scholarly journals Preferential Ribosome Loading on the Stress-Upregulated mRNA Pool Shapes the Selective Translation under Stress Conditions

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 304
Author(s):  
Yan Chen ◽  
Min Liu ◽  
Zhicheng Dong
Keyword(s):  
Enrichment Analysis ◽  
Close Correlation ◽  
Stress Conditions ◽  
Functional Categories ◽  
Molecular Pattern ◽  
Mrna Pool ◽  
Selective Translation ◽  
Stress Responsive Genes ◽  
Highly Correlated ◽  
Response To Water

The reprogramming of gene expression is one of the key responses to environmental stimuli, whereas changes in mRNA do not necessarily bring forth corresponding changes of the protein, which seems partially due to the stress-induced selective translation. To address this issue, we systematically compared the transcriptome and translatome using self-produced and publicly available datasets to decipher how and to what extent the coordination and discordance between transcription and translation came to be in response to wounding (self-produced), dark to light transition, heat, hypoxia, Pi starvation and the pathogen-associated molecular pattern (elf18) in Arabidopsis. We found that changes in total mRNAs (transcriptome) and ribosome-protected fragments (translatome) are highly correlated upon dark to light transition or heat stress. However, this close correlation was generally lost under other four stresses analyzed in this study, especially during immune response, which suggests that transcription and translation are differentially coordinated under distinct stress conditions. Moreover, Gene Ontology (GO) enrichment analysis showed that typical stress responsive genes were upregulated at both transcriptional and translational levels, while non-stress-specific responsive genes were changed solely at either level or downregulated at both levels. Taking wounding responsive genes for example, typical stress responsive genes are generally involved in functional categories related to dealing with the deleterious effects caused by the imposed wounding stress, such as response to wounding, response to water deprivation and response to jasmonic acid, whereas non-stress-specific responsive genes are often enriched in functional categories like S-glycoside biosynthetic process, photosynthesis and DNA-templated transcription. Collectively, our results revealed the differential as well as targeted coordination between transcriptome and translatome in response to diverse stresses, thus suggesting a potential model wherein preferential ribosome loading onto the stress-upregulated mRNA pool could be a pacing factor for selective translation.

scholarly journals An angiogenesis-related long noncoding RNA signature correlates with prognosis in patients with hepatocellular carcinoma

2021 ◽  
Vol 41 (4) ◽  
Author(s):  
Dengliang Lei ◽  
Yue Chen ◽  
Yang Zhou ◽  
Gangli Hu ◽  
Fang Luo
Keyword(s):  
Hepatocellular Carcinoma ◽  
Liver Cancer ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Enrichment Analysis ◽  
Clinical Information ◽  
Roc Curves ◽  
Gene Set Enrichment Analysis ◽  
The Cancer Genome Atlas ◽  
Highly Correlated

Abstract Hepatocellular carcinoma (HCC) is one of the most prevalent and lethal cancers worldwide. Neovascularization is closely related to the malignancy of tumors. We constructed a signature of angiogenesis-related long noncoding RNA (lncRNA) to predict the prognosis of patients with HCC. The lncRNA expression matrix of 424 HCC patients was downloaded from The Cancer Genome Atlas (TCGA). First, gene set enrichment analysis (GSEA) was used to distinguish the differentially expressed genes of the angiogenesis genes in liver cancer and adjacent tissues. Next, a signature of angiogenesis-related lncRNAs was constructed using univariate and multivariate analyses, and receiver operating characteristic (ROC) curves were used to assess the accuracy. The signature and relevant clinical information were used to construct the nomogram. A 5-lncRNA signature was highly correlated with overall survival (OS) in HCC patients and performed well in evaluations using the C-index, areas under the curve, and calibration curves. In summary, the 5-lncRNA model can serve as an accurate signature to predict the prognosis of patients with liver cancer, but its mechanism of action must be further elucidated by experiments.

scholarly journals Effects of Climate Temperature and Water Stress on Plant Growth and Accumulation of Antioxidant Compounds in Sweet Basil (Ocimum basilicum L.) Leafy Vegetable

Scientifica ◽  
2020 ◽  
Vol 2020 ◽  
pp. 1-12 ◽  
Author(s):  
Asma Al-Huqail ◽  
Rehab M. El-Dakak ◽  
Marwa Nme Sanad ◽  
Reem H. Badr ◽  
Mohamed M. Ibrahim ◽  
...  
Keyword(s):  
Water Stress ◽  
Plant Growth ◽  
Growth Parameters ◽  
Stress Conditions ◽  
Total Phenolic ◽  
Antioxidant Compounds ◽  
Chlorophyll Contents ◽  
Sweet Basil ◽  
Stress Markers ◽  
Response To Water

The effects of climate temperature and water stress on growth and several stress markers were investigated in sweet basil plants. Some growth parameters (shoot length and number of leaves) and photosynthetic chlorophyll contents were determined every two days during plant growth, and foliage leaf material was collected after 15 and 21 days of treatment. Both climate temperature and water stress inhibited sweet basil plant growth; especially, total chlorophyll levels were decreased significantly in response to high-temperature treatments. Under strong stresses, basil plants induced the synthesis and accumulation of glycine betaine (GB) as a secondary osmolyte, although at less content when compared with the proline content under the same stress conditions. Proline concentrations particularly increased in leaves of both basil stressed plants, accomplishing levels high enough to play a crucial role in cellular osmoregulation adjustment. Stress-induced accumulation of these antioxidant compounds was detected in sweet basil. Therefore, it appears that sweet basil-treated plants are able to synthesize antioxidant compounds under strong stress conditions. On the other hand, total sugar concentrations decreased in stress-treated basil plants. Both temperature and water stress treatments caused oxidative stress in the treated plants, as indicated by a significant increment in malondialdehyde (MDA) concentrations. An increase in total phenolic and flavonoid concentrations in response to water stress and a highly significant decrease in carotenoid concentrations in basil leaves were observed; flavonoids also increased under high climate temperature conditions.

Regulatory protein genes and microRNAs in response to selenium stimuli in Pueraria lobata (Willd.) Ohwi

Metallomics ◽  
2020 ◽  
Author(s):  
Yanni Li ◽  
Meijun He ◽  
Jishuang Li ◽  
Yiwei Yao ◽  
Li Zhu ◽  
...  
Keyword(s):  
Structural Gene ◽  
Target Genes ◽  
Regulatory Protein ◽  
Enrichment Analysis ◽  
Regulation Of Transcription ◽  
Pueraria Lobata ◽  
Ros Scavenging ◽  
Edible Plant ◽  
Go Enrichment ◽  
Highly Correlated

Abstract Regulatory protein genes and microRNAs (miRNAs) play important roles in response to abiotic and biotic stress, and the biosynthesis of secondary metabolites in plants. However, their responses to selenium (Se) stimuli have not been comprehensively studied in Pueraria lobata (Willd.) Ohwi, a Selenocompound-rich medicinal and edible plant. In this study, we identified a total of 436/556/1161/624 transcription factors (TFs), 134/157/308/172 transcriptional regulators (TRs) and 341/456/250/518 protein kinases (PKs), which were coexpressed with at least one Selenocompound-related structural gene/sulfate transporter or phosphate transporter/ROS scavenging structural gene/isoflavone-related structural gene, respectively. Then, we identified a total of 87 expressed miRNAs by Se disposure, in which 11 miRNAs, including miR171f-3p, miR390b-3P, miR-N111b, miR-N118, miR-N30, miR-N38-3P, miR-N61a, miR-N61b, miR-N80-3p, miR-N84-3P and miR-N90.2-3P were significantly up-regulated. We also identified a total of 1172 target genes for the 87 expressed miRNAs. Go enrichment analysis of these target genes showed that terms of regulation of transcription, DNA-templated, integral component of membrane, nucleus, ATP binding and plasma membrane are the top five subclassifications. Finally, we revealed that 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one Selenocompound-related structural gene or transporter gene; 5 miRNAs targeted 10 regulatory protein genes, which are highly correlated with at least one ROS scavenging structural gene; 5 miRNAs targeted 9 regulatory protein genes, which are potentially involved in the isoflavone biosynthesis. Overall, the study provides us the comprehensive insight of the roles of regulatory proteins and miRNAs in response to Se stimuli in P. lobata.

scholarly journals Knockdown of Cytochrome P450 Genes Gh_D07G1197 and Gh_A13G2057 on Chromosomes D07 and A13 Reveals Their Putative Role in Enhancing Drought and Salt Stress Tolerance in Gossypium hirsutum

Genes ◽  
2019 ◽  
Vol 10 (3) ◽  
pp. 226 ◽  
Author(s):  
Richard Odongo Magwanga ◽  
Pu Lu ◽  
Joy Nyangasi Kirungu ◽  
Qi Dong ◽  
Xiaoyan Cai ◽  
...  
Keyword(s):  
Salt Stress ◽  
Gossypium Hirsutum ◽  
Stress Tolerance ◽  
Common Property ◽  
Stress Conditions ◽  
Tetraploid Cotton ◽  
Salt Stress Tolerance ◽  
Negative Effects ◽  
Drought And Salt Stress ◽  
Stress Responsive Genes

We identified 672, 374, and 379 CYPs proteins encoded by the CYPs genes in Gossypium hirsutum, Gossypium raimondii, and Gossypium arboreum, respectively. The genes were found to be distributed in all 26 chromosomes of the tetraploid cotton, with chrA05, chrA12, and their homeolog chromosomes harboring the highest number of genes. The physiochemical properties of the proteins encoded by the CYP450 genes varied in terms of their protein lengths, molecular weight, isoelectric points (pI), and even grand hydropathy values (GRAVY). However, over 99% of the cotton proteins had GRAVY values below 0, which indicated that the majority of the proteins encoded by the CYP450 genes were hydrophilic in nature, a common property of proteins encoded by stress-responsive genes. Moreover, through the RNA interference (RNAi) technique, the expression levels of Gh_D07G1197 and Gh_A13G2057 were suppressed, and the silenced plants showed a higher concentration of hydrogen peroxide (H2O2) with a significant reduction in the concentration levels of glutathione (GSH), ascorbate peroxidase (APX), and proline compared to the wild types under drought and salt stress conditions. Furthermore, the stress-responsive genes 1-Pyrroline–5-Carboxylate Synthetase (GhP5CS), superoxide dismutase (GhSOD), and myeloblastosis (GhMYB) were downregulated in VIGS plants, but showed upregulation in the leaf tissues of the wild types under drought and salt stress conditions. In addition, CYP450-silenced cotton plants exhibited a high level of oxidative injury due to high levels of oxidant enzymes, in addition to negative effects on CMS, ELWL, RLWC, and chlorophyll content The results provide the basic foundation for future exploration of the proteins encoded by the CYP450 genes in order to understand the physiological and biochemical mechanisms in enhancing drought and salt stress tolerance in plants.

scholarly journals Phenological, Physiological and yield markers as efficient tools to identify drought tolerant rice genotypes in Eastern India

2020 ◽  
Author(s):  
Soumya Kumar Sahoo ◽  
Goutam Kumar Dash ◽  
Arti Guhey ◽  
Mirza Jaynul Baig ◽  
Madhusmita Barik ◽  
...  
Keyword(s):  
Water Stress ◽  
Drought Stress ◽  
Grain Yield ◽  
Stress Conditions ◽  
Eastern Region ◽  
Eastern India ◽  
Drought Tolerant ◽  
Significant Difference ◽  
Rice Genotypes ◽  
Highly Correlated

ABSTRACTRice production is severely threatened by drought stress in Eastern India. To develop drought tolerant varieties, selection of donors for breeding programme is crucial. Twenty one selected rice genotypes including both tolerant and sensitive to drought were grown under well-watered and drought stress conditions in dry seasons of two successive years of 2017 and 2018. Leaf water potential, relative water content displayed significant difference among the genotypes during vegetative screening. At reproductive stage drought screening, days to 50% flowering was delayed in all genotypes except N22 and Anjali (showed early flowering) however grain yield and other yield related traits decreased significantly compared to well watered condition. Correlation analysis of phenological and yield related traits with grain yield revealed that tiller numbers and panicle numbers are highly correlated with grain yield both under well-watered and water stress conditions and contributes maximum towards grain yield. The dendrogram grouped Mahamaya, Sahabhagidhan, Poornima, IBD 1, Hazaridhan, Samleshwari and Danteshwari into one cluster which performed better under water stress conditions and had grain yield more than 1.69 tha−1. Sahabhagidhan, Poornima, Vandana, and N22 displayed tolerance to drought both under vegetative and reproductive conditions which could be a good selection for the breeders to develop drought tolerant rice cultivars for eastern region of India.

scholarly journals Correlations between glycolysis with clinical traits and immune function in bladder urothelial carcinoma

2021 ◽  
Vol 41 (2) ◽  
Author(s):  
Kai Che ◽  
Wenkai Han ◽  
Danxia Li ◽  
Shuxia Cui ◽  
Mingxin Zhang ◽  
...  
Keyword(s):  
Immune Function ◽  
Urothelial Carcinoma ◽  
Immune Surveillance ◽  
Enrichment Analysis ◽  
Close Correlation ◽  
Gene Set Enrichment Analysis ◽  
Immune Checkpoints ◽  
Gene Set ◽  
Glycolytic Gene ◽  
Bladder Urothelial Carcinoma

Abstract Background: Glycolysis was a representative hallmark in the tumor microenvironment (TME), and we aimed to explore the correlations between glycolysis with immune activity and clinical traits in bladder urothelial carcinoma (BLCA). Methods: Our study obtained glycolysis scores for each BLCA samples from TCGA by a single-sample gene set enrichment analysis (ssGSEA) algorithm, based on a glycolytic gene set. The relationship between glycolysis with prognosis, clinical characteristics, and immune function were investigated subsequently. Results: We found that enhanced glycolysis was associated with poor prognosis and metastasis in BLCA. Moreover, glycolysis had a close correlation with immune function, and enhanced glycolysis increased immune activities. In other words, glycolysis had a positive correlation with immune activities. Immune checkpoints such as IDO1, CD274, were up-regulated in high-glycolysis group as well. Conclusion: We speculated that in BLCA, elevated glycolysis enhanced immune function, which caused tumor cells to overexpress immune checkpoints to evade immune surveillance. Inhibition of glycolysis might be a promising assistant for immunotherapy in bladder cancer.

scholarly journals Hippocampal CA3 Transcriptional Modules Associated with Granule Cell Alterations and Cognitive Impairment in Refractory Mesial Temporal Lobe Epilepsy Patients

2021 ◽  
Author(s):  
Silvia Bando ◽  
Fernanda Bertonha ◽  
Luciana Pimentel-Silva ◽  
João Mansano de Oliveira ◽  
Marco Duarte Carneiro ◽  
...  
Keyword(s):  
Granule Cell ◽  
Functional Characterization ◽  
Disease Onset ◽  
Enrichment Analysis ◽  
Mesial Temporal Lobe Epilepsy ◽  
Hippocampal Ca3 ◽  
High Gene ◽  
Cell Alterations ◽  
Highly Correlated ◽  
Patients With Epilepsy

Abstract In about a third of the patients with epilepsy the seizures are not drug-controlled. The current limitation of the antiepileptic drug therapy derives from an insufficient understanding of epilepsy pathophysiology. In order to overcome this situation, it is necessary to consider epilepsy as a disturbed network of interactions, instead of just looking for changes in single molecular components. Here, we studied CA3 transcriptional signatures and dentate gyrus histopathologic alterations in hippocampal explants surgically obtained from 57 RMTLE patients submitted to corticoamygdalohippocampectomy. By adopting a systems biology approach, integrating clinical, histopathological, and transcriptomic data (weighted gene co-expression network analysis), we were able to identify transcriptional modules highly correlated with age of disease onset, cognitive dysfunctions, and granule cell alterations. The enrichment analysis of transcriptional modules and the functional characterization of the highly connected genes in each trait-correlated module allowed us to unveil the modules’ main biological functions, paving the way for further investigations on their roles in RMTLE pathophysiology. Moreover, we found 15 genes with high gene significance values which have the potential to become novel biomarkers and/or therapeutic targets in RMTLE.

Fractal nature of regional ventilation distribution

2000 ◽  
Vol 88 (5) ◽  
pp. 1551-1557 ◽  
Author(s):  
William A. Altemeier ◽  
Steve McKinney ◽  
Robb W. Glenny
Keyword(s):  
Blood Flow ◽  
Regional Blood Flow ◽  
Fractal Dimensions ◽  
Close Correlation ◽  
Aerosol Deposition ◽  
Regional Ventilation ◽  
Significant Difference ◽  
Ventilation Heterogeneity ◽  
Highly Correlated ◽  
Ventilation And Perfusion

High-resolution measurements of pulmonary perfusion reveal substantial spatial heterogeneity that is fractally distributed. This observation led to the hypothesis that the vascular tree is the principal determinant of regional blood flow. Recent studies using aerosol deposition show similar ventilation heterogeneity that is closely correlated with perfusion. We hypothesize that ventilation has fractal characteristics similar to blood flow. We measured regional ventilation and perfusion with aerosolized and injected fluorescent microspheres in six anesthetized, mechanically ventilated pigs in both prone and supine postures. Adjacent regions were clustered into progressively larger groups. Coefficients of variation were calculated for each cluster size to determine fractal dimensions. At the smallest size lung piece, local ventilation and perfusion are highly correlated, with no significant difference between ventilation and perfusion heterogeneity. On average, the fractal dimension of ventilation is 1.16 in the prone posture and 1.09 in the supine posture. Ventilation has fractal properties similar to perfusion. Efficient gas exchange is preserved, despite ventilation and perfusion heterogeneity, through close correlation. One potential explanation is the similar geometry of bronchial and vascular structures.

scholarly journals Transcriptome Analysis Reveals Dynamic Fat Accumulation in the Walnut Kernel

2018 ◽  
Vol 2018 ◽  
pp. 1-13 ◽  
Author(s):  
Shuang Zhao ◽  
Xuemei Zhang ◽  
Yanping Su ◽  
Yilan Chen ◽  
Yang Liu ◽  
...  
Keyword(s):  
High Throughput ◽  
Developmental Stages ◽  
Juglans Regia ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Functional Categories ◽  
Sequencing Technology ◽  
Gene Enrichment ◽  
Three Stages ◽  
Fat Synthesis

Walnut (Juglans regia L.) is an important woody oilseed species cultivated throughout the world. In this study, comparative transcript profiling was performed using high-throughput RNA sequencing technology at the following three stages of walnut fat synthesis in the “Lvling” walnut cultivar: the initial developmental stage (L1), the fast developing stage (L2), and the last developing stage (L3). A total of 68.18 GB of data were obtained on the three developmental stages, and 92% to 94% of clean data were able to be located to the reference genome. Further comparisons of the transcripts in the three libraries revealed that 724, 2027, and 4817 genes were differentially expressed between the L2 and L1 (L2vsL1), L3 and L2 (L3vsL2), and L3 and L1 (L3vsL1) samples, respectively. Through the GO gene enrichment analysis, differentially expressed genes (DEGs) in L2vsL1, L3vsL2, and L3vsL1 were enriched into 3, 0, and 2 functional categories, respectively. According to the KEGG enrichment analysis, DEGs in L2vsL1, L3vsL2, and L3vsL1 were annotated into 77, 110, and 3717 taxonomic metabolic pathways in the KEGG database, respectively. Next, we analyzed expression levels of genes related to fat synthesis. Our results indicated that ACCase, LACS, and FAD7 were the key genes related to fat synthesis. The high-throughput transcriptome sequencing of walnut in different developmental stages has greatly enriched the current genomic available resources. The comparison of DEGs under different developmental stages identified a wealth of candidate genes involved in fat synthesis, which will facilitate further genetic improvement and molecular studies of the walnut.

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