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1.
Ying Yong Sheng Tai Xue Bao ; 32(9): 3288-3298, 2021 Sep.
Artigo em Chinês | MEDLINE | ID: mdl-34658215

RESUMO

Under the background of rapid urbanization, the problem of fragmented habitat patches in economically developed areas is particularly prominent, where biodiversity is seriously threa-tened. Therefore, the construction of ecological network is an important measure to connect habitat patches and protect biological habitats. We extracted ecological source areas of Foshan City by using the connectivity index and morphological spatial pattern analysis (MSPA). Potential ecological corridors were identified based on InVEST model and minimal cumulative resistance (MCR). Combining the radiation channels extracted from hydrological analysis to build an ecological network in Foshan City. The ecological network was optimized by adding ecological source areas, stepping stones, and identifying fracture points. Finally, the network before and after optimization was evalua-ted from the aspects of both structure and function based on network analysis method and circuit theory. The results showed that ecological network in Foshan City was composed of 10 ecological source areas, 8 important corridors, 37 general corridors, and 11 radiation channels. After optimization, 7 new ecological source areas, 17 planning corridors, 13 stepping stones, and 80 fracture points were added. After optimization, the ecological network closure, the line rate index and the connection degree index were 0.59, 1.94, and 0.73, respectively. The maximum current density increased from 1.39 to 9.66 after optimization, indicating that the optimized ecological network structure was more perfect and highly connective.


Assuntos
Conservação dos Recursos Naturais , Ecossistema , Biodiversidade , China , Cidades
2.
BMC Genomics ; 22(1): 687, 2021 Sep 22.
Artigo em Inglês | MEDLINE | ID: mdl-34551703

RESUMO

BACKGROUND: Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a cold-tolerant plant that is vulnerable to high temperature. This study explored the response mechanism of wucai to low temperature. In this study, wucai seedlings were treated with different temperatures, including low temperature (LT), high temperature (HT), and a control. RESULTS: According to transcriptomics analysis, the number of differentially expressed genes (DEGs) in HT and LT was 10,702 and 7267, respectively, compared with the control. The key genes associated with the physiological response of wucai to the treatments were analyzed. The Kyoto Encyclopedia of Genes and Genomes and Gene Ontology annotations indicated the importance of the photosynthesis and photosynthetic-antenna protein pathways. We found that a high-temperature environment greatly inhibited the expression of important genes in the photosynthetic pathway (BrLhc superfamily members, PsaD, PsaE, PsaD, PsaD, PsbO, PsbP, PsbQ, PsbR, PsbS, PsbW, PsbY, Psb27, and Psb28), whereas low temperature resulted in the expression of certain key genes (BrLhc superfamily members, Psa F, Psa H, Psb S, Psb H, Psb 28). In addition, the wucai seedlings exhibited better photosynthetic performance under low-temperature conditions than high-temperature conditions. CONCLUSIONS: Based on the above results, we speculate that upon exposure to low temperature, the plants developed higher cold tolerance by upregulating the expression of genes related to photosynthesis. Conversely, high-temperature stress inhibited the expression of pivotal genes and weakened the self-regulating ability of the plants.


Assuntos
Brassica , Brassica/genética , Brassica/metabolismo , Temperatura Baixa , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fotossíntese/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Estresse Fisiológico/genética , Temperatura , Transcriptoma
3.
BMC Plant Biol ; 21(1): 438, 2021 Sep 28.
Artigo em Inglês | MEDLINE | ID: mdl-34583634

RESUMO

BACKGROUND: Chlorophyll (Chl) is a vital photosynthetic pigment involved in capturing light energy and energy conversion. In this study, the color conversion of inner-leaves from green to yellow in the new wucai (Brassica campestris L.) cultivar W7-2 was detected under low temperature. The W7-2 displayed a normal green leaf phenotype at the seedling stage, but the inner leaves gradually turned yellow when the temperature was decreased to 10 °C/2 °C (day/night), This study facilitates us to understand the physiological and molecular mechanisms underlying leaf color changes in response to low temperature. RESULTS: A comparative leaf transcriptome analysis of W7-2 under low temperature treatment was performed on three stages (before, during and after leaf color change) with leaves that did not change color under normal temperature at the same period as a control. A total of 67,826 differentially expressed genes (DEGs) were identified. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Gene Ontology (GO) analysis revealed that the DEGs were mainly enriched in porphyrin and Chl metabolism, carotenoids metabolism, photosynthesis, and circadian rhythm. In the porphyrin and chlorophyll metabolic pathways, the expression of several genes was reduced [i.e. magnesium chelatase subunit H (CHLH)] under low temperature. Almost all genes [i.e. phytoene synthase (PSY)] in the carotenoids (Car) biosynthesis pathway were downregulated under low temperature. The genes associated with photosynthesis [i.e. photosystem II oxygen-evolving enhancer protein 1 (PsbO)] were also downregulated under LT. Our study also showed that elongated hypocotyl5 (HY5), which participates in circadian rhythm, and the metabolism of Chl and Car, is responsible for the regulation of leaf color change and cold tolerance in W7-2. CONCLUSIONS: The color of inner-leaves was changed from green to yellow under low temperature in temperature-sensitive mutant W7-2. Physiological, biochemical and transcriptomic studies showed that HY5 transcription factor and the downstream genes such as CHLH and PSY, which regulate the accumulation of different pigments, are required for the modulation of leaf color change in wucai under low temperature.

4.
Planta ; 254(3): 50, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34386845

RESUMO

MAIN CONCLUSION: Overexpression of the leaf color (Lc) gene in Ma bamboo substantially increased the accumulation level of anthocyanin, and improved plant tolerance to cold and drought stresses, probably due to the increased antioxidant capacity. Most bamboos, including Ma bamboo (Dendrocalamus latiflorus Munro), are naturally evergreen and sensitive to cold and drought stresses, while it's nearly impossible to make improvements through conventual breeding due to their long and irregular flowering habit. Moreover, few studies have reported bamboo germplasm innovation through genetic engineering as bamboo genetic transformation remains difficult. In this study, we have upregulated anthocyanin biosynthesis in Ma bamboo, to generate non-green Ma bamboo with increased abiotic stress tolerance. By overexpressing the maize Lc gene, a bHLH transcription activator involved in the anthocyanin biosynthesis in Ma bamboo, we generated purple bamboos with increased anthocyanin levels including cyanidin-3-O-rutinoside, peonidin 3-O-rutinoside, and an unknown cyanidin pentaglycoside derivative. The expression levels of 9 anthocyanin biosynthesis genes were up-regulated. Overexpression of the Lc gene improved the plant tolerance to cold and drought stress, probably due to increased antioxidant capacity. The levels of the cold- and drought-related phytohormone jasmonic acid in the transgenic plants were also enhanced, which may also contribute to the plant stress-tolerant phenotypes. High anthocyanin accumulation level did not affect plant growth. Transcriptomic analysis showed higher expressions of genes involved in the flavonoid pathway in Lc transgenic bamboos compared with those in wild-type ones. The anthocyanin-rich bamboos generated here provide an example of ornamental and multiple agronomic trait improvements by genetic engineering in this important grass species.


Assuntos
Secas , Regulação da Expressão Gênica de Plantas , Antocianinas , Resposta ao Choque Frio , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/metabolismo
5.
Angew Chem Int Ed Engl ; 60(41): 22454-22460, 2021 Oct 04.
Artigo em Inglês | MEDLINE | ID: mdl-34347353

RESUMO

Regiodivergent addition reactions provide straightforward and atom-economic approaches to access different regioisomers. However, the regio-chemistry control to access all the possible results is still challenging especially for the reaction involving multiple addition steps. Herein, we reported regio-controllable cobalt-catalyzed sequential hydrosilylation/hydroboration of arylacetylenes, delivering all the possible regio-outcomes with high regioselectivities (up to >20/1 rr for all the cases). Each regioisomer of value-added silylboronates could be efficiently and regioselectively obtained from the same materials. The adjustment of the ligands of cobalt catalysts combined with dual catalysis relay strategy is the key to achieve regio-chemistry control. This regio-controllable research might inspire the exploration of the diversity-oriented synthesis that involves multiple additions and provide full sets of regioisomers of other synthetic useful molecules.

6.
Int J Mol Sci ; 22(13)2021 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-34281238

RESUMO

This study evaluated the effects of different light spectra (white light; WL, blue light; BL and red light; RL) on the root morphological traits and metabolites accumulation and biosynthesis in Sarcandra glabra. We performed transcriptomic and metabolomic profiling by RNA-seq and ultra-performance liquid chromatography-electrospray ionization-tandem mass spectrometry (UPLC-ESI-MS/MS), respectively. When morphological features were compared to WL, BL substantially increased under-ground fresh weight, root length, root surface area, and root volume, while RL inhibited these indices. A total of 433 metabolites were identified, of which 40, 18, and 68 compounds differentially accumulated in roots under WL (WG) vs. roots under BL (BG), WG vs. roots under RL (RG), and RG vs. BG, respectively. In addition, the contents of sinapyl alcohol, sinapic acid, fraxetin, and 6-methylcoumarin decreased significantly in BG and RG. In contrast, chlorogenic acid, rosmarinyl glucoside, quercitrin and quercetin were increased considerably in BG. Furthermore, the contents of eight terpenoids compounds significantly reduced in BG. Following transcriptomic profiling, several key genes related to biosynthesis of phenylpropanoid-derived and terpenoids metabolites were differentially expressed, such as caffeic acid 3-O-methyltransferase) (COMT), hydroxycinnamoyl-CoA shikimate hydroxycinnamoyl transferase (HCT), O-methyltransferase (OMT), and 1-deoxy-D-xylulose-5-phosphate synthetase (DXS). In summary, our findings showed that BL was suitable for growth and accumulation of bioactive metabolites in root tissue of S. glabra. Exposure to a higher ratio of BL might have the potential to improve the production and quality of S. glabra seedlings, but this needs to be confirmed further.


Assuntos
Cor , Magnoliopsida/efeitos da radiação , Raízes de Plantas/efeitos da radiação , Metabolismo Secundário/efeitos da radiação , Plântula/efeitos da radiação , Magnoliopsida/crescimento & desenvolvimento , Magnoliopsida/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Plântula/crescimento & desenvolvimento , Plântula/metabolismo , Terpenos/metabolismo
7.
BMC Genomics ; 22(1): 258, 2021 Apr 12.
Artigo em Inglês | MEDLINE | ID: mdl-33845769

RESUMO

BACKGROUND: Leaf color mutants are the ideal materials to explore the pathways of chlorophyll (Chl) metabolism, chloroplast development, and photosynthesis system. In this study, a spontaneous yellow-green leaf wucai (Brassica campestris L.) mutant "WY16-13" was identified, which exhibited yellow-green leaf color during its entire growth period. However, current understanding of the molecular mechanism underlying Chl metabolism and chloroplast development of "WY16-13" is limited. RESULTS: Total Chl and carotenoid content in WY16-13 was reduced by 60.92 and 58.82%, respectively, as compared with its wild type parental line W16-13. Electron microscopic investigation revealed fewer chloroplasts per cell and looser stroma lamellae in WY16-13 than in W16-13. A comparative transcriptome profiling was performed using leaves from the yellow-green leaf type (WY16-13) and normal green-leaf type (W16-13). A total of 54.12 million (M) (WY16-13) and 56.17 M (W16-13) reads were generated. A total of 40,578 genes were identified from the mapped libraries. We identified 3882 differentially expressed genes (DEGs) in WY16-13 compared with W16-13 (i.e., 1603 upregulated genes and 2279 downregulated genes). According to the Gene Ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, these DEGs are involved in porphyrin and Chl metabolism [i.e., chlorophyllase (CLH), heme oxygenase (HO), chlorophyll (ide) b reductase (NYC), and protochlorophyllide oxidoreductase (POR) genes], carbohydrate metabolism, photosynthesis, and carbon fixation in photosynthetic organisms. Moreover, deficiency in Chl biosynthetic intermediates in WY16-13 revealed that the formation of the yellow-green phenotype was related to the disorder of heme metabolism. CONCLUSIONS: Our results provide valuable insights into Chl deficiency in the yellow-green leaf mutant and a bioinformatics resource for further functional identification of key allelic genes responsible for differences in Chl content.


Assuntos
Brassica , Brassica/genética , Brassica/metabolismo , Clorofila , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Fotossíntese/genética , Folhas de Planta/genética , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Transcriptoma
8.
Endocr J ; 68(6): 631-637, 2021 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-33658438

RESUMO

Metabolic associated fatty liver disease (MAFLD) is a new concept proposed in 2020. This study aimed to explore the relationship between serum 25-hydroxy vitamin D (25(OH)D) level and MAFLD based on a population survey dataset (the third National Health and Nutrition Examination Surveys of the United States). Multivariate logistic regression was used to estimate the odds ratio (OR) of serum 25(OH)D level for MAFLD. A total of 12,878 participants were included in this analysis. Among them, 4,027 (31.27%) cases were diagnosed with MAFLD and 8,851 (66.40%) were without MAFLD (non-MAFLD). Patients with vitamin D sufficiency and insufficiency totaled 6,983 (54.22%) and 5,895 (45.78%), respectively. The incidence of MAFLD and the grade of hepatic steatosis were both significantly higher in vitamin D insufficiency group. Multivariate analysis showed that vitamin D insufficiency was an independent risk factor for MAFLD after adjusted for other confounders (OR: 1.130, 95%CI: 1.035 to 1.234). In MAFLD population, the average serum 25(OH)D level decreased with the numbers of metabolic risks in MAFLD cases. Serum 25(OH)D level was not associated with the severity of fibrosis or steatosis in MAFLD group. In Conclusion, lower serum 25(OH)D level is associated with higher prevalence of MAFLD in general population. No relationship was found between serum 25(OH)D level and the severity of hepatic steatosis or fibrosis in MAFLD.

9.
Plant J ; 106(2): 435-453, 2021 04.
Artigo em Inglês | MEDLINE | ID: mdl-33506534

RESUMO

In mammals, DNA methylation is associated with aging. However, age-related DNA methylation changes during phase transitions largely remain unstudied in plants. Moso bamboo (Phyllostachys edulis) requires a very long time to transition from the vegetative to the floral phase. To comprehensively investigate the association of DNA methylation with aging, we present here single-base-resolution DNA methylation profiles using both high-throughput bisulfite sequencing and single-molecule nanopore-based DNA sequencing, covering the long period of vegetative growth and transition to flowering in moso bamboo. We discovered that CHH methylation gradually accumulates from vegetative to reproductive growth in a time-dependent fashion. Differentially methylated regions, correlating with chronological aging, occurred preferentially at both transcription start sites and transcription termination sites. Genes with CG methylation changes showed an enrichment of Gene Ontology (GO) categories in 'vegetative to reproductive phase transition of meristem'. Combining methylation data with mRNA sequencing revealed that DNA methylation in promoters, introns and exons may have different roles in regulating gene expression. Finally, circular RNA (circRNA) sequencing revealed that the flanking introns of circRNAs are hypermethylated and enriched in long terminal repeat (LTR) retrotransposons. Together, the observations in this study provide insights into the dynamic DNA methylation and circRNA landscapes, correlating with chronological age, which paves the way to study further the impact of epigenetic factors on flowering in moso bamboo.


Assuntos
Envelhecimento/genética , Metilação de DNA , Flores/crescimento & desenvolvimento , Poaceae/genética , RNA Circular/genética , RNA de Plantas/genética , Envelhecimento/fisiologia , Metilação de DNA/genética , Metilação de DNA/fisiologia , Elementos de DNA Transponíveis/genética , Elementos de DNA Transponíveis/fisiologia , Regulação da Expressão Gênica de Plantas/genética , Estudo de Associação Genômica Ampla , Poaceae/crescimento & desenvolvimento , Poaceae/metabolismo , RNA Circular/metabolismo , RNA Circular/fisiologia , RNA de Plantas/metabolismo , RNA de Plantas/fisiologia , Análise de Sequência de DNA/métodos
10.
IEEE J Biomed Health Inform ; 25(2): 337-347, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-32248128

RESUMO

Color consistency is crucial to developing robust deep learning methods for histopathological image analysis. With the increasing application of digital histopathological slides, the deep learning methods are probably developed based on the data from multiple medical centers. This requirement makes it a challenging task to normalize the color variance of histopathological images from different medical centers. In this paper, we propose a novel color standardization module named stain standardization capsule based on the capsule network and the corresponding dynamic routing algorithm. The proposed module can learn and generate uniform stain separation outputs for histopathological images in various color appearance without the reference to manually selected template images. The proposed module is light and can be jointly trained with the application-driven CNN model. The proposed method was validated on three histopathology datasets and a cytology dataset, and was compared with state-of-the-art methods. The experimental results have demonstrated that the SSC module is effective in improving the performance of histopathological image analysis and has achieved the best performance in the compared methods.

11.
IEEE J Biomed Health Inform ; 25(2): 429-440, 2021 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-33216724

RESUMO

Accurate segmentation of lung cancer in pathology slides is a critical step in improving patient care. We proposed the ACDC@LungHP (Automatic Cancer Detection and Classification in Whole-slide Lung Histopathology) challenge for evaluating different computer-aided diagnosis (CADs) methods on the automatic diagnosis of lung cancer. The ACDC@LungHP 2019 focused on segmentation (pixel-wise detection) of cancer tissue in whole slide imaging (WSI), using an annotated dataset of 150 training images and 50 test images from 200 patients. This paper reviews this challenge and summarizes the top 10 submitted methods for lung cancer segmentation. All methods were evaluated using metrics using the precision, accuracy, sensitivity, specificity, and DICE coefficient (DC). The DC ranged from 0.7354 ±0.1149 to 0.8372 ±0.0858. The DC of the best method was close to the inter-observer agreement (0.8398 ±0.0890). All methods were based on deep learning and categorized into two groups: multi-model method and single model method. In general, multi-model methods were significantly better (p 0.01) than single model methods, with mean DC of 0.7966 and 0.7544, respectively. Deep learning based methods could potentially help pathologists find suspicious regions for further analysis of lung cancer in WSI.

12.
IEEE Trans Med Imaging ; 40(3): 1090-1103, 2021 03.
Artigo em Inglês | MEDLINE | ID: mdl-33351756

RESUMO

The development of whole slide imaging techniques and online digital pathology platforms have accelerated the popularization of telepathology for remote tumor diagnoses. During a diagnosis, the behavior information of the pathologist can be recorded by the platform and then archived with the digital case. The browsing path of the pathologist on the WSI is one of the valuable information in the digital database because the image content within the path is expected to be highly correlated with the diagnosis report of the pathologist. In this article, we proposed a novel approach for computer-assisted cancer diagnosis named session-based histopathology image recommendation (SHIR) based on the browsing paths on WSIs. To achieve the SHIR, we developed a novel diagnostic regions attention network (DRA-Net) to learn the pathology knowledge from the image content associated with the browsing paths. The DRA-Net does not rely on the pixel-level or region-level annotations of pathologists. All the data for training can be automatically collected by the digital pathology platform without interrupting the pathologists' diagnoses. The proposed approaches were evaluated on a gastric dataset containing 983 cases within 5 categories of gastric lesions. The quantitative and qualitative assessments on the dataset have demonstrated the proposed SHIR framework with the novel DRA-Net is effective in recommending diagnostically relevant cases for auxiliary diagnosis. The MRR and MAP for the recommendation are respectively 0.816 and 0.836 on the gastric dataset. The source code of the DRA-Net is available at https://github.com/zhengyushan/dpathnet.


Assuntos
Interpretação de Imagem Assistida por Computador , Telepatologia , Bases de Dados Factuais , Diagnóstico por Computador , Software
13.
Comput Methods Programs Biomed ; 198: 105807, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33130497

RESUMO

BACKGROUND AND OBJECTIVE: Cervical cell classification has important clinical significance in cervical cancer screening at early stages. In contrast with the conventional classification methods which depend on hand-crafted or engineered features, Convolutional Neural Network (CNN) generally classifies cervical cells via learned deep features. However, the latent correlations of images may be ignored during CNN feature learning and thus influence the representation ability of CNN features. METHODS: We propose a novel cervical cell classification method based on Graph Convolutional Network (GCN). It aims to explore the potential relationship of cervical cell images for improving the classification performance. The CNN features of all the cervical cell images are firstly clustered and the intrinsic relationships of images can be preliminarily revealed through the clustering. To further capture the underlying correlations existed among clusters, a graph structure is constructed. GCN is then applied to propagate the node dependencies and thus yield the relation-aware feature representation. The GCN features are finally incorporated to enhance the discriminative ability of CNN features. RESULTS: Experiments on the public cervical cell image dataset SIPaKMeD from International Conference on Image Processing in 2018 demonstrate the feasibility and effectiveness of the proposed method. In addition, we introduce a large-scale Motic liquid-based cytology image dataset which provides the large amount of data, some novel cell types with important clinical significance and staining difference and thus presents a great challenge for cervical cell classification. We evaluate the proposed method under two conditions of the consistent staining and different staining. Experimental results show our method outperforms the existing state-of-arts methods according to the quantitative metrics (i.e. accuracy, sensitivity, specificity, F-measure and confusion matrices). CONCLUSIONS: The intrinsic relationship exploration of cervical cells contributes significant improvements to the cervical cell classification. The relation-aware features generated by GCN effectively strengthens the representational power of CNN features. The proposed method can achieve the better classification performance and also can be potentially used in automatic screening system of cervical cytology.


Assuntos
Detecção Precoce de Câncer , Neoplasias do Colo do Útero , Feminino , Humanos , Processamento de Imagem Assistida por Computador , Redes Neurais de Computação , Neoplasias do Colo do Útero/diagnóstico por imagem
14.
Sci Total Environ ; 754: 141935, 2021 Feb 01.
Artigo em Inglês | MEDLINE | ID: mdl-32916486

RESUMO

Climate change due to greenhouse gas (GHG) emissions is one of the global environmental matters of the 21st century. Biochar (BC) amendments have been proposed as a potential solution for improving soil quality and to mitigate GHGs emissions. Therefore, we evaluated the influence of different BCs on soil CO2 and N2O emissions in an outdoor pot experiment. The soil was mixed with three different types of BCs; bamboo, hardwood, and rice straw BCs as BB, BH, and BR, respectively, and control as B0 with four levels (0, 5, 20, and 80 g kg-1 of soil). Gas samples were collected on a bi-monthly basis for six months. A polyvinyl chloride (PVC) static chamber was placed on each replicate to collect the gas samples at 15, 30, 45, and 60 min, respectively. Compared to B0, the lowest cumulative N2O emissions were observed in BH80 (11%) followed by BH20, BH5, and BR80. However, for cumulative CO2 emissions, B0 and BC treatments showed no significant differences except for BB80 (>11%) and BB5 (<2%). BC type and level both had a significant (P < 0.001) impact on the cumulative N2O emissions with a significant interaction (P < 0.001). However, cumulative CO2 emissions were unaffected by BC type but BC level showed a significant influence on cumulative CO2 emissions (P < 0.05) and there was a significant (P < 0.001) interaction between the BC type and level on cumulative CO2 emissions. Overall, higher doses of BR and BB showed a pronounced effect on soil pH over BH. The soil pH and moisture showed a negative correlation with N2O emissions whereas soil temperature showed a positive correlation with the cumulative fluxes of N2O. Our results demonstrate that BC incorporation to soil may help to mitigate GHGs emissions but its influence may vary with BC type and level under different conditions and soil type.


Assuntos
Dióxido de Carbono , Óxido Nitroso , Dióxido de Carbono/análise , Carvão Vegetal , Metano , Óxido Nitroso/análise , Solo
15.
BMC Plant Biol ; 20(1): 476, 2020 Oct 15.
Artigo em Inglês | MEDLINE | ID: mdl-33076818

RESUMO

BACKGROUND: Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. RESULTS: The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin). CONCLUSION: These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.


Assuntos
Magnoliopsida/metabolismo , Plântula/metabolismo , Medicamentos de Ervas Chinesas , Genes de Plantas , Luz , Magnoliopsida/anatomia & histologia , Magnoliopsida/crescimento & desenvolvimento , Magnoliopsida/efeitos da radiação , Metabolômica , Filogenia , Proteínas de Plantas/metabolismo , Plântula/anatomia & histologia , Plântula/crescimento & desenvolvimento , Plântula/efeitos da radiação , Fatores de Transcrição/metabolismo , Transcriptoma
17.
J Integr Plant Biol ; 62(12): 1823-1838, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32735361

RESUMO

N6 -methyladenosine (m6 A) is a prevalent modification in messenger RNAs and circular RNAs that play important roles in regulating various aspects of RNA metabolism. However, the occurrence of the m6 A modification in plant circular RNAs has not been reported. A widely used method to identify m6 A modifications relies on m6 A-specific antibodies followed by next-generation sequencing of precipitated RNAs (MeRIP-Seq). However, one limitation of MeRIP-Seq is that it does not provide the precise location of m6 A at single-nucleotide resolution. Although more recent sequencing techniques such as Nanopore-based direct RNA sequencing (DRS) can overcome such limitations, the technology does not allow sequencing of circular RNAs, as these molecules lack a poly(A) tail. Here, we developed a novel method to detect the precise location of m6 A modifications in circular RNAs using Nanopore DRS. We first enriched our samples for circular RNAs, which we then fragmented and sequenced on the Nanopore platform with a customized protocol. Using this method, we identified 470 unique circular RNAs from DRS reads based on the back-spliced junction region. Among exonic circular RNAs, about 10% contained m6 A sites, which mainly occurred around acceptor and donor splice sites. This study demonstrates the utility of our antibody-independent method in identifying total and methylated circular RNAs using Nanopore DRS. This method has the additional advantage of providing the exact location of m6 A sites at single-base resolution in circular RNAs or linear transcripts from non-coding RNA without poly(A) tails.


Assuntos
Poaceae/genética , RNA Circular/genética , RNA de Plantas/genética , Análise de Sequência de RNA/métodos , Sequenciamento de Nucleotídeos em Larga Escala
18.
Sci Rep ; 10(1): 3522, 2020 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-32103091

RESUMO

Two novel core-shell structured SiO2@AIPA-S-Si-Eu and SiO2@AIPA-S-Si-Eu-phen nanocomposites have been synthesized by a bifunctional organic ligands ((HOOC)2C6H3NHCONH(CH2)3Si(OCH2CH3)3) (defined as AIPA-S-Si) connected with Eu3+ ions and silica via covalent bond. And the corresponding core-shell-shell structured SiO2@AIPA-S-Si-Eu@SiO2 and SiO2@AIPA-S-Si-Eu-phen@SiO2 nanocomposites with enhanced luminescence have been synthesized by tetraethyl orthosilicate (TEOS) hydrolysis co-deposition method. The composition and micromorphology of the nanocomposites were characterized by means of Fourier-transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TG), X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectrometry (EDX) and X-ray photoelectron spectroscopy (XPS). The as-synthesized core-shell and core-shell-shell structured nanocomposites have excellent luminescence intensity and long lifetime. The nanocomposites show bright red light under ultraviolet lamp. However, the core-shell-shell structured nanocomposites have stronger luminescence intensity than the corresponding core-shell structured nanocomposites. Meanwhile, the core-shell-shell structured nanocomposites still exhibit good luminescence stability in aqueous solution. In addition, a large number of Si-OH on the surface of the core-shell-shell structured nanocomposites can be attached to many biomacromolecules. Therefore, they have potential applications in the fields of biology and luminescence.

20.
Tree Physiol ; 40(4): 538-556, 2020 04 08.
Artigo em Inglês | MEDLINE | ID: mdl-31860727

RESUMO

Most bamboo species including Moso bamboo (Phyllostachys edulis) are tropical or subtropical plants that greatly contribute to human well-being. Low temperature is one of the main environmental factors restricting bamboo growth and geographic distribution. Our knowledge of the molecular changes during bamboo adaption to cold stress remains limited. Here, we provided a general overview of the cold-responsive transcriptional profiles in Moso bamboo by systematically analyzing its transcriptomic response under cold stress. Our results showed that low temperature induced strong morphological and biochemical alternations in Moso bamboo. To examine the global gene expression changes in response to cold, 12 libraries (non-treated, cold-treated 0.5, 1 and 24 h at -2 °C) were sequenced using an Illumina sequencing platform. Only a few differentially expressed genes (DEGs) were identified at early stage, while a large number of DEGs were identified at late stage in this study, suggesting that the majority of cold response genes in bamboo are late-responsive genes. A total of 222 transcription factors from 24 different families were differentially expressed during 24-h cold treatment, and the expressions of several well-known C-repeat/dehydration responsive element-binding factor negative regulators were significantly upregulated in response to cold, indicating the existence of special cold response networks. Our data also revealed that the expression of genes related to cell wall and the biosynthesis of fatty acids were altered in response to cold stress, indicating their potential roles in the acquisition of bamboo cold tolerance. In summary, our studies showed that both plant kingdom-conserved and species-specific cold response pathways exist in Moso bamboo, which lays the foundation for studying the regulatory mechanisms underlying bamboo cold stress response and provides useful gene resources for the construction of cold-tolerant bamboo through genetic engineering in the future.


Assuntos
Regulação da Expressão Gênica de Plantas , Poaceae/genética , Temperatura Baixa , Perfilação da Expressão Gênica , Transcriptoma
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