigation [J. Chem. Phys. 157, 114108 (2022)] of the interplay between the electronic strong coupling and molecular nuclear dynamics using the truncated 1-exciton approximation agrees very well with the semiclassical mean-field calculation. [ABSTRACT FROM AUTHOR]

Single-molecule tracking (SMT) methods have been widely employed to offer a high-resolution characterization of synthetic polymers under ambient conditions and, thus, have advanced our understanding of their unique material properties. SMT is based on the systematic monitoring of the diffusive motions of individual fluorescent dye molecules in the as-prepared polymer thin films or thicker monoliths. Quantitative assessment of the recorded SMT video data involves the systematic analysis of the generated diffusion trajectories of a single molecule using well-established and reported methods. The results have offered a wealth of new information on the structural alignment, orientational order, and long-range continuity of the polymer microdomains; the nanoscale material heterogeneities governed by defects, misalignment, and ill-controlled preparation conditions; as well as the various forms of probe–host interactions on the single-molecule level. In the first part of this Tutorial review, we describe the fundamental principles and instrumentation of SMT, before offering interested readers and potential future SMT users a practical guidance on the selection of fluorescent probe molecules, preparation of suitable samples, and optimization of experimental conditions and imaging parameters. Then, we highlight several representative SMT studies in microphase-separated block copolymers, and semicrystalline and amorphous homopolymers to further emphasize the usefulness of SMT methods for polymer characterization without neglecting some of their shortcomings. This Tutorial review is written with the motivation to attract new researchers to the fast-growing field and assist them in starting their own SMT research of synthetic polymers and other technologically useful soft matter systems. [ABSTRACT FROM AUTHOR]

Light‐emitting organic small molecules require high internal and external quantum efficiencies with excellent radiative characteristics for their potential application in next‐generation optoelectronics. Nonetheless, achieving high efficiency in solid states remains a formidable challenge, primarily owing to the non‐radiative processes. Therefore, conformational modulation in solid states is pivotal in influencing emission properties to mitigate non‐radiative decay. Notably, modifying intra‐ and intermolecular non‐covalent interactions (NCIs) is a promising strategy that can simultaneously realize rigidity and stabilization of flexible single bonds, thus suppressing reorganization energy associated with non‐radiative decay. Consequently, considerable emission enhancement is attainable through adept manipulation of NCIs, corresponding to systems ranging from single molecules to multimolecular networks in solid states. This review systematically summarizes and analyzes the influence of diverse NCIs in efficient light‐emitting organic small molecules. The effects of NCIs on single‐and multimolecular‐systems are discussed, based on the fundamentals of light emission mechanism and the correlation between molecular design strategy and photophysical properties. Additionally, strategic perspectives are provided for the advancement of future light‐emitting organic small molecules. Therefore, this review serves as a comprehensive molecular design library, providing an up‐to‐date overview of molecular design leveraging NCIs for efficient light‐emitting organic small molecules. [ABSTRACT FROM AUTHOR]

With the development of metalloimmunology, the potential of platinum drugs in cancer immunotherapy has attracted extensive attention. Although immunochemotherapy combining PD‐1/PD−L1 antibodies with platinum drugs has achieved great success in the clinic, combination therapy commonly brings new problems. Herein, we have developed a platinum‐metformin conjugate as a promising alternative to antibody‐based PD−L1 inhibitors, not only disrupting PD‐1/PD−L1 axis on cell surface but also down‐regulating the total PD−L1 levels in non‐small cell lung cancer (NSCLC) cells comprehensively, thus achieving highly efficient immunochemotherapy by a single small molecule. Mechanism studies demonstrate that Pt‐metformin conjugate can selectively accumulate in lysosomes, promote lysosomal‐dependent PD−L1 degradation via the AMPK‐TFEB pathway, and modulate the upstream regulatory proteins related to PD−L1 expression (e.g. HIF‐1α and NF‐κB), eventually decreasing the total abundance of PD−L1 in NSCLC, overcoming tumor hypoxia, and activating anti‐tumor immunity in vivo. This work suggests an AMPK‐mediated lysosomal degradation pathway of PD−L1 for the first time and provides a unique design perspective for the development of novel platinum drugs for immunochemotherapy. [ABSTRACT FROM AUTHOR]

The Asian green mussel, Perna viridis is an important aquaculture species in the family Mytilidae contributing substantially to molluscan aquaculture. We generated a high-quality chromosome level assembly of this species by combining PacBio single molecule sequencing technique (SMRT), Illumina paired-end sequencing, high-throughput chromosome conformation capture technique (Hi-C) and Bionano mapping. The final assembly resulted in a genome of 723.49 Mb in size with a scaffold N50 of 49.74 Mb with 99% anchored into 15 chromosomes. A total of 49654 protein-coding genes were predicted from the genome. The presence of 634 genes associated with the cancer pathway and 408 genes associated with viral carcinogenesis indicates the potential of this species to be used as a model for cancer studies. The chromosome-level assembly of this species is also a valuable resource for further genomic selection and selective breeding for improving economically important aquaculture traits and augmenting aquaculture productivity. [ABSTRACT FROM AUTHOR]

2'-deoxy-ATP (dATP) improves cardiac function by increasing the rate of crossbridge cycling and Ca2+ transient decay. However, the mechanisms of these effects and how therapeutic responses to dATP are achieved when dATP is only a small fraction of the total ATP pool remain poorly understood. Here, we used a multiscale computational modeling approach to analyze the mechanisms by which dATP improves ventricular function. We integrated atomistic simulations of prepowerstroke myosin and actomyosin association, filament-scale Markov state modeling of sarcomere mechanics, cell-scale analysis of myocyte Ca2+ dynamics and contraction, organ-scale modeling of biventricular mechanoenergetics, and systems level modeling of circulatory dynamics. Molecular and Brownian dynamics simulations showed that dATP increases the actomyosin association rate by 1.9 fold. Markov state models predicted that dATP increases the pool of myosin heads available for crossbridge cycling, increasing steadystate force development at low dATP fractions by 1.3 fold due to mechanosensing and nearest-neighbor cooperativity. This was found to be the dominant mechanism by which small amounts of dATP can improve contractile function at myofilament to organ scales. Together with faster myocyte Ca2+ handling, this led to improved ventricular contractility, especially in a failing heart model in which dATP increased ejection fraction by 16% and the energy efficiency of cardiac contraction by 1%. This work represents a complete multiscale model analysis of a small molecule myosin modulator from single molecule to organ system biophysics and elucidates how the molecular mechanisms of dATP may improve cardiovascular function in heart failure with reduced ejection fraction. [ABSTRACT FROM AUTHOR]

Lujo virus (LUJV) is a human pathogen that was the cause of a deadly hemorrhagic fever outbreak in Africa. LUJV is a divergent member of the Arenaviridae with some similarities to both the "Old World" and "New World" serogroups, but it uses a cell-entry receptor, neuropilin-2 (NRP2), that is distinct from the receptors of OW and NW viruses. Though the receptor binding domain of LUJV has been characterized structurally, the overall organization of the trimeric spike complex and how NRP2 is recognized in this context were unknown. Here, we present the structure of the membrane-embedded LUJV spike complex determined by cryo-electron microscopy. Analysis of the structure suggested that a single NRP2 molecule is bound at the apex of the trimeric spike and that multiple subunits of the trimer contact the receptor. The binding of NRP2 involves an intriguing arginine-methionine interaction, which we analyzed using quantum mechanical modeling methods. We compare the LUJV spike structure with the only other available structure of a complete arenaviral spike, which is the Lassa virus. The similarities and differences between them shed light on Arenavirus evolution, inform vaccine design, and provide information that will be useful in combating future Arenavirus outbreaks. The Lujo virus is a deadly human pathogen. Here, Eilon-Ashkenazy et al. determine the structure of the viral spike complex and elucidate key aspects of its function. [ABSTRACT FROM AUTHOR]

Background: Detecting very minor (< 1%) subpopulations using next-generation sequencing is a critical need for multiple applications, including the detection of drug resistant pathogens and somatic variant detection in oncology. A recently available sequencing approach termed 'sequencing by binding (SBB)' claims to have higher base calling accuracy data "out of the box." This paper evaluates the utility of using SBB for the detection of ultra-rare drug resistant subpopulations in Mycobacterium tuberculosis (Mtb) using a targeted amplicon assay and compares the performance of SBB to single molecule overlapping reads (SMOR) error corrected sequencing by synthesis (SBS) data. Results: SBS displayed an elevated error rate when compared to SMOR error-corrected SBS and SBB techniques. SMOR error-corrected SBS and SBB technologies performed similarly within the linear range studies and error rate studies. Conclusions: With lower sequencing error rates within SBB sequencing, this technique looks promising for both targeted and unbiased whole genome sequencing, leading to the identification of minor (< 1%) subpopulations without the need for error correction methods. [ABSTRACT FROM AUTHOR]

A regular method has been proposed to quantitatively describe the fluorescence of molecules randomly moving in a nanowell. Correlation functions of the fluorescence of single molecules depending on the geometry of the nanowell and the penetration depth of an exciting field into it have been determined. The obtained results can be used to quantitatively analyze the properties of molecules and to extract information on the parameters of the nanowell. [ABSTRACT FROM AUTHOR]

Understanding molecular state evolution is central to many disciplines, including molecular dynamics, precision measurement, and molecule-based quantum technology. Details of this evolution are obscured when observing a statistical ensemble of molecules. Here, we report real-time observations of thermal radiation–driven transitions between individual states (“jumps”) of a single molecule. We reversed these jumps through microwave-driven transitions, which resulted in a 20-fold improvement in the time the molecule dwells in a chosen state. The measured transition rates showed anisotropy in the thermal environment, pointing to the possibility of using single molecules as in situ probes for the strengths of ambient fields. Our approaches for state detection and manipulation could apply to a wide range of species, facilitating their uses in fields including quantum science, molecular physics, and ion-neutral chemistry. [ABSTRACT FROM AUTHOR]

Bipolar‐type electrode materials are capable of improving the specific power and reducing the manufacturing costs for rechargeable symmetric batteries, while their development is plagued by the lack of reliable and affordable bipolar‐type materials. Here, a bipolar‐type indanthrene (IDT) with synergetic coupling effects of two redox centers of p‐type dihydrophenazines and n‐type anthraquinone in a single molecule is proposed to construct a symmetric battery. Due to the mutually affecting of n‐type and p‐type redox couples, the conjugated "p–n fusion" in the IDT material facilitates mutual electron cloud donation and withdrawal between two redox centers, thus a considerable output voltage of 0.62 V is realized in symmetric aqueous battery. Benefiting from its enriched redox centers and extended π‐conjugated structure, the symmetric battery also delivers a specific capacity of 139 mAh g−1 at 0.1 A g−1 and a long cycling stability with a capacity retention of 79% after 600 cycles at 2 A g−1. Comprehensive ex‐situ characterizations paired with density functional theroy calculations reveal both reversible HSO4− and H+ uptake/removal behavior during charging/discharging process. Additionally, a symmetric cell with quasi‐solid electrolyte is established, which exhibits superior practical application capability with a capacity retention of 78% at 2 A g−1 over 1000 cycles. [ABSTRACT FROM AUTHOR]