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Abstract Background In the field of ornamental horticulture, phenotypic mutations, particularly in leaf color, are of great interest due to their potential in developing new plant varieties. The introduction of variegated leaf traits in plants like Heliopsis helianthoides, a perennial herbaceous species with ecological adaptability, provides a rich resource for molecular breeding and research on pigment metabolism and photosynthesis. We aimed to explore the mechanism of leaf variegation of Heliopsis helianthoides (using HY2021F1-0915 variegated mutant named HY, and green-leaf control check named CK in 2020 April, May and June) by analyzing the transcriptome and metabolome. Results Leaf color and physiological parameters were found to be significantly different between HY and CK types. Chlorophyll content of HY was lower than that of CK samples. Combined with the result of Weighted Gene Co-expression Network Analysis (WGCNA), 26 consistently downregulated differentially expressed genes (DEGs) were screened in HY compared to CK subtypes. Among the DEGs, 9 genes were verified to be downregulated in HY than CK by qRT-PCR. The reduction of chlorophyll content in HY might be due to the downregulation of FSD2. Low expression level of PFE2, annotated as ferritin-4, might also contribute to the interveinal chlorosis of HY. Based on metabolome data, differential metabolites (DEMs) between HY and CK samples were significantly enriched on ABC transporters in three months. By integrating DEGs and DEMs, they were enriched on carotenoids pathway. Downregulation of four carotenoid pigments might be one of the reasons for HY’s light color. Conclusion FSD2 and PFE2 (ferritin-4) were identified as key genes which likely contribute to the reduced chlorophyll content and interveinal chlorosis observed in HY. The differential metabolites were significantly enriched in ABC transporters. Carotenoid biosynthesis pathway was highlighted with decreased pigments in HY individuals. These findings not only enhance our understanding of leaf variegation mechanisms but also offer valuable insights for future plant breeding strategies aimed at preserving and enhancing variegated-leaf traits in ornamental plants.

Abstract Background Single cell RNA sequencing technology (scRNA-seq) has been proven useful in understanding cell-specific disease mechanisms. However, identifying genes of interest remains a key challenge. Pseudo-bulk methods that pool scRNA-seq counts in the same biological replicates have been commonly used to identify differentially expressed genes. However, such methods may lack power due to the limited sample size of scRNA-seq datasets, which can be prohibitively expensive. Results Motivated by this, we proposed to use the Bayesian-frequentist hybrid (BFH) framework to increase the power and we showed in simulated scenario, the proposed BFH would be an optimal method when compared with other popular single cell differential expression methods if both FDR and power were considered. As an example, the method was applied to an idiopathic pulmonary fibrosis (IPF) case study. Conclusion In our IPF example, we demonstrated that with a proper informative prior, the BFH approach identified more genes of interest. Furthermore, these genes were reasonable based on the current knowledge of IPF. Thus, the BFH offers a unique and flexible framework for future scRNA-seq analyses.

Objective To conduct Rh blood group serological testing and third-generation sequencing(TGS) on 22 RhD variant voluntary blood donors in Chongqing and explore the phenotypic distribution and genotyping of RhD variants in Chongqing. Methods From January to August 2023, individuals who participated in blood donation in our blood center were selected as the study objects. RhD variant phenotype identification was performed using routine serological methods. Once the RhD variants were identified, tests on different antigenic epitopes of RhD were conducted using a D-screen assay kit. Furthermore, after the genomic DNA from 22 RhD variant blood samples was extracted, imbraided primers design and multi-segment amplification and splicing were used to sequence the full-length RHD gene for TGS. The RHD gene sequence was analyzed using SnapGene software. Results Among the 22 RhD variants, 8 were DVI type 3 (36.36%), with the main mutation of RHD-CE (3-6)-D hybrid allele. Six cases (27.27%) showed partial weak D15 type, with the main mutation of c.845G>A. There were 6 cases of Asia type Del (27.27%), with the main mutation of c.1227G>A. One case was weak D17 type with a mutation of c.340C>T and 1 case speculated to be partial D (c.491A>T, p. Asp164Val, missense mutation). Conclusion The most common RhD variant phenotype among blood donors in Chongqing is DVI type 3, and the full-length haplotype sequence of RHD variant alleles can be obtained by Pacific Bioscience single-molecule real-time sequencing(SMRT).

Abstract Background Hepatitis B virus (HBV) infection is a major concern regarding blood safety in countries with a high HBV prevalence, such as China. We aimed to understand the prevalence of HBV infection among blood donors in Chongqing and provide an important basis for developing appropriate blood screening strategies. Methods Dual enzyme-linked immunosorbent assays (ELISAs) for hepatitis B surface antigen (HBsAg) were conducted in parallel with nucleic acid testing (NAT) of donors. All HBsAg-reactive and/or HBV DNA-positive blood samples were tested for HBsAg and hepatitis B DNA levels. Results A total of 117,927 blood donor samples were collected from the Chongqing Blood Center between April 2020 and November 2020. In total, 473 HBV-ineligible samples were retained for HBsAg and DNA confirmation. A total of 272 samples were confirmed to be HBsAg+, including 2 HBV DNA − and 270 HBV DNA + samples. A total of 201 donations were HBsAg−, including 72 HBV DNA − samples. The rate of HBV infection was 65.33% (309/473) in men, which was significantly higher than that in women (p

Abstract Background Powdery mildew (caused by Blumeria graminis f. sp. tritici (Bgt)) and leaf rust (caused by Puccinia triticina (Pt)) are prevalent diseases in wheat (Triticum aestivum L.) production. Thinopyrum ponticum (2n = 10x = 70, EeEeEbEbExExStStStSt) contains genes that confer high levels of resistance to these diseases. Results An elite wheat-Th. ponticum disomic substitution line, DS5Ag(5D), was developed in the Bainong Aikang 58 (AK58) background. The line was assessed using genomic in situ hybridization (GISH), oligo-nucleotide probe multiplex (ONPM) fluorescence in situ hybridization (FISH), and molecular markers. Twenty eight chromosome-specific molecular markers were identified for the alien chromosome, and 22 of them were co-dominant. Additionally, SNP markers from the wheat 660 K SNP chip were utilized to confirm chromosome identification and they provide molecular tools for tagging the chromosome in concern. The substitution line demonstrated high levels of resistance to powdery mildew throughout its growth period and to leaf rust at the adult stage. Based on the resistance evaluation of five F5 populations between the substitution lines and wheat genotypes with different levels of sensitivity to the two diseases. Results showed that the resistance genes located on 5Ag confered stable resistance against both diseases across different backgrounds. Resistance spectrum analysis combined with diagnostic marker detection of known resistance genes of Th. ponticum revealed that 5Ag contained two novel genes, Pm5Ag and Lr5Ag, which conferred resistance to powdery mildew and leaf rust, respectively. Conclusions In this study, a novel wheat-Th. ponticum disomic substitution line DS5Ag(5D) was successfully developed. The Th. ponticum chromosome 5Ag contain new resistance genes for powdery mildew and leaf rust. Chromosomic—specific molecular markers were generated and they can be used to track the 5Ag chromosome fragments. Consequently, this study provides new elite germplasm resources and molecular markers to facilitate the breeding of wheat varieties that is resistant to powdery mildew and leaf rust.

It is challenging to accurately model the overall uncertainty of the power system when it is connected to large-scale intermittent generation sources such as wind and photovoltaic generation due to the inherent volatility, uncertainty, and indivisibility of renewable energy. Deep reinforcement learning (DRL) algorithms are introduced as a solution to avoid modeling the complex uncertainties and to adapt the fluctuation of uncertainty by interacting with the environment and using feedback to continuously improve their strategies. However, the large-scale nature and uncertainty of the system lead to the sparse reward problem and high-dimensional space issue in DRL. A hierarchical deep reinforcement learning (HDRL) scheme is designed to decompose the process of solving this problem into two stages, using the reinforcement learning (RL) agent in the global stage and the heuristic algorithm in the local stage to find optimal dispatching decisions for power systems under uncertainty. Simulation studies have shown that the proposed HDRL scheme is efficient in solving power system economic dispatch problems under both deterministic and uncertain scenarios thanks to its adaptation system uncertainty, and coping with the volatility of uncertain factors while significantly improving the speed of online decision-making.

The management of crop production in a sandy soil “culture” is difficult, mainly due to its low soil-water-holding capacity, organic matter and poor fertilizer efficiency. Options to increase soil water and nutrient retention for these soils include the addition of surface mulch covers, amendment with biochar and the use of layers of a mixture of charcoal and compost material. Our objective was to measure the distribution of water and nutrients for layers of control 1 (CK1), control 2 (CK2) and compost material of different thicknesses (0.02, 0.05 and 0.10 m) buried 0.01 m from the surface in a column (0.2 m radius, 0.5 m height) filled with sand. The experiment was conducted in a greenhouse located at the Agricultural Science Training Base of Ningxia University, China. There were three replicates per treatment and one soil column per replicate. The soil columns were watered with 2 L via a surface drip emitter and 45 days later, soil samples were obtained in 0.01 m increments across the diameter and depth of 0.4 m, with a total of 12 samples per column. In each sample, we measured soil water, pH, electrical conductivity, ammonium and nitrate nitrogen and available P and K. The results showed that the distribution of water content and nutrient contents were centered on the dripper and diffused to its surroundings. Notably, the horizontal diffusion distance was smaller than that of the vertical direction. In the vertical direction, compared with control 1, adding compost changed the spatial distribution of WC and nutrients and had a greater impact on available potassium (AK) than on inorganic nitrogen (IN) and available phosphorus (AP). Compared with control 1, the composting treatment decreased the content of water in the 0–10 cm surface soil, reduced the electrical conductivity (EC) and nitrate nitrogen (NO3-N), C5 and C10 increased the available potassium. Moreover, composting treatments increased the electrical conductivity, available phosphorus, available potassium and nitrate nitrogen of the 10–30 cm substrate by 61–384%, 10–240%, 11–45% and 133–929%, respectively, when compared with control 1.The nutrients increased as the thickness of the compost interlayer increased. A principal component analysis (PCA) of the C5 and C10 treatments significantly distinguished them from control 1. A linear regression fitting analysis showed that the inorganic nitrogen, available potassium and total nutrients positively correlated with the water content and electrical conductivity of the sand. The 5 cm and 10 cm composting interlayers had a high water content and ability to conserve fertilizer for sand culture, but C10 caused an excessive accumulation of nutrients. Thus, it was concluded that a composting interlayer that was less than 5 cm reduced the base fertilizer input by 24–84%. All these results suggest that applying a composting interlayer of 5 cm could retain more suitable root zone water and fertilizer for the next crop season and provide technological support to reduce fertilizer inputs.

The mode of action is the basis for the rational design of the novel agrochemicals. 3-(4-Methyl-1,2,3-thiadiazolyl)-6-trichloromethyl [1,2,4]triazolo [3,4-b][1,3,4]thiadiazole (YZK-C22) is a novel fungicide candidate. The aim of this study was identification of the mechanism of YZK-C22 against fungi. The results indicated that YZK-C22 inhibited the mycelial growth and spore germination of Botrytis cinerea. Total 56 differentially expressed proteins (DEPs) including 27 up regulated and 29 down regulated proteins were identified by isobaric tags for relative and absolute quantification (iTRAQ). The DEPs mainly concentrated on metabolic pathways, and the results were consistent across the studies of RNA and protein platforms. The pyruvate kinase (PK) activity in the glycolytic pathway was inhibited over 50% by 20 μg/mL of YZK-C22. Molecular docking analysis also validated that YZK-C22 could dock into the active centre of the PK instead of phosphoenolpyruvate. In summary, iTRAQ was an effective way for target identification of YZK-C22.

Plant resistance against biotrophic and necrotrophic pathogens is mediated by mutually synergistic and antagonistic effects of salicylic acid (SA) and jasmonic acid (JA) signals. However, the unique and shared genes responding to the defense mediated by JA/SA signals were largely unclear. To reveal discrete, synergistic and antagonistic JA/SA responsive genes in Arabidopsis thaliana, Meta-Analysis was employed with 257 publicly available Arabidopsis thaliana RNA-Seq gene expression profiles following treatment of mock, JA or SA analogs. JA/SA signalings were found to co-induce broad-spectrum disease-response genes, co-repress the genes related to photosynthesis, auxin, and gibberellin, and reallocate resources of growth toward defense. JA might attenuate SA induced immune response by inhibiting the expression of resistance genes and receptor-like proteins/kinases. Strikingly, co-expression network analysis revealed that JA/SA uniquely regulated genes showing highly coordinated co-expression only in their respective treatment. Using principal component analysis, and hierarchical cluster analysis, JA/SA analogs were segregated into separate entities based on the global differential expression matrix rather than the expression matrix. To accurately classify JA/SA analogs with as few genes as possible, 87 genes, including the SA receptor NPR4, and JA biosynthesis gene AOC1 and JA response biomarkers VSP1/2, were identified by three feature selection algorithms as JA/SA markers. The results were confirmed by independent datasets and provided valuable resources for further functional analyses in JA- or SA- mediated plant defense. These methods would provide cues to build a promising approach for probing the mode of action of potential elicitors.

A molecular dynamics (MD) simulation study was performed to investigate the effects of helium (He) on the mechanical properties of nanocrystalline body-centered cubic iron (BCC Fe). Simulated X-ray diffraction (XRD) was used to explore the relationship between the generation of cracks and the change of the crystal structure in nanocrystalline BCC Fe during tensile deformation. It is observed that the peak stress and the elastic modulus decrease with increasing concentration of He atoms, which are introduced into the grain boundary (GB) region of nanocrystalline Fe. The generation and connection of intergranular cracks are enhanced by He atoms. Significant peak separation, which is associated with the generation of cracks, is found in the simulated XRD patterns of nanocrystalline Fe during the tensile process. The lower diffraction angle of the {211}′ peak suggests a more serious lattice distortion during loading. For all nanocrystalline Fe deformed to 6% strain, the degree and fraction of the lattice distortion increases with the increasing loading stress.

A series of novel 3-(difluoromethyl)-1-methyl-1H-pyrazole-4-carboxylic acid amides were synthesized and their activities were tested against seven phytopathogenic fungi by an in vitro mycelia growth inhibition assay. Most of them displayed moderate to excellent activities. Among them N-(2-(5-bromo-1H-indazol-1-yl)phenyl)-3-(difluoro-methyl)-1-methyl-1H-pyrazole-4-carboxamide (9m) exhibited higher antifungal activity against the seven phytopathogenic fungi than boscalid. Topomer CoMFA was employed to develop a three-dimensional quantitative structure-activity relationship model for the compounds. In molecular docking, the carbonyl oxygen atom of 9m could form hydrogen bonds towards the hydroxyl of TYR58 and TRP173 on SDH.

A series of novel aromatic carboxylic acid amides were synthesized and tested for their activities against six phytopathogenic fungi by an in vitro mycelia growth inhibition assay. Most of them displayed moderate to good activity. Among them N-(2-(1H-indazol-1-yl)phenyl)-2-(trifluoromethyl)benzamide (3c) exhibited the highest antifungal activity against Pythium aphanidermatum (EC50 = 16.75 µg/mL) and Rhizoctonia solani (EC50 = 19.19 µg/mL), compared to the reference compound boscalid with EC50 values of 10.68 and 14.47 µg/mL, respectively. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were employed to develop a three-dimensional quantitative structure-activity relationship model for the activity of the compounds. In the molecular docking, a fluorine atom and the carbonyl oxygen atom of 3c formed hydrogen bonds toward the hydroxyl hydrogens of TYR58 and TRP173.

A simple and efficient strategy for the synthesis of 1-ethynylcyclohex-2-enol derivatives was developed utilizing regioselective addition of acetylides to enediones based on steric effects. Further investigation of the substrate scope of enediones indicated that all the addition reactions ocurred in good yield.

2′,3′-iso-Benzoabscisic acid (iso-PhABA), an excellent selective abscisic acid (ABA) analog, was developed in our previous work. In order to find its more structure-activity information, some structural modifications were completed in this paper, including the substitution of phenyl ring and replacing the ring with heterocycles. Thus, 16 novel analogs of iso-PhABA were synthesized and screened with three bioassays, Arabidopsis and lettuce seed germination and rice seedling elongation. Some of them, i.e., 2′,3′-iso-pyridoabscisic acid (iso-PyABA) and 2′,3′-iso-franoabscisic acid (iso-FrABA), displayed good bioactivities that closed to iso-PhABA and natural (+)-ABA. Some others, for instance, substituted-iso-PhABA, exhibited certain selectivity to different physiological process when compared to iso-PhABA or (+)-ABA. These analogs not only provided new candidates of ABA-like synthetic plant growth regulators (PGRs) for practical application, but also new potential selective agonist/antagonist for probing the specific function of ABA receptors.

Objectives. The presence of motilin receptor in the GI tract of different animal species has been verified. However, the quantitation of motilin receptor expression in different regions of the GI tract remains unclear. The aim of this study was to investigate the expression of motilin receptor in the GI tract and semiquantitatively compare the expression difference in different GI regions in dogs. Methods. Antrum, duodenum, jejunum, ileum, proximal colon, middle colon, and distal colon were obtained from various parts of the GI tract of six sacrificed dogs. The distribution of motilin receptor was determined by immunohistochemistry. The expression levels of motilin receptor mRNA in different regions were measured by RT-PCR. Results. Motilin receptor was expressed throughout the GI tract in dogs. Multiple comparisons of the mean motilin receptor mRNA expression among various regions were significant (P

Low dietary folate intake is associated with several neoplasias, but reports are inconsistent for breast cancer. Additionally, the association of folate with breast cancer estrogen receptor (ER) status is not well established.To determine if dietary intakes of folate, B-vitamins (B2, B6, B12) and methionine are associated with breast cancer risk and ER status in Hispanic, and non-Hispanic White women in the southwestern U.S.Primary breast cancer cases (n = 2,325) in the 4-Corners region (Arizona, Colorado, New Mexico and Utah), diagnosed between October 1999 and May 2004, were identified through state cancer registries. Controls (n = 2,525) were frequency-matched by ethnicity and age (±5 years). Dietary intake, physical activity and other exposures were assessed using in-person interviews. Risk was assessed through multivariable and multinomial logistic regression with adjustment for relevant covariates.While there was no overall association with breast cancer, the highest quartile of folate intake was marginally inversely associated with ER- breast cancer (Odds Ratio (OR) = 0.50, 95% CI 0.25-1.00, p for trend = 0.07). Vitamin B12 intake was inversely associated with breast cancer also (OR = 0.73, 95% CI 0.53-1.00, p for trend = 0.06), particularly for the highest quartile of ER+ breast cancer (OR = 0.67, 95% CI 0.46-0.99, p for trend = 0.06), among NHW women (OR = 0.49, 95% CI 0.29-0.81, p for trend = 0.01) and invasive breast cancer (OR = 0.63; 95% CI: 0.42, 0.93, P(trend) = 0.01). Methionine intake was also inversely associated with ER+ breast cancer (OR for 4th quartile = 0.83, 95% CI 0.66-1.03, p for trend = 0.04), primarily among Hispanic women (OR = 0.71, 95% CI 0.47-1.06, and P for trend = 0.02).Higher intake of folate is marginally associated with a lower risk for ER- breast cancer, and higher intakes of vitamin B-12 and methionine are marginally associated with a lower risk of ER+ breast cancer.