Functional differentiation and genetic diversity of rice cation exchanger (CAX) genes and their potential use in rice improvement.

Cation exchanger (CAX) genes play an important role in plant growth/development and response to biotic and abiotic stresses. Here, we tried to obtain important information on the functionalities and phenotypic effects of CAX gene family by systematic analyses of their expression patterns, genetic diversity (gene CDS haplotypes, structural variations, gene presence/absence variations) in 3010 rice genomes and nine parents of 496 Huanghuazhan introgression lines, the frequency shifts of the predominant gcHaps at these loci to artificial selection during modern breeding, and their association with tolerances to several abiotic stresses. Significant amounts of variation also exist in the cis-regulatory elements (CREs) of the OsCAX gene promoters in 50 high-quality rice genomes. The functional differentiation of OsCAX gene family were reflected primarily by their tissue and development specific expression patterns and in varied responses to different treatments, by unique sets of CREs in their promoters and their associations with specific agronomic traits/abiotic stress tolerances. Our results indicated that OsCAX1a and OsCAX2 as general signal transporters were in many processes of rice growth/development and responses to diverse environments, but they might be of less value in rice improvement. OsCAX1b, OsCAX1c, OsCAX3 and OsCAX4 was expected to be of potential value in rice improvement because of their associations with specific traits, responsiveness to specific abiotic stresses or phytohormones, and relatively high gcHap and CRE diversity. Our strategy was demonstrated to be highly efficient to obtain important genetic information on genes/alleles of specific gene family and can be used to systematically characterize the other rice gene families.

GUGA-based MRCI approach with core-valence separation approximation (CVS) for the calculation of the core-excited states of molecules.

We develop and demonstrate how to use the Graphical Unitary Group Approach (GUGA)-based MRCISD with Core-Valence Separation (CVS) approximation to compute the core-excited states. First, perform a normal Self-Consistent-Field (SCF) or valence MCSCF calculation to optimize the molecular orbitals. Second, rotate the optimized target core orbitals and append to the active space, form an extended CVS active space, and perform a CVS-MCSCF calculation for core-excited states. Finally, construct the CVS-MRCISD expansion space and perform a CVS-MRCISD calculation to optimize the CI coefficients based on the variational method. The CVS approximation with GUGA-based methods can be implemented by flexible truncation of the Distinct Row Table. Eliminating the valence-excited configurations from the CVS-MRCISD expansion space can prevent variational collapse in the Davidson iteration diagonalization. The accuracy of the CVS-MRCISD scheme was investigated for excitation energies and compared with that of the CVS-MCSCF and CVS-CASPT2 methods using the same active space. The results show that CVS-MRCISD is capable of reproducing well-matched vertical core excitation energies that are consistent with experiments by combining large basis sets and a rational reference space. The calculation results also highlight the fact that the dynamic correlation between electrons makes an undeniable contribution in core-excited states.

Programmable RNA N6 -methyladenosine editing with CRISPR/dCas13a in plants.

N6 -methyladenonsine (m6 A) is the most prevalent internal modification of messenger RNA (mRNA) and plays critical roles in mRNA processing and metabolism. However, perturbation of individual m6 A modification to reveal its function and the phenotypic effects is still lacking in plants. Here, we describe the construction and characterization of programmable m6 A editing tools by fusing the m6 A writers, the core catalytic domain of the MTA and MTB complex, and the AlkB homologue 5 (ALKBH5) eraser, to catalytically dead Cas13a (dCas13a) to edit individual m6 A sites on mRNAs. We demonstrated that our m6 A editors could efficiently and specifically deposit and remove m6 A modifications on specific RNA transcripts in both Nicotiana benthamiana and Arabidopsis thaliana. Moreover, we found that targeting SHORT-ROOT (SHR) transcripts with a methylation editor could significantly increase its m6 A levels with limited off-target effects and promote its degradation. This leads to a boost in plant growth with enlarged leaves and roots, increased plant height, plant biomass, and total grain weight in Arabidopsis. Collectively, these findings suggest that our programmable m6 A editing tools can be applied to study the functions of individual m6 A modifications in plants, and may also have potential applications for future crop improvement.

mRNA cleavage by 21-nucleotide phasiRNAs determines temperature-sensitive male sterility in rice.

Temperature-sensitive male sterility is one of the core components for hybrid rice (Oryza sativa) breeding based on the 2-line system. We previously found that knockout of ARGONAUTE 1d (AGO1d) causes temperature-sensitive male sterility in rice by influencing phased small interfering RNA (phasiRNA) biogenesis and function. However, the specific phasiRNAs and their targets underlying the temperature-sensitive male sterility in the ago1d mutant remain unknown. Here, we demonstrate that the ago1d mutant displays normal female fertility but complete male sterility at low temperature. Through a multiomics analysis of small RNA (sRNA), degradome, and transcriptome, we found that 21-nt phasiRNAs account for the greatest proportion of the 21-nt sRNA species in rice anthers and are sensitive to low temperature and markedly downregulated in the ago1d mutant. Moreover, we found that 21-nt phasiRNAs are essential for the mRNA cleavage of a set of fertility- and cold tolerance-associated genes, such as Earlier Degraded Tapetum 1 (EDT1), Tapetum Degeneration Retardation (TDR), OsPCF5, and OsTCP21, directly or indirectly determined by AGO1d-mediated gene silencing. The loss of function of 21-nt phasiRNAs can result in upregulation of their targets and causes varying degrees of defects in male fertility and grain setting. Our results highlight the essential functions of 21-nt phasiRNAs in temperature-sensitive male sterility in rice and suggest their promising application in 2-line hybrid rice breeding in the future.

Effects of Mineralocorticoid Receptor Antagonists for Chronic Kidney Disease: A Systemic Review and Meta-Analysis.

BACKGROUND: Mineralocorticoid receptor blockade could be a potential approach for the inhibition of chronic kidney disease (CKD) progression. The benefits and harms of different mineralocorticoid receptor antagonists (MRAs) in CKD are inconsistent. OBJECTIVES: The aim of the study was to summarize the benefits and harms of MRAs for CKD patients. METHODS: We searched MEDLINE, EMBASE, and the Cochrane databases for trials assessing the effects of MRAs on non-dialysis-dependent CKD populations. Treatment and adverse effects were summarized using meta-analysis. RESULTS: Fifty-three trials with 6 different MRAs involving 22,792 participants were included. Compared with the control group, MRAs reduced urinary albumin-to-creatinine ratio (weighted mean difference [WMD], -90.90 mg/g, 95% CI, -140.17 to -41.64 mg/g), 24-h urinary protein excretion (WMD, -0.20 g, 95% CI, -0.28 to -0.12 g), estimated glomerular filtration rate (eGFR) (WMD, -1.99 mL/min/1.73 m2, 95% CI, -3.28 to -0.70 mL/min/1.73 m2), chronic renal failure events (RR, 0.86, 95% CI, 0.79-0.93), and cardiovascular events (RR, 0.84, 95% CI, 0.77-0.92). MRAs increased the incidence of hyperkalemia (RR, 2.04, 95% CI, 1.73-2.40) and hypotension (RR, 1.80, 95% CI, 1.41-2.31). MRAs reduced the incidence of peripheral edema (RR, 0.65, 95% CI, 0.56-0.75) but not the risk of acute kidney injury (RR, 0.94, 95% CI, 0.79-1.13). Nonsteroidal MRAs (RR, 0.66, 95% CI, 0.57-0.75) but not steroidal MRAs (RR, 0.20, 95% CI, 0.02-1.68) significantly reduced the risk of peripheral edema. Steroidal MRAs (RR, 5.68, 95% CI, 1.26-25.67) but not nonsteroidal MRAs (RR, 0.52, 95% CI, 0.22-1.22) increased the risk of breast disorders. CONCLUSIONS: In the CKD patients, MRAs, particularly in combination with angiotensin-converting enzyme inhibitor/angiotensin receptor blocker, reduced albuminuria/proteinuria, eGFR, and the incidence of chronic renal failure, cardiovascular and peripheral edema events, whereas increasing the incidence of hyperkalemia and hypotension, without the augment of acute kidney injury events. Nonsteroidal MRAs were superior in the reduction of more albuminuria with fewer peripheral edema events and without the augment of breast disorder events.

Aspirin intervention before ICU admission reduced the mortality in critically ill patients with acute kidney injury: results from the MIMIC-IV.

Background: Aspirin, with its pleiotropic effects such as anti-inflammatory and anti-platelet aggregation, has been widely used for anti-inflammatory, analgesic, and cardiovascular diseases. However, the association between the use of aspirin before the intensive care unit (ICU) and clinical outcomes in critically ill patients with acute kidney injury (AKI) is unknown. Methods: Patients with AKI in this retrospective observational study were selected from the Marketplace for Medical Information in Intensive Care IV (MIMIC-IV). The association between aspirin intervention and 30-day mortality was assessed using Cox proportional hazards model. Logistic regression models were used to assess the association of aspirin intervention with the risks of intracranial hemorrhage, gastrointestinal bleeding and blood transfusion. The propensity score matching (PSM) method was adopted to balance the baseline variables. Sensitivity analysis was performed to validate the results by multiple interpolations for the missing data. Results: The study included 4237 pre-ICU aspirin users and 9745 non-users. In multivariate models, we found a decreased risk of mortality in those who received aspirin before ICU compared to those who did not (30-day:hazard ratio [HR], 0.70; 95% CI, 0.62-0.79; p < 0.001; 90-day:HR, 0.70; 95% CI, 0.63-0.77, p < 0.001; 180-day:HR, 0.72; 95%CI,0.65-0.79, p < 0.001). This benefit was consistent in the post-PSM analyses, sensitivity analyses, and subgroup analyses. Moreover, aspirin intervention was associated with a reduced risk of intracranial hemorrhage and gastrointestinal bleeding (HR, 0.16; 95% CI, 0.10-0.25; p < 0.001; HR, 0.59; 95% CI, 0.38-0.88, p = 0.012) after being adjusted by relating covariates, whereas with a increased risk of blood transfusion (HR, 1.28; 95% CI, 1.16-1.46; p < 0.001). Conclusion: Patients with AKI treated with aspirin before ICU admission might have reduced 30-day, 90-day and 180-day mortality without increasing the risk of intracranial hemorrhage (ICH) or gastrointestinal bleeding, but may increase the risk of transfusion.

Plasma D-dimer levels are associated with disease progression in diabetic nephropathy: a two-center cohort study.

BACKGROUND: This study aimed to investigate the relationship between plasma D-dimer levels, clinicopathological features, and clinical outcomes in patients with biopsy-proven diabetic nephropathy (DN). METHODS: A total of 137 patients with biopsy-proven DN were enrolled in this two-center cohort study. Patients were stratified into tertiles based on plasma D-dimer levels. We investigated the relationship between plasma D-dimer levels and clinical outcomes, including a composite of death, a 40% decline in estimated glomerular filtration rate (e-GFR) from baseline, or end-stage renal disease (ESRD) (defined as e-GFR < 15 mL/min/1.73 m2 or need for renal replacement therapy including hemodialysis, peritoneal dialysis, or kidney transplantation), assessed using Cox regression models with adjustment for confounders. RESULTS: At baseline, the mean age was 52.61 ± 11.63 years, and the mean e-GFR was 58.02 ± 28.77 mL/min/1.73 m2. During a median 26-month follow-up period, 65 (47% of patients) achieved clinical outcomes. Compared with the low plasma D-dimer level group, those with higher plasma D-dimer levels were more likely to have higher 24-h proteinuria (p = .002), lower e-GFR (p = .001), lower hemoglobin (p = .001), a higher glomerular lesion class (p = .03), and higher interstitial fibrosis and tubular atrophy (IFTA) scores (p = .002). After adjustment for demographic, DN-specific covariates, and treatments, it was observed that a higher tertile of plasma D-dimer was nonlinearly associated with an increased risk of the clinical outcomes (Hazard Ratio (HR) for tertile 2 vs. 1, 1.7; 95% Confidence Interval (CI), 0.80-3.75; HR for tertile 3 vs. 1, 2.2; 95% CI, 0.93-5.27; p for trend = .001) in the Cox proportional hazards models. CONCLUSION: In this study, DN patients with higher levels of plasma D-dimer had higher 24-h proteinuria, lower e-GFR, a higher glomerular lesion class, and higher IFTA scores. Furthermore, a high level of plasma D-dimer was nonlinearly associated with DN progression.

Optical spectroscopy of the previously unobserved palladium monosulfide (PdS) radical.

The optical spectra of the palladium monosulfide (PdS) molecule in gas phase have been investigated for the first time through laser-induced fluorescence (LIF) and single-vibronic-level (SVL) emission spectroscopies. The I3Σ- - X3Σ- transition system containing 16 vibronic bands was identified in the LIF spectra, covering the energy range of 22 030-23 400 cm-1. The spectra with rotational resolution allowed for the determination of the molecular constants in both the ground X and excited I electronic states, involving the spin-orbit splitting, rotational constant, vibrational frequency, and isotope shift. Isotopically resolved SVL emission spectra permitted the observation of the spin-orbit splitting, vibrational frequency, and vibrational isotope shift of the X3Σ-0+,1 and A3Π2,1,0-,0+ states as they transitioned from the excited I state to the vibrational levels of the X and A states. Ab initio calculations presented plenty of the Λ-S and Ω states of PdS below 28 000 cm-1 and provided strong support for the assignments of the experimental observation.

Short-term use of ceftriaxone sodium leads to intestinal barrier disruption and ultrastructural changes of kidney in SD rats.

OBJECTIVE: Antibiotic treatments are known to disturb gut microbiota, but their effects on the mucosal barrier and extraintestinal diseases are rarely discussed. The aim of this study was to evaluate and visualize the impact of antibiotics on colonic mucus and the microbial community, and to assess whether intestinal dysbacteriosis is involved in the pathogenesis and progression of extraintestinal diseases in vivo. MATERIALS AND METHODS: Twenty-one SD rats were randomly assigned into three groups followed by different experimental treatments. The albumin-creatinine ratio, urinary protein and occult blood semi-quantified test were tested. Fecal samples were collected at different time points (0,4, and 12 weeks) for 16S rRNA gene sequencing. Colon and kidney specimens were examined using light microscopy and transmission electron microscopy (TEM) to identify morphological changes. RESULTS: Ceftriaxone intervention for one week did not cause any symptoms of diarrhea or weight loss, but the alpha and beta diversities of gut microbiota decreased quickly and significantly, a lower Firmicutes/Bacteroidetes (F/B) ratio was observed. At week 12, although the alpha and beta diversities increased to a level similar to that of the control (CON) group, LEfSe analysis indicated that the microbial community composition still differed significantly in each group. In addition, KEGG metabolic prediction revealed different metabolic functions in each group. TEM examination of colon revealed that dramatic morphological changes were observed in the ceftriaxone (Cef) group, wherein microvilli were misaligned and shortened significantly and morphologically intact bacteria were seen on the epithelial cell surface. TEM examination of kidneys from the Cef group showed characteristic glomerular changes in the form of widely irregularly thickened glomerular basement membrane (GBM) and foot process fusion or effacement; mild thickening of the GBM and foot process fusion was detected when ceftriaxone and Resatorvid (TAK242, an inhibitor of TLR4 signaling) are used together in the ceftriaxone + TAK242 (TAK) group. CONCLUSIONS: Short-term use of ceftriaxone induced dynamic changes of gut microbiota and lead to intestinal barrier disruption and ultrastructural changes of kidneys in the SD rats. Moreover, interference with the TLR4-dependent signaling pathway can alleviate the damage to the intestinal barrier and kidney.

A general method for locating stationary points on the mixed-spin surface of spin-forbidden reaction with multiple spin states.

Some chemical reactions proceed on multiple potential energy surfaces and are often accompanied by a change in spin multiplicity, being called spin-forbidden reactions, where the spin-orbit coupling (SOC) effects play a crucial role. In order to efficiently investigate spin-forbidden reactions with two spin states, Yang et al. [Phys. Chem. Chem. Phys. 20, 4129-4136 (2018)] proposed a two-state spin-mixing (TSSM) model, where the SOC effects between the two spin states are simulated by a geometry-independent constant. Inspired by the TSSM model, we suggest a multiple-state spin-mixing (MSSM) model in this paper for the general case with any number of spin states, and its analytic first and second derivatives have been developed for locating stationary points on the mixed-spin potential energy surface and estimating thermochemical energies. To demonstrate the performance of the MSSM model, some spin-forbidden reactions involving 5d transition elements are calculated using the density functional theory (DFT), and the results are compared with the two-component relativistic ones. It is found that MSSM DFT and two-component DFT calculations may provide very similar stationary-point information on the lowest mixed-spin/spinor energy surface, including structures, vibrational frequencies, and zero-point energies. For the reactions containing saturated 5d elements, the reaction energies by MSSM DFT and two-component DFT agree very well within 3 kcal/mol. As for the two reactions OsO+ + CH4 → OOs(CH2)+ + H2 and W + CH4 → WCH2 + H2 involving unsaturated 5d elements, MSSM DFT may also yield good reaction energies of similar accuracy but with some counterexamples. Nevertheless, the energies may be remarkably improved by a posteriori single point energy calculations using two-component DFT at the MSSM DFT optimized geometries, and the maximum error of about 1 kcal/mol is almost independent of the SOC constant used. The MSSM method as well as the developed computer program provides an effective utility for studying spin-forbidden reactions.

Panax notoginseng saponins inhibits NLRP3 inflammasome-mediated pyroptosis by downregulating lncRNA-ANRIL in cardiorenal syndrome type 4.

OBJECTIVE: Cardiorenal syndrome type 4 (CRS4) is a complication of chronic kidney disease. Panax notoginseng saponins (PNS) have been confirmed to be efficient in cardiovascular diseases. Our study aimed to explore the therapeutic role and mechanism of PNS in CRS4. METHODS: CRS4 model rats and hypoxia-induced cardiomyocytes were treated with PNS, with and without pyroptosis inhibitor VX765 and ANRIL overexpression plasmids. Cardiac function and cardiorenal function biomarkers levels were measured by echocardiography and ELISA, respectively. Cardiac fibrosis was detected by Masson staining. Cell viability was determined by cell counting kit-8 and flow cytometry. Expression of fibrosis-related genes (COL-I, COL-III, TGF-ß, α-SMA) and ANRIL was examined using RT-qPCR. Pyroptosis-related protein levels of NLRP3, ASC, IL-1ß, TGF-ß1, GSDMD-N, and caspase-1 were measured by western blotting or immunofluorescence staining. RESULTS: PNS improved cardiac function, and inhibited cardiac fibrosis and pyroptosis in a dose-dependent manner in model rats and injured H9c2 cells (p < 0.01). The expression of fibrosis-related genes (COL-I, COL-III, TGF-ß, α-SMA) and pyroptosis-related proteins (NLRP3, ASC, IL-1ß, TGF-ß1, GSDMD-N, and caspase-1) was inhibited by PNS in injured cardiac tissues and cells (p < 0.01). Additionally, ANRIL was upregulated in model rats and injured cells, but PNS reduced its expression in a dose-dependent manner (p < 0.05). Additionally, the inhibitory effect of PNS on pyroptosis in injured H9c2 cells was enhanced by VX765 and reversed by ANRIL overexpression, respectively (p < 0.05). CONCLUSION: PNS inhibits pyroptosis by downregulating lncRNA-ANRIL in CRS4.

Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice.

Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.

Mapping QTLs and gene validation studies for Mg2+ uptake and translocation using a MAGIC population in rice.

Magnesium (Mg) is an essential element for plant growth and development. Rice is an important food crop in the world, but there are few studies on the uptake and translocation of Mg2+ in rice. We used a multi-parent advanced generation inter-cross (MAGIC) population constructed using four parental lines and genotyped by a 55 K rice SNP array for association analysis to locate QTLs related to Mg2+ uptake and translocation in rice at the seedling stage. Four QTLs (qRMg1, qRMg2, qRMg7 and qRMg8) were detected for the root Mg2+ concentration, which explained 11.45-13.08% of the phenotypic variation. The Mg2+ transporter gene, OsMGT1, was within the region of qRMg1. Three QTLs (qSMg3, qSMg7 and qSMg10) were detected for the shoot Mg2+ concentration, which explained 4.30-5.46% of the phenotypic variation. Two QTLs (qTrMg3 and qTrMg8) were found to affect the translocation of Mg2+ from the roots to the shoots, and explained 10.91% and 9.63% of phenotypic variation. qSMg3 and qTrMg3 might be the same, since they are very close to each other on chromosome 3. Analysis of candidate genes in the region of qSMg3 and qTrMg3 through qRT-PCR, complementation assay in the yeast Mg2+ transport-defective mutant CM66, and sequence analysis of the parental lines suggested that LOC_Os03g04360 may play important roles in Mg2+ uptake, translocation and accumulation in rice. Overexpression of LOC_Os03g04360 can significantly increase the Mg2+ concentration in rice seedlings, especially under the condition of low Mg2+ supply.

XPu(CO)n (X = B, Al, Ga; n = 2 to 4): π Back-Bonding in Heterodinuclear Plutonium Boron Group Compounds with an End-On Carbonyl Ligand.

The bonding situation and the oxidation state of plutonium in heterodinuclear plutonium boron group carbonyl compounds XPu(CO)n (X = B, Al, Ga; n = 2 to 4) were investigated by systematically searching their ground-state geometrical structures and by analyzing their electronic structures. We found that the series of XPu(CO)n compounds show various interesting structures with an increment in n as well as a changeover from X = B to Ga. The first ethylene dione (OCCO) compounds of plutonium are found in AlPu(CO)n (n = 2, 3). A direct Ga-Pu single bond is first predicted in the series of GaPu(CO)n, where the bonding pattern represents a class of the Pu → CO π back-bonding system. There is a trend where the Pu-Ga bonding decreases and the Pu-C(O) covalency increases as the Ga oxidation state increases from Ga(0) to Ga(I). Our finding extends the metal → CO covalence back-bonding concept to plutonium systems and also enriches plutonium-containing bonding chemistry.

OsNAC15 Regulates Tolerance to Zinc Deficiency and Cadmium by Binding to OsZIP7 and OsZIP10 in Rice.

Zinc (Zn) deficiency and cadmium (Cd) stress are severe threats to the growth and development of plants. Increasing Zn content and/or decreasing Cd content in grain are also important objectives of rice breeding. However, the molecular mechanisms of Zn deficiency tolerance (ZDT) and Cd stress tolerance (CDT) are largely unknown in rice. Here, we report that a NAM/CUC2-like transcription factor, OsNAC15, contributes to ZDT and CDT in rice. Knockout of OsNAC15 reduced ZDT and CDT at the vegetative stage. OsNAC15 expresses in all tissues of different developmental stages, and is repressed by Zn deficiency and induced by Cd stress. OsNAC15 is a functional transcription factor with transactivation and DNA binding activities. Expression analysis of rice ZIP family genes suggested that the knockout of OsNAC15 activates or inhibits their transcriptions under Zn deficiency or Cd stress conditions. The yeast one-hybrid assay, transient transcriptional activity assay using the dual-luciferase reporter system and electrophoretic mobility shift assay demonstrated that OsNAC15 directly binds to the zinc deficiency-responsive element motifs in the promoters of OsZIP7 and OsZIP10 to repress their transcriptions. The OsNAC15-OsZIP7/10 module is an essential foundation for further study on the regulatory mechanisms of ZDT and CDT in rice.

Electronic Structures and Unusual Chemical Bonding in Actinyl Peroxide Dimers [An2O6]2+ and [(An2O6)(12-crown-4 ether)2]2+ (An = U, Np, and Pu).

As known, actinyl peroxides play important roles in environmental transport of actinides, and they have strategic importance in the application of nuclear industry. Compared to the most studied uranyl peroxides, the studies of transuranic counterparts are still few, and more information about these species is needed. In this work, experimentally inspired actinyl peroxide dimers ([An2O6]2+, An = U, Np, and Pu) have been studied and analyzed by using density functional theory and multireference wave function methods. This study determines that the three [An2O6]2+ have unique electronic structures and oxidation states, as [(UVIO2)2(O2)2-]2+, [(NpVIIO2)2(O2-)2]2+, and mixed-valent [(PuVI/VO2)2(O2)1-]2+. This study demonstrates the significance of two bridging oxo ligands with at most four electron holes availability in ionically directing actinyl and resulting in the unusual multiradical bonding in [(PuVI/VO2)2(O2)1-]2+. In addition, thermodynamically stable 12-crown-4 ether (12C4) chelated [(An2O6)(12C4)2]2+ complexes have been predicted, that could maintain these unique electronic structures of [An2O6]2+, where the An ← O12C4 dative bonding shows a trend in binding capacity of 12C4 from κ4 (U) to κ3 (Np) and κ4 (Pu). This study reveals the interesting electronic character and bonding feature of a series of early actinide elements in peroxide complexes, which can provide insights into the intrinsic stability of An-containing species.

High-Level Theoretical Study of the C1Π States of GaCl, GaBr, InCl, and InBr.

For the first singlet excited states C1Π of IIIA group monohalides GaCl, GaBr, InCl, and InBr, a very shallow potential well may exist in the flat potential energy curve, which poses a challenge to the theoretical accuracy. In this study, high-level theoretical calculations have been performed through the Feller-Peterson-Dixon composite approach to study the C1Π states, and the obtained spectroscopic constants agree well with the known experimental ones. It is found that the C1Π states are sensitive to the size of basis functions, spin-orbit coupling, and strong correlations mainly due to triple excitations. The final results show that the C1Π states of GaCl and InCl are quasi-bound with one (v' = 0) and four (v' = 0-3) vibrational levels, respectively, being consistent with the experimental findings, whereas the C1Π states of GaBr and InBr are repulsive. Our conclusions deny the existence of higher vibrational levels v' = 1 for GaCl, v' > 3 for InCl, and v' ≥ 0 for InBr in previous experimental and theoretical studies of C1Π.

Multi-Trait Genomic Prediction Models Enhance the Predictive Ability of Grain Trace Elements in Rice.

Multi-trait (MT) genomic prediction models enable breeders to save phenotyping resources and increase the prediction accuracy of unobserved target traits by exploiting available information from non-target or auxiliary traits. Our study evaluated different MT models using 250 rice accessions from Asian countries genotyped and phenotyped for grain content of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), and cadmium (Cd). The predictive performance of MT models compared to a traditional single trait (ST) model was assessed by 1) applying different cross-validation strategies (CV1, CV2, and CV3) inferring varied phenotyping patterns and budgets; 2) accounting for local epistatic effects along with the main additive effect in MT models; and 3) using a selective marker panel composed of trait-associated SNPs in MT models. MT models were not statistically significantly (p < 0.05) superior to ST model under CV1, where no phenotypic information was available for the accessions in the test set. After including phenotypes from auxiliary traits in both training and test sets (MT-CV2) or simply in the test set (MT-CV3), MT models significantly (p < 0.05) outperformed ST model for all the traits. The highest increases in the predictive ability of MT models relative to ST models were 11.1% (Mn), 11.5 (Cd), 33.3% (Fe), 95.2% (Cu) and 126% (Zn). Accounting for the local epistatic effects using a haplotype-based model further improved the predictive ability of MT models by 4.6% (Cu), 3.8% (Zn), and 3.5% (Cd) relative to MT models with only additive effects. The predictive ability of the haplotype-based model was not improved after optimizing the marker panel by only considering the markers associated with the traits. This study first assessed the local epistatic effects and marker optimization strategies in the MT genomic prediction framework and then illustrated the power of the MT model in predicting trace element traits in rice for the effective use of genetic resources to improve the nutritional quality of rice grain.

LModeA-nano: A PyMOL Plugin for Calculating Bond Strength in Solids, Surfaces, and Molecules via Local Vibrational Mode Analysis.

The analysis of chemical bonding in crystal structures and surfaces is an important research topic in theoretical chemistry. In this work, we present a PyMOL plugin, named LModeA-nano, as implementation of the local vibrational mode theory for periodic systems (Tao et al. J. Chem. Theory Comput. 2019, 15, 1761) assessing bond strength in terms of local stretching force constants in extended systems of one, two, and three dimensions. LModeA-nano can also analyze chemical bonds in isolated molecular systems thus enabling a head-to-head comparison of bond strength across systems with different dimensions in periodicity (0-3D). The new code is interfaced to the output generated by various solid-state modeling packages including VASP, CP2K, Quantum ESPRESSO, CASTEP, and CRYSTAL. LModeA-nano is cross-platform, open-source and freely available on GitHub: https://github.com/smutao/LModeA-nano.