TSC22D2 Regulates ACOT8 to Delay the Malignant Progression of Colorectal Cancer.

Purpose: Colorectal cancer (CRC) is one of the cancers with high incidence and mortality rates worldwide. In China, there are approximately 400,000 new CRC cases each year, seriously endangering people's life and health. Transforming growth factor ß-stimulated clone 22 domain family, member 2 (TSC22D2) is widely expression in cancers, but the role of TSC22D2 in CRC are still unknown. Methods: Real­time quantitative PCR (qRT-PCR) and Western blot were applied to determine the TSC22D2 levels. CCK-8, colony formation and transwell assays were used to determine the proliferation and metastasis abilities of CRC cells in vitro. In vivo metastatic potential was assessed using a subcutaneously injected mouse model and. Western-blot and immunoprecipitation experiments were used to study the mechanism of TSC22D2­mediated metastasis. Results: We found TSC22D2 was deregulated in CRC tissues and cells and implied poor prognosis. Overexpression TSC22D2 significantly promoted CRC cells proliferation and tumorigenicity both in vitro and vivo, whereas knockdown TSC22D2 resulted in the opposite effects. Importantly using a co-immunoprecipitation (co-IP) assay combined with mass spectrometry analysis to identify TSC22D2-interacting acyl-coenzyme A thioesterases 8 (ACOT8), TSC22D2 maintained stability of ACOT8. Overexpression of TCC22D2 in CRC cells can promote the expression of ACOT8 and inhibit the proliferation and metastasis of CRC cells through EMT mechanism, highlighting the possibility of TSC22D2 as a potential target in CRC development. Conclusion: In summary, the present study revealed the inhibitory effect of TSC22D2 on the proliferation of colorectal cancer cells, suggesting that TSC22D2 may be an important tumor suppressor and a potential therapeutic target during colorectal carcinogenesis.

Artificial intelligence-based prediction model for the elemental occurrence form of tailings and mine wastes.

With the advent of the second industrial revolution, mining and metallurgical processes generate large volumes of tailings and mine wastes (TMW), which worsens global environmental pollution. Studying the occurrence of metal and metalloid elements in TMW is an effective approach to evaluating pollution linked to TMW. However, traditional laboratory-based measurements are complicated and time-consuming; thus, an empirical method is urgently needed that can rapidly and accurately determine elemental occurrence forms. In this study, a model combining Bayesian optimization and random forest (RF) approaches was proposed to predict TMW occurrence forms. To build the RF model, a dataset of 2376 samples was obtained, with mineral composition, elemental properties, and total concentration composition used as inputs and the percentage of occurrence forms as the model output. The correlation coefficient (R), coefficient of determination, mean absolute error, root mean squared error, and root mean squared logarithmic error metrics were used for model evaluation. After Bayesian optimization, the optimal RF model achieved accurate predictive performance, with R values of 0.99 and 0.965 on the training and test sets, respectively. The feature significance was analyzed using feature importance and Shapley additive explanatory values, which revealed that the electronegativity and total concentration of the elements were the two features with the greatest influence on the model output. As the electronegativity of an element increases, its corresponding residual fraction content gradually decreases. This is because the solubility typically increases with the solvent's polarity and electronegativity. Overall, this study proposes an RF model based on the nature of TMW that can rapidly and accurately predict the percentage values of metal and metalloid element occurrence forms in TMW. This method can minimize testing time requirements and help to assess TMW pollution risks, as well as further promote safe TMW management and recycling.

Histone methylation readers MRG1/2 interact with PIF4 to promote thermomorphogenesis in Arabidopsis.

Warm ambient conditions induce thermomorphogenesis and affect plant growth and development. However, the chromatin regulatory mechanisms involved in thermomorphogenesis remain largely obscure. In this study, we show that the histone methylation readers MORF-related gene 1 and 2 (MRG1/2) are required to promote hypocotyl elongation in response to warm ambient conditions. A transcriptome sequencing analysis indicates that MRG1/2 and phytochrome interacting factor 4 (PIF4) coactivate a number of thermoresponsive genes, including YUCCA8, which encodes a rate-limiting enzyme in the auxin biosynthesis pathway. Additionally, MRG2 physically interacts with PIF4 to bind to thermoresponsive genes and enhances the H4K5 acetylation of the chromatin of target genes in a PIF4-dependent manner. Furthermore, MRG2 competes with phyB for binding to PIF4 and stabilizes PIF4 in planta. Our study indicates that MRG1/2 activate thermoresponsive genes by inducing histone acetylation and stabilizing PIF4 in Arabidopsis.

Improving Photocleavage Efficiency of Photocleavable Protein for Antimicrobial Peptide Histatin 1 Expression.

BACKGROUND: Antimicrobial peptides (AMPs) are promising alternative agents for antibiotics to overcome antibiotic resistance problems. But, it is difficult to produce large-scale antimicrobial research due to the toxicity towards expression hosts or degradation by peptidases in the host. Therefore, heterologous recombinant expression of antimicrobial peptides has always been a challenging issue. OBJECTIVES: To overcome toxicity to the expression host and low expression level, a new photocleavable protein fusion expression method for antimicrobial peptides is provided.3 Methods: Through directed evolution and high throughput screening, a photocleavable protein mutant R6-2-6-4 with a higher photocleavage efficiency was obtained. The DNA coding sequence of antimicrobial peptide Histatin 1 was fused within the sequence of R6-2-6-4 gene. The fusion gene was successfully expressed in Escherichia coli expression system. RESULTS: Antimicrobial peptide Histatin 1 could be successfully expressed and purified by fusing within PhoCl mutant R6-2-6-4. The antimicrobial activity was rarely affected, and the MIC value was 33 ug/mL, which was basically equivalent to 32 ug/mL of the chemically synthesized Histatin 1. After amplification in a 5 L fermenter, the expression of PhoCl mutant (R6-2-6-4)-Histatin1 improved up to 87.6 mg/L in fermenter, and Histatin1 obtained by photocleavage also could up to 11 mg/L. The prepared Histatin1 powder remained stable when stored at 4oC for up to 4 months without any degradation. In addition, the expression and photocleavage of ß -Defensin105 and Lysostaphin verified the certain universality of the PhoCl mutant fusion expression system. CONCLUSION: Antimicrobial peptides Histatin 1, ß -Defensin 105 and Lysostaphin were successfully expressed and purified by photocleavable protein mutant. This may provide a novel strategy to express and purify antimicrobial peptides in the Escherichia coli expression system.

FGF19/FGFR4 signaling contributes to hepatocellular carcinoma survival and immune escape by regulating IGF2BP1-mediated expression of PD-L1.

Immune-checkpoint blockade (ICB) therapies have been widely used in clinical treatment of cancer patients, but only 20-30% of patients benefit from immunotherapy. Therefore, it is important to decipher the molecular mechanism of resistance to ICB and develop new combined treatment strategies. PD-L1 up-regulation in tumor cells contributes to the occurrence of immune escape. Increasing evidence shows that its transcription level is affected by multiple factors, which limits the objective response rate of ICB. Fibroblast growth factor 19 (FGF19), a member of the fibroblast growth factor family, is widely involved in the malignant progression of many tumors by binding to fibroblast growth factor receptor 4 (FGFR4). In this study, we confirmed that FGF19 acts as a driver gene in hepatocellular carcinoma (HCC) progression by binding to FGFR4. The up-regulation of FGF19 and FGFR4 in HCC is associated with poor prognosis. We found that FGF19/FGFR4 promoted the proliferation and invasion of HCC cells by driving IGF2BP1 to promote PD-L1 expression. Knockdown of FGFR4 significantly reduced the expression of IGF2BP1/PD-L1 and inhibited the proliferation and invasion of HCC cells. These biological effects are achieved by inhibiting the PI3K/AKT pathway. The combination of FGFR4 knockdown and anti-PD-1 antibody greatly suppressed tumor growth and enhanced the sensitivity of immunotherapy, highlighting the clinical significance of FGF19/FGFR4 activation in immunotherapy.

Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions.

Trichothecenes are highly toxic mycotoxins produced by Fusarium fungi, while TRI101/201 family enzymes play a crucial role in detoxification through acetylation. Studies on the substrate specificity and catalytic kinetics of TRI101/201 have revealed distinct kinetic characteristics, with significant differences observed in catalytic efficiency toward deoxynivalenol, while the catalytic efficiency for T-2 toxin remains relatively consistent. In this study, we used structural bioinformatics analysis and a molecular dynamics simulation workflow to investigate the mechanism underlying the differential catalytic activity of TRI101/201. The findings revealed that the binding stability between trichothecenes and TRI101/201 hinges primarily on a hydrophobic cage structure within the binding site. An intrinsic disordered loop, termed loop cover, defined the evolutionary patterns of the TRI101/201 protein family that are categorized into four subfamilies (V1/V2/V3/M). Furthermore, the unique loop displayed different conformations among these subfamilies' structures, which served to disrupt (V1/V2/V3) or reinforce (M) the hydrophobic cages. The disrupted cages enhanced the water exposure of the hydrophilic moieties of substrates like deoxynivalenol and thereby hindered their binding to the catalytic sites of V-type enzymes. In contrast, this water exposure does not affect substrates like T-2 toxin, which have more hydrophobic substituents, resulting in a comparable catalytic efficiency of both V- and M-type enzymes. Overall, our studies provide theoretical support for understanding the catalytic mechanism of TRI101/201, which shows how an intrinsic disordered loop could impact the protein-ligand binding and suggests a direction for rational protein design in the future.

The key constituents underlying the combined toxicity of eight cosmetic contaminants towards Vibrio qinghaiensis.

Cosmetic additives (ADDs) and packaging plasticizers (PLAs) probably present potential risks and dangers to the environment and human body as emerging pollutants. To investigate their potential risks and dangers, five ADDs including methyl paraben (MET), ethyl paraben (ETH), propyl paraben (PRO), butyl-hydroxy anisole (BHA), and salicylic acid (SAL), as well as three PLAs including bisphenol A (BPA), bisphenol S (BPS) and tris(2-butoxyethyl) phosphate (TBEP) were selected as research objects, and ten mixture rays (R1-R10) composed of the eight components were designed by the uniform design ray (UD-Ray) method. The toxicities of the eight cosmetic pollutants and their eight-component mixture system towards Vibrio qinghaiensis sp.-Q67 (Q67) were systematically determined by the time-dependent microplate toxicity analysis (t-MTA) method. The three-dimensional (3D) surface of deviation from the concentration addition model (dCA) was utilized to qualitatively and quantitatively analyse the toxicity interaction of the mixtures and the correlation between toxicity interaction and the components' concentration ratios. Finally, eight individual pollutants and representative rays with significant inhibitory and interactive effects were selected to analyse DNA and soluble proteolysis as well as the microstructure and morphology of Q67 after treatment with single chemicals and their mixtures. The results showed that the eight cosmetic pollutants had conspicuous concentration-dependent toxicity and acute toxicity, and none of them, except BPS, BPA and ETH, had time-dependent toxicity. All rays had time/concentration-dependent toxicity and acute toxicity. At the same time, the toxicity interaction of these mixture rays was predominantly antagonism and the strongest antagonism appeared at high concentrations at 12 h. Nevertheless, the components' concentration ratio (pi) was the decisive factor for the type of mixture interaction. The correlation analysis revealed a significant positive linear correlation between mixture toxicity and pETH and pBPA, which indicated that ETH and BPA were the key components of the toxic effects. However, there was a significant negative linear correlation between the antagonism intensity and pBPA and pTBEP, which demonstrated that BPA and TBEP were the key components of the antagonism intensity. Pollutants and their mixtures can also damage cellular structures, and mixtures can exacerbate the dissolution of DNA and soluble proteins.

PIF7-mediated epigenetic reprogramming promotes the transcriptional response to shade in Arabidopsis.

For shade-intolerant plants, changes in light quality through competition from neighbors trigger shade avoidance syndrome (SAS): a series of morphological and physiological adaptations that are ultimately detrimental to plant health and crop yield. Phytochrome-interacting factor 7 (PIF7) is a major transcriptional regulator of SAS in Arabidopsis; however, how it regulates gene expression is not fully understood. Here, we show that PIF7 directly interacts with the histone chaperone anti-silencing factor 1 (ASF1). The ASF1-deprived asf1ab mutant showed defective shade-induced hypocotyl elongation. Histone regulator homolog A (HIRA), which mediates deposition of the H3.3 variant into chromatin, is also involved in SAS. RNA/ChIP-sequencing analyses identified the role of ASF1 in the direct regulation of a subset of PIF7 target genes. Furthermore, shade-elicited gene activation is accompanied by H3.3 enrichment, which is mediated by the PIF7-ASF1-HIRA regulatory module. Collectively, our data reveal that PIF7 recruits ASF1-HIRA to increase H3.3 incorporation into chromatin to promote gene transcription, thus enabling plants to effectively respond to environmental shade.

Research on Application of Data Mining Algorithm in Cardiac Medical Diagnosis System.

Heart disease is a very common high-incidence disease. Due to the wide variety of pathology of heart disease, how to improve the medical diagnosis of heart disease and carry out earlier intervention and treatment is a problem that needs to be solved urgently. The paper adds the decision tree algorithm and its comparison and proposes an optimized classification algorithm Co-SVM. Based on the establishment of a heart disease diagnosis classifier based on data mining algorithms, it is aimed at exploring which of these four algorithms is more suitable for heart disease diagnosis problems and optimizing them. A brief description of the cause, influencing factors, and acquired data of heart disease can be seen from the accuracy and scientificity of the data, which further enhances the authenticity and reliability of the clinical diagnosis model of heart disease. At the same time, the ultrasound diagnosis technology of heart disease is introduced, and the important role of ultrasound diagnosis technology in the medical diagnosis of heart disease is discussed. This thesis uses the heart disease clinical data set to establish a heart disease diagnosis classifier based on the decision tree algorithm, neural network algorithm, support vector machine algorithm, and Co-SVM algorithm. Through experimental comparison and analysis, the optimal classification is selected according to the obtained results. The algorithm is Co-SVM algorithm. The experimental results show that the proposed Co-SVM algorithm has a higher accuracy rate than the other three classic algorithms, and the effectiveness of the Co-SVM algorithm is verified by the evaluation results of multiple algorithms. By applying the Co-SVM algorithm in the medical diagnosis system, it is helpful to assist doctors in making more accurate and precise diagnosis of the condition.

Characterization and functional analysis of RdDFR1 regulation on flower color formation in Rhododendron delavayi.

Rhododendron delavayi is a popular ornamental plant with globular flowers noted for their bright red color, but very limited studies have been reported on its flower color formation. In this study, we successfully isolated a novel DFR gene (RdDFR1) from red flowers of Rhododendron delavayi. Multiple sequence alignments revealed that RdDFR1 had the conserved NADP and substrate binding domain, and was classified into Asn-type DFR. Meanwhile, quantitative real-time PCR analysis showed that transcript levels of RdDFR1 matched the accumulation patterns of anthocyanins during flower development, hinting its potential role involved in anthocyanin biosynthesis. Then in vitro enzymatic analysis indicated that recombinant RdDFR1 protein could catalyze the production of leucoanthocyanidins from dihydroquercetin and dihydromyricetin. Furthermore, the in planta assay, using Arabidopsis thaliana dfr mutant (tt3-1) and tobacco, displayed that RdDFR1 transgenes recovered the defective proanthocyanidin and anthocyanin biosynthesis at seed coats, hypocotyl as well as cotyledon, and altered the flowers color of tobacco from pale pink to dark pink which demonstrated its function as dihydroflavonol 4-reductase in vivo. In summary, our findings suggest that RdDFR1 plays a crucial role in the biosynthesis of anthocyanin and will also make a contribution to understand the mechanisms of flower color formation in Rhododendron delavayi.

Functional analysis of a dihydroflavonol 4-reductase gene in Ophiorrhiza japonica (OjDFR1) reveals its role in the regulation of anthocyanin.

Dihydroflavonol 4-reductase (DFR), a key regulatory enzyme, participated in the biosynthesis of anthocyanins, proanthocyanidins and other flavonoids that essential for plant survival and human health. However, the role of this enzyme in Ophiorrhiza japonica is still unknown. Here, three putative DFR-like genes were firstly isolated from O. japonica. Phylogenetic analysis indicated that OjDFR1 was classified into DFR subgroup, while the rest two were clustered into other NADPH-dependent reductases. Then, functions of the three genes were further characterized. Expression analysis showed that OjDFR1 transcripts had strong correlations with the accumulation pattern of anthocyanin during the flower developmental, whereas other two were not, this suggested the potential roles of OjDFR1 in anthocyanin biosynthesis. Subsequently, all three clones were functionally expressed in Escherichia coli, but confirming that only OjDFR1 encode active DFR proteins that catalyzed the reduction of dihydroflavonols to leucoanthocyanidin. Consistant with the biochemical assay results, overexpressing OjDFR1 in Arabidopsis tt3-1 mutant successfully restored the deficiency of anthocyanin and proanthocyanidin, hinting its function as DFR in planta. Additionally, heterologous expression of OjDFR1 in transgenic tobacco contributed to darker flower color via up-regulating the expressions of endogenous NtANS and NtUFGT, which suggested that OjDFR1 was involved in flower color development. In summary, this study validates the functions of OjDFR1 and expands our understanding of anthocyanin biosynthesis in O. japonica.

Dynamic and quantitative characterization of antagonism within disinfectant mixtures by a modified area-concentration ratio method.

The coexistence of various typical disinfectant pollutants has the potential to produce toxicity interaction towards organisms in the environment. A suitable model is necessary to evaluate the interaction quantitatively. Hence, the area-concentration ratio (ACR) method was modified (MACR) by combing confidence intervals to dynamically and quantitatively evaluate the toxicity interactions within disinfectant mixture pollutants. Disinfectant mixtures were designed by the direct equipartition design ray method using three guanidine disinfectants, chlorhexidine diacetate (CD), chlorhexidine (CHL), and polyhexamethylene biguanidine (POL) and one chlorine-containing disinfectant calcium hypochlorite (CAL). The toxicities of the four disinfectants and their mixtures towards Vibrio qinghaiensis sp.-Q67 (Q67) were determined by the time-dependent toxicity microplate analysis method. And the toxicity mechanism was analyzed by determining the effects of four disinfectants and their binary mixtures on the structure of cell, DNA and proteins (Pro) for Q67. The results show that the toxicities of CD and CHL to Q67vary little with time, but POL and CAL show the obvious time-dependent toxicity. The toxicities of CD, CHL and POL to Q67 are significantly stronger than that of CAL at the same exposure time. The toxicities of three binary mixture systems don't have significant difference in different exposure time. MACR can dynamically, quantitatively and accurately characterize toxicity interactions compared with ACR. According to MACR, the antagonism intensity dynamically changes with the prolongation of exposure time for binary mixture rays of three guanidine disinfectants and CAL, and linearly correlates with the components' concentration ratios. Four disinfectants all can destroy cell membrane and cause desaturation DNA of test organism, and CAL even can destroy the structure of DNA and protein. The probably reason for the antagonism within binary mixtures is the reaction between guanidine group and ClO-, which is called chemical antaogism.

Development of marker-free rice with stable and high resistance to rice black-streaked dwarf virus disease through RNA interference.

The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Asia. RNA interference (RNAi) has been widely applied to develop antiviral varieties in plants. So far, only a few studies reported the application of RNAi in rice against RBSDV and most of them are lack of enough data to support its breeding potential, which limited the progress on developing RBSDV-resistant variety. In this study, we generated three RNAi constructs to specifically target three RBSDV genes (S1, S2 and S6), respectively. We confirmed that RNAi targeting RBSDV S6 conferred rice with almost full immunity to RBSDV through phenotyping test in eight consecutive years in both artificial inoculation and field trials, while RNAi of S1 or S2 only leads to partially increased resistance. The S6RNAi was also found conferring strong resistance to southern rice black-streaked dwarf virus (SRBSDV), a novel species closely related to RBSDV that outbroke recently in Southern China. In particular, no adverse effects on agronomical and developmental traits were found in S6RNAi transgenic lines. The marker-free transgenic lines with S6RNAi, driven by either maize ubiquitin-1 promoter or rice rbcS green tissue expression promoter, in elite rice background should have great potential in breeding of resistant varieties to both RBSDV and SRBSDV and provide a basis for further safety evaluation and commercial application.

Driver Fatigue Detection Based on Convolutional Neural Networks Using EM-CNN.

With a focus on fatigue driving detection research, a fully automated driver fatigue status detection algorithm using driving images is proposed. In the proposed algorithm, the multitask cascaded convolutional network (MTCNN) architecture is employed in face detection and feature point location, and the region of interest (ROI) is extracted using feature points. A convolutional neural network, named EM-CNN, is proposed to detect the states of the eyes and mouth from the ROI images. The percentage of eyelid closure over the pupil over time (PERCLOS) and mouth opening degree (POM) are two parameters used for fatigue detection. Experimental results demonstrate that the proposed EM-CNN can efficiently detect driver fatigue status using driving images. The proposed algorithm EM-CNN outperforms other CNN-based methods, i.e., AlexNet, VGG-16, GoogLeNet, and ResNet50, showing accuracy and sensitivity rates of 93.623% and 93.643%, respectively.

NAP1-Related Protein 1 (NRP1) has multiple interaction modes for chaperoning histones H2A-H2B.

Nucleosome Assembly Protein 1 (NAP1) family proteins are evolutionarily conserved histone chaperones that play important roles in diverse biological processes. In this study, we determined the crystal structure of Arabidopsis NAP1-Related Protein 1 (NRP1) complexed with H2A-H2B and uncovered a previously unknown interaction mechanism in histone chaperoning. Both in vitro binding and in vivo plant rescue assays proved that interaction mediated by the N-terminal α-helix (αN) domain is essential for NRP1 function. In addition, the C-terminal acidic domain (CTAD) of NRP1 binds to H2A-H2B through a conserved mode similar to other histone chaperones. We further extended previous knowledge of the NAP1-conserved earmuff domain by mapping the amino acids of NRP1 involved in association with H2A-H2B. Finally, we showed that H2A-H2B interactions mediated by αN, earmuff, and CTAD domains are all required for the effective chaperone activity of NRP1. Collectively, our results reveal multiple interaction modes of a NAP1 family histone chaperone and shed light on how histone chaperones shield H2A-H2B from nonspecific interaction with DNA.

Total flavonoids of Selaginella pulvinata alleviates cognitive impairment in mice.

Cognitive impairment (CI) refers to dysfunctional cognition, which encompasses a spectrum of disorders, ranging from mild cognitive impairment to dementia. Any factor that results in cortical damage may cause CI. Total flavonoids of Selaginella pulvinata (TFSP), have shown promising antioxidant and protective effects in animal models. In the present study, mice were intraperitoneally treated with scopolamine, sodium nitrite or 45% ethanol to induce memory impairment, and the effects were assessed using a step-down test. After performing the behavioural test, hippocampal sections were collected for anatomical analysis, and the brain and serum levels of memory-related molecules were evaluated. The results showed that TFSP improved memory in a mouse model of CI significantly. Serum data were consistent with the behavioural results: TFSP increased blood acetylcholine levels through modulation of the acetylcholinesterase and choline acetyltransferase levels. It also ameliorated oxidative stress in neurons, increasing superoxide dismutase, glutathione peroxidase and inhibiting nitric oxide synthase levels in the brain. These results suggest that TFSP may exhibit potential as a clinical treatment for neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease, and senile dementia.

Structural insights into target DNA recognition by R2R3-MYB transcription factors.

As the largest group of MYB family transcription factors, R2R3-MYB proteins play essential roles during plant growth and development. However, the structural basis underlying how R2R3-MYBs recognize the target DNA remains elusive. Here, we report the crystal structure of Arabidopsis WEREWOLF (WER), an R2R3-MYB protein, in complex with its target DNA. Structural analysis showed that the third α-helices in both the R2 and R3 repeats of WER fit in the major groove of the DNA, specifically recognizing the DNA motif 5'-AACNGC-3'. In combination with mutagenesis, in vitro binding and in vivo luciferase assays, we showed that K55, N106, K109 and N110 are critical for the function of WER. Although L59 of WER is not involved in DNA binding in the structure, ITC analysis suggested that L59 plays an important role in sensing DNA methylation at the fifth position of cytosine (5mC). Like 5mC, methylation at the sixth position of adenine (6mA) in the AAC element also inhibits the interaction between WER and its target DNA. Our study not only unravels the molecular basis of how WER recognizes its target DNA, but also suggests that 5mC and 6mA modifications may block the interaction between R2R3-MYB transcription factors and their target genes.

Identification of new rice cultivars and resistance loci against rice black-streaked dwarf virus disease through genome-wide association study.

BACKGROUND: The rice black-streaked dwarf virus (RBSDV) disease causes severe rice yield losses in Eastern China and other East Asian countries. Breeding resistant cultivars is the most economical and effective strategy to control the disease. However, few varieties and QTLs for RBSDV resistance have been identified to date. RESULTS: In this study, we conducted a genome-wide association study (GWAS) on RBSDV resistance using the rice diversity panel 1 (RDP1) cultivars that were genotyped by a 44,000 high-density single nucleotide polymorphism (SNP) markers array. We found that less than 15% of these cultivars displayed resistance to RBSDV when tested under natural infection conditions at two locations with serious RBSDV occurrence. The aus, indica and tropical japonica sub-populations displayed higher RBSDV resistance than the aromatic and temperate japonica sub-populations. In particular, we identified four varieties that displayed stable levels of RBSDV resistance at all testing locations. GWAS identified 84 non-redundant SNP loci significantly associated with RBSDV resistance at two locations, leading to the identification of 13 QTLs for RBSDV resistance. Among them, qRBSDV-4.2 and qRBSDV-6.3 were detected at both locations, suggesting their resistance stability against environmental influence. Field disease evaluations showed that qRBSDV-6.3 significantly reduces RBSDV disease severity by 20%. Furthermore, introgression of qRBSDV-6.3 into two susceptible rice cultivars by marker-assisted selection demonstrated the effectiveness of qRBSDV-6.3 in enhancing RBSDV resistance. CONCLUSIONS: The new resistant cultivars and QTLs against RBSDV disease identified in this study provide important information and genetic materials for the cloning of RBSDV resistance genes as well as developing RBSDV resistant varieties through marker-assisted selection.

Linking PHYTOCHROME-INTERACTING FACTOR to Histone Modification in Plant Shade Avoidance.

Shade avoidance syndrome (SAS) allows a plant grown in a densely populated environment to maximize opportunities to access to sunlight. Although it is well established that SAS is accompanied by gene expression changes, the underlying molecular mechanism needs to be elucidated. Here, we identify the H3K4me3/H3K36me3-binding proteins, Morf Related Gene (MRG) group proteins MRG1 and MRG2, as positive regulators of shade-induced hypocotyl elongation in Arabidopsis (Arabidopsis thaliana). MRG2 binds PHYTOCHROME-INTERACTING FACTOR7 (PIF7) and regulates the expression of several common downstream target genes, including YUCCA8 and IAA19 involved in the auxin biosynthesis or response pathway and PRE1 involved in brassinosteroid regulation of cell elongation. In response to shade, PIF7 and MRG2 are enriched at the promoter and gene-body regions and are necessary for increase of histone H4 and H3 acetylation to promote target gene expression. Our study uncovers a mechanism in which the shade-responsive factor PIF7 recruits MRG1/MRG2 that binds H3K4me3/H3K36me3 and brings histone-acetylases to induce histone acetylations to promote expression of shade responsive genes, providing thus a molecular mechanistic link coupling the environmental light to epigenetic modification in regulation of hypocotyl elongation in plant SAS.

The Histone Chaperone NRP1 Interacts with WEREWOLF to Activate GLABRA2 in Arabidopsis Root Hair Development.

NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) defines an evolutionarily conserved family of histone chaperones and loss of function of the Arabidopsis thaliana NAP1 family genes NAP1-RELATED PROTEIN1 (NRP1) and NRP2 causes abnormal root hair formation. Yet, the underlying molecular mechanisms remain unclear. Here, we show that NRP1 interacts with the transcription factor WEREWOLF (WER) in vitro and in vivo and enriches at the GLABRA2 (GL2) promoter in a WER-dependent manner. Crystallographic analysis indicates that NRP1 forms a dimer via its N-terminal α-helix. Mutants of NRP1 that either disrupt the α-helix dimerization or remove the C-terminal acidic tail, impair its binding to histones and WER and concomitantly lead to failure to activate GL2 transcription and to rescue the nrp1-1 nrp2-1 mutant phenotype. Our results further demonstrate that WER-dependent enrichment of NRP1 at the GL2 promoter is involved in local histone eviction and nucleosome loss in vivo. Biochemical competition assays imply that the association between NRP1 and histones may counteract the inhibitory effect of histones on the WER-DNA interaction. Collectively, our study provides important insight into the molecular mechanisms by which histone chaperones are recruited to target chromatin via interaction with a gene-specific transcription factor to moderate chromatin structure for proper root hair development.