Comprehensive Transcriptome Analysis Revealed the Effects of the Light Quality, Light Intensity, and Photoperiod on Phlorizin Accumulation in Lithocarpus polystachyus Rehd.

Lithocarpus polystachyus Rehd. is an important medicinal plant species grown in southern China, with phlorizin as its main active substance. The effects of light conditions on phlorizin biosynthesis in L. polystachyus remain unclear. Thus, we analyzed the transcriptomes of L. polystachyus plants cultivated under diverse light qualities, light intensities, and photoperiods. The light treatments resulted in 5977–8027 differentially expressed genes (DEGs), which were functionally annotated based on the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Genes encoding transcription factors from 89 families were differentially expressed after the light treatments, implying these transcription factors are photoresponsive. Phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) are the key enzymes for the accumulation of phlorizin. The transcription levels of PAL2, PAL, 4CL1 (DN121614), 4CLL7, and 4CL1 (DN102161) were positively correlated with phlorizin accumulation, suggesting that these genes are important for phlorizin biosynthesis. An ultra-high-performance liquid chromatography method was used to quantify the phlorizin content. Phlorizin accumulated in response to the green light treatment and following appropriate decreases in the light intensity or appropriate increases in the duration of the light exposure. The green light, 2000 lx, and 3000 lx treatments increased the PAL activity of L. polystachyus, but the regulatory effects of the light intensity treatments on PAL activity were relatively weak. This study represents the first comprehensive analysis of the light-induced transcriptome of L. polystachyus. The study results may form the basis of future studies aimed at elucidating the molecular mechanism underlying phlorizin biosynthesis in L. polystachyus. Moreover, this study may be relevant for clarifying the regulatory effects of light on the abundance of bioactive components in medicinal plants.

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Identification of hydatidosis-related modules and key regulatory genes

PeerJ ◽

10.7717/peerj.9280 ◽

2020 ◽

Vol 8 ◽

pp. e9280

Author(s):

Jijun Song ◽

Mingxin Song

Keyword(s):

Transcription Factors ◽

Signaling Pathway ◽

Target Genes ◽

Expression Profiles ◽

Differential Expression Analysis ◽

Interaction Network ◽

Enrichment Analysis ◽

Bmp Signaling ◽

Differentially Expressed ◽

Regulatory Effects

Background Echinococcosis caused by larval of Echinococcus is prevalent all over the world. Although clinical experience showed that the presence of tapeworms could not be found in liver lesions, the repeated infection and aggravation of lesions still occur in the host. Here, this study constructed a multifactor-driven disease-related dysfunction network to explore the potential molecular pathogenesis mechanism in different hosts after E.multilocularis infection. Method First, iTRAQ sequencing was performed on human liver infected with E.multilocularis. Second, obtained microRNAs(miRNAs) expression profiles of humans and canine infected with Echinococcus from the GEO database. In addition, we also performed differential expression analysis, protein interaction network analysis, enrichment analysis, and crosstalk analysis to obtain genes and modules related to E.multilocularis infection. Pivot analysis is used to calculate the potential regulatory effects of multiple factors on the module and identify related non-coding RNAs(ncRNAs) and transcription factors(TFs). Finally, we screened the target genes of miRNAs of Echinococcus to further explore its infection mechanism. Results A total of 267 differentially expressed proteins from humans and 3,635 differentially expressed genes from canine were obtained. They participated in 16 human-related dysfunction modules and five canine-related dysfunction modules, respectively. Both human and canine dysfunction modules are significantly involved in BMP signaling pathway and TGF-beta signaling pathway. In addition, pivot analysis found that 1,129 ncRNAs and 110 TFs significantly regulated human dysfunction modules, 158 ncRNAs and nine TFs significantly regulated canine dysfunction modules. Surprisingly, the Echinococcus miR-184 plays a role in the pathogenicity regulation by targeting nine TFs and one ncRNA in humans. Similarly, miR-184 can also cause physiological dysfunction by regulating two transcription factors in canine. Conclusion The results show that the miRNA-184 of Echinococcus can regulate the pathogenic process through various biological functions and pathways. The results laid a solid theoretical foundation for biologists to further explore the pathogenic mechanism of Echinococcosis.

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Artificial complementary chromatic acclimation gene expression system in Escherichia coli

Microbial Cell Factories ◽

10.1186/s12934-021-01621-3 ◽

2021 ◽

Vol 20 (1) ◽

Author(s):

Dwi Ariyanti ◽

Kazunori Ikebukuro ◽

Koji Sode

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Light Exposure ◽

Expression System ◽

Red Light ◽

Green Light ◽

Light Illumination ◽

Multiple Gene ◽

Gene Expression System ◽

Chromatic Acclimation

Abstract Background The development of multiple gene expression systems, especially those based on the physical signals, such as multiple color light irradiations, is challenging. Complementary chromatic acclimation (CCA), a photoreversible process that facilitates the control of cellular expression using light of different wavelengths in cyanobacteria, is one example. In this study, an artificial CCA systems, inspired by type III CCA light-regulated gene expression, was designed by employing a single photosensor system, the CcaS/CcaR green light gene expression system derived from Synechocystis sp. PCC6803, combined with G-box (the regulator recognized by activated CcaR), the cognate cpcG2 promoter, and the constitutively transcribed promoter, the PtrcΔLacO promoter. Results One G-box was inserted upstream of the cpcG2 promoter and a reporter gene, the rfp gene (green light-induced gene expression), and the other G-box was inserted between the PtrcΔLacO promoter and a reporter gene, the bfp gene (red light-induced gene expression). The Escherichia coli transformants with plasmid-encoded genes were evaluated at the transcriptional and translational levels under red or green light illumination. Under green light illumination, the transcription and translation of the rfp gene were observed, whereas the expression of the bfp gene was repressed. Under red light illumination, the transcription and translation of the bfp gene were observed, whereas the expression of the rfp gene was repressed. During the red and green light exposure cycles at every 6 h, BFP expression increased under red light exposure while RFP expression was repressed, and RFP expression increased under green light exposure while BFP expression was repressed. Conclusion An artificial CCA system was developed to realize a multiple gene expression system, which was regulated by two colors, red and green lights, using a single photosensor system, the CcaS/CcaR system derived from Synechocystis sp. PCC6803, in E. coli. The artificial CCA system functioned repeatedly during red and green light exposure cycles. These results demonstrate the potential application of this CCA gene expression system for the production of multiple metabolites in a variety of microorganisms, such as cyanobacteria.

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Transcriptome analyses identify five transcription factors differentially expressed in the hypothalamus of post- versus prepubertal Brahman heifers1

Journal of Animal Science ◽

10.2527/jas.2016-0471 ◽

2016 ◽

Vol 94 (9) ◽

pp. 3693-3702 ◽

Cited By ~ 11

Author(s):

M. R. S. Fortes ◽

L. T. Nguyen ◽

M. M. D. C. A. Weller ◽

A. Cánovas ◽

A. Islas-Trejo ◽

...

Keyword(s):

Transcription Factors ◽

Differentially Expressed ◽

Transcriptome Analyses

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Transcriptome analyses and virus induced gene silencing identify genes in the Rpp4-mediated Asian soybean rust resistance pathway

Functional Plant Biology ◽

10.1071/fp12296 ◽

2013 ◽

Vol 40 (10) ◽

pp. 1029 ◽

Cited By ~ 30

Author(s):

Aguida M. A. P. Morales ◽

Jamie A. O'Rourke ◽

Martijn van de Mortel ◽

Katherine T. Scheider ◽

Timothy J. Bancroft ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Gene Silencing ◽

Differentially Expressed ◽

Soybean Rust ◽

Phakopsora Pachyrhizi ◽

R Gene ◽

Virus Induced Gene Silencing ◽

Asian Soybean Rust ◽

Defence Responses

Rpp4 (Resistance to Phakopsora pachyrhizi 4) confers resistance to Phakopsora pachyrhizi Sydow, the causal agent of Asian soybean rust (ASR). By combining expression profiling and virus induced gene silencing (VIGS), we are developing a genetic framework for Rpp4-mediated resistance. We measured gene expression in mock-inoculated and P. pachyrhizi-infected leaves of resistant soybean accession PI459025B (Rpp4) and the susceptible cultivar (Williams 82) across a 12-day time course. Unexpectedly, two biphasic responses were identified. In the incompatible reaction, genes induced at 12 h after infection (hai) were not differentially expressed at 24 hai, but were induced at 72 hai. In contrast, genes repressed at 12 hai were not differentially expressed from 24 to 144 hai, but were repressed 216 hai and later. To differentiate between basal and resistance-gene (R-gene) mediated defence responses, we compared gene expression in Rpp4-silenced and empty vector-treated PI459025B plants 14 days after infection (dai) with P. pachyrhizi. This identified genes, including transcription factors, whose differential expression is dependent upon Rpp4. To identify differentially expressed genes conserved across multiple P. pachyrhizi resistance pathways, Rpp4 expression datasets were compared with microarray data previously generated for Rpp2 and Rpp3-mediated defence responses. Fourteen transcription factors common to all resistant and susceptible responses were identified, as well as fourteen transcription factors unique to R-gene-mediated resistance responses. These genes are targets for future P. pachyrhizi resistance research.

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PSB27: A thylakoid protein enabling Arabidopsis to adapt to changing light intensity

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1424040112 ◽

2015 ◽

Vol 112 (5) ◽

pp. 1613-1618 ◽

Cited By ~ 17

Author(s):

Xin Hou ◽

Aigen Fu ◽

Veder J. Garcia ◽

Bob B. Buchanan ◽

Sheng Luan

Keyword(s):

Photosystem Ii ◽

Light Intensity ◽

Light Adaptation ◽

Light Exposure ◽

Starch Accumulation ◽

State Transitions ◽

Potential Candidate ◽

Subsequent Work ◽

Variable Intensity ◽

Changing Light

In earlier studies we have identified FKBP20-2 and CYP38 as soluble proteins of the chloroplast thylakoid lumen that are required for the formation of photosystem II supercomplexes (PSII SCs). Subsequent work has identified another potential candidate functional in SC formation (PSB27). We have followed up on this possibility and isolated mutants defective in the PSB27 gene. In addition to lack of PSII SCs, mutant plants were severely stunted when cultivated with light of variable intensity. The stunted growth was associated with lower PSII efficiency and defective starch accumulation. In response to high light exposure, the mutant plants also displayed enhanced ROS production, leading to decreased biosynthesis of anthocyanin. Unexpectedly, we detected a second defect in the mutant, namely in CP26, an antenna protein known to be required for the formation of PSII SCs that has been linked to state transitions. Lack of PSII SCs was found to be independent of PSB27, but was due to a mutation in the previously described cp26 gene that we found had no effect on light adaptation. The present results suggest that PSII SCs, despite being required for state transitions, are not associated with acclimation to changing light intensity. Our results are consistent with the conclusion that PSB27 plays an essential role in enabling plants to adapt to fluctuating light intensity through a mechanism distinct from photosystem II supercomplexes and state transitions.

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Genes Encoding Transcription Factors TaDREB5 and TaNFYC-A7 Are Differentially Expressed in Leaves of Bread Wheat in Response to Drought, Dehydration and ABA

Frontiers in Plant Science ◽

10.3389/fpls.2018.01441 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 6

Author(s):

Lyudmila Zotova ◽

Akhylbek Kurishbayev ◽

Satyvaldy Jatayev ◽

Gulmira Khassanova ◽

Askar Zhubatkanov ◽

...

Keyword(s):

Transcription Factors ◽

Bread Wheat ◽

Differentially Expressed ◽

Genes Encoding

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TFutils: Data structures for transcription factor bioinformatics

F1000Research ◽

10.12688/f1000research.17976.1 ◽

2019 ◽

Vol 8 ◽

pp. 152

Author(s):

Benjamin J. Stubbs ◽

Shweta Gopaulakrishnan ◽

Kimberly Glass ◽

Nathalie Pochet ◽

Celine Everaert ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Data Structures ◽

Binding Sites ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Bioconductor Package ◽

Genome Wide ◽

Study Results ◽

Integrative Analyses

DNA transcription is intrinsically complex. Bioinformatic work with transcription factors (TFs) is complicated by a multiplicity of data resources and annotations. The Bioconductor package TFutils includes data structures and functions to enhance the precision and utility of integrative analyses that have components involving TFs. TFutils provides catalogs of human TFs from three reference sources (CISBP, HOCOMOCO, and GO), a catalog of TF targets derived from MSigDb, and multiple approaches to enumerating TF binding sites. Aspects of integration of TF binding patterns and genome-wide association study results are explored in examples.

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The color of illumination affects the stress response of jundiá (Rhamdia quelen, Quoy & Gaimard, Heptapteridae)

Ciência Rural ◽

10.1590/s0103-84782006000400031 ◽

2006 ◽

Vol 36 (4) ◽

pp. 1249-1252 ◽

Cited By ~ 13

Author(s):

Leonardo José Gil Barcellos ◽

Filipe Ritter ◽

Luiz Carlos Kreutz ◽

Leonardo Bolognesi da Silva ◽

Leonardo Cericato ◽

...

Keyword(s):

Stress Response ◽

South America ◽

Light Exposure ◽

Physiological Responses ◽

Green Light ◽

Fish Production ◽

Rhamdia Quelen ◽

Light Management ◽

Acute Stressor ◽

The Relationship

This paper provides the first data about physiological responses to stress in jundiá (Rhamdia quelen) exposed to different light colours. Jundiá is a species for fish production in the southern part of South America - and suitable for any region with a temperate or subtropical climates. In order to develop a light management for jundiá fingerlings during indoor maintenance and to understand the relationship between welfare and light colour in the jundiá, fingerlings were exposed to white, blue and green light. At the 10th day of light exposure an acute stressor was imposed. One hour after the application of the stressor, fish were sampled. Stress was assessed by means of cortisol determination. Our results show that green light seems to be the worst alternative to illuminate jundiá indoor experimentation facilities, or even fish transportation. The results also suggests that colour affects the stress response of jundia, and may be usefull for the management of this species.

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Potential Prognostic Immune Biomarkers of Overall Survival in Ovarian Cancer Through Comprehensive Bioinformatics Analysis: A Novel Artificial Intelligence Survival Prediction System

Frontiers in Medicine ◽

10.3389/fmed.2021.587496 ◽

2021 ◽

Vol 8 ◽

Author(s):

Tingshan He ◽

Liwen Huang ◽

Jing Li ◽

Peng Wang ◽

Zhiqiao Zhang

Keyword(s):

Artificial Intelligence ◽

Ovarian Cancer ◽

Overall Survival ◽

Transcription Factors ◽

Cancer Patients ◽

Prognostic Model ◽

Cox Regression ◽

Differentially Expressed ◽

Immune Genes ◽

Immune Biomarkers

Background: The tumour immune microenvironment plays an important role in the biological mechanisms of tumorigenesis and progression. Artificial intelligence medicine studies based on big data and advanced algorithms are helpful for improving the accuracy of prediction models of tumour prognosis. The current research aims to explore potential prognostic immune biomarkers and develop a predictive model for the overall survival of ovarian cancer (OC) based on artificial intelligence algorithms.Methods: Differential expression analyses were performed between normal tissues and tumour tissues. Potential prognostic biomarkers were identified using univariate Cox regression. An immune regulatory network was constructed of prognostic immune genes and their highly related transcription factors. Multivariate Cox regression was used to identify potential independent prognostic immune factors and develop a prognostic model for ovarian cancer patients. Three artificial intelligence algorithms, random survival forest, multitask logistic regression, and Cox survival regression, were used to develop a novel artificial intelligence survival prediction system.Results: The current study identified 1,307 differentially expressed genes and 337 differentially expressed immune genes between tumour samples and normal samples. Further univariate Cox regression identified 84 prognostic immune gene biomarkers for ovarian cancer patients in the model dataset (GSE32062 dataset and GSE53963 dataset). An immune regulatory network was constructed involving 63 immune genes and 5 transcription factors. Fourteen immune genes (PSMB9, FOXJ1, IFT57, MAL, ANXA4, CTSH, SCRN1, MIF, LTBR, CTSD, KIFAP3, PSMB8, HSPA5, and LTN1) were recognised as independent risk factors by multivariate Cox analyses. Kaplan-Meier survival curves showed that these 14 prognostic immune genes were closely related to the prognosis of ovarian cancer patients. A prognostic nomogram was developed by using these 14 prognostic immune genes. The concordance indexes were 0.760, 0.733, and 0.765 for 1-, 3-, and 5-year overall survival, respectively. This prognostic model could differentiate high-risk patients with poor overall survival from low-risk patients. According to three artificial intelligence algorithms, the current study developed an artificial intelligence survival predictive system that could provide three individual mortality risk curves for ovarian cancer.Conclusion: In conclusion, the current study identified 1,307 differentially expressed genes and 337 differentially expressed immune genes in ovarian cancer patients. Multivariate Cox analyses identified fourteen prognostic immune biomarkers for ovarian cancer. The current study constructed an immune regulatory network involving 63 immune genes and 5 transcription factors, revealing potential regulatory associations among immune genes and transcription factors. The current study developed a prognostic model to predict the prognosis of ovarian cancer patients. The current study further developed two artificial intelligence predictive tools for ovarian cancer, which are available at https://zhangzhiqiao8.shinyapps.io/Smart_Cancer_Survival_Predictive_System_17_OC_F1001/ and https://zhangzhiqiao8.shinyapps.io/Gene_Survival_Subgroup_Analysis_17_OC_F1001/. An artificial intelligence survival predictive system could help improve individualised treatment decision-making.

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In vitro studies on the induction of sporogenous tissue on leaves of cinnamon fern. I. Environmental factors

Canadian Journal of Botany ◽

10.1139/b72-341 ◽

1972 ◽

Vol 50 (12) ◽

pp. 2673-2682 ◽

Cited By ~ 7

Author(s):

William H. Harvey ◽

James D. Caponetti

Keyword(s):

Environmental Factors ◽

Light Intensity ◽

Environmental Conditions ◽

Light Exposure ◽

Progressive Increase ◽

Light Phase ◽

Sporogenous Tissue ◽

Light Darkness

Intact, set III, cinnamon fern cataphyll and frond primordia, which were shown to have no predisposition to fertility in situ, produced sporangia when excised and cultured under sterile conditions in Knudson's medium supplemented with various levels of sucrose and maintained on 11 different regimens of light, darkness, and temperature for 10 weeks. Increasing levels of sucrose resulted in increased fertility under all environmental conditions, but the highest percentage of fertility was obtained under conditions of continuous dark at 26 °C. As the length of the light phase of the photoperiods decreased, a progressive increase in induction of fertile leaves was observed, suggesting that periods of long light exposure are inhibitory to the initiation of sporangia. Conversely, as the light intensity was increased, an inhibition of sporophyll differentiation occurred. Sporangia excised from dark-induced sporophylls and cultured in the light produced viable spores which germinated yielding haploid gametophytes that ultimately produced sporophytes.

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