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1.
Plant Cell ; 34(9): 3425-3442, 2022 08 25.
Article in English | MEDLINE | ID: mdl-35642941

ABSTRACT

Plants manage the high cost of immunity activation by suppressing the expression of defense genes during normal growth and rapidly switching them on upon pathogen invasion. TGAs are key transcription factors controlling the expression of defense genes. However, how TGAs function, especially in monocot plants like rice with continuously high levels of endogenous salicylic acid (SA) remains elusive. In this study, we characterized the role of OsTGA5 as a negative regulator of rice resistance against blast fungus by transcriptionally repressing the expression of various defense-related genes. Moreover, OsTGA5 repressed PTI responses and the accumulation of endogenous SA. Importantly, we showed that the nucleus-localized casein kinase II (CK2) complex interacts with and phosphorylates OsTGA5 on Ser-32, which reduces the affinity of OsTGA5 for the JIOsPR10 promoter, thereby alleviating the repression of JIOsPR10 transcription and increasing rice resistance. Furthermore, the in vivo phosphorylation of OsTGA5 Ser-32 was enhanced by blast fungus infection. The CK2 α subunit, depending on its kinase activity, positively regulated rice defense against blast fungus. Taken together, our results provide a mechanism for the role of OsTGA5 in negatively regulating the transcription of defense-related genes in rice and the repressive switch imposed by nuclear CK2-mediated phosphorylation during blast fungus invasion.


Subject(s)
Magnaporthe , Oryza , Casein Kinase II , Disease Resistance , Gene Expression Regulation, Plant , Phosphorylation , Plant Diseases , Plant Proteins , Salicylic Acid , Transcription, Genetic
2.
Plant Biotechnol J ; 2024 May 27.
Article in English | MEDLINE | ID: mdl-38803114

ABSTRACT

Although thousands of genes have been identified or cloned in rice (Oryza sativa) in the last two decades, the majority of them have only been separately characterized in specific varieties or single-gene modified backgrounds, thus limiting their practical application. We developed an optimized multiplex genome editing (MGE) toolbox that can efficiently assemble and stably express up to twelve sgRNA targets in a single plant expression vector. In this study, we established the MGE-based Rapid Directional Improvement (MRDI) strategy for directional improvement of complex agronomic traits in one small-scale rice transformation. This approach provides a rapid and practical procedure, encompassing sgRNA assembly, transgene-free screening and the creation of promising germplasm, by combining the precision of gene editing with phenotype-based field breeding. The MRDI strategy was used to generate the full diversity of twelve main agronomic genes in rice cultivar FXZ for the directional improvement of its growth duration and plant architecture. After applying the MRDI to FXZ, ideal plants with the desired traits of early heading date reduced plant height, and more effective panicles were generated without compromising yield, blast resistance and grain quality. Furthermore, the results of whole-genome sequencing (WGS), including the analysis of structural variations (SVs) and single nucleotide variations (SNVs) in the MGE plants, confirmed the high specificity and low frequency of unwanted mutations associated with this strategy. The MRDI breeding strategy would be a robust approach for exploring and applying crucial agronomic genes, as well as for generating novel elite germplasm in the future.

3.
Appl Opt ; 63(14): 3854-3862, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38856348

ABSTRACT

Star trackers are typically used in a spacecraft to provide absolute attitude information to the on-board attitude control system so as to promote high accuracy. The performance of the star tracker is rather important. Attitude incorrectness provided by star trackers may lead to bad navigation with big deviations, even failure of satellites. Therefore, how to realize and verify the accuracy is crucial. As a matter of fact, it is difficult to validate accuracy of star trackers on the ground, especially for star trackers under highly dynamic conditions. In this paper, an accuracy measurement method for star trackers under dynamic conditions is proposed, utilizing a high-accuracy swing table to provide reference to compare. To this end, a swing table, star tracker, and the test equipment are synchronized, in order to reduce systematic errors. As the motion trajectory of the swing table can be set beforehand, the initial attitude of the star tracker can be predicted through a set of coordinate transformations. As a result, the star tracker is able to keep tracking, regardless of the angular velocity of the swing table. This makes the statistical sample points more sufficient and the results more reliable. Moreover, it can evaluate the angular velocity of star trackers up to 20°/s. In comparison with the conventional method with simulated stars, this method utilizes real navigation stars as observation targets making the measurement results much closer to the on-orbit performance. Lastly, but much more importantly, it can also verify the performance of a star tracker in one experiment, such as sensitivity, static performance, capture probability, and so on. Experimental results demonstrate that the proposed method is effective, especially for highly dynamic star trackers. Such a measurement environment is close to the in-orbit conditions, and it can satisfy the stringent requirement for star trackers under high dynamics.

4.
Plant Mol Biol ; 111(4-5): 415-428, 2023 Mar.
Article in English | MEDLINE | ID: mdl-36867321

ABSTRACT

Prolonged storage of rice seeds can lead to a decrease in seed vigor and seedling quality. The Lipoxygenase (LOX) gene family is widely distributed in plants, and LOX activity is closely related to seed viability and stress tolerance. In this study, the lipoxygenase OsLOX10 gene from the 9-lipoxygenase metabolic pathway was cloned from rice, and its roles in determining seed longevity and tolerance to saline-alkaline stress caused by Na2CO3 in rice seedlings were mainly investigated. CRISPR/Cas9 knockout of OsLOX10 increased seed longevity compared with the wild-type and OsLOX10 overexpression lines in response to artificial aging. The expression levels of other 9-lipoxygenase metabolic pathway related genes, such as LOX1, LOX2 and LOX3, were increased in the LOX10 overexpression lines. Quantitative real-time PCR and histochemical staining analysis showed that the expression of LOX10 was highest in seed hulls, anthers and the early germinating seeds. KI-I2 staining of starch showed that LOX10 could catalyze the degradation of linoleic acid. Furthermore, we found that the transgenic lines overexpressing LOX10 showed better tolerance to saline-alkaline stress than the wild-type and knockout mutant lines. Overall, our study demonstrated that the knockout LOX10 mutant increased seed longevity, whereas overexpression of LOX10 enhanced tolerance to saline-alkaline stress in rice seedlings.


Subject(s)
Lipoxygenase , Oryza , Lipoxygenase/genetics , Seedlings/metabolism , Oryza/genetics , Longevity , Seeds/genetics
5.
BMC Plant Biol ; 23(1): 11, 2023 Jan 06.
Article in English | MEDLINE | ID: mdl-36604645

ABSTRACT

BACKGROUND: The sterile lemma is a unique organ of the rice (Oryza sativa L.) spikelet. However, the characteristics and origin of the rice sterile lemma have not been determined unequivocally, so it is important to elucidate the molecular mechanism of the development of the sterile lemma. RESULTS: In the paper, we outline the regulatory mechanism of sterile lemma development by LONG STERILE LEMMA1 (G1), which has been identified as the gene controlling sterile lemma development. Based on the comprehensive analyses of transcriptome dynamics during sterile lemma development with G1 alleles between wild-type (WT) and mutant (MT) in rice, we obtained co-expression data and regulatory networks related to sterile lemma development. Co-transfection assays of rice protoplasts confirmed that G1 affects the expression of various phytohormone-related genes by regulating a number of critical transcription factors, such as OsLBD37 and OSH1. The hormone levels in sterile lemmas from WT and MT of rice supports the hypotheses that lower auxin, lower gibberellin, and higher cytokinin concentrations are required to maintain a normal phenotype of sterile lemmas. CONCLUSION: The regulatory networks have considerable reference value, and some of the regulatory relationships exhibiting strong correlations are worthy of further study. Taken together, these work provided a detailed guide for further studies into the molecular mechanism of sterile lemma development.


Subject(s)
Oryza , Gene Regulatory Networks , Plant Proteins/genetics , Plant Proteins/metabolism , Gene Expression Regulation, Plant , Mutation
6.
BMC Plant Biol ; 23(1): 55, 2023 Jan 25.
Article in English | MEDLINE | ID: mdl-36698063

ABSTRACT

Drought is a major abiotic stress to rice (Oryza sativa) during growth. Ideal Plant Architecture (IPA1), the first cloned gene controlling the ideal plant type in rice, has been reported to function in both ideal rice plant architecture and biotic resistance. Here, we report that the IPA1/OsSPL14, encoding a transcriptional factor, positively regulates drought tolerance in rice. The IPA1 is constitutively expressed and regulated by H2O2, abscisic acid, NaCl and polyethylene glycol 6000 treatments in rice. Furthermore, the IPA1-knockout plants showed much greater accumulation of H2O2 as measured by 3,3'-diaminobenzidine staining in leaves compared with WT plants. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assays indicated that the IPA1 directly activates the promoter of SNAC1. Expression of SNAC1 is significantly down-regulated in IPA1 knockout plants. Further investigation indicated that the IPA1 plays a positive role in drought-stress tolerance by inducing reactive oxygen species scavenging in rice. Together, these findings indicated that the IPA1 played important roles in drought tolerance by regulating SNAC1, thus activating the antioxidant system in rice.


Subject(s)
Oryza , Oryza/metabolism , Drought Resistance , Plants, Genetically Modified/genetics , Hydrogen Peroxide/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Stress, Physiological/genetics , Droughts , Gene Expression Regulation, Plant
7.
Small ; 19(48): e2303500, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37541661

ABSTRACT

Optical Fourier surface is a unique patterned optical surface containing the precise sum of sinusoidal waves, each with a well-defined spatial frequency and amplitude. It can manipulate the desired diffracted light field through its Fourier transform, which brings a straightforward mathematical method for designing complex diffractive optics. However, the fabrication techniques typically have the drawbacks of low efficiency, limiting the large-scale industrial application of optical Fourier surfaces. This study presents a powerful approach, the multi-frequency vibration cutting (MFVC), to enable the high-efficiency fabrication of optical Fourier surfaces. A specific optical Fourier surface consisting of arbitrary frequency components of linear gratings has been fabricated on metallic surfaces using MFVC. Due to the capacity of multicomponent gratings in coupling red, green, and blue lights at the same incident angle, the RGB true color has been prepared. The additive and subtractive principles of mixing the three primary colors are demonstrated. The former relies on the light dispersion induced by grating diffraction, while the latter is based on the light absorption induced by the subwavelength grating-coupled surface plasma polarization (SPP). The experimental results of authentic structural true color on the aluminum surface verify the efficacy of MFVC in the fabrication of optical Fourier surfaces.

8.
Planta ; 255(2): 43, 2022 Jan 19.
Article in English | MEDLINE | ID: mdl-35044566

ABSTRACT

MAIN CONCLUSION: We identified a typical rice premature senescence leaf mutant 86 (psl86) and exhibited the first global ubiquitination data during rice leaf senescence. Premature leaf senescence affects the yield and quality of rice, causing irreparable agricultural economic losses. In this study, we reported a rice premature senescence leaf mutant 86 (psl86) in the population lines of rice (Oryza sativa) japonica cultivar 'Yunyin' (YY) mutagenized using ethyl methane sulfonate (EMS) treatment. Immunoblotting analysis revealed that a higher ubiquitination level in the psl86 mutant compared with YY. Thus, we performed the proteome and ubiquitylome analyses to identify the differential abundance proteins and ubiquitinated proteins (sites) related to leaf senescence. Among 885 quantified lysine ubiquitination (Kub) sites in 492 proteins, 116 sites in 94 proteins were classified as up-regulated targets and seven sites in six proteins were classified as down-regulated targets at a threshold of 1.5. Proteins with up-regulated Kub sites were mainly enriched in the carbon fixation in photosynthetic organisms, glycolysis/gluconeogenesis and the pentose phosphate pathway. Notably, 14 up-regulated Kub sites in 11 proteins were enriched in the carbon fixation in photosynthetic organism pathway, and seven proteins (rbcL, PGK, GAPA, FBA5, ALDP, CFBP1 and GGAT) were down-regulated, indicating this pathway is tightly regulated by ubiquitination during leaf senescence. To our knowledge, we present the first global data on ubiquitination during rice leaf senescence.


Subject(s)
Oryza , Gene Expression Regulation, Plant , Oryza/genetics , Oryza/metabolism , Plant Leaves/metabolism , Plant Proteins/genetics , Plant Proteins/metabolism , Plant Senescence , Proteome
9.
Opt Express ; 30(6): 8829-8846, 2022 Mar 14.
Article in English | MEDLINE | ID: mdl-35299327

ABSTRACT

Optically variable devices (OVDs) are well received for anti-counterfeiting and decorative applications. In this study, new strategies to develop highly decoupled OVDs were proposed and demonstrated based on the fast patterning of blazed gratings by vibration-assisted diamond texturing. A unique surface generation mechanism was revealed as a combined cutting and forming process. One facet of blazed grating is generated by the cutting motion defined by the tool tip trajectory. The other facet is formed by the tool flank face, which establishes the blaze angle. This process is able to generate high-resolution, structurally colored graphics by modulating cutting velocity to control the grating distribution. Due to the unique surface generation mechanism, the orientation of the created blazed gratings is intrinsically perpendicular to the cutting direction. Thus, it enables the flexible control of concentration directions of diffracted light by tuning the orientation of blazed gratings. We designed and demonstrated two types of highly decoupled OVDs based on vibration-induced blazed gratings. The orthogonal-type OVD utilizes the azimuth angle dependence of blazed gratings to encode two images in orthogonal cutting directions. The in-plane-type OVD utilizes the optimized diffraction efficiency of blazed gratings in a given diffraction order to encode two images in opposite cutting directions. The fabricated OVDs are presented and compared with optical simulation results based on an extended scalar diffraction theory.

10.
Mol Breed ; 42(3): 13, 2022 Mar.
Article in English | MEDLINE | ID: mdl-37309407

ABSTRACT

The induction of embryogenic calli plays a vital role in the genetic transformation and regeneration of rice (Oryza sativa L.). Despite progress in rice tissue culture, the molecular mechanisms of embryogenic callus induction remain unknown. In this study, gene expression profiles associated with calli were comprehensively analyzed during callus induction of japonica rice 'Yunyin'. We first confirmed that NMB medium with 24 h of light and 0 h of dark (NMB-L) was the optimal condition for 'Yunyin' callus induction, while J3 medium with 0 h of light and 24 h of dark (J3-D) was the worst condition. After transcriptome analysis, 33,597 unigenes were assembled, among which we identified 6,063 DEGs (Differentially Expressed Genes) related to media and seven DEGs related to photoperiod. Phenylpropanoid biosynthesis, plant hormone signal, and starch and sucrose metabolism were the top three pathways affected by media, while the circadian rhythm-plant pathway was associated with photoperiod. Furthermore, we identified two candidate genes, Os01g0965900 and Os12g0555200, affected by both medium and photoperiod. Statistical analysis of RNA-seq libraries showed that the expression levels of these two genes in J3-D calli were over 2.5 times higher than those in NMB-L calli, which was further proved by RT-qPCR analysis. Based on FPKM (Fragments Per Kilobase of transcript Per Million mapped reads), unigenes belonging to the NMB-L group were mainly assigned to ribosome, carbon metabolism, biosynthesis of amino acids, protein processing in endoplasmic reticulum, and plant hormone signal transduction pathways. We transformed Os12g0555200Nip and Os12g05552009311 into 'Nipponbare' calli and observed their effects on the growth and development process of rice calli using TEM (Transmission Electron Microscopy) and SEM (Scanning Electron Microscopy). Observations showed that Os12g05552009311 was more disadvantageous to rice callus growth than Os12g0555200Nip. Our results reveal that the Os12g0555200, identified from transcriptomic profiles, has a negative influence during 'Yunyin' callus induction. Supplementary information: The online version contains supplementary material available at 10.1007/s11032-022-01283-y.

11.
BMC Plant Biol ; 21(1): 287, 2021 Jun 24.
Article in English | MEDLINE | ID: mdl-34167489

ABSTRACT

BACKGROUND: Phosphoenolpyruvate carboxylase (PEPC) plays an important role in the primary metabolism of higher plants. Several studies have revealed the critical importance of PEPC in the interaction of carbon and nitrogen metabolism. However, the function mechanism of PEPC in nitrogen metabolism is unclear and needs further investigation. RESULTS: This study indicates that transgenic rice expressing the sugarcane C4-PEPC gene displayed shorter primary roots and fewer crown roots at the seedling stage. However, total nitrogen content was significantly higher in transgenic rice than in wild type (WT) plants. Proteomic analysis revealed that there were more differentially expressed proteins (DEPs) responding to nitrogen changes in transgenic rice. In particular, the most enriched pathway "glutathione (GSH) metabolism", which mainly contains GSH S-transferase (GST), was identified in transgenic rice. The expression of endogenous PEPC, GST and several genes involved in the TCA cycle, glycolysis and nitrogen assimilation changed in transgenic rice. Correspondingly, the activity of enzymes including GST, citrate synthase, 6-phosphofructokinase, pyruvate kinase and ferredoxin-dependent glutamate synthase significantly changed. In addition, the levels of organic acids in the TCA cycle and carbohydrates including sucrose, starch and soluble sugar altered in transgenic rice under different nitrogen source concentrations. GSH that the substrate of GST and its components including glutamic acid, cysteine and glycine accumulated in transgenic rice. Moreover, the levels of phytohormones including indoleacetic acid (IAA), zeatin (ZT) and isopentenyladenosine (2ip) were lower in the roots of transgenic rice under total nutrients. Taken together, the phenotype, physiological and biochemical characteristics of transgenic rice expressing C4-PEPC were different from WT under different nitrogen levels. CONCLUSIONS: Our results revealed the possibility that PEPC affects nitrogen metabolism through regulating GST, which provide a new direction and concepts for the further study of the PEPC functional mechanism in nitrogen metabolism.


Subject(s)
Glutathione Transferase/metabolism , Nitrogen/metabolism , Oryza/enzymology , Phosphoenolpyruvate Carboxylase/metabolism , Saccharum/enzymology , Carbon/metabolism , Oryza/genetics , Oryza/metabolism , Phosphoenolpyruvate Carboxylase/genetics , Plants, Genetically Modified , Proteomics , Saccharum/genetics , Transcriptome
12.
Biochem Biophys Res Commun ; 522(2): 448-455, 2020 02 05.
Article in English | MEDLINE | ID: mdl-31767151

ABSTRACT

Trichomes are specialized epidermal cells that play crucial roles in resisting environmental stress and enhancing plant development. In Arabidopsis thaliana, the main genes controlling trichome formation have been consecutively identified. However, few genes like this were reported in rice. In this study, we identified the hairy phenotype of indica variety 75-1-127. This was used to construct a segregation population with a cross of hairless variety Minghui63 (MH63) to fine map the trichome formation genes. Genetic analysis indicated that hairy phenotype was controlled by a pair of dominant genes on chromosome 6, which was designated as GLABRA6 (OsGL6). OsGL6 was an allele of HL6 gene whose sequences containing rich variations in genomes. Compared to wild type, the overexpressing transgenic lines revealed that OsGL6 promoted trichome initiation. We found that OsGL6 interacted with serine/threonine protein kinase OSK3 (OSK3) or COP9 signalosome complex subunit 5a (CSN5) in yeast. These results provide potential information for understanding the molecular mechanism of trichome formation in rice.


Subject(s)
Conserved Sequence , Organogenesis , Oryza/growth & development , Plant Proteins/chemistry , Plant Proteins/metabolism , Gene Expression Regulation, Plant , Oryza/genetics , Phenotype , Plant Leaves/metabolism , Plant Proteins/genetics , Protein Binding , Protein Domains , Saccharomyces cerevisiae/metabolism , Subcellular Fractions/metabolism , Trichomes/metabolism
13.
BMC Plant Biol ; 20(1): 76, 2020 Feb 14.
Article in English | MEDLINE | ID: mdl-32059642

ABSTRACT

BACKGROUND: Rice ratooning has traditionally been an important component of the rice cropping system in China. However, compared with the rice of the first harvest, few studies on factors effecting ratoon rice yield have been conducted. Because ratoon rice is a one-season rice cultivated using axillary buds that germinate on rice stakes and generate panicles after the first crop's harvest, its production is mainly affected by the growth of axillary buds. The objectives of this study were to evaluate the sprouting mechanism of axillary buds to improve the ratoon rice yield. RESULTS: First, we observed the differentiation and growth dynamics of axillary buds at different nodes of Shanyou 63, and found that they differentiated from bottom to top before the heading of the mother stem, and that they developed very slowly. After heading they differentiated from top to bottom, and the ones on the top, especially the top 2nd node, developed much faster than those at the other nodes. The average length and dry weight of the axillary buds were significantly greater than those at other nodes by the yellow ripe stage, and they differentiated into pistils and stamens by 6 d after the yellow ripe stage. The morphology of vegetative organs from regenerated tillers of Shanyou 63 also suggested the superior growth of the upper buds, which was regulated by hormones, in ratoon rice. Furthermore, a comprehensive proteome map of the rice axillary buds at the top 2nd node before and after the yellow ripe stage was established, and some proteins involved in steroid biosynthesis were significantly increased. Of these, four took part in brassinosteroid (BR) biosynthesis. Thus, BR signaling may play a role in the germination of axillary buds of ratoon rice. CONCLUSIONS: The data provide insights into the molecular mechanisms underlying BR signaling, and may allow researchers to explore further the biological functions of endogenous BRs in the germination of axillary buds of ratoon rice.


Subject(s)
Brassinosteroids/metabolism , Flowers/physiology , Germination , Oryza/physiology , Signal Transduction
14.
Ann Hematol ; 99(3): 443-449, 2020 Mar.
Article in English | MEDLINE | ID: mdl-31970447

ABSTRACT

This current study retrospectively analyzed the clinical characteristics of 69 adult patients with acquired pure red cell aplasia (PRCA) including 40 elderly and 29 non-elderly patients from September 2009 to June 2019. The remission induction therapy regimens included cyclosporine A (CsA), corticosteroids (CS), or other immunosuppressive agents. The overall response rate was 55% (22/40) in the elderly group compared with 75.9% (22/29) in non-elderly patients (P = 0.075). In elderly patients, the best remission was achieved in the group treated with CsA than those treated with CS or other immunosuppressive agents (83.3% vs 26.7% vs 42.9%%, P = 0.004). However, outcomes of remission were similar among different treatment groups (P = 0.458) in non-elderly patients. CS induced a higher response rate in the non-elderly than that in the elderly (88.9% vs 26.7%, P = 0.009). By univariate and multivariate analysis, the clinical efficacy of elderly patients with acquired PRCA was closely associated with an induction regimen of CsA (P = 0.009; P = 0.017). In conclusion, CsA might produce higher response rate than CS and other drugs in elderly patients with acquired PRCA.


Subject(s)
Cyclosporine/administration & dosage , Immunosuppression Therapy , Red-Cell Aplasia, Pure/drug therapy , Remission Induction , Adult , Age Factors , Aged , Aged, 80 and over , Female , Humans , Male , Middle Aged , Red-Cell Aplasia, Pure/immunology , Red-Cell Aplasia, Pure/pathology
15.
Angew Chem Int Ed Engl ; 59(40): 17525-17532, 2020 09 28.
Article in English | MEDLINE | ID: mdl-32613694

ABSTRACT

Histone deacetylase (HDAC) is a major class of deacetylation enzymes. Many HDACs exist in large protein complexes in cells and their functions strongly depend on the complex composition. The identification of HDAC-associated proteins is highly important in understanding their molecular mechanisms. Although affinity probes have been developed to study HDACs, they were mostly targeting the direct binder HDAC, while other proteins in the complex remain underexplored. We report a DNA-based affinity labeling method capable of presenting different probe configurations without the need for preparing multiple probes. Using one binding probe, 9 probe configurations were created to profile HDAC complexes. Notably, this method identified indirect HDAC binders that may be inaccessible to traditional affinity probes, and it also revealed new biological implications for HDAC-associated proteins. This study provided a simple and broadly applicable method for characterizing protein-protein interactions.


Subject(s)
Affinity Labels/chemistry , DNA/chemistry , Histone Deacetylases/metabolism , Acetylation , DNA/metabolism , HeLa Cells , Histone Deacetylase Inhibitors/chemistry , Histone Deacetylase Inhibitors/metabolism , Histone Deacetylases/chemistry , Humans , Light , Protein Binding , Protein Isoforms/metabolism
16.
Angew Chem Int Ed Engl ; 59(35): 14965-14972, 2020 08 24.
Article in English | MEDLINE | ID: mdl-32436364

ABSTRACT

Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.


Subject(s)
DNA/chemistry , Gene Library , Humans
17.
BMC Infect Dis ; 19(1): 992, 2019 Nov 21.
Article in English | MEDLINE | ID: mdl-31752711

ABSTRACT

BACKGROUND: Histoplasmosis is one of the invasive fungal infections and presents with symptoms mainly in the lungs. Disseminated histoplasmosis (DH) is rare and its lesions in the gastrointestinal tract are even uncommon. The concomitant involvement of the upper and lower gastrointestinal tract has never been described in the immunocompetent individuals. CASE PRESENTATION: A 44-year-old immunocompetent Chinese man presented with fever, hepatosplenomegaly, fungal esophagitis and protuberant lesions with central depression and erosion along the mucous membrane of the colon. The patient was diagnosed as disseminated histoplasmosis by gastrointestinal endoscopy. CONCLUSIONS: Histoplasmosis should be taken caution in patients with fever and hepatosplenomegaly. Actions should be taken to avoid its disseminated infection associated high mortality.


Subject(s)
Histoplasma/isolation & purification , Histoplasmosis/diagnosis , Adult , Colon/diagnostic imaging , Colon/pathology , Endoscopy, Gastrointestinal , Histoplasma/classification , Histoplasma/genetics , Histoplasmosis/diagnostic imaging , Histoplasmosis/immunology , Histoplasmosis/microbiology , Humans , Immunocompromised Host , Male
18.
J Am Chem Soc ; 140(46): 15859-15867, 2018 11 21.
Article in English | MEDLINE | ID: mdl-30412395

ABSTRACT

Dynamic combinatorial library (DCL) has emerged as an efficient tool for ligand discovery and become an important discovery modality in biomedical research. However, the applications of DCLs have been significantly hampered by low library diversity and limited analytical methods capable of processing large libraries. Here, we report a strategy that has addressed this limitation and can select cooperatively binding small-molecule pairs from large-scale dynamic libraries. Our approach is based on DNA-mediated dynamic hybridization, DNA-encoding, and a photo-cross-linking-based decoding scheme. To demonstrate the generality and performance of this approach, a 10 000-member DNA-encoded dynamic library has been prepared and selected against six protein targets. Specific binders have been identified for each target, and we have validated the biological activities of selected ligands for the targets that are implicated in important cellular functions including protein deacetylation and sumoylation. Notably, a series of novel and selective sirtuin-3 inhibitors have been developed. Our study has circumvented a major obstacle in DCL and may provide a broadly applicable method for ligand discovery against biological targets.


Subject(s)
DNA/chemistry , Drug Discovery , Small Molecule Libraries/chemistry , Ligands , Molecular Conformation
19.
Biochem Biophys Res Commun ; 495(1): 461-467, 2018 01 01.
Article in English | MEDLINE | ID: mdl-29128357

ABSTRACT

Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H2O2 scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K+-deficiency tolerance in rice. We found that OsPRX2 was localized in the chloroplast. Overexpressed OsPRX2 causes the stomatal closing and K+-deficiency tolerance increasing, while knockout of OsPRX2 lead to serious defects in leaves phenotype and the stomatal opening under the K+-deficiency tolerance. Detection of K+ accumulation, antioxidant activity of transgenic plants under the starvation of potassium, further confirmed that OsPRX2 is a potential target for engineering plants with improved potassium deficiency tolerance.


Subject(s)
Oryza/metabolism , Peroxiredoxins/metabolism , Plant Proteins/metabolism , Plant Stomata/metabolism , Potassium/metabolism , Cloning, Molecular , Gene Expression Regulation, Plant , Oryza/anatomy & histology , Oryza/genetics , Oryza/ultrastructure , Peroxiredoxins/analysis , Peroxiredoxins/genetics , Phylogeny , Plant Proteins/analysis , Plant Proteins/genetics , Plant Stomata/anatomy & histology , Plant Stomata/genetics , Plant Stomata/ultrastructure , Plants, Genetically Modified/anatomy & histology , Plants, Genetically Modified/genetics , Plants, Genetically Modified/metabolism , Plants, Genetically Modified/ultrastructure , Up-Regulation
20.
Bioorg Med Chem Lett ; 27(3): 361-369, 2017 02 01.
Article in English | MEDLINE | ID: mdl-28011218

ABSTRACT

DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.


Subject(s)
DNA/metabolism , Small Molecule Libraries/metabolism , Combinatorial Chemistry Techniques , DNA/chemistry , Drug Discovery , High-Throughput Screening Assays , Ligands , Nucleic Acid Hybridization , Small Molecule Libraries/chemistry
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