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PubMed Journals Articles About "Transcriptome Analysis Reveals Dysregulation Genes Involved Oxidative Phosphorylation" RSS

12:46 EDT 30th March 2020 | BioPortfolio

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Showing "Transcriptome analysis reveals dysregulation genes involved oxidative phosphorylation" PubMed Articles 1–25 of 45,000+

Transcriptome analysis reveals dysregulation of genes involved in oxidative phosphorylation in a murine model of retinopathy of prematurity.

Retinal gene expression pattern is severely altered after exposition to hyperoxia in mice with oxygen-induced retinopathy (OIR), a common model of retinopathy of prematurity. Gene ontology and signaling pathway analyses may add new insights into a better understanding of the pathogenesis of this disease.


Transcriptome analysis of maize reveals potential key genes involved in the response to belowground herbivore H. parallela larvae feeding.

The larvae of Holotrichia parallela, a destructive belowground herbivore, causes tremendous damages to maize plants. However, little is known if there are any defense mechanisms in maize roots to defend themselves against this herbivore. In the current research, we carried out RNA-sequencing to investigate the changes in gene transcription level in maize roots after the H. parallela larvae infestation. A total of 644 up-regulated genes and 474 down-regulated genes was found. In addition, Gene ontology (GO) ...

Transcriptome analysis of Xanthomonas oryzae pv. oryzicola exposed to H2O2 reveals horizontal gene transfer contributes to its oxidative stress response.

Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of bacterial leaf streak, is one of the most severe seed-borne bacterial diseases of rice. However, the molecular mechanisms underlying Xoc in response to oxidative stress are still unknown. In this study, we performed a time-course RNA-seq analysis on the Xoc in response to H2O2, aiming to reveal its oxidative response network. Overall, our RNA sequence analysis of Xoc revealed a significant global gene expression profile when it was exposed to H2O2....


SRNAome and transcriptome analysis provide insight into strawberry fruit ripening.

Strawberry fruit ripening is a complex process affected by multiple factors at different regulation levels. To elucidate the regulation mechanisms, the combined analysis of sRNAome and transcriptome were used. A total of 124 known and 190 novel miRNAs were found, 62 of them were significantly differentially expressed (DE). The targets of the DE miRNAs were parsed and several TFs, such as SPL, ARF, WRKY, and TCP, were found to be involved in ripening. Elevated CO can significantly postpone ripening and miR15...

Integrated analysis of the transcriptome and metabolome of purple and green leaves of Tetrastigma hemsleyanum reveals gene expression patterns involved in anthocyanin biosynthesis.

To gain better insight into the regulatory networks of anthocyanin biosynthesis, an integrated analysis of the metabolome and transcriptome in purple and green leaves of Tetrastigma hemsleyanum was conducted. Transcript and metabolite profiles were archived by RNA-sequencing data analysis and LC-ESI-MS/MS, respectively. There were 209 metabolites and 4211 transcripts that were differentially expressed between purple and green leaves. Correlation tests of anthocyanin contents and transcriptional changes show...

Transcriptome analysis reveals gene expression changes of the fat body of silkworm (Bombyx mori L.) in response to selenium treatment.

A comparative transcriptome analysis was conducted to investigate the gene expression changes in the fat body of silkworm after treatment with different concentrations (50 μM and 200 μM) of selenium (Se). 912 differential expression genes (DEGs) (371 up-regulated and 541 down-regulated) and 1420 DEGs (1078 up-regulated and 342 down-regulated) were identified in silkworm fat body treated with 50 μM and 200 μM of Se, respectively. In case of 50 μM group, DEGs were mainly enriched in the peroxisome p...

Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder.

Evaluation of expression profile in autism spectrum disorder (ASD) patients is an important approach to understand possible similar functional consequences that may underlie disease pathophysiology regardless of its genetic heterogeneity. Induced pluripotent stem cell (iPSC)-derived neuronal models have been useful to explore this question, but larger cohorts and different ASD endophenotypes still need to be investigated. Moreover, whether changes seen in this in vitro model reflect previous findings in ASD...

Comparative transcriptome analysis reveals a potential role for CaMK4 in γδT17 cells from systemic lupus erythematosus patients with lupus nephritis.

γδ T cells may be involved in the onset of systemic lupus erythematosus (SLE) though the production of pro-inflammatory cytokines. IL-17 has been shown to play an important role in the pathogenesis of SLE with lupus nephritis (LN). Although some investigations have indicated that γδ T cells are the major producing cells of IL-17 (γδT17 cells), the function of γδT17 cells in SLE with LN has not yet been fully established. In the present study, transcriptome sequencing analysis was performed to identi...

Poly(Adp-Ribose) Polymerase-1 inhibition potentiates cell death and phosphorylation of Dna damage response proteins in oxidative stressed retinal cells.

Oxidative stress (OxS) is involved in the development of cell injures occurring in retinal diseases while Poly(ADP-ribose) Polymerase-1 (PARP-1) is a key protein involved in the repair of the DNA damage caused by OxS. Inhibition of PARP-1 activity with the pharmacological inhibitor PJ34 in mouse retinal explants subjected to HO-induced oxidative damage resulted in an increase of apoptotic cells. Reduction of cell growth was also observed in the mouse cone like cell line 661 W in the presence of PJ34 under...

A transcriptome-based signature of pathological angiogenesis predicts breast cancer patient survival.

The specific genes and molecules that drive physiological angiogenesis differ from those involved in pathological angiogenesis, suggesting distinct mechanisms for these seemingly related processes. Unveiling genes and pathways preferentially associated with pathologic angiogenesis is key to understanding its mechanisms, thereby facilitating development of novel approaches to managing angiogenesis-dependent diseases. To better understand these different processes, we elucidated the transcriptome of the mouse...

De novo transcriptome analysis of halotolerant bacterium Staphylococcus sp. strain P-TSB-70 isolated from East coast of India: In search of salt stress tolerant genes.

In the present study, we identified salt stress tolerant genes from the marine bacterium Staphylococcus sp. strain P-TSB-70 through transcriptome sequencing. In favour of whole-genome transcriptome profiling of Staphylococcus sp. strain P-TSB-70 (GenBank Accn. No. KP117091) which tolerated upto 20% NaCl stress, the strain was cultured in the laboratory condition with 20% NaCl stress. Transcriptome analyses were performed by SOLiD4.0 sequencing technology from which 10280 and 9612 transcripts for control and...

Comprehensive analysis of Q gene near isogenic lines reveals key molecular pathways for wheat domestication and improvement.

The wheat AP2-like transcription factor gene Q played a major role in domestication by conferring the free-threshing character and pleiotropically affecting numerous other traits. However, little is known regarding the molecular mechanisms associated with the regulation of these traits by Q, especially for the structural determination of threshability. Here, transcriptome analysis of immature spike tissues in three lines nearly isogenic for Q revealed over 3,000 differentially expressed genes (DEGs) involve...

Transcriptome-wide analysis of MADS-box family genes involved in aluminum and fluoride assimilation in .

MADS-box transcription factors (TFs) are involved in a variety of processes in flowering plants ranging from root growth to flower and fruit development. However, studies of the tolerance-related functions of MADS-box genes are very limited, and to date no such studies have been conducted on . To gain insight into the functions of genes of this family and to elucidate the role they may play in tissue development and Al and F response, we identified 45 MADS-box genes through transcriptomic analysis of . Phyl...

Transcriptome analysis reveals the mechanism underlying improved glutathione biosynthesis and secretion in Candida utilis during selenium enrichment.

The effect of sodium selenite on batch culture of Candida utilis CCTCC M 209298 was investigated. Cell growth was inhibited while glutathione biosynthesis and secretion were improved during selenium enrichment. To reveal the mechanism underlying the decrease in biomass and the increase in glutathione, both metabolic flux analysis of key intermediates involved in glutathione metabolic pathway and transcriptome analysis of C. utilis by RNA-seq were carried out for selenized cells and the control without selen...

Transcriptome analysis clarified genes involved in resistance to Phytophthora capsici in melon.

Phytophthora blight caused by Phytophthora capsici is a devastating disease for melon plant. However, the underlying resistance mechanisms are still poorly understood. In this study, the transcriptome differences between the resistant ZQK9 and susceptible E31 at 0, 3, and 5 days post-inoculation (dpi) were identified by RNA-seq. A total of 1,195 and 6,595 differentially expressed genes (DEGs) were identified in ZQK9 and E31, respectively. P. capsici infection triggered massive transcript changes in the inoc...

The Arabidopsis Transcriptome Responds Specifically and Dynamically to High Light Stress.

The dynamic and specific transcriptome for high light (HL) stress in plants is poorly understood because heat has confounded previous studies. Here, we perform an in-depth temporal responsive transcriptome analysis and identify the core HL-responsive genes. By eliminating the effect of heat, we uncover a set of genes specifically regulated by high-intensity light-driven signaling. We find that 79% of HL-responsive genes restore their expression to baseline within a 14-h recovery period. Our study reveals t...

Energy metabolism involved in fertility of the wheat TCMS line YS3038.

In the wheat TCMS line YS3038, the anther development is inhibited from late uninucleate stage to the binucleate stage. The disruption of energy metabolism pathways by aberrant transcriptional regulation causes the male sterility under low temperatures. The utilization of thermosensitive male sterile (TMS) lines provides a basis for two-line breeding. Previous work, including morphological and cytological observations, has shown that the development process of the TMS line YS3038 is inhibited from the late ...

Investigating Phosphorylation-Induced Conformational Changes in WNK1 Kinase by Molecular Dynamics Simulations.

The With-No-Lysine (WNK) kinase is considered to be a master regulator for various cation-chloride cotransporters involved in maintaining cell-volume and ion homeostasis. Here, we have investigated the phosphorylation-induced structural dynamics of the WNK1 kinase bound to an inhibitor via atomistic molecular dynamics simulations. Results from our simulations show that the phosphorylation at Ser could stabilize the otherwise flexible activation loop (A-loop). The intrahelix salt-bridge formed between Arg an...

Metabolite profiling and transcriptome analyses provide insights into the flavonoid biosynthesis in the developing seed of tartary buckwheat (Fagopyrum tataricum).

Tartary buckwheat (Fagopyrum tataricum) seeds are rich in flavonoids. However, the detailed flavonoid compositions and the molecular basis of flavonoid biosynthesis in tartary buckwheat seeds remain largely unclear. Here, we performed a combined metabolite profiling and transcriptome analysis to identify flavonoid compositions and characterize genes involved in flavonoid biosynthesis in the developing tartary buckwheat seeds. In total, 234 flavonoids, including 10 isoflavones, were identified. Of these, 80 ...

Transcriptome analysis and histopathology of the mud crab (Scylla paramamosain) after air exposure.

The mud crab, Scylla paramamosain, is an economically-important crab in China. Air exposure is an important environmental stressor during mud crab culture and transportation. Adaptive mechanisms responding to air exposure in mud crabs are still poorly understood. In this study, mud crabs were exposed to air for 120 h. Air exposure decreased total hemocyte counts, led to cytological damage, and caused high mortality. Transcriptomic analysis was conducted at 0, 6 and 96 h after air exposure. A total of 35...

Transcriptome analysis of Aconitum carmichaelii and exploration of the salsolinol biosynthetic pathway.

Aconitum carmichaelii has been used in traditional Chinese medicine for treating various diseases for several thousand years. Based on the biosynthetic pathway of some alkaloids such as C19-diterpenoid alkaloids and obvious differences in alkaloid content between leaves of two A. carmichaelii varieties has been reported, we performed leaves transcriptome analysis of two A. carmichaelii varieties. Besides we characterized the biosynthetic pathway of salsolinol. A total of 56 million raw reads (8.28 G) and ...

Transcriptome analysis of Actinidia chinensis in response to Botryosphaeria dothidea infection.

Ripe rot caused by Botryosphaeria dothidea causes extensive production losses in kiwifruit (Actinidia chinensis Planch.). Our previous study showed that kiwifruit variety "Jinyan" is resistant to B. dothidea while "Hongyang" is susceptible. For a comparative analysis of the response of these varieties to B. dothidea infection, we performed a transcriptome analysis by RNA sequencing. A total of 305.24 Gb of clean bases were generated from 36 libraries of which 175.76 Gb was from the resistant variety and 129...

Gene Expression Profile Reveals Hematopoietic-Related Molecule Changes in Response to Hypoxic Exposure.

The Qing-Tibet Plateau is characterized by low oxygen pressure, which is an important biomedical and ecological stressor. However, the variation in gene expression during periods of stay on the plateau has not been well studied. We recruited eight volunteers to stay on the plateau for 3, 7, and 30 days. Human Clariom D arrays were used to measure transcriptome changes in the mRNA expression profiles in these volunteers' blood. Analysis of variance (ANOVA) indicated that 699 genes were significantly differen...

Application of transcriptome analysis: Oxidative stress, inflammation and microtubule activity disorder caused by ammonia exposure may be the primary factors of intestinal microvilli deficiency in chicken.

Ammonia (NH), an inhaled harmful gas, is not only an important volatile in fertilizer production and ranching, but also the main basic component of haze. However, the effect and mechanism of NH on the intestines are still unclear. To investigate the intestinal toxicity of NH inhalation, morphological changes, transcriptome profiles and oxidative stress indicators of jejunum in broiler chicken exposed to NH for 42 days were examined. Results of morphological observation showed that NH exposure caused defic...

Simultaneous transcriptome analysis of oil palm clones and Phytophthora palmivora reveals oil palm defense strategies.

Phytophthora palmivora is an oomycete that causes oil palm bud rot disease. To understand the molecular mechanisms of this disease, palm clones with contrasting responses (Ortet 34, resistant and Ortet 57, susceptible) were inoculated with P. palmivora, and RNAseq gene expression analysis was performed. The transcriptome was obtained by sequencing using Illumina HiSeq2500 technology during the asymptomatic phase (24, 72 and 120 hours postinfection, hpi). A simultaneous analysis of differentially expressed g...


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