Chiral ligands and photothermal synergistic effects of inorganic nanoparticles for bacteria-killing.

As the drawbacks of antibiotics in treating bacterial infections emerged, physical methods such as near-infrared-activated (NIR-activated) bacterial killing, have attracted great interests for their advantages of no resistance, short action time and few side effects. In this manuscript, NIR-activated bacteria-killing performance of chiral copper sulphide nanoparticles (L-/d-CuS NPs) was investigated using linearly polarized light (LPL) and circularly polarized light (CPL) as illumination sources, respectively. Chiral CuS NPs showed enhanced NIR-activated bacteria-killing effect compared with achiral CuS NPs under the same conditions. Moreover, these chiral CuS NPs showed obvious chirality-related antibacterial effect: the bacterial killing was more efficient under CPL activation, and L- and d-CuS NPs had higher antibacterial efficiency under left circularly polarized light (LCPL) and right circularly polarized light (RCPL), respectively. The possible mechanism of bacteria-killing performance for chiral CuS NPs was discussed in detailed. Photothermal bacteria-killing tests of chiral CuS NPs "sealed" in polydimethylsiloxane (PDMS) demonstrated the individual influence of photothermal effect. These observations in this paper could provide ideas for the potential applications of chiral nanostructures with enhanced photothermal effect in efficient bacterial killing.

Specific metabolic and cellular mechanisms of the vegetative desiccation tolerance in resurrection plants for adaptation to extreme dryness.

MAIN CONCLUSION: Substantial advancements have been made in our comprehension of vegetative desiccation tolerance in resurrection plants, and further research is still warranted to elucidate the mechanisms governing distinct cellular adaptations. Resurrection plants are commonly referred to as a small group of extremophile vascular plants that exhibit vegetative desiccation tolerance (VDT), meaning that their vegetative tissues can survive extreme drought stress (> 90% water loss) and subsequently recover rapidly upon rehydration. In contrast to most vascular plants, which typically employ water-saving strategies to resist partial water loss and optimize water absorption and utilization to a limited extent under moderate drought stress, ultimately succumbing to cell death when confronted with severe and extreme drought conditions, resurrection plants have evolved unique mechanisms of VDT, enabling them to maintain viability even in the absence of water for extended periods, permitting them to rejuvenate without harm upon water contact. Understanding the mechanisms associated with VDT in resurrection plants holds the promise of expanding our understanding of how plants adapt to exceedingly arid environments, a phenomenon increasingly prevalent due to global warming. This review offers an updated and comprehensive overview of recent advances in VDT within resurrection plants, with particular emphasis on elucidating the metabolic and cellular adaptations during desiccation, including the intricate processes of cell wall folding and the prevention of cell death. Furthermore, this review highlights existing unanswered questions in the field, suggests potential avenues for further research to gain deeper insights into the remarkable VDT adaptations observed in resurrection plants, and highlights the potential application of VDT-derived techniques in crop breeding to enhance tolerance to extreme drought stress.

Functional Characterization of Pheromone Receptors in the Beet Webworm, Loxostege sticticalis (Lepidoptera: Pyralidae).

Lepidopteran insects mainly rely on sex pheromones to complete sexual communications. Pheromone receptors (PRs) are expressed on the olfactory receptor neurons (ORNs) of the sensilla trichodea and play an essential role in sexual communication. Despite extensive investigations into the mechanisms of peripheral recognition of sex pheromones in Lepidoptera, knowledge about these mechanisms in L. sticticalis remains limited. In this study, five candidate LstiPRs were analyzed in a phylogenetic tree with those of other Lepidopteran insects. Electroantennography (EAG) assays showed that the major sex pheromone component E11-14:OAc elicited a stronger antennal response than other compounds in male moths. Moreover, two types of neurons in sensilla trichodea were classified by single sensillum recordings, of which the "a" neuron specifically responded to E11-14:OAc. Five candidate PRs were functionally assayed by the heterologous expression system of Xenopus oocytes, and LstiPR2 responded to the major sex pheromone E11-14:OAc. Our findings suggest that LstiPR2 is a PR sensitive to L. sticticalis's major sex pheromone compound, E11-14:OAc. Furthermore, this study offers valuable insights into the sexual communication behavior of L. sticticalis, forming a foundation for further analysis of the species' central nervous system.

Chromosome-scale genome assembly and insights into the metabolome and gene regulation of leaf color transition in an important oak species, Quercus dentata.

Quercus dentata Thunb., a dominant forest tree species in northern China, has significant ecological and ornamental value due to its adaptability and beautiful autumn coloration, with color changes from green to yellow into red resulting from the autumnal shifts in leaf pigmentation. However, the key genes and molecular regulatory mechanisms for leaf color transition remain to be investigated. First, we presented a high-quality chromosome-scale assembly for Q. dentata. This 893.54 Mb sized genome (contig N50 = 4.21 Mb, scaffold N50 = 75.55 Mb; 2n = 24) harbors 31 584 protein-coding genes. Second, our metabolome analyses uncovered pelargonidin-3-O-glucoside, cyanidin-3-O-arabinoside, and cyanidin-3-O-glucoside as the main pigments involved in leaf color transition. Third, gene co-expression further identified the MYB-bHLH-WD40 (MBW) transcription activation complex as central to anthocyanin biosynthesis regulation. Notably, transcription factor (TF) QdNAC (QD08G038820) was highly co-expressed with this MBW complex and may regulate anthocyanin accumulation and chlorophyll degradation during leaf senescence through direct interaction with another TF, QdMYB (QD01G020890), as revealed by our further protein-protein and DNA-protein interaction assays. Our high-quality genome assembly, metabolome, and transcriptome resources further enrich Quercus genomics and will facilitate upcoming exploration of ornamental values and environmental adaptability in this important genus.

Genomics assisted functional characterization of Bacillus velezensis E as a biocontrol and growth promoting bacterium for lily.

Lily (Lilium spp.) is one of the most famous ornamental flowers globally. Lily basal rot (also known as root rot or stem rot) and lily gray mold have seriously affected the yield and quality of lily, resulting in huge economic losses. In this study, bacterial strain E was isolated from a continuous lily cropping field. Strain E displayed high control efficiency against lily basal rot and gray mold, caused by Fusarium oxysporum and Botrytis cinerea respectively, and promoted the occurrence of scale bulblets. Strain E displayed strong inhibitory effects against several other plant pathogenic fungi and two pathogenic bacteria in dual culture and disc diffusion assays, respectively. Whole genome sequencing revealed that strain E contained a 3,929,247 bp circular chromosome with 4,056 protein-coding genes and an average GC content of 47.32%. Strain E was classified as Bacillus velezensis using genome-based phylogenetic analysis and average nucleotide identity and digital DNA-DNA hybridization analyses. A total of 86 genes and 13 secondary metabolite biosynthetic gene clusters involved in antifungal and antibacterial activity, plant growth promotion, colonization, nutrient uptake and availability were identified in the genome of strain E. In vitro biochemical assays showed that strain E produced siderophores, proteases, cellulases, biofilms, antifungal and antibacterial substances, and exhibited organic phosphate solubilization and swimming and swarming motility, which were consistent with the results of the genome analysis. Colonization analysis showed that strain E could colonize the root of the lily, but not the leaf. Overall, these results demonstrate that B. velezensis strain E can be used as a potential biofertilizer and biocontrol agent for lily production.

Transcriptome analysis identifies key gene LiMYB305 involved in monoterpene biosynthesis in Lilium 'Siberia'.

Lilium is a popular cut flower that is highly favored by consumers due to its snowy white color and strong fragrance, which originates from the release of monoterpenes. However, the underlying molecular mechanism of monoterpene synthesis remains poorly understood. In this study, the content of three main monoterpenes (linalool, ocimene, and myrcene) was examined in Lilium 'Siberia', and RNA sequencing of the 11 stages of flower development was conducted. The biosynthesis of the three monoterpenes increased with flower development, reaching their peak levels at the full flowering stage. Transcriptome data revealed 257,140 unigenes, with an average size of 794 bp, from which 43,934 differentially expressed genes were identified and enriched in the KEGG pathways partly involved in plant hormone signal transduction and monoterpenoid biosynthesis. Furthermore, the essential factor LiMYB305 was identified by WGCNA after the release of the flower fragrance. The transient silencing of LiMYB305 in petals using VIGS technology showed that the mRNA expression levels of LiLiS, LiOcS, and LiMyS were significantly downregulated and that the release of linalool, ocimene, and myrcene had decreased significantly. Y1H, LUC, and EMSA experiments revealed that LiMYB305 directly bound and activated the LiOcS promoter to increase the synthesis of monoterpenes. Taken together, these results provide insight into the molecular mechanism of monoterpene synthesis and provide valuable information to investigate the formation of the flower fragrance in Lilium.

Theoretical study on thermal decomposition mechanism of 1-nitroso-2-naphthol.

1-nitroso-2-naphthol has thermal instability of thermal decomposition, spontaneous combustion and even explosion. Its thermal decomposition characteristics were tested by synchronous thermal analyzer (TGA/DSC); The activation energy of the thermal decomposition process was calculated by Kissinger method; The infrared absorption characteristic spectra of the gas products produced in the thermal decomposition process were measured by TGA/DSC-FTIR, and the thermal decomposition reaction process was speculated. The results show that the initial temperature (Tonset) of TGA exothermic decomposition of 1-nitroso-2 naphthol is between 129.01 and 155.69 °C, and the faster the heating rate(ß), the higher the Tonset, but the faster the thermal decomposition rate, the greater the heat release and the worse the thermal stability. The activation energy (E) of the thermal decomposition process is 83.323 kJ/mol calculated by Kissinger method. The dynamic test results of TGA/DSC-FTIR show that the main reaction of 1-nitroso-2 naphthol during heating is intermolecular dehydration to form ether, and the secondary reaction is decomposition into aliphatic nitro compounds, carbonyl compounds and amines. Sodium hydroxide will reduce the thermal stability of 1-nitroso-2 naphthol. After adding sodium hydroxide, the thermal decomposition process of 1-nitroso-2 naphthol has changed. The main reaction is that 1-nitroso-2-naphthol reacts with sodium hydroxide to produce sodium nitrophenol, which is further decomposed into aliphatic nitro compounds. The research results have guiding significance for finding the reasonable conditions and temperature of 1-nitroso-2 naphthol during storage and transportation.

Compute-in-Memory for Numerical Computations.

In recent years, compute-in-memory (CIM) has been extensively studied to improve the energy efficiency of computing by reducing data movement. At present, CIM is frequently used in data-intensive computing. Data-intensive computing applications, such as all kinds of neural networks (NNs) in machine learning (ML), are regarded as 'soft' computing tasks. The 'soft' computing tasks are computations that can tolerate low computing precision with little accuracy degradation. However, 'hard' tasks aimed at numerical computations require high-precision computing and are also accompanied by energy efficiency problems. Numerical computations exist in lots of applications, including partial differential equations (PDEs) and large-scale matrix multiplication. Therefore, it is necessary to study CIM for numerical computations. This article reviews the recent developments of CIM for numerical computations. The different kinds of numerical methods solving partial differential equations and the transformation of matrixes are deduced in detail. This paper also discusses the iterative computation of a large-scale matrix, which tremendously affects the efficiency of numerical computations. The working procedure of the ReRAM-based partial differential equation solver is emphatically introduced. Moreover, other PDEs solvers, and other research about CIM for numerical computations, are also summarized. Finally, prospects and the future of CIM for numerical computations with high accuracy are discussed.

Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24.

CRISPR-Cas systems are prokaryotic adaptive immune systems and phages use anti-CRISPR proteins (Acrs) to counteract these systems. Here, we report the structures of AcrIF24 and its complex with the crRNA-guided surveillance (Csy) complex. The HTH motif of AcrIF24 can bind the Acr promoter region and repress its transcription, suggesting its role as an Aca gene in self-regulation. AcrIF24 forms a homodimer and further induces dimerization of the Csy complex. Apart from blocking the hybridization of target DNA to the crRNA, AcrIF24 also induces the binding of non-sequence-specific dsDNA to the Csy complex, similar to AcrIF9, although this binding seems to play a minor role in AcrIF24 inhibitory capacity. Further structural and biochemical studies of the Csy-AcrIF24-dsDNA complexes and of AcrIF24 mutants reveal that the HTH motif of AcrIF24 and the PAM recognition loop of the Csy complex are structural elements essential for this non-specific dsDNA binding. Moreover, AcrIF24 and AcrIF9 display distinct characteristics in inducing non-specific DNA binding. Together, our findings highlight a multifunctional Acr and suggest potential wide distribution of Acr-induced non-specific DNA binding.

Nomenclatural and taxonomic notes on Rubusdavidianus Kuntze and R.viburnifolius Franch.

Critical examinations of specimens, with literature reviews, have shown that Rubusdavidianus is conspecific with R.lambertianus. Therefore, we treat R.davidianus as a new synonym within Rubus. We propose a new name, Rubusloirensis Ti R. Huang nom. nov. to replace the later homonym of R.pycnanthus Genev. Additionally, lectotypification of three names, R.davidianus Kuntze, R.malifolius Focke and R.viburnifolius Franch., are designated here after examination of previous works.

Detection of ryanodine receptor G4911E and I4754M mutation sites and analysis of binding modes of diamide insecticides with RyR on Galeruca daurica (Coleoptera: Chrysomelidae).

In recent years, the leaf beetle Galeruca daurica has broken out in the northern grasslands of Inner Mongolia, its management still mainly depends on chemical control using traditional insecticides or with novel action. The study was aim to identify mutation locus associated with resistance to diamide insecticides in field population of G. daurica, to provide a reference for rational selection of insecticides and to avoid the rapid resistance development to diamide insecticides. We cloned the full length of the ryanodine receptor gene of G. daurica (GdRyR), constructed 3D model and transmembrane regions by homologous modeling based on deduced amino acid sequence. Two potential mutation loci (Gly4911Glu and Ile4754Met) and allelic mutation frequencies were detected in individuals of G. daurica. In addition, their binding patterns to two diamide insecticides (chlorantraniliprole, cyantraniliprole) were analyzed separately using a molecular docking method. The full-length cDNA sequence of GdRyR (GenBank accession number: OP828593) was obtained by splicing and assembling, which is 15,399 bp in length and encodes 5,133 amino acids. The amino acid similarity of GdRyR with that of other Coleopteran insects were 86.70%-91.33%, which possessed the typical structural characteristics. An individual resistance allelic mutation frequency test on fifty field leaf beetles has identified 12% and 32% heterozygous individuals at two potential mutation loci Gly4911Glu and Ile4754Met, respectively. The affinity of the I4754M mutant model of GdRyR for chlorantraniliprole and cyantraniliprole was not significantly different from that of the wild type, and all had non-covalent interactions such as hydrogen bonding, hydrophobic interactions and π-cation interactions. However, the G4911E mutant model showed reduced affinity and reduced mode of action with two diamide insecticides, thus affecting the binding stability of the ryanodine receptor to the diamide insecticides. In conclusion, the G4911E mutation in GdRyR may be a potential mechanism for the development of resistance to diamide insecticides on G. daurica and should be a key concern for resistance risk assessment and reasonable applications of diamide insecticides for control in future. Moreover, this study could provide a reference for ryanodine receptor structure-based insecticides design.

Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR-Cas surveillance complex.

CRISPR-Cas systems are bacterial adaptive immune systems, and phages counteract these systems using many approaches such as producing anti-CRISPR (Acr) proteins. Here, we report the structures of both AcrIF14 and its complex with the crRNA-guided surveillance (Csy) complex. Our study demonstrates that apart from interacting with the Csy complex to block the hybridization of target DNA to the crRNA, AcrIF14 also endows the Csy complex with the ability to interact with non-sequence-specific dsDNA as AcrIF9 does. Further structural studies of the Csy-AcrIF14-dsDNA complex and biochemical studies uncover that the PAM recognition loop of the Cas8f subunit of the Csy complex and electropositive patches within the N-terminal domain of AcrIF14 are essential for the non-sequence-specific dsDNA binding to the Csy-AcrIF14 complex, which is different from the mechanism of AcrIF9. Our findings highlight the prevalence of Acr-induced non-specific DNA binding and shed light on future studies into the mechanisms of such Acr proteins.

Boosting chiral amplification in plasmon-coupled circular dichroism using discrete silver nanorods as amplifiers.

Remarkable chiral amplification in plasmon-coupled circular dichroism spectroscopy (CD) is demonstrated by using discrete Ag nanorods as amplifiers. An unprecedented CD enhancement factor of over 3000 times is achieved without resonant or near-resonant exciton-plasmon couplings.

Facile in-situ synthesis of heazlewoodite on nitrogen-doped reduced graphene oxide for enhanced sodium storage.

Nickel sulfide based anode materials, featuring rich types, high specific capacities and favorable conversion kinetics, have been proved to be promisingly applied in high-performance sodium-ion batteries (SIBs). Unfortunately, the poor electronic/ionic conductivity, together with the structure change induced degraded capacity upon cycling, restricts their further development. In this work, heazlewoodite nanoparticles decorated on nitrogen doped reduced graphene oxide (Ni3S2/NrGO) were fabricated via a facile combined approach with freeze-drying and subsequent in-situ sulfidation. In the obtained hybrid structure, the synergistic effect between Ni3S2 and NrGO endows the composite with highly conductive pathways, thus accelerating the charge transfer. Benefitting from the buffering matrix offered by NrGO as well as the tight combination between Ni3S2 and NrGO, this novel Ni3S2/NrGO demonstrates satisfying sodium storage performance, with a stable reversible capacity of 299.2 mAh g-1 up to 100 cycles (0.1 A g-1) and a high initial Coulombic efficiency of 76.8%. Importantly, the rational structure design and synthesis method, as well as the insights on the improved electrochemical performance reported in this work, should be helpful for the development of new-type host materials with high performance for SIBs.

Corrigendum: Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana.

[This corrects the article DOI: 10.3389/fpls.2020.00157.].

Atomic structure of human TOM core complex.

The translocase of the outer mitochondrial membrane (TOM) complex is the main entry gate for mitochondrial precursor proteins synthesized on cytosolic ribosomes. Here we report the single-particle cryo-electron microscopy (cryo-EM) structure of the dimeric human TOM core complex (TOM-CC). Two Tom40 ß-barrel proteins, connected by two Tom22 receptor subunits and one phospholipid, form the protein-conducting channels. The small Tom proteins Tom5, Tom6, and Tom7 surround the channel and have notable configurations. The distinct electrostatic features of the complex, including the pronounced negative interior and the positive regions at the periphery and center of the dimer on the intermembrane space (IMS) side, provide insight into the preprotein translocation mechanism. Further, two dimeric TOM complexes may associate to form tetramer in the shape of a parallelogram, offering a potential explanation into the unusual structural features of Tom subunits and a new perspective of viewing the import of mitochondrial proteins.

Crystal Structure of the Chloroplastic Glutamine Phosphoribosylpyrophosphate Amidotransferase GPRAT2 From Arabidopsis thaliana.

Chloroplastic glutamine phosphoribosylpyrophosphate amidotransferase (GPRATase) catalyzes the first committed step of de novo purine biosynthesis in Arabidopsis thaliana, and DAS734 is a direct and specific inhibitor of AtGPRAT, with phytotoxic effects similar to the leaf beaching phenotypes of known AtGPRAT genetic mutants, especially cia1 and atd2. However, the structure of AtGPRAT and the inhibition mode of DAS734 still remain poorly understood. In this study, we solved the structure of AtGPRAT2, which revealed structural differences between AtGPRAT2 and bacterial enzymes. Kinetics assay demonstrated that DAS734 behaves as a competitive inhibitor for the substrate phosphoribosyl pyrophosphate (PRPP) of AtGPRAT2. Docking studies showed that DAS734 forms electrostatic interactions with R264 and hydrophobic interactions with several residues, which was verified by binding assays. Collectively, our study provides important insights into the inhibition mechanism of DAS734 to AtGPRAT2 and sheds light on future studies into further development of more potent herbicides targeting Arabidopsis GPRATases.

Improving the limit of detection in portable luminescent assay readers through smart optical design.

Critical biomarkers of disease are increasingly being detected by point-of-care assays. Chemiluminescence (CL) and electrochemiluminescence (ECL) are often used in such assays due to their convenience and that they do not require light sources or other components that could complicate or add cost to the system. Reports of these assays often include readers built on a cellphone platform or constructed from low-cost components. However, the impact the optical design has on the limit of detection (LOD) in these systems remains unexamined. Here, we report a theoretical rubric to evaluate different optical designs in terms of maximizing the use of photons emitted from a CL or ECL assay to improve the LOD. We demonstrate that the majority of cellphone designs reported in the literature are not optimized, in part due to misunderstandings of the optical tradeoffs in collection systems, and in part due to limitations imposed on the designs arising from the use of a mobile phone with a very small lens aperture. Based on the theoretical rubric, we design a new portable reader built using off-the-shelf condenser optics, and demonstrate a nearly 10× performance enhancement compared to prior reports on an ECL assays running on a portable chip.

Transcriptome Sequencing Analysis Provides Insights Into the Response to Fusarium oxysporum in Lilium pumilum.

Lily basal rot, caused by Fusarium oxysporum f. sp. lilii, is one of the most serious diseases of lily. Although the lily germplasm which is resistant to F. oxysporum has been used in disease-resistant breeding, few studies on its molecular mechanism of disease resistance have been reported. To comprehensively study the mechanism of resistance to F. oxysporum, transcriptome sequencings of root tissues from Lilium pumilum inoculated with F. oxysporum or sterile water for 6, 12, or 24 h were performed. A total of 50 GB of data were obtained from the transcriptome sequencings of the 6 L. pumilum samples, and 217 098 Unigenes were obtained after the de novo assembly, of which 38.36% Unigenes were annotated. The sequencing results showed that the numbers of differentially expressed genes at 6, 12, and 24 h after inoculation compared with the control were 111, 254, and 2500, respectively. The functional enrichment analysis of the differentially expressed genes showed that several pathways were involved in responses of L. pumilum, mainly including starch and sucrose metabolism, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, vitamin B6 (VB6) biosynthesis, acid biosynthesis, proteasome, and ribosome. Transcription factor analysis revealed that the WRKY and ERF families played important roles in responses of L. pumilum to F. oxysporum. The results of this study elucidate the molecular responses to F. oxysporum in lily and lay a theoretical foundation for improving lily breeding and strategies for lily basal rot resistance.

Structural basis of ubiquitin modification by the Legionella effector SdeA.

Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.