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In the realm of medicinal chemistry, the primary objective is to swiftly optimize a multitude of chemical properties of a set of compounds to yield a clinical candidate poised for clinical trials. In recent years, two computational techniques, machine learning (ML) and physics-based methods, have evolved substantially and are now frequently incorporated into the medicinal chemist's toolbox to enhance the efficiency of both hit optimization and candidate design. Both computational methods come with their own set of limitations, and they are often used independently of each other. ML's capability to screen extensive compound libraries expediently is tempered by its reliance on quality data, which can be scarce especially during early-stage optimization. Contrarily, physics-based approaches like free energy perturbation (FEP) are frequently constrained by low throughput and high cost by comparison; however, physics-based methods are capable of making highly accurate binding affinity predictions. In this study, we harnessed the strength of FEP to overcome data paucity in ML by generating virtual activity data sets which then inform the training of algorithms. Here, we show that ML algorithms trained with an FEP-augmented data set could achieve comparable predictive accuracy to data sets trained on experimental data from biological assays. Throughout the paper, we emphasize key mechanistic considerations that must be taken into account when aiming to augment data sets and lay the groundwork for successful implementation. Ultimately, the study advocates for the synergy of physics-based methods and ML to expedite the lead optimization process. We believe that the physics-based augmentation of ML will significantly benefit drug discovery, as these techniques continue to evolve.

ZBP1 senses viral Z-RNAs to induce necroptotic cell death to restrain viral infection. ZBP1 is also thought to recognize host cell-derived Z-RNAs to regulate organ development and tissue inflammation in mice. However, it remains unknown how the host-derived Z-RNAs are formed and how these endogenous Z-RNAs are sensed by ZBP1. Here, we report that oxidative stress strongly induces host cell endogenous Z-RNAs, and the Z-RNAs then localize to stress granules for direct sensing by ZBP1 to trigger necroptosis. Oxidative stress triggers dramatically increase Z-RNA levels in tumor cells, and the Z-RNAs then directly trigger tumor cell necroptosis through ZBP1. Localization of the induced Z-RNAs to stress granules is essential for ZBP1 sensing. Oxidative stress-induced Z-RNAs significantly promote tumor chemotherapy via ZBP1-driven necroptosis. Thus, our study identifies oxidative stress as a critical trigger for Z-RNA formation and demonstrates how Z-RNAs are directly sensed by ZBP1 to trigger anti-tumor necroptotic cell death., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

In the field of lithium-sulfur batteries (LSBs) and all-solid-state batteries, lithium sulfide (Li 2 S) is a critical raw material. However, its practical application is greatly hindered by its high price due to its deliquescent property and production at high temperatures (above 700 °C) with carbon emission. Hereby, we report a new method of preparing Li 2 S, in air and at low temperatures (∼200 °C), which presents enriched and surprising chemistry. The synthesis relies on the solid-state reaction between inexpensive and air-stable raw materials of lithium hydroxide (LiOH) and sulfur (S), where lithium sulfite (Li 2 SO 3 ), lithium thiosulfate (Li 2 S 2 O 3 ), and water are three major byproducts. About 57% of lithium from LiOH is converted into Li 2 S, corresponding to a material cost of ∼$64.9/kg_Li 2 S, less than 10% of the commercial price. The success of conducting this water-producing reaction in air lies in three-fold: (1) Li 2 S is stable with oxygen below 220 °C; (2) the use of excess S can prevent Li 2 S from water attack, by forming lithium polysulfides (Li 2 S n ); and (3) the byproduct water can be expelled out of the reaction system by the carrier gas and also absorbed by LiOH to form LiOH·H 2 O. Two interesting and beneficial phenomena, i.e., the anti-hydrolysis of Li 2 S n and the decomposition of Li 2 S 2 O 3 to recover Li 2 S, are explained with density functional theory computations. Furthermore, our homemade Li 2 S (h-Li 2 S) is at least comparable with the commercial Li 2 S (c-Li 2 S), when being tested as cathode materials for LSBs.

Lithium sulfide (Li 2 S) is a critical material for clean energy technologies, i.e., the cathode material in lithium-sulfur batteries and the raw material for making sulfide solid electrolytes in all-solid-state batteries. However, its practical application at a large scale is hindered by its industrial production method of reducing lithium sulfate with carbon materials at high temperatures, which emits carbon dioxide and is time-consuming. We hereby report a method of synthesizing Li 2 S by thermally reducing lithium sulfate with aluminum. Compared with the carbothermal method, this aluminothermal approach has several advantages, such as operation at lower temperatures, completion in minutes, no emission of greenhouse gases, and valuable byproducts of aluminum oxide (Al 2 O 3 ). The home-made Li 2 S demonstrates competitive performance in battery tests versus the commercial counterpart. Moreover, using the byproduct Al 2 O 3 to coat the cathode side of the separator can enhance the battery's capacity without influencing its rate capability. Thus, this "one stone two birds" method has great potential for practical applications of developing Li-S batteries.

Striga asiatica (L.) Kuntze 1891 is a hemiparasitic plant native to Asia and Africa. It is invasive and causes yield losses in crops such as corn, rice and sorghum. Lack of chloroplast genomic data has limited research into its obligate parasitic lifestyle. In this study, the complete chloroplast genome of Striga asiatica was sequenced and characterized. It is a quadripartite structure with a total length of 191,085 bp and a GC content of 37.86%. It has a large single copy region (LSC) of 51,406 bp, a small single copy region (SSC) of 273 bp, and two copies of the reverse repeat sequence (IRA and IRB) of 69,703 bp. A total of 122 protein-coding genes, 8 rRNA genes, and 44 tRNA genes were annotated in the chloroplast genome. There were a lot of ndh gene deletions and pseudogenizations in this chloroplast genome. For example, ndh A, D, E, H, I, and K were all pseudogenes because they were missing the 5' end start codon. ndh B, C, and J had shorter gene lengths than their homologs, and ndh F and ndh G were missing genes. The phylogenetic tree reveals that all Striga species form a clade, and a bootstrap value of 100 indicates that S. asiatica is closely related to Striga hermonthica and Striga sepera . The comprehensive chloroplast genomic resource of S. asiatica would assist researchers in comprehending hemiparasitic mechanisms, molecular markers, and evolutionary patterns of the genus  Striga ., Competing Interests: No potential conflict of interest was reported by the author(s)., (© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.)

Microbes are accepted as the foremost drivers of the rhizosphere ecology that influences plant health in direct or indirect ways. In recent years, the rapid development of gene sequencing technology has greatly facilitated the study of plant microbiome structure and function, and various plant-associated microbiomes have been categorized. Additionally, there is growing research interest in plant-disease-related microbes, and some specific microflora beneficial to plant health have been identified. This Review discusses the plant-associated microbiome's biological control pathways and functions to modulate plant defense against pathogens. How do plant microbiomes enhance plant resistance? How does the plant core microbiome-associated synthetic microbial community (SynCom) improve plant health? This Review further points out the primary need to develop smart agriculture practices using SynComs against plant diseases. Finally, this Review provides ideas for future opportunities in plant disease control and mining new microbial resources.

Bletilla striata (Thunb.) Rchb. f. (Orchidaceae) is an essential traditional Chinese medicinal plant used to treat hemorrhage, swelling, inflammation, ulcers, and pulmonary diseases (Xu et al. 2019). In April of 2020, an unknown leaf spot disease was observed on B. striata in a plantation (~ 0.2 ha) in Nanning, Guangxi province, China. Disease incidence was estimated at approximately 25% ( n = 150 plants). The initial symptoms were small brown circular spots, which then expanded into reddish to brown, circular to irregular lesions 5-10 mm in diameter. As the disease developed, the whole leaf became densely covered with lesions. Finally, the lesions coalesced, killing the leaf and resulting in defoliation. To isolate the causal agent, six symptomatic leaves were collected from individual plants. Small pieces (~ 5 mm 2 ) were cut from the margin of the necrotic lesions ( n = 18), disinfected in 1% NaOCl for 2 min before rinsing three times in sterile water, and placed on potato dextrose agar (PDA) at 26°C for 3 days. Hyphal tips from the resulting cultures were transferred to PDA to obtain pure cultures. Fifteen isolates were obtained, of which twelve isolates exhibited similar morphology. Colonies on PDA were initially white, then turned dark gray after 7 days. Pycnidia were produced on the surface of PDA after 50 days. Conidia were hyaline, aseptate, ellipsoidal to fusiform, externally smooth, thin-walled, and measuring 11.5 to 15.2 × 4.9 to 6.1 μm (mean ± SD: 13.4 ± 1.0 × 5.4 ± 0.3 μm, n = 60). Morphological features were similar to N. parvum (Phillips et al. 2013). For further molecular identification, the internal transcribed spacer (ITS) region, partial translational elongation factor subunit 1-α ( EF-1α ), β-tubulin ( TUB2 ) genes were amplified and sequenced using the primer pairs ITS1/ITS4 (White et al. 1990), EF1-728F (Carbone and Kohn 1999)/EF-2 (O'Donnell et al. 1998), and Bt2a/Bt2b (Glass and Donaldson 1995), respectively. Sequences of the two isolates BJ-111.1 and BJ-111.4 were deposited in NCBI GenBank under the following accession numbers: OM348509-10, OM397537-40. The obtained ITS, EF1-α, and TUB2 sequences showed 99% (514/516, and 513/516 bp), 99% (275/276, and 274/275 bp), and 99% (429/431, and 429/430 bp) homology with several GenBank sequences of the ex-type strain N. parvum CMW 9081 (AY236943, AY236888, and AY236917, respectively) (Zhang et al. 2017). In addition, a phylogenetic analysis confirmed the isolates as N. parvum . Therefore, the isolates were identified as N. parvum based on morphological and molecular evidence. Furthermore, pathogenicity tests were carried out on 1.5-year-old B. striata plants. Healthy leaves on six plants (1 leaf per plant) were inoculated with a 10-μl droplet of conidial suspensions (106 conidia/mL). Three plants treated with sterile water served as the control. All plants were covered with transparent plastic bags and incubated in a greenhouse at 26°C with a 12 h photoperiod. Six days post-inoculation, the inoculated leaves showed leaf spot symptoms, while the control plants remained healthy. The experiments repeated three times showed similar results. Finally, N. parvum was consistently re-isolated from the infected leaves and confirmed by morphology and sequencing, fulfilling Koch's postulates. No fungus was isolated from the controls. To our knowledge, this is the first report of N. parvum causing leaf spot of B. striata worldwide. This result will help develop disease management strategies against this pathogen.

Li 6 PS 5 Cl is an extensively studied sulfide-solid-electrolyte for developing all-solid-state lithium batteries. However, its practical application is hindered by the high cost of its raw material lithium sulfide (Li 2 S), the difficulty in its massive production, and its substandard performance. Herein we report an economically viable and scalable method, denoted as "de novo liquid phase method", which enables in synthesizing high-performance Li 6 PS 5 Cl without using commercial Li 2 S but instead in situ making Li 2 S from cheap materials of lithium chloride (LiCl) and sodium sulfide. LiCl, a raw material needed for making both Li 2 S and Li 6 PS 5 Cl, can be added at a full-scale in the beginning and unrequired to separate when making the intermediate Li 3 PS 4 . Such a consecutive feature makes this method time-efficient; and the excess amount of LiCl in the step of making Li 2 S also facilitates removing the byproduct of sodium chloride via the common ion effect. The materials cost of this method for Li 6 PS 5 Cl is ∼ $55/kg, comparable with the practical need of $50/kg. Moreover, the obtained Li 6 PS 5 Cl shows high ionic conductivity and outstanding cyclability in full battery tests, that is, ∼2 mS/cm and >99.8% retention for 400+ cycles at 1 C, respectively. Thus, this innovative method is expected to pave the way to develop practical sulfide-solid-electrolytes for all-solid-state lithium batteries.

We report a synthesis of lithium sulfide, the cost-determining material for making sulphide solid electrolytes (SSEs), via spontaneous metathesis reactions between lithium salts (halides and nitrate) and sodium sulfide. This innovative method is economical, scalable and green. It will pave the way to developing practical SSE-based solid-state lithium batteries.

Background: Miscanthus  ×  giganteus is widely recognized as a promising lignocellulosic biomass crop due to its advantages of high biomass production, low environmental impacts, and the potential to be cultivated on marginal land. However, the high costs of bioethanol production still limit the current commercialization of lignocellulosic bioethanol. The lignin in the cell wall and its by-products released in the pretreatment step is the main component inhibiting the enzymatic reactions in the saccharification and fermentation processes. Hence, genetic modification of the genes involved in lignin biosynthesis could be a feasible strategy to overcome this barrier by manipulating the lignin content and composition of M . ×  giganteus . For this purpose, the essential knowledge of these genes and understanding the underlying regulatory mechanisms in M . ×  giganteus is required., Results: In this study, MgPAL1 , MgPAL5 , Mg4CL1 , Mg4CL3 , MgHCT1 , MgHCT2 , MgC3'H1 , MgCCoAOMT1 , MgCCoAOMT3 , MgCCR1 , MgCCR2 , MgF5H , MgCOMT , and MgCAD were identified as the major monolignol biosynthetic genes in M . ×  giganteus based on genetic and transcriptional evidence. Among them, 12 genes were cloned and sequenced. By combining transcription factor binding site prediction and expression correlation analysis, MYB46, MYB61, MYB63, WRKY24, WRKY35, WRKY12, ERF021, ERF058, and ERF017 were inferred to regulate the expression of these genes directly. On the basis of these results, an integrated model was summarized to depict the monolignol biosynthesis pathway and the underlying regulatory mechanism in M . ×  giganteus ., Conclusions: This study provides a list of potential gene targets for genetic improvement of lignocellulosic biomass quality of M . ×  giganteus , and reveals the genetic, transcriptional, and regulatory landscape of the monolignol biosynthesis pathway in M . ×  giganteus ., Competing Interests: Competing interestsThe authors declare that they have no competing interests., (© The Author(s) 2020.)

In the era of opioid abuse epidemics, there is an increased demand for understanding how opioid receptors can be allosterically modulated to guide the development of more effective and safer opioid therapies. Among the modulators of the μ-opioid (MOP) receptor, which is the pharmacological target for the majority of clinically used opioid drugs, are monovalent and divalent cations. Specifically, the monovalent sodium cation (Na + ) has been known for decades to affect MOP receptor signaling by reducing agonist binding, whereas the divalent magnesium cation (Mg 2+ ) has been shown to have the opposite effect, notwithstanding the presence of sodium chloride. Although ultra-high-resolution opioid receptor crystal structures have revealed a specific Na + binding site and molecular dynamics (MD) simulation studies have supported the idea that this monovalent ion reduces agonist binding by stabilizing the receptor inactive state, the putative binding site of Mg 2+ on the MOP receptor, as well as the molecular determinants responsible for its positive allosteric modulation of the receptor, are unknown. In this work, we carried out tens of microseconds of all-atom MD simulations to investigate the simultaneous binding of Mg 2+ and Na + cations to inactive and active crystal structures of the MOP receptor embedded in an explicit lipid-water environment and confirmed adequate sampling of Mg 2+ ion binding with a grand canonical Monte Carlo MD method. Analyses of these simulations shed light on 1) the preferred binding sites of Mg 2+ on the MOP receptor, 2) details of the competition between Mg 2+ and Na + cations for specific sites, 3) estimates of binding affinities, and 4) testable hypotheses of the molecular mechanism underlying the positive allosteric modulation of the MOP receptor by the Mg 2+ cation., (Copyright © 2019 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

We revealed the potential biomarker and pathway of gelanxinning capsule on rat model with coronary heart disease, which aims to clarify holistic therapeutic effect and predict quality-markers of gelanxinning capsule. Ultra-high performance liquid chromatography coupled with mass spectrometry based on metabolomics technique was used to find the biomarkers and related metabolic pathways of coronary heart disease model, which evaluates the intervention effect of gelanxinning capsule. Using serum pharmacochemistry of traditional Chinese medicine and Pearson correlation analysis, effective ingredients in serum is analyzed to characterize the activity of gelanxinning capsule on coronary heart disease under valid state. A total of 20 biomarkers from coronary heart disease were identified and 12 of them were regulated by gelanxinning capsule treatment, which is mainly involved in sphingolipid metabolism and glycerophospholipid metabolism. With the high sensitivity liquid chromatography coupled with mass spectrometry technology, a total of 46 compounds from gelanxinning capsule were identified in vitro and 25 of them were absorbed in blood. The correlation analysis of serum biomarkers and absorbed components was used to find 11 compounds as quality-markers to be responsible for the efficacy of gelanxinning capsule. This strategy was successfully applied to screening of potential mechanism and quality-markers from herbal medicine., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Sodium ions have long been known to reduce the binding of agonists in many class-A GPCRs while having little effect on antagonist binding. Here, using long-time scale classical all-atom molecular dynamics simulations, we explore, in atomic detail, the motion of sodium ions within the ligand-binding pocket of the A 2A adenosine receptor (A2A-AR) both in the presence and absence of ligands and in the active and inactive state. We identify novel secondary ion binding sites within the pocket and find that the types of ion motions within the pocket are highly dependent on the presence and type of ligand within the pocket. Our results provide a first step toward developing a molecular understanding of the impact of sodium ions on class-A GPCRs.

Fracture characterization is necessary to evaluate fracturing operations and forecast well performance. However, it is challenging to quantitatively characterize the complex fracture network in shale gas reservoirs because of the unknown density and reactivation of natural fractures. The flowback water transients can provide useful information about the complexity of the fracture network after the fracturing operations. In this paper, a mathematical model for modeling fracturing fluid flowback of hydraulically fractured shale gas wells is established. This proposed model characterizes the flow of water and gas in a hydraulic fracture-induced natural fracture-shale matrix system. Hydraulic, capillary, and osmotic convections; gas adsorption; and natural fracture closure are considered in this model. Flowback simulation of a hydraulically fractured shale gas well is conducted using the developed numerical simulator, and the water/gas transients between hydraulic fractures, natural fractures, and matrix are obtained. Finally, two field cases from the Longmaxi Formation, Southern Sichuan Basin, China, are used for comparison of the flowback data with the model results. The good match of the two water transients provides a group of fracture network parameters, that is, the effective length and conductivity of main hydraulic fractures and the density of induced natural fractures. The proposed model for describing the flowback process and its meaningful relationship with the fracture-network complexity provides an alternative approach for post-stimulation evaluation., Competing Interests: The authors declare no competing financial interest.

The differential modulation of agonist and antagonist binding to opioid receptors (ORs) by sodium (Na+) has been known for decades. To shed light on the molecular determinants, thermodynamics, and kinetics of Na+ translocation through the μ-OR (MOR), we used a multi-ensemble Markov model framework combining equilibrium and non-equilibrium atomistic molecular dynamics simulations of Na+ binding to MOR active or inactive crystal structures embedded in an explicit lipid bilayer. We identify an energetically favorable, continuous ion pathway through the MOR active conformation only, and provide, for the first time: i) estimates of the energy differences and required timescales of Na+ translocation in inactive and active MORs, ii) estimates of Na+-induced changes to agonist binding validated by radioligand measurements, and iii) testable hypotheses of molecular determinants and correlated motions involved in this translocation, which are likely to play a key role in MOR signaling., Competing Interests: The authors have declared that no competing interests exist.

Neutrons scatter quasielastically from stochastic, diffusive processes, such as overdamped vibrations, localized diffusion and transitions between energy minima. In biological systems, such as proteins and membranes, these relaxation processes are of considerable physical interest. We review here recent methodological advances and applications of quasielastic neutron scattering (QENS) in biology, concentrating on the role of molecular dynamics simulation in generating data with which neutron profiles can be unambiguously interpreted. We examine the use of massively-parallel computers in calculating scattering functions, and the application of Markov state modeling. The decomposition of MD-derived neutron dynamic susceptibilities is described, and the use of this in combination with NMR spectroscopy. We discuss dynamics at very long times, including approximations to the infinite time mean-square displacement and nonequilibrium aspects of single-protein dynamics. Finally, we examine how neutron scattering and MD can be combined to provide information on lipid nanodomains. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo., (Copyright © 2016 Elsevier B.V. All rights reserved.)

The genome sizes of five Miscanthus species, including 79 accessions of M. lutarioriparius, 8 of M. floridulus, 6 of M. sacchariflorus, 7 of M. sinensis, and 4 of M. × giganteus were examined using flow cytometry. The overall average nuclear DNA content were 4.256 ± 0.6 pg/2C in M. lutarioriparius, 5.175 ± 0.3 pg/2C in M. floridulus, 3.956 ± 0.2 pg/2C in M. sacchariflorus, 5.272 ± 0.2 pg/2C in M. sinensis, and 6.932 ± 0.1 pg/2C in M. × giganteus. Interspecific variation was found at the diploid level, suggesting that DNA content might be a parameter that can be used to differentiate the species. Tetraploid populations were found in M. lutarioriparius, M. sacchariflorus, and M. sinensis, and their DNA content were 8.34 ± 1.2, 8.52, and 8.355 pg, respectively. The association between the DNA content of M. lutarioriparius, collected from representative ranges across the Yangtze River, and its geographic distribution was statistically analyzed. A consistent pattern of DNA content variation in 79 M. lutarioriparius accessions across its entire geographic range was found in this study. Along the Yangtze River, the DNA content of M. lutarioriparius tended to increase from the upstream to the downstream areas, and almost all tetraploids gathered in the upstream area extended to coastal regions.

NMR spectroscopy experiments and molecular dynamics simulations were performed to describe the dynamic properties of the aminoglycoside acetyltransferase (3)-IIIb (AAC) in its apo and coenzyme A (CoASH) bound forms. The (15)N-(1)H HSQC spectra indicate a partial structural change and coupling of the CoASH binding site with another region in the protein upon the CoASH titration into the apo enzyme. Molecular dynamics simulations indicate a significant structural and dynamic variation of the long loop in the antibiotic binding domain in the form of a relatively slow (250 ns), concerted opening motion in the CoASH-enzyme complex and that binding of the CoASH increases the structural flexibility of the loop, leading to an interchange between several similar equally populated conformations.

The electric field dependence of the structure and dynamics of water at 77 K, i.e., below the glass transition temperature (136 K), is investigated using molecular dynamics simulations. Transitions are found at two critical field strengths, denoted E(1) and E(2). The transition around E(1)≈3.5 V/nm is characterized by the onset of significant structural disorder, a rapid increase in the orientational polarization, and a maximum in the dynamical fluctuations. At E(2)≈40 V/nm, the system crystallizes in discrete steps into a body-centered-cubic unit cell that minimizes the potential energy by simultaneous superpolarization of the water molecular dipoles and maximization of the intermolecular hydrogen bonds. The stepwise and discontinuous increase of the orientational polarization with the increasing electric field indicates that the dipole relaxation in the electric field is highly cooperative., (© 2011 American Institute of Physics)