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The TRPA1 ion channel is a sensitive detector of reactive chemicals, found primarily on sensory neurons. The phenotype exhibited by mice lacking TRPA1 suggests its potential as a target for pharmacological intervention. Antibody-based detection for distribution analysis is a standard technique. In the case of TRPA1, however, there is no antibody with a plausible validation in knockout animals or functional studies, but many that have failed in this regard. To this end we employed the single molecule in situ hybridization technique RNAscope on sensory neurons immediately after detection of calcium responses to the TRPA1 agonist allyl isothiocyanate. There is a clearly positive correlation between TRPA1 calcium imaging and RNAscope detection (R = 0.43), although less than what might have been expected. Thus, the technique of choice should be carefully considered to suit the research question. The marginal correlation between TRPV1 RNAscope and the specific agonist capsaicin indicates that such validation is advisable for every RNAscope target. Given the recent description of a long-awaited TRPA1 reporter mouse, TRPA1 RNAscope detection might still have its use cases, for detection of RNA at particular sites, for example, defined structurally or by other molecular markers. [ABSTRACT FROM AUTHOR]

The endo-β-1,4-xylanase glycosyl hydrolase (GH11) decomposes the backbone of xylan into xylooligosaccharides or xylose. These enzymes are important for industrial applications in the production of biofuel, feed, food, and value-added materials. β-D-xylopyranose (XYP, also known as β-D-xylose) is the fundamental unit of the substrate xylan, and understanding its recognition is fundamental for the initial steps of GH11's molecular mechanism. However, little is known about the recognition of a single XYP molecule by GH11. In this study, the crystal structures of GH11 from Thermoanaerobacterium saccharolyticum (TsaGH11) complexed with an XYP molecule were determined at a resolution of 1.7–1.9 Å. The XYP molecule binds to subsite −2 of the substrate-binding cleft. The XYP molecule is mainly stabilized by a π–π interaction with the conserved Trp36 residue. The O2 and O3 atoms of XYP are stabilized by hydrogen bond interactions with the hydroxyl groups of Tyr96 and Tyr192. The conformation of the thumb domain of TsaGH11 does not play a critical role in XYP binding, and XYP binding induces a shift in the thumb domain of TsaGH11 toward the XYP molecule. A structural comparison of TsaGH11 with other GH11 xylanases revealed that the XYP molecule forms π–π stacking with the center between the phenyl and indoline ring of Trp36, whereas the XYP molecule unit from xylobiose or xylotetraose forms π–π stacking with the indoline of Trp36, which indicates that the binding modes of the substrate and XYP differ. These structural results provide a greater understanding of the recognition of XYP by the GH11 family. [ABSTRACT FROM AUTHOR]

Chiral surfaces are an object of interest due to their application in catalysis, separation and sensors. Such surfaces can exhibit chirality on the molecular or supramolecular level. Previously, we have studied the thermodynamic features of adsorption on non-porous surfaces with supramolecular chirality. However, for their application in enantiomer separation, enantioselectivity and capacity should be greater. Porous adsorbents are promising for this purpose. In this work, the enantioselectivity of copper borophosphate LiCu2[BP2O8(OH)2] was studied. This zeotype material was obtained by hydrothermal synthesis without any source of chirality. Supramolecular chirality was achieved by spontaneous symmetry breaking via Viedma ripening. XRD and SEM were used to prove the synthesis accuracy. Enantioselectivity during adsorption was studied using the adsorption isotherms of α-pinene and limonene enantiomer analysis. The experimental isotherms were approximated by Langmuir, Dubinin–Radushkevich, Freundlich and Fowler–Guggenheim equations. The t-test was used to prove the reliability of the differences in enantiomer adsorption. The isosteric heats of adsorption were calculated from the adsorption isotherms. The data obtained have shown the ability of the LiCu2[BP2O8(OH)2] surface to recognize both α-pinene and limonene enantiomers. The molecules of α-pinenes adsorbed without pores, with the maximum enantioselectivity coefficient of 1.23 at 80 °C. Limonene molecules adsorbed in pore volume as single molecules or 1D chains. This phenomenon was proved by analysis of isosteric heats. The enantioselectivity of copper borophosphate to limonenes and α-pinenes was similar. The ability of pores with supramolecular chirality (and without molecular chirality) to recognize enantiomers was discovered in this paper for the first time. [ABSTRACT FROM AUTHOR]

Chiral surfaces are an object of interest due to their application in catalysis, separation and sensors. Such surfaces can exhibit chirality on the molecular or supramolecular level. Previously, we have studied the thermodynamic features of adsorption on non-porous surfaces with supramolecular chirality. However, for their application in enantiomer separation, enantioselectivity and capacity should be greater. Porous adsorbents are promising for this purpose. In this work, the enantioselectivity of copper borophosphate LiCu2[BP2O8(OH)2] was studied. This zeotype material was obtained by hydrothermal synthesis without any source of chirality. Supramolecular chirality was achieved by spontaneous symmetry breaking via Viedma ripening. XRD and SEM were used to prove the synthesis accuracy. Enantioselectivity during adsorption was studied using the adsorption isotherms of α-pinene and limonene enantiomer analysis. The experimental isotherms were approximated by Langmuir, Dubinin–Radushkevich, Freundlich and Fowler–Guggenheim equations. The t-test was used to prove the reliability of the differences in enantiomer adsorption. The isosteric heats of adsorption were calculated from the adsorption isotherms. The data obtained have shown the ability of the LiCu2[BP2O8(OH)2] surface to recognize both α-pinene and limonene enantiomers. The molecules of α-pinenes adsorbed without pores, with the maximum enantioselectivity coefficient of 1.23 at 80 °C. Limonene molecules adsorbed in pore volume as single molecules or 1D chains. This phenomenon was proved by analysis of isosteric heats. The enantioselectivity of copper borophosphate to limonenes and α-pinenes was similar. The ability of pores with supramolecular chirality (and without molecular chirality) to recognize enantiomers was discovered in this paper for the first time. [ABSTRACT FROM AUTHOR]

Protein diffusion is a critical factor governing the functioning and organization of a cell's cytoplasm. In this study, we investigate the influence of (poly)ribosome distribution, cell aging, protein aggregation, and biomolecular condensate formation on protein mobility within the E. coli cytoplasm. We employ nanoscale single-molecule displacement mapping (SMdM) to determine the spatial distribution of the proteins and to meticulously track their diffusion. We show that the distribution of polysomes does not impact the lateral diffusion coefficients of proteins. However, the degradation of mRNA induced by rifampicin treatment leads to an increase in protein mobility within the cytoplasm. Additionally, we establish a significant correlation between cell aging, the asymmetric localization of protein aggregates and reduced diffusion coefficients at the cell poles. Notably, we observe variations in the hindrance of diffusion at the poles and the central nucleoid region for small and large proteins, and we reveal differences between the old and new pole of the cell. Collectively, our research highlights cellular processes and mechanisms responsible for spatially organizing the bacterial cytoplasm into domains with different structural features and apparent viscosity. Single molecule diffusion study to determine the impact of (poly)ribosome distribution, cell aging, protein aggregation, and biomolecular condensate formation on the spatial organization and mobility of proteins in bacteria. [ABSTRACT FROM AUTHOR]

Metal ions can perform multiple roles ranging from regulatory to structural and are crucial for cell function. While some metal ions like Na+ are ubiquitously present at high concentrations, other ions, especially Ca2+ and transition metals, such as Zn2+ or Cu+/2+ are regulated. The concentrations above or below the physiological range cause severe changes in the behavior of biomolecules that bind them and subsequently affect the cell wellbeing. This has led to the development of specialized protocols to study metal ion binding biomolecules in bulk conditions that mimic the cell environment. Recently, there is growing evidence of influence of post-transcriptional and post-translational modifications on the affinity of the metal ion binding sites. However, such targets are difficult to obtain in amounts required for classical biophysical experiments. Single molecule techniques have revolutionized the field of biophysics, molecular and structural biology. Their biggest advantage is the ability to observe each molecule's interaction independently, without the need for synchronization. An additional benefit is its extremely low sample consumption. This feature allows characterization of designer biomolecules or targets obtained coming from natural sources. All types of biomolecules, including proteins, DNA and RNA were characterized using single molecule methods. However, one group is underrepresented in those studies. These are the metal ion binding biomolecules. Single molecule experiments often require separate optimization, due to extremely different concentrations used during the experiments. In this review we focus on single molecule methods, such as single molecule FRET, nanopores and optical tweezers that are used to study metal ion binding biomolecules. We summarize various examples of recently characterized targets and reported experimental conditions. Finally, we discuss the potential promises and pitfalls of single molecule characterization on metal ion binding biomolecules. [ABSTRACT FROM AUTHOR]

The giant protein titin is an essential component of muscle sarcomeres. A single titin molecule spans half a sarcomere and mediates diverse functions along its length by virtue of its unique domains. The A-band of titin functions as a molecular blueprint that defines the length of the thick filaments, the I-band constitutes a molecular spring that determines cell-based passive stiffness, and various domains, including the Z-disk, I-band, and M-line, serve as scaffolds for stretch-sensing signaling pathways that mediate mechanotransduction. This review aims to discuss recent insights into titin’s functional roles and their relationship to cardiac function. The role of titin in heart diseases, such as dilated cardiomyopathy and heart failure with preserved ejection fraction, as well as its potential as a therapeutic target, is also discussed. [ABSTRACT FROM AUTHOR]

Single‐molecule white‐light and near‐infrared circularly polarized luminescent materials are effective complements to the demonstrated enhancements of visible emission in the high contrast 3D images or organic light‐emitting diodes. In this contribution, two binaphthalene‐containing luminogenic enantiomers (BIT or BITM) with aggregation‐induced emission are synthesized which exhibit circularly polarized luminescence in solution with dissymmetry factors of ±5.0 × 10−3 and ±4.8 × 10−3, respectively. Additionally, the dual‐fluorescence spectra of single‐molecule white emission (CIE: 0.33, 0.34) in toluene solution are observed with (R)/(S)‐BIT in low polarity solvent originating from locally excited and twisted intramolecular charge‐transfer emission. While (R)/(S)‐BITM only shows single NIR luminescence with peaks at 720 nm in powder state. The nondoped OLEDs exhibit high maximum external quantum efficiencies of up to 4.2% with small efficiency roll‐off and NIR electroluminescence peak at 709 nm. [ABSTRACT FROM AUTHOR]

Solid‐state assembling modes are as crucial as the chemical structures of single molecules for real applications. In this work, solid‐state structures and phase‐transition temperatures are investigated for a series of fluoranthene‐fused [3.3.3]propellanes consisting of a rigid three‐dimensional (3D) π‐core and varying lengths of alkoxy groups. Compounds in this series with n‐butoxy or longer alkoxy groups take an amorphous state at room temperature. In these molecules, rotatable biaryl‐type bonds are not incorporated and high D3h molecular symmetry is retained. Therefore, π‐fused [3.3.3]propellanes present a unique platform for amorphous molecular materials with low ratios of flexible alkoxy atoms to rigid π‐core ones. [ABSTRACT FROM AUTHOR]

Direct RNA sequencing offers the possibility to simultaneously identify canonical bases and epi-transcriptomic modifications in each single RNA molecule. Thus far, the development of computational methods has been hampered by the lack of biologically realistic training data that carries modification labels at molecular resolution. Here, we report on the synthesis of such samples and the development of a bespoke algorithm, mAFiA (m6A Finding Algorithm), that accurately detects single m6A nucleotides in both synthetic RNAs and natural mRNA on single read level. Our approach uncovers distinct modification patterns in single molecules that would appear identical at the ensemble level. Compared to existing methods, mAFiA also demonstrates improved accuracy in measuring site-level m6A stoichiometry in biological samples. Direct RNA-seq offers the possibility to identify RNA modifications on single molecules. Here, the authors report on the synthesis of biologically realistic training data and the development of mAFiA that accurately detects m6A on single read level. [ABSTRACT FROM AUTHOR]

Background: Cold hardiness is fundamental for amphibians to survive during the extremely cold winter on the Qinghai-Tibet plateau. Exploring the gene regulation mechanism of freezing-tolerant Rana kukunoris could help us to understand how the frogs survive in winter. Results: Transcriptome of liver and muscle of R. kukunoris collected in hibernation and spring were assisted by single molecule real-time (SMRT) sequencing technology. A total of 10,062 unigenes of R. kukunoris were obtained, and 9,924 coding sequences (CDS) were successfully annotated. Our examination of the mRNA response to whole body freezing and recover in the frogs revealed key genes concerning underlying antifreeze proteins and cryoprotectants (glucose and urea). Functional pathway analyses revealed differential regulated pathways of ribosome, energy supply, and protein metabolism which displayed a freeze-induced response and damage recover. Genes related to energy supply in the muscle of winter frogs were up-regulated compared with the muscle of spring frogs. The liver of hibernating frogs maintained modest levels of protein synthesis in the winter. In contrast, the liver underwent intensive high levels of protein synthesis and lipid catabolism to produce substantial quantity of fresh proteins and energy in spring. Differences between hibernation and spring were smaller than that between tissues, yet the physiological traits of hibernation were nevertheless passed down to active state in spring. Conclusions: Based on our comparative transcriptomic analyses, we revealed the likely adaptive mechanisms of R. kukunoris. Ultimately, our study expands genetic resources for the freezing-tolerant frogs. [ABSTRACT FROM AUTHOR]

Single molecule fluorescence in situ hybridisation (smFISH) has become a valuable tool to investigate the mRNA expression of single cells. However, it requires a considerable amount of programming expertise to use currently available open-source analytical software packages to extract and analyse quantitative data about transcript expression. Here, we present FISHtoFigure, a new software tool developed specifically for the analysis of mRNA abundance and co-expression in QuPath-quantified, multi-labelled smFISH data. FISHtoFigure facilitates the automated spatial analysis of transcripts of interest, allowing users to analyse populations of cells positive for specific combinations of mRNA targets without the need for computational image analysis expertise. As a proof of concept and to demonstrate the capabilities of this new research tool, we have validated FISHtoFigure in multiple biological systems. We used FISHtoFigure to identify an upregulation in the expression of Cd4 by T-cells in the spleens of mice infected with influenza A virus, before analysing more complex data showing crosstalk between microglia and regulatory B-cells in the brains of mice infected with Trypanosoma brucei brucei. These analyses demonstrate the ease of analysing cell expression profiles using FISHtoFigure and the value of this new tool in the field of smFISH data analysis. [ABSTRACT FROM AUTHOR]

Background: The use of single-chain variable fragments (scFvs) for treating human diseases, such as cancer and immune system disorders, has attracted significant attention. However, a critical drawback of scFv is its extremely short serum half-life, which limits its therapeutic potential. Thus, there is a critical need to prolong the serum half-life of the scFv for clinical applications. One promising serum half-life extender for therapeutic proteins is human serum albumin (HSA), which is the most abundant protein in human serum, known to have an exceptionally long serum half-life. However, conjugating a macromolecular half-life extender to a small protein, such as scFv, often results in a significant loss of its critical properties. Results: In this study, we conjugated the HSA to a permissive site of scFv to improve pharmacokinetic profiles. To ensure minimal damage to the antigen-binding capacity of scFv upon HSA conjugation, we employed a site-specific conjugation approach using a heterobifunctional crosslinker that facilitates thiol-maleimide reaction and inverse electron-demand Diels-Alder reaction (IEDDA). As a model protein, we selected 4D5scFv, derived from trastuzumab, a therapeutic antibody used in human epithermal growth factor 2 (HER2)-positive breast cancer treatment. We introduced a phenylalanine analog containing a very reactive tetrazine group (frTet) at conjugation site candidates predicted by computational methods. Using the linker TCO-PEG4-MAL, a single HSA molecule was site-specifically conjugated to the 4D5scFv (4D5scFv-HSA). The 4D5scFv-HSA conjugate exhibited HER2 binding affinity comparable to that of unmodified 4D5scFv. Furthermore, in pharmacokinetic profile in mice, the serum half-life of 4D5scFv-HSA was approximately 12 h, which is 85 times longer than that of 4D5scFv. Conclusions: The antigen binding results and pharmacokinetic profile of 4D5scFv-HSA demonstrate that the site-specifically albumin-conjugated scFv retained its binding affinity with a prolonged serum half-life. In conclusion, we developed an effective strategy to prepare site-specifically albumin-conjugated 4D5scFv, which can have versatile clinical applications with improved efficacy. [ABSTRACT FROM AUTHOR]

In recent years, an increasing interest in phytotherapy has been observed. Parallel to the research on the total extracts of plant material, numerous studies on the activity of single molecules derived from plants are being conducted to address their mechanisms of action and determine active doses and eventual interactions. Despite this phenomenon, the isolation of individual compounds is a bottleneck due to its difficulty and cost. This work presents the results of a careful optimization of magnoflorine and berberine (isoquinoline alkaloids) recovery from a commonly distributed shrub, Berberis vulgaris, growing in Poland and Georgia, using CPC. Both compounds are known for their numerous medicinal properties, which makes the isolation methodology an important area of research. Additionally, CPC has the ability to isolate high-quality compounds in large quantities, which makes it an effective and easy-to-commercialize method. For a successful separation, the biphasic solvent system composed of hexane, butanol, ethanol, and water in a ratio (3:12:4:16 v/v/v/v) was used in the ascending mode, together with the flow rate of 8 mL/min and rotation speed of 1600 rpm. The method was selective for both compounds, and it delivered good results for both root and stem extracts from the plant. The qualitative composition of alkaloids in the studied extracts determined by HPLC-ESI-QTOF-MS/MS confirmed the presence of berberine, magnoflorine, jatrorhizine, and palmatine alkaloids from the group of isoquinolines. The isolates, magnoflorine and berberine, were subjected to the Helicobacter pylori growth inhibition assay and urease inhibition test to assess whether, next to the previously proved anticancer properties, these compounds are characterized by H. pylori inhibition. MGN was found to exhibit inhibitory potential against urease (IC50 = 25 mg/L). [ABSTRACT FROM AUTHOR]

The year 2024 marks the 125th anniversary of aspirin, still one of the most frequently used drugs worldwide. Despite its veritable age, it is still relevant in pharmacotherapy and its use has spread to new areas over time. Due to aspirin's multiple pharmacological actions unified in one single molecule (i.e., analgesic, antipyretic, anti-inflammatory, antithrombotic, and antiviral effects), it continues to attract considerable attention in the scientific community and is subject to intense basic and clinical research. In fact, recent results confirmed aspirin's potential role as an antiviral drug and as an agent that can block harmful platelet functions in inflammatory/immunological processes. These features may open up new horizons for this ancient drug. The future of aspirin looks, therefore, bright and promising. Aspirin is not yet ready for retirement; on the contrary, its success story continues. This 125th anniversary paper will concisely review the various therapeutic uses of aspirin with a particular emphasis on the latest research results and their implications (e.g., use as an antiviral agent). In addition, the reader is provided with future perspectives for this remarkable drug. [ABSTRACT FROM AUTHOR]

Sap-feeding insects often maintain two or more nutritional endosymbionts that act in concert to produce compounds essential for insect survival. Many mealybugs have endosymbionts in a nested configuration: one or two bacterial species reside within the cytoplasm of another bacterium, and together, these bacteria have genomes that encode interdependent sets of genes needed to produce key nutritional molecules. Here, we show that the mealybug Pseudococcus viburni has three endosymbionts, one of which contributes only two unique genes that produce the host nutrition-related molecule chorismate. All three bacterial endosymbionts have tiny genomes, suggesting that they have been coevolving inside their insect host for millions of years. [ABSTRACT FROM AUTHOR]

It is a matter of debate whether the discipline independence in discipline formation narrows its interdisciplinarity. It is also less well understood how disruptive works emerge in investigative practice rather than a theory‐driven approach. Aggregation‐induced emission (AIE) is an atypical photophysical phenomenon, in which the whole (aggregate) is brighter than the sum of its parts (single molecule). Through measuring and computing the cognitive extent and evolution of research on AIE, including topics, epistemic‐social collaborative networks, interdisciplinarity, emergent concepts, core concept networks and knowledge flow, this study shows that a cross‐research scales concept and its practice can establish new bridges in the sciences and promote disruptive work. Focusing on mesoscale entities, scientists from many different branches of science are involved in theoretical research on mechanisms, as well as developing different AIE systems for applications. The data analysis in this study provides details showing how non‐reductionist concepts based on new scientific discoveries cross traditional disciplinary boundaries and aggregate interdisciplinary research. The emergence and evolution of the AIE field implies that scientists may be motivated to embrace nonreductionist ideas at different research scales, leading to a more permeable field boundary. [ABSTRACT FROM AUTHOR]

Recently, immunotherapy has arisen as a novel treatment approach for patients with colorectal cancer (CRC), but the effectiveness of immunotherapy varies in these patients. We hypothesized that immune checkpoint molecules (ICMs), which are the targets of immunotherapy, are often exhibited concomitantly. Our objective was to investigate the patterns of ICM expression in patients with CRC and the differences in ICM expression based on microsatellite instability status. The immunohistochemical expression of programmed cell death protein 1 (PD-1), programmed cell death ligand 1 (PD-L1), T cell immunoglobulin and mucin-domain containing-3 (TIM-3), and lymphocyte-activation gene 3 (LAG-3) in the tumor center and periphery was assessed in patients with non-metastatic colorectal cancer. We enrolled 83 patients with CRC: a total of 40 microsatellite-stable (MSS) and 43 microsatellite-instability-high (MSI-H) cancer patients. PD-L1 was more frequently expressed in the tumor center in the MSI-H patients with than that in the MSS patients (18 [41.9%] vs. 3 [7.5%], respectively; p < 0.001), and the same trend was observed for TIM-3 expression (30 [69.8%] vs. 19 [47.5%], respectively; p = 0.047). The concomitant expression of two or more ICMs was more frequently observed than no expression or the expression of a single molecule in both the MSS and MSI-H groups; a total of 34 (79.7%) patients with MSI-H cancer and 23 (57.5%) with MSS cancer showed ICM expression at the tumor center, whereas 34 (79.7%) patients with MSI-H cancer and 22 (55%) with MSS cancer showed expression at the tumor periphery. Patients with the genetic characteristics of MSI-H cancer showed higher expression levels of ICMs than those in patients with MSS cancer, and predominantly, two or more ICMs were concurrently expressed. Our findings highlight the potential efficacy of the dual-blockade approach in immunotherapy, particularly in patients with MSI-H CRC. [ABSTRACT FROM AUTHOR]

Single‐molecule fluorescence (smFL) imaging techniques have evolved greatly over the past two decades to encompass the ability to monitor chemical reactions, providing unique advantages of non‐invasive sample preparation and characterization, labeling specificity, and high spatial and temporal resolutions. This work summarizes the recent progress in this important area by first providing a brief overview of different smFL techniques, including their common optical setups and working principles. We then introduce recent developments of smFL to characterize various model chemical reaction systems, such as biochemical synthesis, catalyzed systems, and nanomaterial assembly. Furthermore, several representative areas of using smFL to understand polymer reactions are discussed, including understanding interfacial phenomenon and polymerization kinetics, as well as characterizing electrochemical reactions. We also highlight the outlook of this exciting field and potential opportunities for further development and application of smFL to enable advances in polymer chemistry and physics. [ABSTRACT FROM AUTHOR]

Single‐molecule force spectroscopy is a powerful tool for the quantitative investigation of the biophysics, polymer physics and mechanochemistry of individual polymer strands. One limitation of this technique is that the attachment between the tip of the atomic force microscope and the covalent or noncovalent analyte in a given pull is typically not strong enough to sustain the force at which the event of interest occurs, which makes the experiments time‐consuming and inhibits throughput. Here we report a polyelectrolyte handle for single‐molecule force spectroscopy that offers a combination of high (several hundred pN) attachment forces, good (~4%) success in obtaining a high‐force (>200 pN) attachment, a non‐fouling detachment process that allows for repetition, and specific attachment locations along the polymer analyte. [ABSTRACT FROM AUTHOR]

Betaine structural analogs are compounds characterized by the presence of positive and negative charges in a single molecule and have been reported to have physiological properties, such as anti-inflammatory activities. In this study, we performed a metabolomic analysis of metabolite composition changes during the fermentation of Neopyropia yezoensis, an edible red alga, with Aspergillus oryzae for 72 h. The results indicated that three specific betaine structural analogs (betaine, stachydrine, and carnitine) exhibited significant changes in production by the end of the 72 h fermentation period. Time-course analysis suggested that betaine was generated from the precursor choline at 12–24 h during the late stage of fungal growth, while stachydrine was generated from the precursor-related compound glutamic acid at 48–72 h during the sporulation stage. However, the contribution of the precursor lysine to the increased production of carnitine during the 12–72 h period was unclear. This study provides useful information on the efficient production of betaine structural analogs by the fungal fermentation of seaweed as well as various other food materials. [ABSTRACT FROM AUTHOR]

The utilization of single molecule electronic devices represents a significant avenue toward advancing next-generation circuits. Recent investigations have notably augmented our understanding of the optoelectronic characteristics exhibited by diverse single molecule materials. This comprehensive review underscores the latest progressions in probing photo-induced electron transport behaviors within molecular junctions. Encompassing both single molecule and self-assembled monolayer configurations, this review primarily concentrates on unraveling the fundamental mechanisms and guiding principles underlying photo-switchable devices within single molecule junctions. Furthermore, it presents an outlook on the obstacles faced and future prospects within this dynamically evolving domain. [ABSTRACT FROM AUTHOR]

Honey can beneficially act against different human diseases, helping our body to improve its health. The aim of the present study was first to increase knowledge of some biochemical characteristics (amount and composition of polyphenols and volatile organic compounds, vitamin C content) of five Italian legume honeys (alfalfa, astragalus, carob, indigo, and sainfoin). Furthermore, we evaluated their potential health properties by studying their antioxidant and in vitro anti-inflammatory activities and in vitro inhibitory effects on three enzymes involved in neurodegenerative diseases (acetylcholinesterase, butyrylcholinesterase, and tyrosinase). Alfalfa honey showed the highest total polyphenol content (TPC) (408 μg g−1 of product). Indigo honey showed the lowest TPC (110 μg g−1 of product). The antioxidant activity was noteworthy, especially in the case of sainfoin honey (IC50 = 6.08 mg), which also exhibited excellent inhibitory action against butyrylcholinesterase (74%). Finally, the correlation between the biochemical and functional results allowed us to identify classes of molecules, or even single molecules, present in these five honeys, which are capable of influencing the properties indicated above. [ABSTRACT FROM AUTHOR]

Biopolymer topology is critical for determining interactions inside cell environments, exemplified by DNA where its response to mechanical perturbation is as important as biochemical properties to its cellular roles. The dynamic structures of chiral biopolymers exhibit complex dependence with extension and torsion, however the physical mechanisms underpinning the emergence of structural motifs upon physiological twisting and stretching are poorly understood due to technological limitations in correlating force, torque and spatial localization information. We present COMBI-Tweez (Combined Optical and Magnetic BIomolecule TWEEZers), a transformative tool that overcomes these challenges by integrating optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy, demonstrated on single DNA molecules, that can controllably form and visualise higher order structural motifs including plectonemes. This technology combined with cutting-edge MD simulations provides quantitative insight into complex dynamic structures relevant to DNA cellular processes and can be adapted to study a range of filamentous biopolymers. It is hard to correlate force, torque and localization information. The authors report Combined Optical and Magnetic BIomolecule TWEEZers, COMBI-Tweez, that integrates optical trapping, time-resolved electromagnetic tweezers, and fluorescence microscopy: they demonstrate visualisation of higher order structural motifs in DNA. [ABSTRACT FROM AUTHOR]

Protein kinase A (PKA) is a ubiquitous, promiscuous kinase whose activity is specified through subcellular localization mediated by A-kinase anchoring proteins (AKAPs). PKA has complex roles as both an effector and a regulator of integrin-mediated cell adhesion to extracellular matrix (ECM). Recent observations demonstrate that PKA is an active component of focal adhesions (FA), suggesting the existence of one or more FA AKAPs. Using a promiscuous biotin ligase fused to PKA type-IIα regulatory (RIIα) subunits and subcellular fractionation, we identify the archetypal FA protein talin1 as an AKAP. Talin is a large, mechanosensitive scaffold that directly links integrins to actin filaments and promotes FA assembly by recruiting additional components in a force-dependent manner. The rod region of talin1 consists of 62 α-helices bundled into 13 rod domains, R1 to R13. Direct binding assays and NMR spectroscopy identify helix41 in the R9 subdomain of talin as the PKA binding site. PKA binding to helix41 requires unfolding of the R9 domain, which requires the linker region between R9 and R10. Experiments with single molecules and in cells manipulated to alter actomyosin contractility demonstrate that the PKA--talin interaction is regulated by mechanical force across the talin molecule. Finally, talin mutations that disrupt PKA binding also decrease levels of total and phosphorylated PKA RII subunits as well as phosphorylation of VASP, a known PKA substrate, within FA. These observations identify a mechanically gated anchoring protein for PKA, a force-dependent binding partner for talin1, and a potential pathway for adhesion-associated mechanotransduction. [ABSTRACT FROM AUTHOR]

Encouraged by the successful fabrication of C60‐GNR (GNR=graphene nanoribbon) single‐molecule transistors in experiments, four Fe‐containing derived double‐layered devices of Fe@C60‐GNR are designed by employing different electrode linkages and their transport properties are investigated by using density functional theory (DFT) and nonequilibrium Green's function (NEGF) methods. Regardless of electrode connection, all these devices give rise to a smaller negative differential resistance (NDR) peak at V=0.2 and a higher peak at 1.2 V, suggesting their stable maneuverability as molecular devices and good candidates for developing on(off)‐off(on)‐on(off) current switches. The macroscopic NDR performance depends on the delocalization character and the crossing mechanism of the frontier orbitals. The peak‐to‐valley current ratios (Rmax) range from 454 to 2737, determined by the electrode linkage. Such a large Rmax‐value is necessary for developing dynamic random‐access memory (DRAM) cells. Encapsulating the Fe atom inside C60 not only improves the conductivity but also introduces the spin‐polarized transport property. The spin‐filtering efficiency (SFE) of almost all devices oscillates up and down in response to the bias voltage, indicating the possibility of designing on(off)‐off(on)‐on(off) spin switches and up‐down spin switches. All these fascinating properties provide an important clue for designing similar molecular devices with multiple functions by trapping magnetic transition metal atoms inside fullerenes. [ABSTRACT FROM AUTHOR]

Single particle tracking (SPT) combined with total internal reflection fluorescence microscopy (TIRFm) is an outstanding approach to decipher mechanisms on the cell membrane at the nanoscale. Multicolor configurations, needed to investigate interactions, are still hindered by several challenges. This work systematically and quantitatively analyzes the impact of necessary elements of SPT‐TIRFm setups on the signal‐to‐noise ratio (SNR), which must be optimized especially in dynamic studies needing minimally invasive dyes for biomolecule labeling. Autofluorescence originating from commonly used optical glass results in the dominant limiting factor in TIRFm, and a cover glass material is tested yielding significant SNR improvements in multichannel TIRFm. Moreover, methodologies are optimized for reducing fluorophore photobleaching in multicolor implementations requiring simultaneous stabilization of multiple dyes. The developed strategies are applied to the fast p75NTR receptors labeled by two fluorophores on the membrane of living cells, achieving reliable, simultaneous two‐color SPT, contrary to configurations using standard cover glasses. This work highlights the importance of optical materials suitable for microscopy and with reduced autofluorescence for increasing sensitivity toward ultimate spatiotemporal resolutions. In particular, the present protocols can pave the way for multicolor super‐resolved localization and tracking of single molecules by TIRFm, greatly expanding the potential of SPT. [ABSTRACT FROM AUTHOR]

DNA motors that consume chemical energy to generate processive mechanical motion mimic natural motor proteins and have garnered interest due to their potential applications in dynamic nanotechnology, biosensing, and drug delivery. Such motors translocate by a catalytic cycle of binding, cleavage, and rebinding between DNA "legs" on the motor body and RNA "footholds" on a track. Herein, we address the well‐documented trade‐off between motor speed and processivity and investigate how these parameters are controlled by the affinity between DNA legs and their complementary footholds. Specifically, we explore the role of DNA leg length and GC content in tuning motor performance by dictating the rate of leg‐foothold dissociation. Our investigations reveal that motors with 0 % GC content exhibit increased instantaneous velocities of up to 150 nm/sec, three‐fold greater than previously reported DNA motors and comparable to the speeds of biological motor proteins. We also demonstrate that the faster speed and weaker forces generated by 0 % GC motors can be leveraged for enhanced capabilities in sensing. We observe single‐molecule sensitivity when programming the motors to stall in response to the binding of nucleic acid targets. These findings offer insights for the design of high‐performance DNA motors with promising real‐world biosensing applications. [ABSTRACT FROM AUTHOR]

Encouraged by the promising performance of C60-graphene single-molecule transistors observed in experiments, two types of Fen/C60-GNR (n = 2 and 4 and GNR = graphene nanoribbon) molecules with Fe atoms sandwiched between the upper and lower GNR layers were designed and their electronic and transport properties were investigated by employing density functional theory (DFT) and nonequilibrium Green's function (NEGF) methods. Adding the Fe atoms induces high spin magnetism in the systems. Within the considered bias, almost all Fe2/C60-GNR devices generate double NDR peaks, and some of the Fen/C60-GNR devices (n = 2 and 4) possess a large peak-to-valley current ratio R = Ipeak/Ivalley (>400), implying potential applications in developing on–off–on/off–on–off current switches. The NDR character originates from the crossing of the frontier molecular orbitals. In addition, these systems show distinct spin-polarized transport characteristics, with up-spin channels displaying higher conductivity than down-spin pathways. The spin filter efficiency (SFE) oscillates up and down as bias is scanned for almost all devices, suggesting the possibility of designing on–off–on/off–on–off current switches as well as up–down spin switches. All these findings provide guidance for exploring single molecular devices with promising properties combined with graphene, fullerenes, and transition metals. [ABSTRACT FROM AUTHOR]

Long non-coding RNAs (lncRNAs) could modulate expression of immune checkpoints (ICPs) by cooperating with immunity genes in tumor immunization. However, precise functions in immunity and potential for predicting ICP inhibitors (ICI) response have been described for only a few lncRNAs. Here we present an integrated framework that leverages network-based analyses and Bayesian network inference to identify the regulated relationships including lncRNA, ICP and immunity genes as ICP-related LncRNAs mediated Core Regulatory Circuitry Triplets (ICP-LncCRCTs) that can make robust predictions. Hub ICP-related lncRNAs such as MIR155HG and ADAMTS9-AS2 were highlighted to play central roles in immune regulation. Specific ICP-related lncRNAs could distinguish cancer subtypes. Moreover, the ICP-related lncRNAs are likely to significantly correlated with immune cell infiltration, MHC, CYT. Some ICP-LncCRCTs such as CXCL10-MIR155HG-ICOS could better predict one-, three- and five-year prognosis compared to single molecule in melanoma. We also validated that some ICP-LncCRCTs could effectively predict ICI-response using three kinds of machine learning algorithms follow five independent datasets. Specially, combining ICP-LncCRCTs with the tumor mutation burden (TMB) improves the prediction of ICI-treated melanoma patients. Altogether, this study will improve our grasp of lncRNA functions and accelerating discovery of lncRNA-based biomarkers in ICI treatment. An integrated framework to identify immune checkpoint-related lncRNA core regulatory circuitry triplets has the potential to improve our understanding of lncRNA functions and accelerate the discovery of lncRNA-based biomarkers for immune checkpoint inhibitor treatment. [ABSTRACT FROM AUTHOR]

Interactions between monatomic ions and water molecules are fundamental to understanding the hydration of complex polyatomic ions and ionic process. Among the simplest and well-established ion-related reactions is dissolution of salt in water, which is an endothermic process requiring an increase in entropy. Extensive efforts have been made to date; however, most studies at single-ion level have been limited to theoretical approaches. Here, we demonstrate the salt dissolution process by manipulating a single water molecule at an under-coordinated site of a sodium chloride film. Manipulation of molecule in a controlled manner enables us to understand ion–water interaction as well as dynamics of water molecules at NaCl interfaces, which are responsible for the selective dissolution of anions. The water dipole polarizes the anion in the NaCl ionic crystal, resulting in strong anion–water interaction and weakening of the ionic bonds. Our results provide insights into a simple but important elementary step of the single-ion chemistry, which may be useful in ion-related sciences and technologies. The strong ionic bond in salt is broken by electrostatic interactions with water, but direct observation at the level of a single ion is challenging. Here, the authors have visualized the preferential dissolution of an anion by manipulating a single water molecule. [ABSTRACT FROM AUTHOR]

Natural fruits contain a large variety of cis-diols. However, due to the lack of a high-resolution sensor that can simultaneously identify all cis-diols without a need of complex sample pretreatment, direct and rapid analysis of fruits in a hand-held device has never been previously reported. Nanopore, a versatile single molecule sensor, can be specially engineered to perform this task. A hetero-octameric Mycobacterium smegmatis porin A (MspA) nanopore modified with a sole phenylboronic acid (PBA) adapter is prepared. This engineered MspA accurately recognizes 1,2-diphenols, alditols, α-hydroxy acids and saccharides in prune, grape, lemon, different varieties of kiwifruits and commercial juice products. Assisted with a custom machine learning program, an accuracy of 99.3% is reported and the sample pretreatment is significantly simplified. Enantiomers such as DL-malic acids can also be directly identified, enabling sensing of synthetic food additives. Though demonstrated with fruits, these results suggest wide applications of nanopore in food and drug administration uses. Fruits contain a large variety of cis-diols but their rapid and direct analysis without complex sample pretreatment was not achieved. Here, the authors report a Mycobacterium smegmatis porin A nanopore modified with a phenylboronic acid adapter for recognition of 1,2-diphenols, alditols, α-hydroxy acids and saccharides in fruits. [ABSTRACT FROM AUTHOR]

Water molecules play an important role in the structure, function, and dynamics of (bio‐) materials. A direct access to the number of water molecules in nanoscopic volumes can thus give new molecular insights into materials and allow for fine‐tuning their properties in sophisticated applications. The determination of the local water content has become possible by the finding that H2O quenches the fluorescence of red‐emitting dyes. Since deuterated water, D2O, does not induce significant fluorescence quenching, fluorescence lifetime measurements performed in different H2O/D2O‐ratios yield the local water concentration. We combined this effect with the recently developed fluorescence lifetime single molecule localization microscopy imaging (FL‐SMLM) in order to nanoscopically determine the local water content in microgels, i.e. soft hydrogel particles consisting of a cross‐linked polymer swollen in water. The change in water content of thermo‐responsive microgels when changing from their swollen state at room temperature to a collapsed state at elevated temperature could be analyzed. A clear decrease in water content was found that was, to our surprise, rather uniform throughout the entire microgel volume. Only a slightly higher water content around the dye was found in the periphery with respect to the center of the swollen microgels. [ABSTRACT FROM AUTHOR]

Determining absolute electron impact ionization cross-sections for atoms and molecules, whether through experimental or theoretical means, poses a formidable challenge and is typically limited to a narrow selection of species. In this paper, by using measured cross-sections and polarizability data, it was obtained empirical scaling laws for total single ionization and non-dissociative single ionization cross-section maximum of neutral molecules by collisions with electrons. It is found that the total single ionization cross-sections scale linearly with the target electric static polarizability, while the non-dissociate cross-sections exhibit a saturation effect for large target polarizabilities. This saturation effect is interpreted as the increasing role of fragmentation with polarizability. [ABSTRACT FROM AUTHOR]

The chemical etching of germanium in Br2 environment at elevated temperatures is described by the Michaelis–Menten equation. The validity limit of Michaelis–Menten kinetics is subjected to the detailed analysis. The steady-state etching rate requires synergy of two different process parameters. High purity gas should be directed to the substrate on which intermediate reaction product does not accumulate. Theoretical calculations indicate that maximum etching rate is maintained when 99.89% of the germanium surface is covered by the reaction product, and 99.9999967% of the incident Br2 molecules are reflected from the substrate surface. Under these conditions, single GeBr2 molecule is formed after 30 million collisions of Br2 molecules with the germanium surface. [ABSTRACT FROM AUTHOR]

Homochirality is an obvious feature of life on Earth. On the other hand, extraterrestrial samples contain largely racemic compounds. The same is true for any common organic synthesis. Therefore, it has been a perplexing puzzle for decades how these racemates could have formed enantiomerically enriched fractions as a basis for the origin of homochiral life forms. Numerous hypotheses have been put forward as to how preferentially homochiral molecules could have formed and accumulated on Earth. In this article, it is shown that homochirality of the abiotic organic pool at the time of formation of the first self-replicating molecules is not necessary and not even probable. It is proposed to abandon the notion of a molecular ensemble and to focus on the level of individual molecules. Although the formation of the first self-replicating, most likely homochiral molecule, is a seemingly improbable event, on a closer look, it is almost inevitable that some homochiral molecules have formed simply on a statistical basis. In this case, the non-selective leap to homochirality would be one of the first steps in chemical evolution directly out of a racemic "ocean". Moreover, most studies focus on the chirality of the primordial monomers with respect to an asymmetric carbon atom. However, any polymer with a minimal size that allows folding to a secondary structure would spontaneously lead to asymmetric higher structures (conformations). Most of the functions of these polymers would be influenced by this inherently asymmetric folding. Furthermore, a concept of physical compartmentalization based on rock nanopores in analogy to nanocavities of digital immunoassays is introduced to suggest that complex cell walls or membranes were also not required for the first steps of chemical evolution. To summarize, simple and universal mechanisms may have led to homochiral self-replicating systems in the context of chemical evolution. A homochiral monomer pool is deemed unnecessary and probably never existed on primordial Earth. [ABSTRACT FROM AUTHOR]

Simple Summary: Clustered regularly interspaced short palindromic repeats (CRISPR) ribonucleoprotein (RNP)-mediated precise genome editing can modify a specific targeted gene to establish cell models and improve animal traits, thus playing a significant role in animal breeding. However, the efficiency of precise gene editing is low, which limits its widespread use. To overcome this problem in porcine cells, we used small molecules to improve the efficiency of CRISPR RNP-mediated precise genome editing in porcine fetal fibroblasts (PFFs). We demonstrated that a single small molecule including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A increased the efficiency of homology-directed repair (HDR) during precise gene editing in PFFs, respectively. These results provided methodological support for the establishment of an efficient and precise gene editing system in pigs. The aim of this study was to verify whether small molecules can improve the efficiency of precision gene editing using clustered regularly interspaced short palindromic repeats (CRISPR) ribonucleoprotein (RNP) in porcine cells. CRISPR associated 9 (Cas9) protein, small guide RNA (sgRNA), phosphorothioate-modified single-stranded oligonucleotides (ssODN), and different small molecules were used to generate precise nucleotide substitutions at the insulin (INS) gene by homology-directed repair (HDR) in porcine fetal fibroblasts (PFFs). These components were introduced into PFFs via electroporation, followed by polymerase chain reaction (PCR) for the target site. All samples were sequenced and analyzed, and the efficiencies of different small molecules at the target site were compared. The results showed that the optimal concentrations of the small molecules, including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A, for in vitro-cultured PFFs' viability were determined. Compared with the control group, the single small molecules including L-189, NU7441, SCR7, L755507, RS-1, and Brefeldin A increased the efficiency of HDR-mediated precise gene editing from 1.71-fold to 2.28-fold, respectively. There are no benefits in using the combination of two small molecules, since none of the combinations improved the precise gene editing efficiency compared to single small molecules. In conclusion, these results suggested that a single small molecule can increase the efficiency of CRISPR RNP-mediated precise gene editing in porcine cells. [ABSTRACT FROM AUTHOR]

SecA is a widely conserved ATPase that drives the secretion of proteins across the cell membrane via the SecYEG translocon, while the SRP system is a key player in the insertion of membrane proteins via SecYEG. How SecA gains access to substrate proteins in Bacillus subtilis cells and copes with an increase in substrate availability during biotechnologically desired, high-level expression of secreted proteins is poorly understood. Using single molecule tracking, we found that SecA localization closely mimics that of ribosomes, and its molecule dynamics change similarly to those of ribosomes after inhibition of transcription or translation. These data suggest that B. subtilis SecA associates with signal peptides as they are synthesized at the ribosome, similar to the SRP system. In agreement with this, SecA is a largely mobile cytosolic protein; only a subset is statically associated with the cell membrane, i.e., likely with the Sec translocon. SecA dynamics were considerably different during the late exponential, transition, and stationary growth phases, revealing that single molecule dynamics considerably alter during different genetic programs in cells. During overproduction of a secretory protein, AmyE, SecA showed the strongest changes during the transition phase, i.e., where general protein secretion is high. To investigate whether the overproduction of AmyE also has an influence on other proteins that interact with SecYEG, we analyzed the dynamics of SecDF, YidC, and FtsY with and without AmyE overproduction. SecDF and YidC did not reveal considerable differences in single molecule dynamics during overexpression, while the SRP component FtsY changed markedly in its behavior and became more statically engaged. These findings indicate that the SRP pathway becomes involved in protein secretion upon an overload of proteins carrying a signal sequence. Thus, our data reveal high plasticity of the SecA and SRP systems in dealing with different needs for protein secretion. [ABSTRACT FROM AUTHOR]

Kymograph analysis is employed across the biological atomic force microscopy (AFM) community to boost temporal resolution. The method is well suited for revealing protein dynamics at the single molecule level in near-native conditions. Yet, kymograph analysis comes with limitations that depend on several factors including protein geometry and instrumental drift. This work focuses on conformational dynamics of difficult-to-study sparse distributions of membrane proteins. We compare and contrast AFM kymograph analysis for two proteins, one of which (SecDF) exhibits conformational dynamics primarily in the vertical direction (normal to the membrane surface) and the other (Pgp) exhibits a combination of lateral dynamics and vertical motion. Common experimental issues are analyzed including translational and rotational drift. Conformational transition detection is evaluated via kymograph simulations followed by state detection algorithms. We find that kymograph analysis is largely robust to lateral drift. Displacement of the AFM line scan trajectory away from the protein center of mass by a few nanometers, roughly half of the molecule diameter, does not significantly affect transition detection nor generate undue dwell time errors. On the other hand, for proteins like Pgp that exhibit significant azimuthal maximum height dependence, rotational drift can potentially produce artifactual transitions. Measuring the height of a membrane protein protrusion is generally superior to measurement of width, confirming intuition based on vertical resolution superiority. In low signal-to-noise scenarios, common state detection algorithms struggle with transition detection as opposed to infinite hidden Markov models. AFM kymography represents a valuable addition to the membrane biophysics toolkit; continued hardware and software improvements are poised to expand the method's impact in the field. [ABSTRACT FROM AUTHOR]

• GMIA integrates the atom node and the incoming edge information to learn the node representation. • GMIA can capture the mutual interaction context between two molecular graphs in a drug pair. • GMIA provides interpretability and can discover key molecular substructures for drug-drug pairs. • Comprehensive experiments demonstrated the performance of GMIA. • A novel graph learning framework of mutual interaction attention mechanism is proposed to predict DDIs. Effective representation of molecules is a crucial step in AI-driven drug design and drug discovery, especially for drug-drug interaction (DDIs) prediction. Previous work usually models the drug information from the drug-related knowledge graph or the single drug molecules, but the interaction information between molecular substructures of drug pair is seldom considered, thus often ignoring the influence of bond information on atom node representation, leading to insufficient drug representation. Moreover, key molecular substructures have significant contribution to the DDIs prediction results. Therefore, in this work, we propose a novel Graph learning framework of Mutual Interaction Attention mechanism (called GMIA) to predict DDIs by effectively representing the drug molecules. Specifically, we build the node-edge message communication encoder to aggregate atom node and the incoming edge information for atom node representation and design the mutual interaction attention decoder to capture the mutual interaction context between molecular graphs of drug pairs. GMIA can bridge the gap between two encoders for the single drug molecules by attention mechanism. We also design a co-attention matrix to analyze the significance of different-size substructures obtained from the encoder-decoder layer and provide interpretability. In comparison with other recent state-of-the-art methods, our GMIA achieves the best results in terms of area under the precision-recall-curve (AUPR), area under the ROC curve (AUC), and F1 score on two different scale datasets. The case study indicates that our GMIA can detect the key substructure for potential DDIs, demonstrating the enhanced performance and interpretation ability of GMIA. [ABSTRACT FROM AUTHOR]

This article discusses the advancements and challenges in nanopore protein sequencing. While DNA sequencing has been successful, protein sequencing presents unique complexities due to the diverse amino acids and heterogeneous charges in peptides. The article explores two methodologies for nanopore protein sequencing: full-length chain sequencing and enzyme-assisted sequencing. The authors propose a strategy combining enzymatic cleavage and host-guest interaction-assisted nanopore sensing for comprehensive peptide sequencing. The article concludes by highlighting the potential of nanopore protein sequencing in revolutionizing diagnostics and biomedical breakthroughs. [Extracted from the article]

Anisotropic colloidal particles have attracted great attention over the past few decades because of their significant properties that differ from isotropic particles. Molecular self‐assembly provides the possibility to design and construct anisotropic colloidal particles from the single‐molecule level, and molecular assemblies can both inherit the properties of molecules in single states and integrate the functions of molecules in collective states, which has attracted great interest to researchers. Even in recent years, the self‐assembly strategy of anisotropic colloidal particles has been greatly developed. This review article briefly summarizes the research progress of molecules from small molecules, block copolymers and homopolymers to anisotropic particles, including their self‐assembly strategies and applications. Finally, we discuss the remaining challenges of this topic and we expect that by manipulating the design of diverse molecules/polymers, anisotropic colloidal particles can evolve into a new era. [ABSTRACT FROM AUTHOR]

N-acyl hydrazone (NAH) is recognized as a promising framework in drug design due to its versatility, straightforward synthesis, and attractive range of biological activities, including antimicrobial, antitumoral, analgesic, and anti-inflammatory properties. In the global context of increasing resistance of pathogenic bacteria to antibiotics, NAHs represent potential solutions for developing improved treatment alternatives. Therefore, this research introduces six novel derivatives of (EZ)-N'-benzylidene-2-(6-chloro-9H-carbazol-2-yl)propanehydrazide, synthesized using a microwave-assisted method. In more detail, we joined two pharmacophore fragments in a single molecule, represented by an NSAID-type carprofen structure and a hydrazone-type structure, obtaining a new series of NSAID-N-acyl hydrazone derivatives that were further characterized spectrally using FT-IR, NMR, and HRMS investigations. Additionally, the substances were assessed for their tuberculostatic activity by examining their impact on four strains of M. tuberculosis, including two susceptible to rifampicin (RIF) and isoniazid (INH), one susceptible to RIF and resistant to INH, and one resistant to both RIF and INH. The results of our research highlight the potential of the prepared compounds in fighting against antibiotic-resistant M. tuberculosis strains. [ABSTRACT FROM AUTHOR]

Abstract The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase–AMP complex and the ligase–AMP–DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase–AMP complex that persist in the ligase–AMP–DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.

In a recent study [J. Phys. Chem. B 126, 4584–4598 (2022)], we have used infrared spectroscopy to investigate the solvation and dynamics of solitary water in ionic liquids and dipolar solvents. Complex shapes observed for water OH-stretching bands, common to all high-polarity solvents, were assigned to water in several solvation states. In the present study, classical molecular dynamics simulations of a single water molecule in four ionic liquids and three dipolar solvents were used to test and refine this interpretation. Consistent with past assignments, simulations show solitary water usually donates two hydrogen bonds to distinct solvent molecules. Such symmetrically solvated water produces the primary pair of peaks identified in the OH spectra of water in nearly all solvents. We had further proposed that additional features flanking this main peak are due to asymmetric solvation states, states in which only one OH group makes a hydrogen bond to solvent. Such states were found in significant concentrations in all of the systems simulated. Simulations of the OH stretching spectra using a semiclassical description and the vibrational map developed by Auer and Skinner [J. Chem. Phys. 128, 224511–224512 (2008)] provided semi-quantitative agreement with experiment. Analysis of species-specific spectra confirmed assignment of the additional features in the experimental spectra to asymmetrically solvated water. The simulations also showed that rapid water motions cause a marked motional narrowing compared with the inhomogeneous limit. This narrowing is largely responsible for making the additional features due to minority solvation states manifest in the spectra. [ABSTRACT FROM AUTHOR]

In order to improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. As an example application, a potential-energy surface is generalized for a small DNA duplex, taking into account explicit solvation and long-range electron exchange–correlation effects. A long-standing problem in molecular science is that experimental studies of the structural and thermodynamic behavior of DNA under tension are not well confirmed by simulation; study of the potential energy vs extension taking into account a novel correction shows that leading classical DNA models have excessive stiffness with respect to stretching. This discrepancy is found to be common across multiple forcefields. The quantum correction is in qualitative agreement with the experimental thermodynamics for larger DNA double helices, providing a candidate explanation for the general and long-standing discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. The new dataset of quantum calculations should facilitate multiple types of nucleic acid simulation, and the associated Kernel Modified Molecular Dynamics method (KMMD) is applicable to biomolecular simulations in general. KMMD is made available as part of the AMBER22 simulation software. [ABSTRACT FROM AUTHOR]

This article discusses the development of a new model of immune cells called Langerhans-like cells (LCs) for studying tick-borne encephalitis virus (TBEV) infection. LCs play a crucial role in the early-stage infection by transporting viral antigens from the skin to the lymph nodes. The researchers derived primary LCs from murine bone marrow and confirmed their suitability for TBEV infection experiments. The LCs were found to be susceptible to TBEV infection, with high cell viability and viral replication. This new model provides a valuable tool for studying TBEV infection and the dissemination of the virus. [Extracted from the article]

This editorial published in the journal Frontiers in Physiology provides a historical perspective on the classification and discovery of unconventional myosins, which are molecular motors involved in cellular movement. It discusses the identification of the first unconventional myosin, myosin I, in 1973 and subsequent research that led to the discovery of other unconventional myosins. The document includes articles and reviews on specific unconventional myosins, such as myosin Va and myosin 5c, and their roles in cellular processes. The editorial also highlights recent research on different isoforms of unconventional myosins, including myosin VI and class-18 myosins, and their functions in various cellular structures and processes. The article concludes by acknowledging the contributions of researchers in the field and providing a historic perspective on the discovery of unconventional myosins. [Extracted from the article]

The article discusses the field of academic foreign compound metabolism, specifically focusing on the identification and characterization of drug metabolites. In the past, it was acceptable to identify metabolites down to a certain percentage of the given dose, but regulatory authorities now require the identification of metabolites representing 10% or more of the dosed product. Modern technology allows for the detection of metabolites at extremely low levels. The article also explores the significance of the absolute number of drug metabolite molecules and the challenges in detecting minor metabolites. It concludes by discussing the future directions of xenobiochemistry, including the study of polymorphic variation, genetic and epigenetic associations, and the importance of the microbiome. [Extracted from the article]