Lipid Productivity and Biosynthesis Genes Response of Indigenous Chlorella sp. T4 Strain under Different Nitrogen and Phosphorus Load

Abstract Microalgae can synthesize and accumulate high neutral lipids upon exposure to abiotic stress such as nutrient starvation or limitation. In this study, indigenous microalgae Chlorella sp. T4 was cultivated in nitrogen and phosphorus under both limiting and replete conditions. Growth, lipid yield, fatty acid profiles and biosynthetic gene expression levels were determined to ascertain cell’s response under these conditions. An impaired cell growth was observed under nitrogen limiting condition, evident by the lowest biomass yield (0.58±0.03 g L−1) as revealed by low quantum efficiency of photosystem II (Fv/Fm) value and chlorophyll a content. An increase in lipid content yield was observed under nitrogen and phosphorus limiting conditions as compared to the control. Nutrient limiting conditions produced fatty acid methyl ester that is suitable for biodiesel production compared to the control (BG-11). Gene expression analysis using real time q-PCR for photosynthesis (rbcL) and lipid biosynthesis (accD, KAS-1, ω-6 FAD, ω-3 FAD) genes revealed different expression levels under both limiting and replete conditions. Under nutrient limiting conditions, increase in the expression of accD, KAS-1, ω-6 FAD and ω-3 FAD genes was observed, whereas a decrease in rbcL gene expression level was noted. A significant correlation could be drawn between the expression levels of the biosynthetic genes and growth rate, biomass yield, physiological response, lipid yield and fatty acid composition. These results provide an insight into the physiological response and gene expression level under different nutrient levels, which could be harnessed for future genetic engineering of Chlorella sp. T4 for improved lipid production.

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Influence of dietary linseed oil as substitution of fish oil on whole fish fatty acid composition, lipid metabolism and oxidative status of juvenile Manchurian trout, Brachymystax lenok

Scientific Reports ◽

10.1038/s41598-019-50243-8 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 1

Author(s):

Jianhua Yu ◽

Shuguo Li ◽

Huaxin Niu ◽

Jie Chang ◽

Zongfu Hu ◽

...

Keyword(s):

Gene Expression ◽

Fatty Acid ◽

Lipid Metabolism ◽

Fish Oil ◽

Linseed Oil ◽

Gene Expression Level ◽

Expression Level ◽

Manchurian Trout ◽

Inclusion Level ◽

Brachymystax Lenok

Abstract In this study, juvenile Manchurian trout, Brachymystax lenok (initial weight: 6.43 ± 0.02 g, mean ± SE) were received for nine weeks with five types of diets prepared by gradually replacing the proportion of fish oil (FO) with linseed oil (LO) from 0% (LO0) to 25% (LO25), 50% (LO50), 75% (LO75), and 100% (LO100). The eicosapentaenoic (EPA) and docosahexaenoic (DHA) composition decreased with increasing inclusion level of LO (P < 0.05). With increasing LO inclusion level, triglyceride (TAG) content of serum increased significantly, however, there was a decrease in high-density lipoprotein cholesterol (HDL) (P < 0.05). LO substitution of FO up-regulated the gene expression level of lipid metabolism-related genes Fatty Acid Desaturases 6 (FAD6), Acetyl-Coa Carboxylase (ACCα), Sterol Regulatory Element Binding Protein 1 (SREBP-1), and Sterol O- Acyl Transferase 2 (SOAT2), and down-regulated the gene expression level of Peroxisome Proliferator-Activated Receptor a (PPARα) (P < 0.05). The SOD activities of both serum and liver in LO100 were significantly lower than in LO25 (P < 0.05). The CAT activity of the liver in LO100 was significantly lower than in LO0 and LO25 (P < 0.05). This study indicates that the Manchurian trout may have the ability to synthesize LC-PUFAs from ALA, and an appropriate LO in substitution of FO (<75%) could improve both the lipid metabolism and the oxidation resistance.

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Gene Expression Level, Immunolocalization, and Function of Fatty Acid-Binding Protein from Schistosoma japonicum

Journal of Parasitology ◽

10.1645/19-42 ◽

2021 ◽

Vol 107 (4) ◽

Author(s):

Chun-Lian Tang ◽

Yan-hong Li ◽

Wen-Qin Dai ◽

Ya-Wen Zhu ◽

Zhao-Xia Wu ◽

...

Keyword(s):

Gene Expression ◽

Fatty Acid ◽

Schistosoma Japonicum ◽

Fatty Acid Binding Protein ◽

Binding Protein ◽

Gene Expression Level ◽

Expression Level ◽

Fatty Acid Binding ◽

Acid Binding Protein ◽

And Function

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Chromatin Signature and Transcription Factor Binding Provide a Predictive Basis for Understanding Plant Gene Expression

Plant and Cell Physiology ◽

10.1093/pcp/pcz051 ◽

2019 ◽

Vol 60 (7) ◽

pp. 1471-1486 ◽

Cited By ~ 6

Author(s):

Zefeng Wu ◽

Jing Tang ◽

Junjie Zhuo ◽

Yuhan Tian ◽

Feiyang Zhao ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Histone Modifications ◽

Gene Expression Level ◽

Expression Level ◽

Good Prediction ◽

Chromatin Modifications ◽

Chromatin Signature ◽

Expression Levels ◽

Gene Expression Levels

Abstract Chromatin accessibility and post-transcriptional histone modifications play important roles in gene expression regulation. However, little is known about the joint effect of multiple chromatin modifications on the gene expression level in plants, despite that the regulatory roles of individual histone marks such as H3K4me3 in gene expression have been well-documented. By using machine-learning methods, we systematically performed gene expression level prediction based on multiple chromatin modifications data in Arabidopsis and rice. We found that as few as four histone modifications were sufficient to yield good prediction performance, and H3K4me3 and H3K36me3 being the top two predictors with known functions related to transcriptional initiation and elongation, respectively. We demonstrated that the predictive powers differed between protein-coding and non-coding genes as well as between CpG-enriched and CpG-depleted genes. We also showed that the predictive model trained in one tissue or species could be applied to another tissue or species, suggesting shared underlying mechanisms. More interestingly, the gene expression levels of conserved orthologs are easier to predict than the species-specific genes. In addition, chromatin state of distal enhancers was moderately correlated to gene expression but was dispensable if given the chromatin features of the proximal regions of genes. We further extended the analysis to transcription factor (TF) binding data. Strikingly, the combinatorial effects of only a few TFs were roughly fit to gene expression levels in Arabidopsis. Overall, by using quantitative modeling, we provide a comprehensive and unbiased perspective on the epigenetic and TF-mediated regulation of gene expression in plants.

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Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression level with cell volume

10.1101/2021.01.26.428201 ◽

2021 ◽

Author(s):

Jie Lin

Keyword(s):

Gene Expression ◽

Cell Volume ◽

Direct Consequence ◽

Rna Polymerases ◽

Gene Expression Level ◽

Expression Level ◽

Expression Levels ◽

Genes Expression ◽

Biophysical Mechanism ◽

Cycle Regulation

Many experiments have shown that most genes’ expression levels are typically proportional to cell volumes in growing cells. However, a finite number of genes often exhibit nonlinear scaling of expression levels with cell volume. Their corresponding mRNA and protein concentrations are therefore not constant as the cell volume increases. While these genes with changing concentrations often have important biological functions such as cell cycle regulation, the biophysical mechanism underlying the nonlinear scaling between the gene expression level and the cell volume is still unclear. In this manuscript, we show that the nonlinear scaling is, in fact, a direct consequence of heterogeneous recruitment abilities of promoters to RNA polymerases. Those genes with weaker (stronger) recruitment abilities compared with the average ability spontaneously exhibit superlinear (sublinear) scaling with cell volume. Our model makes predictions in agreement with experimental observations, including a correlation between the expression levels and nonlinear scaling degrees with cell volume among genes.

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Multiparametric MRI Features Predict the SYP Gene Expression in Low-Grade Glioma Patients: A Machine Learning-Based Radiomics Analysis

Frontiers in Oncology ◽

10.3389/fonc.2021.663451 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zheng Xiao ◽

Shun Yao ◽

Zong-ming Wang ◽

Di-min Zhu ◽

Ya-nan Bie ◽

...

Keyword(s):

Neural Network ◽

Gene Expression ◽

Survival Rate ◽

Convolutional Neural Network ◽

Multiparametric Mri ◽

Low Grade Glioma ◽

Gene Expression Level ◽

Expression Level ◽

Low Grade ◽

Expression Levels

PurposeSynaptophysin (SYP) gene expression levels correlate with the survival rate of glioma patients. This study aimed to explore the feasibility of applying a multiparametric magnetic resonance imaging (MRI) radiomics model composed of a convolutional neural network to predict the SYP gene expression in patients with glioma.MethodUsing the TCGA database, we examined 614 patients diagnosed with glioma. First, the relationship between the SYP gene expression level and outcome of survival rate was investigated using partial correlation analysis. Then, 7266 patches were extracted from each of the 108 low-grade glioma patients who had available multiparametric MRI scans, which included preoperative T1-weighted images (T1WI), T2-weighted images (T2WI), and contrast-enhanced T1WI images in the TCIA database. Finally, a radiomics features-based model was built using a convolutional neural network (ConvNet), which can perform autonomous learning classification using a ROC curve, accuracy, recall rate, sensitivity, and specificity as evaluation indicators.ResultsThe expression level of SYP decreased with the increase in the tumor grade. With regard to grade II, grade III, and general patients, those with higher SYP expression levels had better survival rates. However, the SYP expression level did not show any significant association with the outcome in Level IV patients.ConclusionOur multiparametric MRI radiomics model constructed using ConvNet showed good performance in predicting the SYP gene expression level and prognosis in low-grade glioma patients.

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Improving the Effects of Omega-3 Fatty Acid on the In Vitro Maturation of Oocytes

Jurnal Ilmu Ternak dan Veteriner ◽

10.14334/jitv.v25i4.2555 ◽

2020 ◽

Vol 25 (4) ◽

pp. 153

Author(s):

Masume Ghorbani Vahed ◽

Ramazan Khanbabaee ◽

Mehrdad Shariati ◽

Mohammad Amin Edalatmanesh

Keyword(s):

Gene Expression ◽

Fatty Acid ◽

In Vitro Maturation ◽

Cumulus Cells ◽

Gene Expression Level ◽

Expression Level ◽

Maturation Stage ◽

High Dose ◽

Omega 3

This research was conducted in order to determine the effects of omega-3 on oocyte in vitro maturation and the level of expression of tribbles (TRIB1, TRIB2 and TRIB3 genes) in cumulus cells. Eight-ten weeks old NMRI mice were super-ovulated using 7.5 IU pregnant mare’s serum gonadotropin (PMSG, Intraperitoneal) and they were killed after 44 hours and their ovaries were removed. The oocytes were used for <em>in vitro</em> maturation and the cumulus-oocyte complexes (COCs) were released. Cumulus cells and oocytes were assigned into control, ethanol-treated and groups exposed to 10 and 100 μg/ml of omega-3. The cells were prepared to assess the maturation stage in order to evaluate the gene expression level. The data were statistically analyzed. Exposing oocytes to low dose (10 μg/ml) and high dose (100 μg/ml) of omega-3 resulted in a reduced rate of GV-stage oocytes, decreased MI-oocytes and increased MII-oocytes. The enhanced maturity of COCs was also detected in response to a high dose of omega-3 (100 μg/ml). Exposure of cumulus cells to omega-3 (10 and 100 μg/ml) induced TRIB2 and inhibited TRIB3 gene expression level; however, TRIB1 gene expression level increased and decreased in response to low (10 μg/ml) and high (100 μg/ml) concentrations of omega-3, respectively. The addition of omega-3 to the environment of oocytes or cumulus cells affected the maturation of oocytes and cumulus cells, which was followed by the differential expression of TRIB genes, suggesting that there was a role of fatty acid metabolism in the differentiation and maturation of cumulus cells.

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