Analyzing the response of rice to tefuryltrione herbicide: Haplotype variation and evolutionary dynamics of the HIS1 gene.

Weeds pose multifaceted challenges in rice cultivation, leading to substantial economic losses through reduced yield and poor grain quality. Harnessing the natural genetic diversity in germplasm collections becomes crucial for identifying novel herbicide resistance loci in crops. A comprehensive analysis was conducted on 475 rice accessions from the KRICE depository, assessing their response to TFT (tefuryltrione) and probing the underlying HIS1 (HPPD INHIBITOR SENSITIVE 1) genotypic variations. The HIS1 gene, responsible for detoxifying benzobicyclon (BBC) and imparting broad-spectrum herbicide resistance, holds significant promise in rice breeding. This study explores the genetic landscape of HIS1 within Korean rice collection (KRICE), aiming to unveil genetic variations, haplotype diversity, and evolutionary relationships across diverse rice ecotypes. The indica ecotype showed the highest nucleotide diversity, while the wild and temperate japonica groups exhibited low diversity, hinting at selective sweeps and possible population expansion. Negative Tajima's D values in temperate japonica and wild groups indicate an excess of low-frequency mutations, potentially resulting from selective sweeps. In contrast, with positive Tajima's D values, admixture, indica, and aus groups suggest balancing selection. Furthermore, haplotype analysis uncovered 42 distinct haplotypes within KRICE, with four shared haplotypes between cultivated and wild accessions, four specific to cultivated accessions, and 34 specific to wild types. Phenotypic assessments of these haplotypes revealed that three haplotypes, viz., Hap_1 (predominant in japonica), Hap_2 (predominant in indica), and Hap_3 (specific to indica), displayed significant differences from aus-specific Hap_4 and indica-specific Hap_5. This study offers insights into genetic diversity, selective pressures, and ecotype-specific responses, ultimately paving the way for developing HPPD-inhibiting herbicide-resistant rice cultivars.

Harnessing γ-TMT Genetic Variations and Haplotypes for Vitamin E Diversity in the Korean Rice Collection.

Gamma-tocopherol methyltransferase (γ-TMT), a key gene in the vitamin E biosynthesis pathway, significantly influences the accumulation of tocochromanols, thereby determining rice nutritional quality. In our study, we analyzed the γ-TMT gene in 475 Korean rice accessions, uncovering 177 genetic variants, including 138 SNPs and 39 InDels. Notably, two functional SNPs, tmt-E2-28,895,665-G/A and tmt-E4-28,896,689-A/G, were identified, causing substitutions from valine to isoleucine and arginine to glycine, respectively, across 93 accessions. A positive Tajima's D value in the indica group suggests a signature of balancing selection. Haplotype analysis revealed 27 haplotypes, with two shared between cultivated and wild accessions, seven specific to cultivated accessions, and 18 unique to wild types. Further, profiling of vitamin E isomers in 240 accessions and their association with haplotypes revealed that Hap_2, distinguished by an SNP in the 3' UTR (tmt-3UTR-28,897,360-T/A) exhibited significantly lower α-tocopherol (AT), α-tocotrienol (AT3), total tocopherol, and total tocotrienol, but higher γ-tocopherol (GT) in the japonica group. Additionally, in the indica group, Hap_2 showed significantly higher AT, AT3, and total tocopherol, along with lower GT and γ-tocotrienol, compared to Hap_19, Hap_20, and Hap_21. Overall, this study highlights the genetic landscape of γ-TMT and provides a valuable genetic resource for haplotype-based breeding programs aimed at enhancing nutritional profiles.

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice.

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.

Synthesis and anti-diabetic activity of novel biphenylsulfonamides as glucagon receptor antagonists.

Type 2 diabetes is characterized by chronic hyperglycemia. Insulin, a hormone secreted from pancreatic ß-cells, decreases blood glucose levels, and glucagon, a hormone secreted from pancreatic α-cells, increases blood glucose levels by counterregulation of insulin through stimulation of hepatic glucose production. In diabetic patients, dysregulation of glucagon secretion contributes to hyperglycemia. Thus, inhibition of the glucagon receptor is one strategy for the treatment of hyperglycemia in type 2 diabetes. In this paper, we report a series of biphenylsulfonamide derivatives that were designed, synthesized, and then evaluated by cAMP and hepatic glucose production assays as glucagon receptor antagonists. Of these, compound 7aB-3 decreased glucagon-induced cAMP production and glucagon-induced glucose production in the in vitro assays. Glucagon challenge tests and glucose tolerance tests showed that compound 7aB-3 significantly inhibited glucagon-induced glucose increases and improved glucose tolerance. These results suggest that compound 7aB-3 has therapeutic potential for the treatment of type 2 diabetes.

A consistent approach to the genotype encoding problem in a genome-wide association study of continuous phenotypes.

In this study, we suggested a hypothesis test method that was robust to different genotype encodings in a genome-wide association analysis of continuous traits. When the population stratification is corrected for using a method based on principal component analysis, ordinally (or categorically) encoded genotypes are adjusted and turn into continuous values. Due to the adjustment of the encoded genotype, the association test result using conventional methods, such as the test of Pearson's correlation coefficient, was shown to be dependent on how genotypes were encoded. To overcome this shortcoming, we proposed a non-parametric test based on Kendall's tau. Because Kendall's tau deals with rank, rather than value, associations between adjusted genotype and phenotype values, Kendall's test can be more robust than Pearson's test under different genotype encodings. We assessed the robustness of Kendall's test and compared with that of Pearson's test in terms of the difference in p-values obtained by using different genotype encodings. With simulated as well as real data set, we demonstrated that Kendall's test was more robust than Pearson's test under different genotype encodings. The proposed method can be applicable to the broad topics of interest in population genetics and comparative genomics, in which novel genetic variants are associated with traits. This study may also bring about a cautious approach to the genotype encoding in the numerical analysis.

The fractal dimension as a measure for characterizing genetic variation of the human genome.

Motivated by the characteristics of highly clustered single nucleotide polymorphism (SNP) across the human genome, we propose a set of chromosome-wise fractal dimensions as a measure for identifying an individual for human polymorphism. The fractal dimension quantifies the degree of clustered distribution of SNPs and represents parsimoniously the genetic variation in a chromosome. In this sense, the proposed scheme projects the SNP genotype data into a new space which is simpler and lower in dimension. As an illustrative example, we estimate the chromosome-wise fractal dimensions of SNPs that are extracted from the HapMap of Phase III data set. To determine the validity of the proposed measure, we apply principal component analysis (PCA) to the set of estimated fractal dimensions and demonstrate that the set more or less described the population structure of 11 global populations. We also use multidimensional scaling to relate the genetic distances based on PCA to the geographical distances between global populations. This shows that, similar to the SNP genotype data, the fractal dimensions also has a role in genetic distance in the population structure. In addition, we apply the proposed measure to a signature for the classification of global populations by developing a support vector machine model. The selected feature model predicts the global population with a balanced accuracy of about 77%. These results support that the fractal dimension is an efficient way to describe the genetic variation of global populations.

The Intraocular Pressure-Lowering Effect of Persimmon leaves (Diospyros kaki) in a Mouse Model of Glaucoma.

The aim of this study was to evaluate the pharmacological efficacy of persimmon leaves in two glaucoma models, microbeads-induced ocular hypertension (OHT) and DBA/2 mouse. Thus, we demonstrated that Ethanol Extract of Diospyros kaki (EEDK) reduced elevated intraocular pressure (IOP) in both mouse models of glaucoma by measurements with a tonometer. In particular, we revealed that retinal ganglion cell loss and optic nerve damage caused by IOP elevation were markedly diminished as assessed by TUNEL assay, H&E staining, and fluorescent staining, while the expression of soluble guanylate cyclase (sGCα-1) increased, when EEDK was administered, as revealed by western blot. Moreover, the b-wave magnitude indicating functional scotopic vision was significantly improved in EEDK-administered DBA/2 mice during the 10-week follow-up study, as observed with electroretinography. Collectively, our results suggested that EEDK could be an effective therapeutic and IOP-lowering agent for preventing and treating retinal degenerative diseases such as glaucoma.

Inhibition of STAT3 signaling induces apoptosis and suppresses growth of lung cancer: good and bad.

Signal transducer and activator of transcription 3 (STAT3) modulates a variety of genes involved in the regulation of critical functions, including cell proliferation, differentiation, apoptosis, angiogenesis, metastasis, and immunity. For many cancers, elevated levels of STAT3 signaling have been associated with a poor prognosis and the development of chemotherapy resistance. In this study, we investigated the inhibitory effects of a novel small-molecule inhibitor of STAT3, STX-0119, on the cell viability and survival of human lung cancer cells. STX-0119 inhibited activated STAT3 and the expression of STAT3-regulated oncoproteins such as c-Myc, cyclin D1, and survivin in lung cancer cells. STX-0119 also decreased the amount of STAT3 in the nuclear fraction as well as induced apoptosis of these lung cancer cell lines as evidenced by increases in apoptotic cells (Annexin V positive) and poly (ADP-ribose) polymerase (PARP) cleavage. The efficacy of STX-0119 in a mouse xenograft model was confirmed. However, a hematological side effect, which had not been previously reported, was observed. The level of white blood cells was significantly lowered when treated at the dose at which STX-0119 alone showed a significant tumor-suppressive effect. In conclusion, we suggest that STX-0119 may be a potent therapeutic agent against lung cancer. Consideration of the side effect suggests, it is necessary to study whether low-dose STX-0119 is effective for lung treatment with a combination of classic lung cancer therapeutics.

Design, synthesis, and effects of novel phenylpyrimidines as glucagon receptor antagonists.

The hormone glucagon increases blood glucose levels through increasing hepatic glucose output. In diabetic patients, dysregulation of glucagon secretion contributes to hyperglycemia. Thus, the inhibition of glucagon receptor is one target for the treatment of hyperglycemia in type 2 diabetes. Here we designed and synthesized a series of small molecules based on phenylpyrimidine. Of these, the compound (R)-7a most significantly decreased the glucagon-induced cAMP production and glucagon-induced glucose production during in vitro and in vivo assays. In addition, (R)-7a showed good efficacy in glucagon challenge tests and lowered blood glucose levels in diabetic db/db mice. Our results suggest that the compound (R)-7a could be a potential glucose-lowering agent for treating type 2 diabetes.

Kartogenin inhibits pain behavior, chondrocyte inflammation, and attenuates osteoarthritis progression in mice through induction of IL-10.

Osteoarthritis (OA) is a major degenerative joint condition that causes articular cartilage destruction. It was recently found that enhancement of chondroclasts and suppression in Treg cell differentiation are involved in the pathogenesis of OA. Kartogenin (KGN) is a small drug-like molecule that induces chondrogenesis in mesenchymal stem cells (MSCs). This study aimed to identify whether KGN can enhance severe pain behavior and improve cartilage repair in OA rat model. Induction of OA model was loaded by IA-injection of MIA. In the OA rat model, treatment an intra-articular injection of KGN. Pain levels were evaluated by analyzing PWL and PWT response in animals. Histological analysis and micro-CT images of femurs were used to analyze cartilage destruction. Gene expression was measured by real-time PCR. Immunohistochemistry was analyzed to detect protein expression. KGN injection significantly decreased pain severity and joint destruction in the MIA-induced OA model. KGN also increased mRNA levels of the anti-inflammatory cytokine IL-10 in OA patients' chondrocytes stimulated by IL-1ß. Decreased chondroclast expression, and increased Treg cell expression. KGN revealed therapeutic activity with the potential to reduce pain and improve cartilage destruction. Thus, KGN could be a therapeutic molecule for OA that inhibits cartilage damage.

Streptavidin-mirror DNA tetrahedron hybrid as a platform for intracellular and tumor delivery of enzymes.

Despite the extremely high substrate specificity and catalytically amplified activity of enzymes, the lack of efficient cellular internalization limits their application as therapeutics. To overcome this limitation and to harness enzymes as practical biologics for targeting intracellular functions, we developed the streptavidin-mirror DNA tetrahedron hybrid as a platform for intracellular delivery of various enzymes. The hybrid consists of streptavidin, which provides a stoichiometrically controlled loading site for the enzyme cargo and an L-DNA (mirror DNA) tetrahedron, which provides the intracellular delivery potential. Due to the cell-penetrating ability of the mirror DNA tetrahedron of this hybrid, enzymes loaded on streptavidin can be efficiently delivered into the cells, intracellularly expressing their activity. In addition, we demonstrate tumor delivery of enzymes in an animal model by utilizing the potential of the hybrid to accumulate in tumors. Strikingly, the hybrid is able to transfer the apoptotic enzyme specifically into tumor cells, leading to strong suppression of tumor growth without causing significant damage to other tissues. These results suggest that the hybrid may allow anti-proliferative enzymes and proteins to be utilized as anticancer drugs.

Gingerenone A Attenuates Monocyte-Endothelial Adhesion via Suppression of I Kappa B Kinase Phosphorylation.

During the early stages of atherosclerosis, monocytes bind and migrate into the endothelial layer, promoting inflammation within the aorta. In order to prevent the development of atherosclerosis, it is critical to inhibit such inflammation. The therapeutic effects of ginger have been investigated in several models of cardiovascular disease. However, although a number of previous studies have focused on specific compounds, the mechanisms of action responsible remain unclear. Here, we investigated five major compounds present in ginger, and observed that gingerenone A exhibited the strongest inhibitory effects against tumor necrosis factor (TNF)-α and lipopolysaccharide (LPS) induced monocyte-endothelial adhesion. Furthermore, gingerenone A significantly suppressed the expression of TNF-α and LPS-induced vascular cell adhesion molecule-1 (VCAM-1) and chemokine (C-C motif) ligand 2 (CCL2), key mediators of the interaction between monocytes, and endothelial cells. Transactivation of nuclear factor-κB (NF-κB), which is a key transcription factor of VCAM-1 and CCL2, was induced by TNF-α and LPS, and inhibited by treatment of gingerenone A. Gingerenone A also inhibited the phosphorylation of NF-κB inhibitor (IκB) α and IκB Kinase. Taken together, these results demonstrate that gingerenone A attenuates TNF-α and LPS-induced monocyte adhesion and the expression of adhesion factors in endothelial cells via the suppression of NF-κB signaling. J. Cell. Biochem. 119: 260-268, 2018. © 2017 Wiley Periodicals, Inc.

PKCι is a target of 7,8,4'-trihydroxyisoflavone for the suppression of UVB-induced MMP-1 expression.

The soy isoflavone daidzein is bioconverted to 7,8,4'-trihydroxyisoflavone (7,8,4'-THIF) by microorganisms. Here, we investigated the matrix metalloproteinase (MMP)-1 inhibitory properties of 7,8,4'-THIF that arise through the suppression of UVB-induced MMP-1 expression. 7,8,4'-THIF reduced UVB-induced MMP-1 expression at the transcriptional level in primary human dermal fibroblasts and inhibited UVB-induced transcriptional activity of AP-1, a major activator of MMP-1 expression. Additionally, it was observed that the mitogen-activated protein kinase (MAPK) pathway, a crucial signalling cascade for MMP-1 expression, was suppressed by 7,8,4'-THIF. Protein kinase C iota (PKCι) was suspected to be a direct target of 7,8,4'-THIF. The direct interaction between 7,8,4'-THIF and PKCι was confirmed using pull-down assays and immobilized metal ion affinity-based fluorescence polarization assays. Finally, we observed that 7,8,4'-THIF inhibited UVB-induced MMP-1 expression in a human skin equivalent model. Taken together, these results suggest that 7,8,4'-THIF, a bioconversion product of daidzein, suppresses UVB-induced MMP-1 expression.

A major daidzin metabolite 7,8,4'-trihydroxyisoflavone found in the plasma of soybean extract-fed rats attenuates monocyte-endothelial cell adhesion.

Among many functional foods and their phytochemicals, ingestion of soybean (Glycine max) is highly correlated to reduced risk of cardiovascular diseases. Validation of potential health benefits of functional foods requires information about the bioavailability and metabolism of bioactive compounds. In this context, several phase I and II metabolites of isoflavones were target-analyzed in the plasma of rats acutely supplemented with soybean embryo extract. A daidzein metabolite, 7,8,4'-trihydroxyisoflavone (7,8,4'-THI), was found to have the highest average area under curve value (574.3±112.8). Therefore, its potential prevention effect on atherosclerosis was investigated using monocyte-endothelial cell adhesion assay. Different from its precursor daidzein or daidzin, 7,8,4'-THI attenuated adhesion of THP-1 monocytes to tumor necrosis factor-alpha (TNF-α) stimulated human umbilical vein endothelial cells (HUVECs). In addition, 7,8,4'-THI significantly downregulated TNF-α stimulated the expression of vascular cell adhesion molecule-1 and monocyte chemotactic protein-1 and phosphorylation of IκB kinase and IκBα involved in the initiation of atherosclerosis in HUVECs. Therefore, 7,8,4'-THI, a highly bioavailable hydroxylated isoflavone metabolite, has potential anti-atherosclerotic effect via inhibiting monocyte-endothelial adhesion.

5-(3',4'-Dihydroxyphenyl-γ-valerolactone), a Major Microbial Metabolite of Proanthocyanidin, Attenuates THP-1 Monocyte-Endothelial Adhesion.

Several metabolomics of polymeric flavan-3-ols have reported that proanthocyanidins are extensively metabolized by gut microbiota. 5-(3',4'-dihydroxyphenyl)-γ-valerolactone (DHPV) has been reported to be the major microbial metabolite of proanthocyanidins. We demonstrated that DHPV has stronger prevention effect on tumor necrosis factor (TNF)-α-stimulated adhesion of THP-1 human monocytic cells to human umbilical vein endothelial cells compared to its potential precursors such as procyanidin A1, A2, B1 and B2, (+)catechin, (-)epicatechin and its microbial metabolites such as 3-(3,4-dihydroxyphenyl)propionic acid and 2-(3,4-dihydroxyphenyl)acetic acid. Mechanism study showed that DHPV prevents THP-1 monocyte-endothelial cell adhesion by downregulating TNF-α-stimulated expressions of the two biomarkers of atherosclerosis such as vascular cell adhesion molecule-1 and monocyte chemotactic protein-1, activation of nuclear factor kappa B transcription and phosphorylation of I kappa-B kinase and IκBα. We suggested that DHPV has higher potentiality in prevention of atherosclerosis among the proanthocyanidin metabolites.

Comprehensive phenolic composition analysis and evaluation of Yak-Kong soybean (Glycine max) for the prevention of atherosclerosis.

Yak-Kong (YK) (Glycine max), a small black soybean cultivar with a green embryo, was evaluated for functional constituents with a focus on atherosclerosis prevention. In comparison to common yellow and black soybean cultivars, YK contains significantly higher concentrations of antioxidants, particularly in its seed coat. A comprehensive phenolic composition analysis revealed that proanthocyanidins were the major phenolic group in YK. In contrast to other proanthocyanidin-rich foods, YK was rich in bioavailable proanthocyanidins (with a degree of polymerization ≤3) specifically with A-type dimers. Significant concentrations of phloridzin and coumestrol were also exclusively found in YK seed coat and the embryo, respectively. Extracts of both the proanthocyanidin-rich seed coat and isoflavonoid-rich embryo of YK attenuated adhesion of THP-1 to LPS-stimulated human umbilical vascular endothelial cells, suggesting that they are important sources of coronary heart disease-preventive phenolics. YK has promising potential for further development as a functional food source targeted at atherosclerosis prevention.

Systemic structure-activity relationship study of phenyl polyyne diols as potential chemopreventive agents.

The present study reports the cancer chemopreventive activities of phenyl polyyne diols derived from polyacetylene triol. Thirty-seven analogues based on a 1-phenylhexa-2,4-diyne-1,6-diol scaffold were prepared and their effects on QR activity were elucidated, as well as their cytotoxicities. We found that most of the derivatives based on phenylhexa-2,4-diyne-1,6-diol exhibited good QR induction activity and relatively low cytotoxicity and systemic structure-activity relationship was revealed. In particular, 4-fluorophenyl, 3-chlorophenyl, and 3,4-dioxolophenyl derivatives showed the best profiles in terms of QR induction, cytotoxicity, and CI.

Nanometer scale fabrication and optical response of InGaN/GaN quantum disks.

In this work, we demonstrate homogeneously distributed In0.3Ga0.7N/GaN quantum disks (QDs), with an average diameter below 10 nm and a high density of 2.1 × 10(11) cm(-2), embedded in 20 nm tall nanopillars. The scalable top-down fabrication process involves the use of self-assembled ferritin bio-templates as the etch mask, spin coated on top of a strained In0.3Ga0.7N/GaN single quantum well (SQW) structure, followed by a neutral beam etch (NBE) method. The small dimensions of the iron cores inside ferritin and nearly damage-free process enabled by the NBE jointly contribute to the observation of photoluminescence (PL) from strain-relaxed In0.3Ga0.7N/GaN QDs at 6 K. The large blueshift of the peak wavelength by over 70 nm manifests a strong reduction of the quantum-confined Stark effect (QCSE) within the QD structure, which also agrees well with the theoretical prediction using a 3D Schrödinger equation solver. The current results hence pave the way towards the realization of large-scale III-N quantum structures using the combination of bio-templates and NBE, which is vital for the development of next-generation lighting and communication devices.

A model for the clustered distribution of SNPs in the human genome.

Motivated by a non-random but clustered distribution of SNPs, we introduce a phenomenological model to account for the clustering properties of SNPs in the human genome. The phenomenological model is based on a preferential mutation to the closer proximity of existing SNPs. With the Hapmap SNP data, we empirically demonstrate that the preferential model is better for illustrating the clustered distribution of SNPs than the random model. Moreover, the model is applicable not only to autosomes but also to the X chromosome, although the X chromosome has different characteristics from autosomes. The analysis of the estimated parameters in the model can explain the pronounced population structure and the low genetic diversity of the X chromosome. In addition, correlation between the parameters reveals the population-wise difference of the mutation probability. These results support the mutational non-independence hypothesis against random mutation.

Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.

BACKGROUND: Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. RESULTS: Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. CONCLUSION: This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.