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1.
Virol J ; 21(1): 122, 2024 May 30.
Article in English | MEDLINE | ID: mdl-38816865

ABSTRACT

Hand, Foot and Mouth Disease (HFMD) is a highly contagious viral illness primarily affecting children globally. A significant epidemiological transition has been noted in mainland China, characterized by a substantial increase in HFMD cases caused by non-Enterovirus A71 (EV-A71) and non-Coxsackievirus A16 (CVA16) enteroviruses (EVs). Our study conducts a retrospective examination of 36,461 EV-positive specimens collected from Guangdong, China, from 2013 to 2021. Epidemiological trends suggest that, following 2013, Coxsackievirus A6 (CVA6) and Coxsackievirus A10 (CVA10) have emerged as the primary etiological agents for HFMD. In stark contrast, the incidence of EV-A71 has sharply declined, nearing extinction after 2018. Notably, cases of CVA10 infection were considerably younger, with a median age of 1.8 years, compared to 2.3 years for those with EV-A71 infections, possibly indicating accumulated EV-A71-specific herd immunity among young children. Through extensive genomic sequencing and analysis, we identified the N136D mutation in the 2 A protein, contributing to a predominant subcluster within genogroup C of CVA10 circulating in Guangdong since 2017. Additionally, a high frequency of recombination events was observed in genogroup F of CVA10, suggesting that the prevalence of this lineage might be underrecognized. The dynamic landscape of EV genotypes, along with their potential to cause outbreaks, underscores the need to broaden surveillance efforts to include a more diverse spectrum of EV genotypes. Moreover, given the shifting dominance of EV genotypes, it may be prudent to re-evaluate and optimize existing vaccination strategies, which are currently focused primarily target EV-A71.


Subject(s)
Genome, Viral , Genotype , Hand, Foot and Mouth Disease , Phylogeny , China/epidemiology , Humans , Hand, Foot and Mouth Disease/epidemiology , Hand, Foot and Mouth Disease/virology , Child, Preschool , Infant , Retrospective Studies , Female , Male , Child , Molecular Epidemiology , Enterovirus/genetics , Enterovirus/classification , Enterovirus/isolation & purification , Enterovirus A, Human/genetics , Enterovirus A, Human/isolation & purification , Genomics , Incidence , Adolescent , Enterovirus Infections/epidemiology , Enterovirus Infections/virology
2.
Chem Soc Rev ; 52(17): 5968-6002, 2023 Aug 29.
Article in English | MEDLINE | ID: mdl-37498342

ABSTRACT

Biomolecular electronics is a rapidly growing multidisciplinary field that combines biology, nanoscience, and engineering to bridge the two important fields of life sciences and molecular electronics. Proteins are remarkable for their ability to recognize molecules and transport electrons, making the integration of proteins into electronic devices a long sought-after goal and leading to the emergence of the field of protein-based bioelectronics, also known as proteotronics. This field seeks to design and create new biomolecular electronic platforms that allow for the understanding and manipulation of protein-mediated electronic charge transport and related functional applications. In recent decades, there have been numerous reports on protein-based bioelectronics using a variety of nano-gapped electrical devices and techniques at the single molecular level, which are not achievable with conventional ensemble approaches. This review focuses on recent advances in physical electron transport mechanisms, device fabrication methodologies, and various applications in protein-based bioelectronics. We discuss the most recent progress of the single or few protein-bridged electrical junction fabrication strategies, summarise the work on fundamental and functional applications of protein bioelectronics that enable high and dynamic electron transport, and highlight future perspectives and challenges that still need to be addressed. We believe that this specific review will stimulate the interdisciplinary research of topics related to protein-related bioelectronics, and open up new possibilities for single-molecule biophysics and biomedicine.


Subject(s)
Electronics , Wearable Electronic Devices , Electron Transport , Nanotechnology
3.
Angew Chem Int Ed Engl ; 63(15): e202400582, 2024 Apr 08.
Article in English | MEDLINE | ID: mdl-38308672

ABSTRACT

Large-scale deployment of proton exchange membranes water electrolysis (PEM-WE) requires a substantial reduction in usage of platinum group metals (PGMs) as indispensable electrocatalyst for cathodic hydrogen evolution reaction (HER). Ultra-fine PGMs nanocatalysts possess abundant catalytic sites at lower loading, but usually exhibit reduced stability in long-term operations under corrosive acidic environments. Here we report grafting the ultra-fine PtRu crystalline nanoalloys with PtxRuySez "amorphous skin" (c-PtRu@a-PtxRuySez) by in situ atomic layer selenation to simultaneously improve catalytic activity and stability. We found that the c-PtRu@a-PtxRuySez-1 with ~0.6 nm thickness amorphous skin achieved an ultra-high mass activity of 26.7 A mg-1 Pt+Ru at -0.07 V as well as a state-of-the-art durability maintained for at least 1000 h at -10 mA cm-2 and 550 h at -100 mA⋅cm-2 for acid HER. Experimental and theoretical investigations suggested that the amorphous skin not only improved the electrochemical accessibility of the catalyst surface and increasing the intrinsic activity of the catalytic sites, but also mitigated the dissolution/diffusion of the active species, thus resulting in improved catalytic activity and stability under acidic electrolyte. This work demonstrates a direction of designing ultra-fine PGMs electrocatalysts both with high utilization and robust durability, offers an in situ "amorphous skin" engineering strategy.

4.
Small ; 19(35): e2300876, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37127875

ABSTRACT

The rational design of efficient and cost-effective electrocatalysts for oxygen evolution reaction (OER) with sluggish kinetics, is imperative to diverse clean energy technologies. The performance of electrocatalyst is usually governed by the number of active sites on the surface. Crystalline/amorphous heterostructure has exhibited unique properties and opens new paradigms toward designing electrocatalysts with abundant active sites for improved performance. Hence, Fe doped Ni-Co phosphite (Fe-NiCoHPi) electrocatalyst with cauliflower-like structure, comprising crystalline@amorphous core-shell nanorod, is reported. The experiments uncover that Fe is enriched in the amorphous shell due to the flexibility of the amorphous component. Further density functional theory calculations indicate that the strong electronic interaction between the enriched Fe in the amorphous shell and crystalline core host at the core-shell interface, leads to balanced binding energies of OER intermediates, which is the origin of the catalyst-activity. Eventually, the Fe-NiCoHPi exhibits remarkable activity, with low overpotentials of only 206 and 257 mV at current density of 15 and 100 mA cm-2 . Unceasing durability over 90 h is achieved, which is superior to the effective phosphate electrocatalysts. Although the applications at high current remain challenges , this work provides an approach for designing advanced OER electrocatalysts for sustainable energy devices.

5.
Bioinformatics ; 37(8): 1125-1134, 2021 05 23.
Article in English | MEDLINE | ID: mdl-33135051

ABSTRACT

MOTIVATION: Expression quantitative trait loci (eQTL) harbor genetic variants modulating gene transcription. Fine mapping of regulatory variants at these loci is a daunting task due to the juxtaposition of causal and linked variants at a locus as well as the likelihood of interactions among multiple variants. This problem is exacerbated in genes with multiple cis-acting eQTL, where superimposed effects of adjacent loci further distort the association signals. RESULTS: We developed a novel algorithm, TreeMap, that identifies putative causal variants in cis-eQTL accounting for multisite effects and genetic linkage at a locus. Guided by the hierarchical structure of linkage disequilibrium, TreeMap performs an organized search for individual and multiple causal variants. Via extensive simulations, we show that TreeMap detects co-regulating variants more accurately than current methods. Furthermore, its high computational efficiency enables genome-wide analysis of long-range eQTL. We applied TreeMap to GTEx data of brain hippocampus samples and transverse colon samples to search for eQTL in gene bodies and in 4 Mbps gene-flanking regions, discovering numerous distal eQTL. Furthermore, we found concordant distal eQTL that were present in both brain and colon samples, implying long-range regulation of gene expression. AVAILABILITY AND IMPLEMENTATION: TreeMap is available as an R package enabled for parallel processing at https://github.com/liliulab/treemap. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Subject(s)
Genome-Wide Association Study , Quantitative Trait Loci , Chromosome Mapping , Colon , Gene Expression , Hippocampus , Humans , Linkage Disequilibrium , Polymorphism, Single Nucleotide , Quantitative Trait Loci/genetics
6.
Eur Radiol ; 32(2): 1106-1114, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34467454

ABSTRACT

OBJECTIVES: To develop and validate a magnetic resonance imaging (MRI)-based radiomics nomogram model combining radiomic features and clinical factors for the prediction of radiotherapy-induced temporal lobe injury (RTLI) in patients with nasopharyngeal carcinoma (NPC). METHODS: From 203 NPC cases receiving radiotherapy, 128 RTLI-positive and 278 RTLI-negative lobes were retrospectively analyzed. They were randomly divided into training (n = 285) and validation (n = 121) sets. Three hundred ninety-six texture features based on T2WI images were extracted from each temporal lobe. The minimum redundancy maximum relevance (mRMR) and the least absolute shrinkage and selection operator (LASSO) were used to reduce the dimension of the features and establish a radiomics signature model. Clinical risk factors and the radiomics signature were combined by multivariable logistic regression analysis to construct a radiomics nomogram model. We assessed the performance of the radiomics nomogram on discrimination, calibration, and clinical utility. RESULTS: The radiomics signature consisted of 14 selected features that were significantly associated with RTLI. In the training set, the radiomics nomogram model demonstrated a better predictive performance (AUC, 0.87; 95% CI, 0.82-0.91) than the radiomics model (AUC, 0.71; 95% CI, 0.65-0.78) and clinical model (AUC, 0.73; 95% CI, 0.67-0.79). These results were confirmed in the validation set. The radiomics nomogram model demonstrated good calibration and was clinically useful by decision curve analysis. CONCLUSION: The radiomics nomogram model combining radiomics signatures and clinical factors is an effective method for the noninvasive prediction of RTLI in NPC patients after radiotherapy. KEY POINTS: • The radiomics model based on T2WI images at the end of intensity-modulated radiotherapy can predict radiotherapy-induced temporal lobe injury in patients with NPC. • Dosimetric factors can improve the prediction performance of the radiomics model in predicting radiotherapy-induced temporal lobe injury. • An MRI-based radiomics nomogram combining radiomics signatures and clinical factors had better prediction performance than both radiomics and clinical model for the prediction of radiotherapy-induced temporal lobe injury in patients with NPC.


Subject(s)
Nasopharyngeal Neoplasms , Nomograms , Humans , Magnetic Resonance Imaging , Nasopharyngeal Carcinoma/radiotherapy , Nasopharyngeal Neoplasms/diagnostic imaging , Nasopharyngeal Neoplasms/radiotherapy , Retrospective Studies , Temporal Lobe
7.
BMC Pulm Med ; 22(1): 402, 2022 Nov 07.
Article in English | MEDLINE | ID: mdl-36344945

ABSTRACT

BACKGROUND: Radiotherapy is an important treatment for patients with stage III/IV non-small cell lung cancer (NSCLC), and due to its high incidence of radiation pneumonitis, it is essential to identify high-risk people as early as possible. The present work investigates the value of the application of different phase data throughout the radiotherapy process in analyzing risk of grade ≥ 2 radiation pneumonitis in stage III/IV NSCLC. Furthermore, the phase data fusion was gradually performed with the radiotherapy timeline to develop a risk assessment model. METHODS: This study retrospectively collected data from 91 stage III/IV NSCLC cases treated with Volumetric modulated arc therapy (VMAT). Patient data were collected according to the radiotherapy timeline for four phases: clinical characteristics, radiomics features, radiation dosimetry parameters, and hematological indexes during treatment. Risk assessment models for single-phase and stepwise fusion phases were established according to logistic regression. In addition, a nomogram of the final fusion phase model and risk classification system was generated. Receiver operating characteristic (ROC), decision curve, and calibration curve analysis were conducted to internally validate the nomogram to analyze its discrimination. RESULTS: Smoking status, PTV and lung radiomics feature, lung and esophageal dosimetry parameters, and platelets at the third week of radiotherapy were independent risk factors for the four single-phase models. The ROC result analysis of the risk assessment models created by stepwise phase fusion were: (area under curve [AUC]: 0.67,95% confidence interval [CI]: 0.52-0.81), (AUC: 0.82,95%CI: 0.70-0.94), (AUC: 0.90,95%CI: 0.80-1.00), and (AUC:0.90,95%CI: 0.80-1.00), respectively. The nomogram based on the final fusion phase model was validated using calibration curve analysis and decision curve analysis, demonstrating good consistency and clinical utility. The nomogram-based risk classification system could correctly classify cases into three diverse risk groups: low-(ratio:3.6%; 0 < score < 135), intermediate-(ratio:30.7%, 135 < score < 160) and high-risk group (ratio:80.0%, score > 160). CONCLUSIONS: In our study, the risk assessment model makes it easy for physicians to assess the risk of grade ≥ 2 radiation pneumonitis at various phases in the radiotherapy process, and the risk classification system and nomogram identify the patient's risk level after completion of radiation therapy.


Subject(s)
Carcinoma, Non-Small-Cell Lung , Lung Neoplasms , Pneumonia , Radiation Pneumonitis , Radiotherapy, Intensity-Modulated , Humans , Carcinoma, Non-Small-Cell Lung/drug therapy , Radiation Pneumonitis/etiology , Retrospective Studies , Radiotherapy, Intensity-Modulated/adverse effects , Lung Neoplasms/complications , Risk Assessment , Pneumonia/complications
8.
Phys Chem Chem Phys ; 23(6): 3949-3962, 2021 Feb 19.
Article in English | MEDLINE | ID: mdl-33544099

ABSTRACT

Graphene, a new two-dimensional (2D) material, has attracted considerable attention in recent years because of the metallic characteristics at terahertz frequencies. The phase coupling of multilayer graphene-coupled grating structures is normally used to realize multiple plasmon-induced transparency (PIT) spectral responses. However, the device becomes more complicated with the increase in the number of graphene layers. In this work, we propose a five-step-coupled pyramid-shaped monolayer graphene metamaterial and predict a dynamically controllable PIT with four transparency peaks for the first time in the monolayer graphene metamaterial. A tunable multi-switch and good slow light effect is predicted over the wide PIT window, and the maximum modulation depth is high up to 16.89 dB, which corresponds to 97.95%, while the time delay of the induced transparent window is as high as 0.488 ps, where the corresponding group refractive index is 586. The electric field distributions and quantum level theory are used to explain the physical mechanism of the PIT with four transparency peaks. The coupled mode theory (CMT) is employed to establish the mathematical model of the PIT with four transparency peaks, and the consistency between the simulated and the calculated results is nearly perfect. We believe that the pyramid-shaped monolayer graphene metamaterial could be useful in efficient filters, switches, and slow light devices.

9.
Am J Hum Genet ; 100(2): 228-237, 2017 02 02.
Article in English | MEDLINE | ID: mdl-28065468

ABSTRACT

We analyzed the mRNA levels for 36,778 transcript expression traits (probes) from 2,765 individuals to comprehensively investigate the genetic architecture and degree of missing heritability for gene expression in peripheral blood. We identified 11,204 cis and 3,791 trans independent expression quantitative trait loci (eQTL) by using linear mixed models to perform genome-wide association analyses. Furthermore, using information on both closely and distantly related individuals, heritability was estimated for all expression traits. Of the set of expressed probes (15,966), 10,580 (66%) had an estimated narrow-sense heritability (h2) greater than zero with a mean (median) value of 0.192 (0.142). Across these probes, on average the proportion of genetic variance explained by all eQTL (hCOJO2) was 31% (0.060/0.192), meaning that 69% is missing, with the sentinel SNP of the largest eQTL explaining 87% (0.052/0.060) of the variance attributed to all identified cis- and trans-eQTL. For the same set of probes, the genetic variance attributed to genome-wide common (MAF > 0.01) HapMap 3 SNPs (hg2) accounted for on average 48% (0.093/0.192) of h2. Taken together, the evidence suggests that approximately half the genetic variance for gene expression is not tagged by common SNPs, and of the variance that is tagged by common SNPs, a large proportion can be attributed to identifiable eQTL of large effect, typically in cis. Finally, we present evidence that, compared with a meta-analysis, using individual-level data results in an increase of approximately 50% in power to detect eQTL.


Subject(s)
Gene Expression , Inheritance Patterns , Quantitative Trait Loci , RNA, Messenger/blood , Genetic Association Studies , Genome, Human , Genotype , HapMap Project , Humans , Linear Models , Linkage Disequilibrium , Models, Genetic , Phenotype , Polymorphism, Single Nucleotide , RNA, Messenger/genetics
10.
Small ; 16(48): e2004720, 2020 Dec.
Article in English | MEDLINE | ID: mdl-33155382

ABSTRACT

Recent progress in addressing electrically driven single-molecule behaviors has opened up a path toward the controllable fabrication of molecular devices. Herein, the selective fabrication of single-molecule junctions is achieved by employing the external electric field. For molecular junctions with methylthio (-SMe), thioacetate (-SAc), amine (-NH2 ), and pyridyl (-PY), the evolution of their formation probabilities along with the electric field is extracted from the plateau analysis of individual single-molecule break junction traces. With the increase of the electric field, the SMe-anchored molecules show a different trend in the formation probability compared to the other molecular junctions, which is consistent with the density functional theory calculations. Furthermore, switching from an SMe-anchored junction to an SAc-anchored junction is realized by altering the electric field in a mixed solution. The results in this work provide a new approach to the controllable fabrication and modulation of single-molecule junctions and other bottom-up nanodevices at molecular scales.

11.
Bioinformatics ; 35(6): 1061-1063, 2019 03 15.
Article in English | MEDLINE | ID: mdl-30165584

ABSTRACT

MOTIVATION: Expression quantitative loci (eQTL) are being used widely to annotate and interpret GWAS hits. Recent studies have demonstrated that individual gene expression is often regulated by multiple independent cis-acting eQTL. Diverse methods, frequentist and Bayesian, have already been developed to simultaneously detect and fine-map such multiple eQTL, but most of these ignore sample relatedness and potential population structure. This can result in false positives and disrupt the accuracy of fine-mapping. Here we introduce PolyQTL software for identifying and estimating eQTL effects. The package incorporates a genetic relatedness matrix to remove the influence of population structure and sample relatedness, while utilizing a Bayesian multiple eQTL detection pipeline to identify the most plausible candidate causal variants at one or more independent loci influencing abundance of a transcript. RESULTS: Simulations demonstrate that our approach improves the rate of discovery of causal variants relative to methods that do not account for relatedness. AVAILABILITY AND IMPLEMENTATION: The software is written in C++, and freely available for download at https://github.com/jxzb1988/PolyQTL.


Subject(s)
Genome-Wide Association Study , Quantitative Trait Loci , Bayes Theorem , Gene Expression , Polymorphism, Single Nucleotide , Software
12.
Chemistry ; 26(23): 5264-5269, 2020 Apr 21.
Article in English | MEDLINE | ID: mdl-32022327

ABSTRACT

Heteroatom substitution into the cores of alternant, aromatic hydrocarbons containing only even-membered rings is attracting increasing interest as a method of tuning their electrical conductance. Here, the effect of heteroatom substitution into molecular cores of non-alternant hydrocarbons, containing odd-membered rings, is examined. Benzodichalcogenophene (BDC) compounds are rigid, planar π-conjugated structures, with molecular cores containing five-membered rings fused to a six-membered aryl ring. To probe the sensitivity or resilience of constructive quantum interference (CQI) in these non-bipartite molecular cores, two C2 -symmetric molecules (I and II) and one asymmetric molecule (III) were investigated. I (II) contains S (O) heteroatoms in each of the five-membered rings, while III contains an S in one five-membered ring and an O in the other. Differences in their conductances arise primarily from the longer S-C and shorter O-C bond lengths compared with the C-C bond and the associated changes in their resonance integrals. Although the conductance of III is significantly lower than the conductances of the others, CQI was found to be resilient and persist in all molecules.

13.
Genome Res ; 24(1): 167-76, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24131563

ABSTRACT

Genetic imprinting is a specific epigenetic phenomenon in which a subset of genes is expressed depending on their parent-of-origin. Two types of chromatin modifications, DNA methylation and histone modification, are generally believed to be involved in the regulation of imprinting. However, the genome-wide correlation between allele-specific chromatin modifications and imprinted gene expression in maize remains elusive. Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. For DNA methylation, thousands of parent-of-origin dependent differentially methylated regions (pDMRs) were identified. All pDMRs were uniformly paternally hypermethylated and maternally hypomethylated. We also identified 1131 allele-specific H3K27me3 peaks that are preferentially present in the maternal alleles. Maternally expressed imprinted genes (MEGs) and paternally expressed imprinted genes (PEGs) had different patterns of allele-specific DNA methylation and H3K27me3. Allele-specific expression of MEGs was not directly related to allele-specific H3K27me3, and only a subset of MEGs was associated with maternal-specific DNA demethylation, which was primarily located in the upstream and 5' portion of gene body regions. In contrast, allele-specific expression of a majority of PEGs was related to maternal-specific H3K27me3, with a subgroup of PEGs also associated with maternal-specific DNA demethylation. Both pDMRs and maternal H3K27me3 peaks associated with PEGs are enriched in gene body regions. Our results indicate highly complex patterns of regulation on genetic imprinting in maize endosperm.


Subject(s)
DNA, Plant/genetics , Endosperm/genetics , Histones/metabolism , Zea mays/genetics , Alleles , Endosperm/metabolism , Epigenesis, Genetic , Gene Expression Profiling , Gene Expression Regulation, Plant , Genes, Plant , Genome, Plant , Genomic Imprinting , Histones/genetics , Methylation , Plant Proteins/genetics , Plant Proteins/metabolism , Zea mays/metabolism
14.
Biomed Environ Sci ; 30(6): 460-464, 2017 Jun.
Article in English | MEDLINE | ID: mdl-28705271

ABSTRACT

Laboratory-based pathogen isolation, identification, and toxicity determination were performed on samples from a suspected case of infant botulism. Mice injected with cultures generated from the enema sample and ingested Powered infant formula (PIF) presented typical signs of botulism. Antitoxins to polyvalent botulinum neurotoxins (BoNTs) and monovalent BoNT type B antitoxin had protective effects. Clostridium botulinum isolated from the enema and residual PIF samples were positive for type B toxin. Pulsed-field gel electrophoresis (PFGE) revealed that the two strains of C. botulinum isolated from the two samples produced indistinguishable pulsotypes. These findings confirmed this case of type B infant botulism associated with the ingestion of PIF contaminated by type B C. botulinum spores.


Subject(s)
Botulinum Toxins/toxicity , Botulism/diagnosis , Botulism/epidemiology , Clostridium botulinum/isolation & purification , Animals , Beijing/epidemiology , Botulinum Toxins/isolation & purification , Gastrointestinal Tract/microbiology , Humans , Infant , Mice , Toxicity Tests
15.
Lang Speech ; 60(4): 562-570, 2017 12.
Article in English | MEDLINE | ID: mdl-29216812

ABSTRACT

This study used the perceptual-migration paradigm to explore whether Mandarin tones and syllable rhymes are processed separately during Mandarin speech perception. Following the logic of illusory conjunctions, we calculated the cross-ear migration of tones, rhymes, and their combination in Chinese and English listeners. For Chinese listeners, tones migrated more than rhymes. For English listeners, the opposite pattern was found. The results lend empirical support to autosegmental theory, which claims separability and mobility between tonal and segmental representations. They also provide evidence that such representations and their involvement in perception are deeply shaped by a listener's linguistic experience.


Subject(s)
Phonetics , Pitch Discrimination , Speech Acoustics , Speech Perception , Voice Quality , Acoustic Stimulation , China , Dichotic Listening Tests , Humans , Pattern Recognition, Physiological
16.
Plant J ; 84(6): 1206-18, 2015 Dec.
Article in English | MEDLINE | ID: mdl-26568274

ABSTRACT

Plants can respond to environmental changes with various mechanisms occurred at transcriptional and translational levels. Thus far, there have been relatively extensive understandings of stress responses of plants on transcriptional level, while little information is known about that on translational level. To uncover the landscape of translation in plants in response to drought stress, we performed the recently developed ribosome profiling assay with maize seedlings growing under normal and drought conditions. Comparative analysis of the ribosome profiling data and the RNA-seq data showed that the fold changes of gene expression at transcriptional level were moderately correlated with that of translational level globally (R(2) = 0.69). However, less than half of the responsive genes were shared by transcription and translation under drought condition, suggesting that drought stress can introduce transcriptional and translational responses independently. We found that the translational efficiencies of 931 genes were changed significantly in response to drought stress. Further analysis revealed that the translational efficiencies of genes were highly influenced by their sequence features including GC content, length of coding sequences and normalized minimal free energy. In addition, we detected potential translation of 3063 upstream open reading frames (uORFs) on 2558 genes and these uORFs may affect the translational efficiency of downstream main open reading frames (ORFs). Our study indicates that plant can respond to drought stress with highly dynamic translational mechanism, that acting synergistically with that of transcription.


Subject(s)
Gene Expression Regulation, Plant/physiology , Ribosomes/metabolism , Seedlings/metabolism , Transcriptome , Water , Zea mays/metabolism , Protein Biosynthesis , Ribosomes/genetics , Seedlings/genetics , Transcription, Genetic , Zea mays/genetics
17.
Chem Biodivers ; 13(5): 596-601, 2016 May.
Article in English | MEDLINE | ID: mdl-27088891

ABSTRACT

Following an in vitro bioactivity-guided fractionation procedure, 14 compounds including eight flavonoids and six phenylpropanoids were isolated and identified from the AcOEt fraction of Clinopodium chinense (Benth.) O. Kuntze. All constituents were tested for α-glucosidase and high glucose-induced injury in human umbilical vein endothelial cells (HUVECs) inhibitory activities. All constituents exhibited varying degrees α-glucosidase inhibitory activity and protective activity on HUVECs. Among them, luteolin (2), eriodictyol (5), ethyl rosmarinate (13), and clinopodic acids B (14) were proved to be potent α-glucosidase inhibitors with IC50 value ranging from 0.6 to 2.0 µm. Additionally, luteolin (2), naringenin (4), eriodictyol (5), ethyl (2R)-3-(3, 4-dihydroxyphenyl)-2-hydroxypropanate (9), caffeic acid (11), ethyl rosmarinate (13), and clinopodic acids B (14) significantly ameliorate HUVECs injury induced by high glucose with an approximate EC50 value of 3 - 36 µm. These results suggest that the 14 bioactive constituents were responsible for hypoglycemic and protective vascular endothelium effect of C. chinense (Benth.) O. Kuntze and their structure-activity relationship was also analyzed briefly. Eriodictyol, luteolin, ethyl rosmarinate, and clinopodic acids B were the potential lead compounds of antidiabetic drugs.


Subject(s)
Glycoside Hydrolase Inhibitors/pharmacology , Human Umbilical Vein Endothelial Cells/drug effects , Lamiaceae/chemistry , Phenols/pharmacology , alpha-Glucosidases/metabolism , Dose-Response Relationship, Drug , Glucose/pharmacology , Glycoside Hydrolase Inhibitors/chemistry , Glycoside Hydrolase Inhibitors/isolation & purification , Human Umbilical Vein Endothelial Cells/pathology , Humans , Molecular Structure , Phenols/chemistry , Phenols/isolation & purification , Structure-Activity Relationship
19.
Plant Physiol ; 166(1): 252-64, 2014 Sep.
Article in English | MEDLINE | ID: mdl-25037214

ABSTRACT

Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues. A total of 26,105 genes were found to be involved in programming seed development, including 1,614 transcription factors. Global comparisons of gene expression highlighted the fundamental transcriptomic reprogramming and the phases of development. Coexpression analysis provided further insight into the dynamic reprogramming of the transcriptome by revealing functional transitions during maturation. Combined with the published nonseed high-throughput RNA sequencing data, we identified 91 transcription factors and 1,167 other seed-specific genes, which should help elucidate key mechanisms and regulatory networks that underlie seed development. In addition, correlation of gene expression with the pattern of DNA methylation revealed that hypomethylation of the gene body region should be an important factor for the expressional activation of seed-specific genes, especially for extremely highly expressed genes such as zeins. This study provides a valuable resource for understanding the genetic control of seed development of monocotyledon plants.


Subject(s)
Endosperm/growth & development , Endosperm/metabolism , Plant Development , Zea mays/growth & development , Zea mays/metabolism , Gene Expression Profiling , Sequence Analysis, RNA , Transcriptome , Zein/genetics
20.
Molecules ; 20(8): 14879-88, 2015 Aug 14.
Article in English | MEDLINE | ID: mdl-26287144

ABSTRACT

A new skeleton of diterpenoid, 1,2,3,4,4α,9,10,10α-octahydro-(4α-hydroxyymethyl) -1,1-dimethyl-9-(1-methylethyl)-(2S,3S,4αR,9R,10αS)-2,3,5,7-phenanthrenetertrol, named plebeianiol A (1), along with four known diterpenoids (2-5), were isolated from Salvia plebeia R. Br. Their structures were determined on the basis of spectral analysis. In the bioactivity tests, compounds 1, 2 and 5 showed 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging activities with IC50 values of 20.0-29.6 µM. In addition, these three compounds had significant inhibitory effects on reactive oxygen species (ROS) production in lipopolysaccharide (LPS)-induced macrophages. Compounds 1-3 inhibited nitric oxide (NO) production in LPS-induced macrophages with IC50 values of 18.0-23.6 µM. These results showed that compounds 1, 2 had significant antioxidant and anti-inflammatory activities and might provide basis for the treatment of diseases associated with oxidative lesions and inflammation.


Subject(s)
Anti-Inflammatory Agents/pharmacology , Antioxidants/pharmacology , Diterpenes/pharmacology , Salvia/chemistry , Animals , Anti-Inflammatory Agents/chemistry , Antioxidants/chemistry , Biosynthetic Pathways/drug effects , Biphenyl Compounds/chemistry , Carbon-13 Magnetic Resonance Spectroscopy , Cell Survival/drug effects , Diterpenes/chemistry , Macrophages/drug effects , Macrophages/metabolism , Mice , Nitric Oxide/biosynthesis , Picrates/chemistry , Proton Magnetic Resonance Spectroscopy , RAW 264.7 Cells
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