scholarly journals Comparison of the Transcriptomic Responses of Two Chrysanthemum Morifolium Cultivars to Low Light

2021 ◽  
Author(s):  
Shuang Han ◽  
Qingchen Zhang ◽  
Xiaoqin Zhu ◽  
Dongli Pei
Keyword(s):  
Elongation Factor ◽  
Chrysanthemum Morifolium ◽  
Stem Length ◽  
Shade Avoidance ◽  
Biological Processes ◽  
Low Light ◽  
Helix Loop Helix ◽  
Molecular Functions ◽  
Upregulated Genes ◽  
Cellular Components

Abstract Low light is a primary regulator of chrysanthemum growth. Herein, we conducted a transcriptomic analysis of leaf samples from the ‘Nannonggongfen’ and ‘Nannongxuefeng’ chrysanthemum cultivars following a 5-day exposure to optimal light (70%, control [CK]) or low-light (20%, LL) conditions. Gene Ontology (GO) classification of upregulated genes revealed these genes to be associated with 11 cellular components, 9 molecular functions, and 15 biological processes, with the majority being localized to the chloroplast, highlighting the role of chloroplast proteins as regulators of shading tolerance. Downregulated genes were associated with 11 cellular components, 8 molecular functions, and 16 biological processes. Heat map analyses suggested that basic helix–loop–helix domain genes and elongation factors were markedly downregulated in ‘Nannongxuefeng’ leaves, consistent with the maintenance of normal stem length, whereas no comparable changes were observed in ‘Nanonggongfen’ leaves. Subsequent qPCR analyses revealed that phytochrome-interacting factors and dormancy-associated genes were significantly upregulated under LL conditions relative to CK conditions, while succinate dehydrogenase 1, elongated hypocotyls 5, and auxin-responsive gene of were significantly downregulated under LL conditions. These findings suggest that LL plants were significantly lower than those of the CK plants. Low-light tolerant chrysanthemum cultivars may maintain reduced indole-3-acetic acid (IAA) and elongation factor expression as a means of preventing the onset of shade-avoidance symptoms.

scholarly journals NSUN5 is Upregulated and Positively Correlated with Translation in Human Cancers: A Bioinformatics-based Study

2020 ◽  
Author(s):  
Xiao-wen Zhang ◽  
Yan Huang ◽  
Lu-yi Wu ◽  
Qin Qi ◽  
Rui Zhong ◽  
...  
Keyword(s):  
Methylation Level ◽  
Biological Processes ◽  
Kegg Pathways ◽  
Normal Tissues ◽  
Human Cancers ◽  
Molecular Functions ◽  
Cellular Components

Abstract The role of RNA m5C (5-methylcytosine) and RNA m5C methyltransferases (RCMTs, including NSUN1, NSUN2, NSUN3, NSUN4, NSUN5, NSUN6, NSUN7 and TRDMT1) in human cancers remains largely unknown. In this study, GEPIA2 was used to compare the expression of RCMTs in human cancers and that in associated normal tissues, and to analyze the prognosis value of NSUN5 expression. UALCAN was used to compare the methylation level of NSUN5 promoter in human cancers and that in associated normal tissues. LinkedOmics was used perform BPs (biological processes), CCs (cellular components), MFs (molecular functions) and KEGG pathways analyses of NSUN5-correlated genes in each cancer one by one. We found that six RCMTs (NSUN1-NSUN5 and TRDMT1), especially NSUN5, were generally upregulated in human cancers, that the hypomethylation of NSUN5 promoter may be responsible for its upregulation, and that overexpressed NSUN5 predicted poorer prognosis and was positively correlated with translation in human cancers. The function of NSUN5 in human cancers and its mechanism need to be validated by biological experiments.

Study of NSCLC cell migration promoted by NSCLC-Derived Extracellular Vesicle using atomic force microscopy

2021 ◽  
Author(s):  
Shuwei Wang ◽  
Jiajia Wang ◽  
Tuoyu Ju ◽  
Kaige Qu ◽  
Fan Yang ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Cell Migration ◽  
Cancer Cells ◽  
Extracellular Vesicles ◽  
Extracellular Vesicle ◽  
Cancer Microenvironment ◽  
Biological Processes ◽  
Force Microscopy ◽  
Atomic Force ◽  
Cellular Components

Extracellular Vesicles (EVs) secreted by cancer cells have a key role in the cancer microenvironment and progression. Previous studies have mainly focused on molecular functions, cellular components and biological processes...

scholarly journals Insights into how environment shapes post-mortem RNA transcription in mouse brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Raphael Severino Bonadio ◽  
Larissa Barbosa Nunes ◽  
Patricia Natália S. Moretti ◽  
Juliana Forte Mazzeu ◽  
Stefano Cagnin ◽  
...  
Keyword(s):  
Lipid Metabolism ◽  
Mouse Brain ◽  
Molecular Mechanisms ◽  
Cell Communication ◽  
Rna Degradation ◽  
The Body ◽  
Biological Processes ◽  
Post Mortem ◽  
Gene Expression Alterations ◽  
Upregulated Genes

AbstractMost biological features that occur on the body after death were already deciphered by traditional medicine. However, the molecular mechanisms triggered in the cellular microenvironment are not fully comprehended yet. Previous studies reported gene expression alterations in the post-mortem condition, but little is known about how the environment could influence RNA degradation and transcriptional regulation. In this work, we analysed the transcriptome of mouse brain after death under three concealment simulations (air exposed, buried, and submerged). Our analyses identified 2,103 genes differentially expressed in all tested groups 48 h after death. Moreover, we identified 111 commonly upregulated and 497 commonly downregulated genes in mice from the concealment simulations. The gene functions shared by the individuals from the tested environments were associated with RNA homeostasis, inflammation, developmental processes, cell communication, cell proliferation, and lipid metabolism. Regarding the altered biological processes, we identified that the macroautophagy process was enriched in the upregulated genes and lipid metabolism was enriched in the downregulated genes. On the other hand, we also described a list of biomarkers associated with the submerged and buried groups, indicating that these environments can influence the post-mortem RNA abundance in its particular way.

scholarly journals Targeting the Ubiquitin Signaling Cascade in Tumor Microenvironment for Cancer Therapy

2021 ◽  
Vol 22 (2) ◽  
pp. 791
Author(s):  
Qi Liu ◽  
Bayonle Aminu ◽  
Olivia Roscow ◽  
Wei Zhang
Keyword(s):  
Tumor Microenvironment ◽  
Cancer Therapy ◽  
Therapeutic Agents ◽  
Biological Processes ◽  
Post Translational Modification ◽  
E3 Ligases ◽  
Tumor Microenvironments ◽  
Cellular Immune ◽  
Ubiquitin Conjugating Enzymes ◽  
Cellular Components

Tumor microenvironments are composed of a myriad of elements, both cellular (immune cells, cancer-associated fibroblasts, mesenchymal stem cells, etc.) and non-cellular (extracellular matrix, cytokines, growth factors, etc.), which collectively provide a permissive environment enabling tumor progression. In this review, we focused on the regulation of tumor microenvironment through ubiquitination. Ubiquitination is a reversible protein post-translational modification that regulates various key biological processes, whereby ubiquitin is attached to substrates through a catalytic cascade coordinated by multiple enzymes, including E1 ubiquitin-activating enzymes, E2 ubiquitin-conjugating enzymes and E3 ubiquitin ligases. In contrast, ubiquitin can be removed by deubiquitinases in the process of deubiquitination. Here, we discuss the roles of E3 ligases and deubiquitinases as modulators of both cellular and non-cellular components in tumor microenvironment, providing potential therapeutic targets for cancer therapy. Finally, we introduced several emerging technologies that can be utilized to develop effective therapeutic agents for targeting tumor microenvironment.

scholarly journals Identification of Key Candidate Genes Involved in the Progression of Idiopathic Pulmonary Fibrosis

Molecules ◽  
2021 ◽  
Vol 26 (4) ◽  
pp. 1123
Author(s):  
Yu Cui ◽  
Jie Ji ◽  
Jiwei Hou ◽  
Yi Tan ◽  
Xiaodong Han
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Candidate Genes ◽  
Expression Profiles ◽  
Biological Processes ◽  
Protein Protein Interaction ◽  
Novel Treatments ◽  
Kegg Pathway Analysis ◽  
Cell Components ◽  
Upregulated Genes

Idiopathic pulmonary fibrosis (IPF) is a lethal, agnogenic interstitial lung disease with limited therapeutic options. To investigate vital genes involved in the development of IPF, we integrated and compared four expression profiles (GSE110147, GSE53845, GSE24206, and GSE10667), including 87 IPF samples and 40 normal samples. By reanalyzing these datasets, we managed to identify 62 upregulated genes and 20 downregulated genes in IPF samples compared with normal samples. Differentially expressed genes (DEGs) were analyzed by gene ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis to illustrate relevant pathways of IPF, biological processes, molecular function, and cell components. The DEGs were then subjected to protein–protein interaction (PPI) for network analysis, serving to find 11 key candidate genes (ANXA3, STX11, THBS2, MMP1, MMP9, MMP7, MMP10, SPP1, COL1A1, ITGB8, IGF1). The result of RT-qPCR and immunohistochemical staining verified our finding as well. In summary, we identified 11 key candidate genes related to the process of IPF, which may contribute to novel treatments of IPF.

scholarly journals The Yin and Yang of tumour-derived extracellular vesicles in tumour immunity

2020 ◽  
Author(s):  
Takayoshi Yamauchi ◽  
Toshiro Moroishi
Keyword(s):  
Extracellular Vesicles ◽  
Tumour Progression ◽  
Tumour Microenvironment ◽  
Host Immunity ◽  
Biological Processes ◽  
Small Particles ◽  
Tumour Immunity ◽  
Heterogeneous Nature ◽  
Yin And Yang ◽  
Cellular Components

Abstract Extracellular vesicles (EVs) are small particles that are naturally released from various types of cells. EVs contain a wide variety of cellular components, such as proteins, nucleic acids, lipids and metabolites, which facilitate intercellular communication in diverse biological processes. In the tumour microenvironment, EVs have been shown to play important roles in tumour progression, including immune system–tumour interactions. Although previous studies have convincingly demonstrated the immunosuppressive functions of tumour-derived EVs, some studies have suggested that tumour-derived EVs can also stimulate host immunity, especially in therapeutic conditions. Recent studies have revealed the heterogeneous nature of EVs with different structural and biological characteristics that may account for the divergent functions of EVs in tumour immunity. In this review article, we provide a brief summary of our current understanding of tumour-derived EVs in immune activation and inhibition. We also highlight the emerging utility of EVs in the diagnosis and treatment of cancers and discuss the potential clinical applications of tumour-derived EVs.

Gene of the month: BECN1

2014 ◽  
Vol 67 (8) ◽  
pp. 656-660 ◽  
Author(s):  
Sumit Sahni ◽  
Angelica M Merlot ◽  
Sukriti Krishan ◽  
Patric J Jansson ◽  
Des R Richardson
Keyword(s):  
Neurological Disorders ◽  
Viral Infections ◽  
Critical Role ◽  
Beclin 1 ◽  
Biological Processes ◽  
Disease States ◽  
Binding Partners ◽  
Future Drug ◽  
Cellular Components ◽  
Important Therapeutic Target

The BECN1 gene encodes the Beclin-1 protein, which is a well-established regulator of the autophagic pathway. It is a mammalian orthologue of the ATG6 gene in yeast and was one of the first identified mammalian autophagy-associated genes. Beclin-1 interacts with a number of binding partners in the cell which can lead to either activation (eg, via PI3KC3/Vps34, Ambra 1, UV radiation resistance-associated gene) or inhibition (eg, via Bcl-2, Rubicon) of the autophagic pathway. Apart from its role as a regulator of autophagy, it is also shown to effect important biological processes in the cell such as apoptosis and embryogenesis. Beclin-1 has also been implicated to play a critical role in the pathology of a variety of disease states including cancer, neurological disorders (eg, Alzheimer's disease, Parkinson's disease) and viral infections. Thus, understanding the functions of Beclin-1 and its interactions with other cellular components will aid in its development as an important therapeutic target for future drug development.

Changes in the responses to light quality during ontogeny in Chenopodium album

2003 ◽  
Vol 81 (2) ◽  
pp. 152-163 ◽  
Author(s):  
Humberto Fabio Causin ◽  
Renata D Wulff
Keyword(s):  
Plant Growth ◽  
Light Quality ◽  
Chenopodium Album ◽  
Intraspecific Variability ◽  
Reproductive Fitness ◽  
Stem Length ◽  
Shade Avoidance ◽  
Late Flowering ◽  
Total Leaf ◽  
Avoidance Responses

Morphological shade-avoidance responses have been hypothesized to be a form of adaptive plasticity to improve competition for light; however, little is known about their intraspecific variability and their effect on reproductive fitness. To compare plant responses either at a common age or at a common phenological stage, two experiments were conducted with early- and late-flowering Chenopodium album plants exposed to different red (660 nm) to far red (730 nm) ratios. In the first experiment, plant height and number of leaves were recorded at several times during the vegetative stage, and at the onset of flowering, each plant was harvested and other growth traits were measured. In the second experiment, three destructive harvests were performed across the whole plant cycle. Plant growth and development markedly differed between early- and late-flowering plants in all of the conditions tested. Light treatments significantly affected stem length, total leaf number, total leaf area, and relative allocation to leaf biomass. In all families, the response of stem elongation to light treatments decreased later in the development, while changes in the other plastic responses were mostly due to variations in plant growth. No significant treatment effect was found on relative biomass allocation to reproductive structures. However, individual seed mass significantly differed between certain groups, indicating that light quality can affect reproductive fitness through changes in traits other than fruit or seed set.Key words: Chenopodium album, fitness, intraspecific variability, phenotypic plasticity, red to far red ratio, shade-avoidance responses.

scholarly journals Transcriptome Reveals the Specificity of Phyllostachys edulis ‘Pachyloen’ Shoots at Different Developmental Stages

Forests ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 861 ◽  
Author(s):  
Yaping Hu ◽  
Ying Zhang ◽  
Jie Zhou ◽  
Guibing Wang ◽  
Qirong Guo
Keyword(s):  
Metabolic Pathways ◽  
Developmental Stages ◽  
Moso Bamboo ◽  
Biological Processes ◽  
Phyllostachys Edulis ◽  
Monthly Basis ◽  
Bamboo Shoots ◽  
Tyrosine Metabolism ◽  
Culm Wall ◽  
Cellular Components

Phyllostachys edulis ‘Pachyloen’ can have a stalk wall thickness of up to 2.5 cm at a height of 1.3 m, which is 1.8 times that of normal Moso bamboo (Phyllostachys edulis); this serves as an excellent cultivar, comprising both wood and bamboo shoots. We collected bamboo shoot samples of Phyllostachys edulis ‘Pachyloen’ and Moso bamboo on a monthly basis from September to April and used transcriptome sequencing to explore the differences in their development. The results showed that there were 666–1839 Phyllostachys edulis ‘Pachyloen’-specific genes at different developmental stages enriched in 20 biological processes, 15 cellular components, 12 molecular functions, and 137 metabolic pathways, 52 of which were significant. Among these, 27 metabolic pathways such as tyrosine metabolism and their uniquely expressed genes were found to play important roles in the thickening of Phyllostachys edulis ‘Pachyloen’. This study provides insights into the mechanisms underlying the thickening of the culm wall of Phyllostachys edulis ‘Pachyloen’.

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