BPB1 regulates rice (Oryza sative L.) panicle length and panicle branch development by promoting lignin and inhibiting cellulose accumulation.

Panicle structure is one of the most important agronomic traits directly related to rice yield. This study identified a rice mutant basal primary branch 1 (bpb1), which exhibited a phenotype of reduced panicle length and arrested basal primary branch development. In addition, lignin content was found to be increased while cellulose content was decreased in bpb1 young panicles. Map-based cloning methods characterized the gene BPB1, which encodes a peptide transporter (PTR) family transporter. Phylogenetic tree analysis showed that the BPB1 family is highly conserved in plants, especially the PTR2 domain. It is worth noting that BPB1 is divided into two categories based on monocotyledonous and dicotyledonous plants. Transcriptome analysis showed that BPB1 mutation can promote lignin synthesis and inhibit cellulose synthesis, starch and sucrose metabolism, cell cycle, expression of various plant hormones, and some star genes, thereby inhibiting rice panicle length, resulting in basal primary branch development stagnant phenotypes. In this study, BPB1 provides new insights into the molecular mechanism of rice panicle structure regulation by BPB1 by regulating lignin and cellulose content and several transcriptional metabolic pathways. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01389-x.

The miR167-OsARF12 module regulates rice grain filling and grain size downstream of miR159.

Grain weight and quality are always determined by grain filling. Plant microRNAs have drawn attention as key targets for regulation of grain size and yield. However, the mechanisms that underlie grain size regulation remain largely unclear because of the complex networks that control this trait. Our earlier studies demonstrated that suppressed expression of miR167 (STTM/MIM167) substantially increased grain weight. In a field test, the yield increased up to 12.90%-21.94% because of a significantly enhanced grain filling rate. Here, biochemical and genetic analyses revealed the regulatory effects of miR159 on miR167 expression. Further analysis indicated that OsARF12 is the major mediator by which miR167 regulates rice grain filling. Overexpression of OsARF12 produced grain weight and grain filling phenotypes resembling those of STTM/MIM167 plants. Upon in-depth analysis, we found that OsARF12 activates OsCDKF;2 expression by directly binding to the TGTCGG motif in its promoter region. Flow cytometry analysis of young panicles from OsARF12-overexpressing plants and examination of cell number in cdkf;2 mutants verified that OsARF12 positively regulates grain filling and grain size by targeting OsCDKF;2. Moreover, RNA sequencing results suggested that the miR167-OsARF12 module is involved in the cell development process and hormone pathways. OsARF12-overexpressing plants and cdkf;2 mutants exhibited enhanced and reduced sensitivity to exogenous auxin and brassinosteroid (BR) treatment, confirming that targeting of OsCDKF;2 by OsARF12 mediates auxin and BR signaling. Our results reveal that the miR167-OsARF12 module works downstream of miR159 to regulate rice grain filling and grain size via OsCDKF;2 by controlling cell division and mediating auxin and BR signals.

Differences in methane and nitrous oxide emissions and soil bacteria communities between straw return methods in central China.

It is well recognized that straw return (SR) can improve soil fertility and soil organic carbon (SOC) storage. Increasing planting density and reducing nitrogen fertilizer application is considered an effective cultivation technique for japonica rice in central and northern China. However, few are known about the mechanisms of differences between wheat SR with rice planting densification and N reduction (SRD) and wheat SR on greenhouse gas emissions and soil bacteria communities in central China. A 2-year experiment was conducted to evaluate the effects of SR and SRD compared with straw removal (NS) on methane (CH4) and nitrous oxide (N2O) emission, rice yield, and soil properties in Henan Province, China, in 2019 and 2020. We found that SRD increased SOC, available phosphorous (AP), and available potassium (AK) compared to SR and NS in 2019 and 2020. The mean CH4 flux was positively correlated with SOC, and the cumulative CH4 emissions of SR and SRD plots were significantly higher than those of NS plots. No significant difference in cumulative CH4 emissions was detected between the SR and SRD treatments. N2O emissions were significantly lower under SRD than SR. SRD significantly affected soil bacteria diversity and composition at a depth of 0-15 cm. The relative abundance of Bacteroidota in SRD soil was 1.37- and 3.73-fold higher than that in NS and SR soils, respectively. The relative abundance of nitrate reduction-related operational taxonomic units enriched under SRD was significantly lower than that under SR, indicating that lower nitrate reduction of N2O production was induced by soil bacteria under SRD. N partial factor productivity was 21.4% and 28.5% higher under SRD than SR in 2019 and 2020, respectively. Our results suggest that SRD decreased soil bacteria N2O emissions; increased SOC, AP, and AK; and improved N fertilizer use efficiency, thereby improving rice yield in central China.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.).

BACKGROUND: Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development. RESULTS: In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation. CONCLUSIONS: Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Lattice distortion inducing local antiferromagnetic behaviors in FeAl alloys.

In this work, we study the local magnetic moment as a function of order degree in solid-solution FeAl alloys. Using the combination of ab initio method and similar atomic environment model, we find that the decrease of magnetic moment, even antiferromagnetic behavior, of the Fe atoms derives from the distorted local atomic clusters centered at Fe atoms on the Fe-atom sublattice sites in B2 FeAl alloys. While the local magnetic moment of Fe atoms is up to 2.2 µ B on the Al and Fe solid-solution sublattice sites. The ordering results in the decrease of Curie temperature and magnetic moment of solid-solution FeAl alloys.

A structural modeling approach to solid solutions based on the similar atomic environment.

A solid solution is one of the important ways to enhance the structural and functional performance of materials. In this work, we develop a structural modeling approach to solid solutions based on the similar atomic environment (SAE). We propose a similarity function associated with any type of atom cluster to describe quantitatively the configurational deviation from the desired solid-solution structure that is fully disordered or contains short-range order (SRO). In this manner, the structural modeling for solid solutions is transferred to a minimization problem in the configuration space. Moreover, we strive to enhance the practicality of this approach. The approach and implementation are demonstrated by cross validations with the special quasi-random structure method. We apply the SAE method to the typical quinary CoCrFeMnNi high-entropy alloy, continuous binary Ta-W alloy, and ternary CoCrNi medium-entropy alloy with SRO as prototypes. In combination with ab initio calculations, we investigate the structural properties and compare the calculation results with experiments.

Insoluble dietary fiber from soy hulls regulates the gut microbiota in vitro and increases the abundance of bifidobacteriales and lactobacillales.

We evaluated soy hull dietary fibers (SHDF) extracted from different raw materials, in terms of their chemical composition, physicochemical properties, structure, and ability to regulate fecal microflora, in order to investigate the properties and functions of SHDF. The structures of insoluble dietary fiber from soy hull with oxalic acid extraction (IDFO) and insoluble dietary fiber from soy hull with citric acid extraction (IDFC) were characterized by scanning electron microscopy, Fourier transform infrared spectroscopy, and X-ray diffraction. Compared with IDFO, IDFC had larger crystalline regions, and a higher water retention capacity (4.92 g/g), water swelling capacity (4.77 mL/g), oil adsorption capacity (1.60%), α-amylase activity inhibition ratio (12.72%), glucose adsorption capacity (1.59-13.42%), and bile acid retardation index (5.18-26.61%). Given that the gut microbiota plays a pivotal role in health homeostasis, we performed a detailed investigation of the effects of dietary fiber on fecal microbiota through 16S rDNA high-throughput sequencing. As revealed by Venn, principal component analysis, and 3D-principal co-ordinates analysis analysis, the structure of the fecal microbiota community was markedly altered by intake of IDFO and IDFC. In particular, the abundance of Bifidobacteriales and Lactobacillales significantly increased to varying degrees as a result of IDFO and IDFC intake. Altogether, this study demonstrates a prebiotic effect of SHDF on the fecal microbiota in vitro and provides a basis for the development of SHDF as a novel gut microbiota modulator for health promotion.

Chemical structure, chain conformation and rheological properties of pectic polysaccharides from soy hulls.

We obtained a new acidic soy hull polysaccharide (SHP-1) with a molecular weight (Mw) of 4.81 × 105 g/mol through ammonium oxalate and microwave assisted extraction. SHP-1 was mainly composed of galacturonic acid, galactose, rhamnose and arabinose (molar ratio = 46.59%:17.95%:14.77%:13.97%) with small amounts of fucose, glucose, mannose and xylose. The chemical structure was presumed to be of pectin-I type, consisting of 2/3 HGA and 1/3 RG-I. Furthermore, the rheological information and the chain morphology of SHP-1 were different in five solvents. Surfactant, salt and alkali solutions enhanced the solubility and flexibility of the polysaccharide, but the polysaccharide showed decreased fluidity under acidic conditions. The addition of ions and alkali increased the consistency coefficient of the solution, but the effect was far less than that of the cross-linking morphology. The structural and morphological information of purified SHP should aid in further study of its structure-function relationships and applications.

miR1432-OsACOT (Acyl-CoA thioesterase) module determines grain yield via enhancing grain filling rate in rice.

Rice grain filling rate contributes largely to grain productivity and accumulation of nutrients. MicroRNAs (miRNAs) are key regulators of development and physiology in plants and become a novel key target for engineering grain size and crop yield. However, there is little studies, so far, showing the miRNA regulation of grain filling and rice yield, in consequence. Here, we show that suppressed expression of rice miR1432 (STTM1432) significantly improves grain weight by enhancing grain filling rate and leads to an increase in overall grain yield up to 17.14% in a field trial. Molecular analysis identified rice Acyl-CoA thioesterase (OsACOT), which is conserved with ACOT13 in other species, as a major target of miR1432 by cleavage. Moreover, overexpression of miR1432-resistant form of OsACOT (OXmACOT) resembled the STTM1432 plants, that is, a large margin of an increase in grain weight up to 46.69% through improving the grain filling rate. Further study indicated that OsACOT was involved in biosynthesis of medium-chain fatty acids. In addition, RNA-seq based transcriptomic analyses of transgenic plants with altered expression of miR1432 demonstrated that downstream genes of miR1432-regulated network are involved in fatty acid metabolism and phytohormones biosynthesis and also overlap with the enrichment analysis of co-expressed genes of OsACOT, which is consistent with the increased levels of auxin and abscisic acid in STTM1432 and OXmACOT plants. Overall, miR1432-OsACOT module plays an important role in grain filling in rice, illustrating its capacity for engineering yield improvement in crops.

TGMin: An efficient global minimum searching program for free and surface-supported clusters.

In this article, we introduce an efficient global-minimum structural search program named Tsinghua Global Minimum 2 (TGMin-2), which is the successor of the original TGMin algorithm that was developed in our group in 2011. We have introduced a number of new features and improvements into TGMin-2, including a symmetric structure generation algorithm that can produce good initial seeds for small- and medium-size clusters, the duplicated structure identification algorithm, and the improved structure adaption algorithm that was implemented in the original TGMin code. To predict the simulated photoelectron spectrum (PE spectrum) automatically, we also implemented a standalone program named AutoPES (Auto Photoelectron Spectroscopy), which can be used to simulate PE spectra and compare them with experimental results automatically. We have demonstrated that TGMin-2 and AutoPES are powerful tools for studying free and surface-supported molecules, clusters, and nanoclusters. © 2018 Wiley Periodicals, Inc.

A Resource for Inactivation of MicroRNAs Using Short Tandem Target Mimic Technology in Model and Crop Plants.

microRNAs (miRNAs) are endogenous small non-coding RNAs that bind to mRNAs and target them for cleavage and/or translational repression, leading to gene silencing. We previously developed short tandem target mimic (STTM) technology to deactivate endogenous miRNAs in Arabidopsis. Here, we created hundreds of STTMs that target both conserved and species-specific miRNAs in Arabidopsis, tomato, rice, and maize, providing a resource for the functional interrogation of miRNAs. We not only revealed the functions of several miRNAs in plant development, but also demonstrated that tissue-specific inactivation of a few miRNAs in rice leads to an increase in grain size without adversely affecting overall plant growth and development. RNA-seq and small RNA-seq analyses of STTM156/157 and STTM165/166 transgenic plants revealed the roles of these miRNAs in plant hormone biosynthesis and activation, secondary metabolism, and ion-channel activity-associated electrophysiology, demonstrating that STTM technology is an effective approach for studying miRNA functions. To facilitate the study and application of STTM transgenic plants and to provide a useful platform for storing and sharing of information about miRNA-regulated gene networks, we have established an online Genome Browser (https://blossom.ffr.mtu.edu/designindex2.php) to display the transcriptomic and miRNAomic changes in STTM-induced miRNA knockdown plants.

Anion photoelectron spectroscopy and chemical bonding of ThO2- and ThO3.

We conducted a study of electronic structures and chemical bonding of gaseous ThO2- and ThO3- using velocity-map imaging and ab initio calculations. The electron affinity of neutral ThO2 molecule is reported for the first time with the value of 1.21(5) eV. We obtained a vibrationally resolved photoelectron spectroscopy of ThO2- and observed the symmetric stretching frequency of 824(40) cm-1 for neutral molecules. One hot band transition is observed in the spectrum of ThO2-, which allows the measurement of symmetric stretching mode for ThO2-. The ground state of ThO2- is 2A1 with C2v symmetry: the detachment of an electron from the singly occupied molecular orbital (SOMO) results in the ground state of ThO2. Kohn-Sham molecular orbital analyses reveal an σ and two weak π bonds for Th-O multiple bonds in ThO2. Global minimum search methodology combined with quantum chemical calculations are used to find the minima of ThO3 and ThO3-, and the adiabatic detachment energy of ThO3- is calculated to be 3.26 eV at the coupled cluster with singles and doubles plus perturbative triples level. Our theoretical calculations suggest that the ground state of ThO3 is 1A' with a symmetry of Cs, while the most stable ThO3- is 2A1 with C2v symmetry; thus, the transition from ThO3- to ThO3 undergoes a significant geometry reorganization. Molecular orbital analyses suggest that the SOMO of ThO3- is mainly participated by O 2p and O to Th back donation was found in HOMO-2 molecular orbital. This investigation will shed some light on the understanding of covalent bonding in Th-contained molecules.

Suppression of microRNA159 impacts multiple agronomic traits in rice (Oryza sativa L.).

BACKGROUND: microRNAs (miRNAs) are important regulators in plant growth and development. miR159 is a conserved miRNA among different plant species and has various functions in plants. Studies on miR159 are mostly done on model plant, Arabidopsis thaliana. In rice, studies on miR159 were either based upon genome-wide expression analyses focused upon responses to different nitrogen forms and abiotic stress or upon phenotypic studies of transgenic plants overexpressing its precursor. STTM (Short Tandem Target Mimic) is an effective tool to block the activity of endogenous mature miRNA activity in plant. Therefore, specific roles of miR159 in rice could be explored by down regulating miR159 through STTM. RESULTS: In this study, expression of mature miR159 was successfully suppressed by STTM which resulted in the increased expressions of its two targets genes, OsGAMYB and OsGAMYBL1 (GAMYB-LIKE 1). Overall, STTM159 plants exhibited short stature along with smaller organ size and reduction in stem diameter, length of flag leaf, main panicle, spikelet hulls and grain size. Histological analysis of stem, leaf and mature spikelet hull showed the reduced number of small vascular bundles (SVB), less number of small veins (SV) between two big veins (LV) and less cell number in outer parenchyma. Gene Ontology (GO) enrichment analysis of differentially expressed genes between wild type plants and STTM159 transgenic plants showed that genes involved in cell division, auxin, cytokinin (CK) and brassinosteroids (BRs) biosynthesis and signaling are significantly down-regulated in STTM159 plants. CONCLUSION: Our data suggests that in rice, miR159 positively regulates organ size, including stem, leaf, and grain size due to the promotion of cell division. Further analysis from the RNA-seq data showed that the decreased cell divisions in STTM159 transgenic plants may result, at least partly from the lower expression of the genes involved in cell cycle and hormone homeostasis, which provides new insights of rice miR159-specific functions.

Observation and characterization of the smallest borospherene, B28(-) and B28.

Free-standing boron nanocages or borospherenes have been observed recently for B40(-) and B40. There is evidence that a family of borospherenes may exist. However, the smallest borospherene is still not known. Here, we report experimental and computational evidence of a seashell-like borospherene cage for B28(-) and B28. Photoelectron spectrum of B28(-) indicated contributions from different isomers. Theoretical calculations showed that the seashell-like B28(-) borospherene is competing for the global minimum with a planar isomer and it is shown to be present in the cluster beam, contributing to the observed photoelectron spectrum. The seashell structure is found to be the global minimum for neutral B28 and the B28(-) cage represents the smallest borospherene observed to date. It is composed of two triangular close-packed B15 sheets, interconnected via the three corners by sharing two boron atoms. The B28 borospherene was found to obey the 2(n + 1)(2) electron-counting rule for spherical aromaticity.

Dynamic Analysis of Gene Expression in Rice Superior and Inferior Grains by RNA-Seq.

Poor grain filling of inferior grains located on lower secondary panicle branch causes great drop in rice yield and quality. Dynamic gene expression patterns between superior and inferior grains were examined from the view of the whole transcriptome by using RNA-Seq method. In total, 19,442 genes were detected during rice grain development. Genes involved in starch synthesis, grain storage and grain development were interrogated in particular in superior and inferior grains. Of the genes involved in sucrose to starch transformation process, most were expressed at lower level in inferior grains at early filling stage compared to that of superior grains. But at late filling stage, the expression of those genes was higher in inferior grains and lower in superior grains. The same trends were observed in the expression of grain storage protein genes. While, evidence that genes involved in cell cycle showed higher expression in inferior grains during whole period of grain filling indicated that cell proliferation was active till the late filling stage. In conclusion, delayed expression of most starch synthesis genes in inferior grains and low capacity of sink organ might be two important factors causing low filling rate of inferior grain at early filling stage, and shortage of carbohydrate supply was a limiting factor at late filling stage.

Structure Evolution and Associated Catalytic Properties of Pt-Sn Bimetallic Nanoparticles.

Bimetallic nanoparticles (NPs) often show new catalytic properties that are different from those of the parent metals. Carefully exploring the structures of bimetallic NPs is a prerequisite for understanding the structure-associated properties. Herein, binary PtSn NPs with tunable composition are prepared in a controllable manner. X-ray characterizations reveal that their structures evolve from SnO2-x -patched PtSn alloys to SnO2-x -patched Pt clusters when more tin is incorporated. An obvious composition-dependent catalytic performance is observed for the hydrogenation of α,ß-unsaturated aldehydes: the selectivity to unsaturated alcohol increases substantially at high tin content, whereas the reaction rate follows a volcano shape. Furthermore, Pt sites are responsible for hydrogen dissociation, whereas oxygen vacancy (Ovac ) sites, provided by SnO2-x , drastically enhance the adsorption of carbonyl group.

[Relationship between serum adiponectin and bone mineral density in preterm infants].

OBJECTIVE: To examine serum adiponectin level in preterm infants and to evaluate the relationship between serum adiponectin and bone mineral density in preterm infants. METHODS: Seventy-two appropriate-for-gestational-age neonates were classified into three groups according to their gestational ages: early preterm (31-33(+6) weeks, 13 cases), late preterm (34-36(+6) weeks, 16 cases), and full-term (37-42 weeks, 43 cases). Venous blood was collected at one week of their life to measure serum adiponectin concentration. During the period, omnisense ultrasound bone sonometer was applied to measure speed of sound (SOS) of the left tibia. RESULTS: The median of tibia SOS in the early preterm group was significantly lower than in the late preterm and full term groups (P<0.05), and the median of tibia SOS in the late preterm group was lower than in the full-term group (P<0.05). Serum adiponectin level was lowest in the early preterm group, and the full-term group had the highest serum adiponectin level. Serum adiponectin level was positively correlated with tibia SOS in preterm infants (r=0.664, P<0.05). According to the result of multivariate linear stepwise regression analysis, serum adiponectin and birth weight were independent predictor of tibia SOS in preterm infants. CONCLUSIONS: Serum adiponectin level is lower in preterm infants than that in full-term infants. There is a positive correlation between serum adiponectin and bone mineral density in preterm infants.

Experimental and theoretical evidence of an axially chiral borospherene.

Chirality plays an important role in chemistry, biology, and materials science. The recent discovery of the B40(-/0) borospherenes marks the onset of a class of boron-based nanostructures. Here we report the observation of axially chiral borospherene in the B(39)(-) nanocluster on the bases of photoelectron spectroscopy, global minimum searches, and electronic structure calculations. Extensive structural searches in combination with density functional and CCSD(T) calculations show that B(39)(-) has a C3 cage global minimum with a close-lying C2 cage isomer. Both the C3 and C2 B(39)(-) cages are chiral with degenerate enantiomers. The C3 global minimum consists of three hexagons and three heptagons around the vertical C3 axis. The C2 isomer is built on two hexagons on the top and at the bottom of the cage with four heptagons around the waist. Both the C3 and C2 axially chiral isomers of B(39)(-) are present in the experiment and contribute to the observed photoelectron spectrum. The chiral borospherenes also exhibit three-dimensional aromaticity, featuring σ and π double delocalization for all valence electrons. Molecular dynamics simulations reveal that these chiral B(39)(-) cages are structurally fluxional above room temperature, compared to the highly robust D(2d)B40 borospherene. The current findings add chiral members to the borospherene family and indicate the structural diversity of boron-based nanomaterials.

The B35 cluster with a double-hexagonal vacancy: a new and more flexible structural motif for borophene.

Elemental boron is electron-deficient and cannot form graphene-like structures. Instead, triangular boron lattices with hexagonal vacancies have been predicted to be stable. A recent experimental and computational study showed that the B36 cluster has a planar C6v structure with a central hexagonal hole, providing the first experimental evidence for the viability of atom-thin boron sheets with hexagonal vacancies, dubbed borophene. Here we report a boron cluster with a double-hexagonal vacancy as a new and more flexible structural motif for borophene. Photoelectron spectrum of B35(-) displays a simple pattern with certain similarity to that of B36(-). Global minimum searches find that both B35(-) and B35 possess planar hexagonal structures, similar to that of B36, except a missing interior B atom that creates a double-hexagonal vacancy. The closed-shell B35(-) is found to exhibit triple π aromaticity with 11 delocalized π bonds, analogous to benzo(g,h,i)perylene (C22H12). The B35 cluster can be used to build atom-thin boron sheets with various hexagonal hole densities, providing further experimental evidence for the viability of borophene.