Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.

Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.

A Natural Allele of a Transcription Factor in Rice Confers Broad-Spectrum Blast Resistance.

Rice feeds half the world's population, and rice blast is often a destructive disease that results in significant crop loss. Non-race-specific resistance has been more effective in controlling crop diseases than race-specific resistance because of its broad spectrum and durability. Through a genome-wide association study, we report the identification of a natural allele of a C2H2-type transcription factor in rice that confers non-race-specific resistance to blast. A survey of 3,000 sequenced rice genomes reveals that this allele exists in 10% of rice, suggesting that this favorable trait has been selected through breeding. This allele causes a single nucleotide change in the promoter of the bsr-d1 gene, which results in reduced expression of the gene through the binding of the repressive MYB transcription factor and, consequently, an inhibition of H2O2 degradation and enhanced disease resistance. Our discovery highlights this novel allele as a strategy for breeding durable resistance in rice.

Raman spectroscopy coupled with chemometrics for identification of adulteration and fraud in muscle foods: a review.

Muscle foods, valued for their significant nutrient content such as high-quality protein, vitamins, and minerals, are vulnerable to adulteration and fraud, stemming from dishonest vendor practices and insufficient market oversight. Traditional analytical methods, often limited to laboratory-scale., may not effectively detect adulteration and fraud in complex applications. Raman spectroscopy (RS), encompassing techniques like Surface-enhanced RS (SERS), Dispersive RS (DRS), Fourier transform RS (FTRS), Resonance Raman spectroscopy (RRS), and Spatially offset RS (SORS) combined with chemometrics, presents a potent approach for both qualitative and quantitative analysis of muscle food adulteration. This technology is characterized by its efficiency, rapidity, and noninvasive nature. This paper systematically summarizes and comparatively analyzes RS technology principles, emphasizing its practicality and efficacy in detecting muscle food adulteration and fraud when combined with chemometrics. The paper also discusses the existing challenges and future prospects in this field, providing essential insights for reviews and scientific research in related fields.

Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals.

The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.

Exogenous Indole-3-Acetic Acid Suppresses Rice Infection of Magnaporthe oryzae by Affecting Plant Resistance and Fungal Growth.

Auxin is an important phytohormone that regulates diverse biologic processes, including plant growth and immunity. Indole-3-acetic acid (IAA), known as one of the main forms of auxin, is able to activate plant immunity. However, it is unknown whether IAA enhances plant resistance and/or suppresses the growth of the fungal pathogen Magnaporthe oryzae. Here, we found that IAA could induce expression levels of pathogenesis-related genes to enhance disease resistance and could control the development of blast disease through inhibiting M. oryzae infection. Exogenous IAA suppressed mycelial growth and delayed spore germination by inhibiting fungal endogenous IAA biosynthesis and impairing redox homeostasis, respectively. When applied to a field test, two IAA analogues, 1-naphthaleneacetic acid and 2,4-dichlorophenoxy acetic acid, can effectively control rice blast disease. Our study advances the understanding of IAA in controlling rice blast disease through suppressing pathogen growth and enhancing plant resistance.

Accurate carbon storage estimation for the salt marsh ecosystem based on Bayesian maximum entropy approach - A case study for the Spartina alterniflora ecosystem.

The blue carbon ecosystem, including the salt marsh ecosystem, possesses a significant carbon sequestration potential. Therefore, accurately quantifying the carbon storage within such ecosystems is crucial for the adequate accounting of carbon sequestration. The present work chose a Spartina alterniflora ecosystem in the Xiaogan Island (China) as the study area (approximately 11 ha), and employed the Bayesian maximum entropy (BME) approach to assimilate both hard organic carbon (OC) data and soft OC data measured from 2 cm and 10 cm stratified samples. A 3-dimensional model was developed for space-time OC estimation purposes based on the sediment chronology results. The 10-fold BME cross validation results demonstrated a high estimation accuracy, with the R2, RMSE and MAE values equal to 0.8564, 0.1026 % and 0.0748 %, respectively. A noteworthy outcome was the BME-generated carbon storage density maps with 1 m spatial resolution. These maps revealed that the carbon storage density at the top 30 cm sediment depth in the stable zone (with elder stand age of S. alterniflora) was higher than that in the rapid expansion zone, i.e., 71.79 t/ha vs. 69.82 t/ha, respectively. Additionally, the study found that the averaged carbon burial rate and the total carbon storage at the top 30 cm sediment depth across the study area were 266 g C/m2/yr and 781.50 t, respectively. Lastly, the proposed BME-based framework of carbon storage estimation was found to be versatile and applicable to other blue carbon ecosystems. This approach can foster the development of a standardized carbon sink metrological methodology for diverse blue carbon ecosystems.

Developing active and intelligent biodegradable packaging from food waste and byproducts: A review of sources, properties, film production methods, and their application in food preservation.

Food waste and byproducts (FWBP) are a global issue impacting economies, resources, and health. Recycling and utilizing these wastes, due to processing and economic constraints, face various challenges. However, valuable components in food waste inspire efficient solutions like active intelligent packaging. Though research on this is booming, its material selectivity, effectiveness, and commercial viability require further analysis. This paper categorizes FWBP and explores their potential for producing packaging from both animal and plant perspectives. In addition, the preparation/fabrication methods of these films/coatings have also been summarized comprehensively, focusing on the advantages and disadvantages of these methods and their commercial adaptability. Finally, the functions of these films/coatings and their ultimate performance in protecting food (meat, dairy products, fruits, and vegetables) are also reviewed systematically. FWBP provide a variety of methods for the application of edible films, including being made into coatings, films, and fibers for food preservation, or extracting active substances directly or indirectly from them (in the form of encapsulation) and adding them to packaging to endow them with functions such as barrier, antibacterial, antioxidant, and pH response. In addition, the casting method is the most commonly used method for producing edible films, but more film production methods (extrusion, electrospinning, 3D printing) need to be tried to make up for the shortcomings of the current methods. Finally, researchers need to conduct more in-depth research on various active compounds from FWBP to achieve better application effects and commercial adaptability.

Total Syntheses of Polycyclic Diterpenes Phomopsene, Methyl Phomopsenonate, and iso-Phomopsene via Reorganization of C-C Single Bonds.

The first total syntheses of polycyclic diterpenes phomopsene (1), methyl phomopsenonate (2), and iso-phomopsene (3) have been accomplished through the unusual cascade reorganization of C-C single bonds. This approach features: (i) a synergistic Nazarov cyclization/double ring expansions in one-step, developed by authors, to rapid and stereospecific construction of the 5/5/5/5 tetraquinane scaffold bearing contiguous quaternary centers and (ii) a one-pot strategic ring expansion through Beckmann fragmentation/recombination to efficiently assemble the requisite 5/5/6/5 tetracyclic skeleton of the target molecules 1-3. This work enables us to determine that the correct structure of iso-phomopsene is, in fact, the C7 epimer of the originally assigned structure. Finally, the absolute configurations of three target molecules were confirmed through enantioselective synthesis.

Film Thickness Dependent Stability and Glass Transition Temperature of Polymer Films Produced by Physical Vapor Deposition.

We report measurements of the onset temperature of rejuvenation, T_{onset}, and the fictive temperature, T_{f}, for ultrathin stable polystyrene with thicknesses from 10 to 50 nm prepared by physical vapor deposition. We also measure the T_{g} of these glasses on the first cooling after rejuvenation as well as the density anomaly of the as-deposited material. Both the T_{g} in rejuvenated films and the T_{onset} in stable films decrease with decreasing film thickness. The T_{f} value increases for decreasing film thickness. The density increase typical of stable glasses also decreases with decreasing film thickness. Collectively, the results are consistent with a decrease in apparent T_{g} due to the existence of a mobile surface layer, as well as a decrease in the film stability as the thickness is decreased. The results provide the first self-consistent set of measurements of stability in ultrathin films of stable glass.

Surface and bulk relaxation of vapor-deposited polystyrene glasses.

We have studied the liquid-like response of the surface of vapor-deposited glassy films of polystyrene to the introduction of gold nanoparticles on the surface. The build-up of polymer material was measured as a function of time and temperature for both as-deposited films, as well as films that have been rejuvenated to become normal glasses cooled from the equilibrium liquid. The temporal evolution of the surface profile is well described by the characteristic power law of capillary-driven surface flows. In all cases, the surface evolution of the as-deposited films and the rejuvenated films is enhanced compared to bulk and is not easily distinguishable from each other. The temperature dependence of the measured relaxation times determined from the surface evolution is found to be quantitatively comparable to similar studies for high molecular weight spincast polystyrene. Comparisons to numerical solutions of the glassy thin film equation provide quantitative estimates of the surface mobility. For temperatures sufficiently close to the glass-transition temperature, particle embedding is also measured and used as a probe of bulk dynamics, and, in particular, bulk viscosity.

The PGS1 basic helix-loop-helix protein regulates Fl3 to impact seed growth and grain yield in cereals.

Plant transcription factors (TFs), such as basic helix-loop-helix (bHLH) and AT-rich zinc-binding proteins (PLATZ), play critical roles in regulating the expression of developmental genes in cereals. We identified the bHLH protein TaPGS1 (T. aestivum Positive Regulator of Grain Size 1) specifically expressed in the seeds at 5-20 days post-anthesis in wheat. TaPGS1 was ectopically overexpressed (OE) in wheat and rice, leading to increased grain weight (up to 13.81% in wheat and 18.55% in rice lines) and grain size. Carbohydrate and total protein levels also increased. Scanning electron microscopy results indicated that the starch granules in the endosperm of TaPGS1 OE wheat and rice lines were smaller and tightly embedded in a proteinaceous matrix. Furthermore, TaPGS1 was bound directly to the E-box motif at the promoter of the PLATZ TF genes TaFl3 and OsFl3 and positively regulated their expression in wheat and rice. In rice, the OsFl3 CRISPR/Cas9 knockout lines showed reduced average thousand-grain weight, grain width, and grain length in rice. Our results reveal that TaPGS1 functions as a valuable trait-associated gene for improving cereal grain yield.

Loss of Gn1a/OsCKX2 confers heavy-panicle rice with excellent lodging resistance.

Significant achievements have been made in breeding programs for the heavy-panicle-type (HPT) rice (Oryza sativa) in Southwest China. The HPT varieties now exhibit excellent lodging resistance, allowing them to overcome the greater pressures caused by heavy panicles. However, the genetic mechanism of this lodging resistance remains elusive. Here, we isolated a major quantitative trait locus, Panicle Neck Diameter 1 (PND1), and identified the causal gene as GRAIN NUMBER 1A/CYTOKININ OXIDASE 2 (Gn1A/OsCKX2). The null gn1a allele from rice line R498 (gn1aR498 ) improved lodging resistance through increasing the culm diameter and promoting crown root development. Loss-of-function of Gn1a/OsCKX2 led to cytokinin accumulation in the crown root tip and accelerated the development of adventitious roots. Gene pyramiding between the null gn1aR498 allele with two gain-of-function alleles, STRONG CULM 2 (SCM2) and SCM3, further improved lodging resistance. Moreover, Gn1a/OsCKX2 had minimal influence on overall rice quality. Our research thus highlights the distinct genetic components of lodging resistance of HPT varieties and provides a strategy for tailor-made crop improvement of both yield and lodging resistance in rice.

Ultrastable monodisperse polymer glass formed by physical vapour deposition.

Stable glasses prepared by vapour deposition are an analogue of glassy materials aged for geological timescales. The ability to prepare such materials allows the study of near-ideal glassy systems. We report the preparation and characterization of stable glasses of polymers prepared by physical vapour deposition. By controlling the substrate temperature, deposition rate and polydispersity, we prepared and characterized a variety of stable polymer glasses. These materials display the kinetic stability, low fictive temperatures and high-density characteristic of stable glasses. Extrapolation of the measured transformation times between the stable and normal glass provides estimates of the relaxation times of the equilibrium supercooled liquid at temperatures as much as 30 K below the glass transition temperature. These results demonstrate that polymer stable glasses are an exciting and powerful tool in the study of ultrastable glass and disordered materials in general.

Loss of function of a rice TPR-domain RNA-binding protein confers broad-spectrum disease resistance.

Crops carrying broad-spectrum resistance loci provide an effective strategy for controlling infectious disease because these loci typically confer resistance to diverse races of a pathogen or even multiple species of pathogens. Despite their importance, only a few crop broad-spectrum resistance loci have been reported. Here, we report the identification and characterization of the rice bsr-k1 (broad-spectrum resistance Kitaake-1) mutant, which confers broad-spectrum resistance against Magnaporthe oryzae and Xanthomonas oryzae pv oryzae with no major penalty on key agronomic traits. Map-based cloning reveals that Bsr-k1 encodes a tetratricopeptide repeats (TPRs)-containing protein, which binds to mRNAs of multiple OsPAL (OsPAL1-7) genes and promotes their turnover. Loss of function of the Bsr-k1 gene leads to accumulation of OsPAL1-7 mRNAs in the bsr-k1 mutant. Furthermore, overexpression of OsPAL1 in wild-type rice TP309 confers resistance to M. oryzae, supporting the role of OsPAL1 Our discovery of the bsr-k1 allele constitutes a significant conceptual advancement and provides a valuable tool for breeding broad-spectrum resistant rice.

Adaptive transgenerational effects remain significant.

The comment by Sánchez-Tójar et al. (2020, Ecol Lett) questioned the methodology, transparency and conclusion of our study (Ecol Lett, 22, 2019, 1976). The comment has overlooked important evolutionary assumptions in their reanalysis, and the issues raised were in fact dealt with through the peer-review process. Far from being biased, the key conclusion of our meta-analysis still stands; transgenerational effects are largely adaptive.

Sclerenchyma cell thickening through enhanced lignification induced by OsMYB30 prevents fungal penetration of rice leaves.

Broad-spectrum resistance is highly preferred in crop breeding programmes. Previously, we have reported the identification of the broad-spectrum resistance-Digu 1 (bsr-d1) allele from rice Digu. The bsr-d1 allele prevents activation of Bsr-d1 expression by Magnaporthe oryzae infection and degradation of H2 O2 by peroxidases, leading to resistance to M. oryzae. However, it remains unknown whether defence pathways other than H2 O2 burst and peroxidases contribute to the bsr-d1-mediated immunity. Blast resistance was determined in rice leaves by spray and punch inoculations. Target genes of OsMYB30 were identified by one-hybrid assays in yeast and electrophoretic mobility shift assay. Lignin content was measured by phloroglucinol-HCl staining, and acetyl bromide and thioacidolysis methods. Here, we report the involvement of the OsMYB30 gene in bsr-d1-mediated blast resistance. Expression of OsMYB30 was induced during M. oryzae infection or when Bsr-d1 was knocked out or downregulated, as occurs in bsr-d1 plants upon infection. We further found that OsMYB30 bound to and activated the promoters of 4-coumarate:coenzyme A ligase genes (Os4CL3 and Os4CL5) resulting in accumulation of lignin subunits G and S. This action led to obvious thickening of sclerenchyma cells near the epidermis, inhibiting M. oryzae penetration at the early stage of infection. Our study revealed novel components required for bsr-d1-mediated resistance and penetration-dependent immunity, and advanced our understanding of broad-spectrum disease resistance.

Crystallization and melting of highly monodisperse poly(ethylene-oxide).

We present a quantitative study of the crystallization and melting behaviours of highly monodisperse PEO oligomers, and compare to previous studies. Through evaporative purification, we were able to isolate low molecular weight PEO oligomers that are much more monodisperse than the as-purchased material (as measured by mass spectrometry). Crystal structure, crystal growth rate and melting temperatures were characterized. Melting temperatures of isolated fractions were described by the Gibbs-Thomson relation. We show that during crystallization the isolated fractions are able to form crystal lamellae not only with extended chains, but also with once-folded chains. This chain folding is unexpected for polymers with such short chain lengths. We use these samples to investigate the effects of polydispersity on crystal formation and chain folding, and discuss both qualitative and quantitative differences from previous studies on similar but more polydisperse small chains.

Rh(i)-Catalyzed enantioselective and scalable [4 + 2] cycloaddition of 1,3-dienes with dialkyl acetylenedicarboxylates.

An asymmetric intermolecular [4 + 2] cycloaddition of 1,3-dienes with dialkyl acetylenedicarboxylates, which was catalyzed by a rhodium(i)-chiral phosphoramidite complex, was developed. This protocol provided a highly enantioselective access to prepare carbonyl substituted cyclohexa-1,4-dienes with up to 96% yield and >99% ee. Notably, a cycloaddition on the 10 g scale gave the product in 92% yield and with 99% ee, which showed great potential for the scale-up synthesis of carbonyl substituted cyclohexa-1,4-dienes. In addition, oxidative aromatizations and hydrolysis of the products were also investigated.

Transgenerational effects benefit offspring across diverse environments: a meta-analysis in plants and animals.

The adaptive value of transgenerational effects (the ancestor environmental effects on offspring) in changing environments has received much attention in recent years, but the related empirical evidence remains equivocal. Here, we conducted a meta-analysis summarising 139 experimental studies in plants and animals with 1170 effect sizes to investigate the generality of transgenerational effects across taxa, traits, and environmental contexts. It was found that transgenerational effects generally enhanced offspring performance in response to both stressful and benign conditions. The strongest effects are in annual plants and invertebrates, whereas vertebrates appear to benefit mostly under benign conditions, and perennial plants show hardly any transgenerational responses at all. These differences among taxonomic/life-history groups possibly reflect that vertebrates can avoid stressful conditions through their mobility, and longer-lived plants have alternative strategies. In addition to environmental contexts and taxonomic/life-history groups, transgenerational effects also varied among traits and developmental stages of ancestors and offspring, but the effects were similarly strong across three generations of offspring. By way of a more comprehensive data set and a different effect size, our results differ from those of a recent meta-analysis, suggesting that transgenerational effects are widespread, strong and persistent and can substantially impact the responses of plants and animals to changing environments.

Influences of simulated gastrointestinal environment on physicochemical properties of gold nanoparticles and their implications on intestinal epithelial permeability.

Gold nanoparticles (Au NPs) hold great promise in food, industrial and biomedical applications due to their unique physicochemical properties. However, influences of the gastrointestinal tract (GIT), a likely route for Au NPs administration, on the physicochemical properties of Au NPs has been rarely evaluated. Here, we investigated the influence of GIT fluids on the physicochemical properties of Au NPs (5, 50, and 100 nm) and their implications on intestinal epithelial permeability in vitro. Au NPs aggregated in fasted gastric fluids and generated hydroxyl radicals in the presence of H2O2. Cell studies showed that GIT fluids incubation of Au NPs affected the cellular uptake of Au NPs but did not induce cytotoxicity or disturb the intestinal epithelial permeability.