scholarly journals Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology

2020 ◽  
Vol 69 (1) ◽  
pp. 39-48
Author(s):  
RUIRUI LIU ◽  
LULU LI ◽  
ZHIYING LI ◽  
WEIWEI WANG
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Rna Sequencing ◽  
Metabolic Pathways ◽  
Sinorhizobium Meliloti ◽  
Hydrogen Treatment ◽  
Sequencing Technology ◽  
Pathway Analyses ◽  
The Relationship ◽  
Surrounding Soil

Hydrogen formed during nitrogen fixation in legumes can enter the surrounding soil and confer multiple benefits to crops. Here, we used Sinorhizobium meliloti 1021, whose genome was sequenced in 2001, as a model bacterium to study the relationship between the bacterium and legume. We investigated the effects of hydrogen on the gene expression in S. meliloti using RNA-sequencing technology. We identified 43 genes whose expression was altered by hydrogen treatment; among these, 39 were downregulated, and 4 were upregulated. These genes accounted for 1.5% of the total 2941 annotated genes of the S. meliloti genome. Gene ontology and pathway analyses revealed that the hydrogen-regulated genes were associated with catalytic activity and binding. Further, these genes were primarily involved in arginine, proline, and β-alanine metabolism. Real-time PCR revealed that the transcription levels of SMc02983, cyoB, cyoC, and cyoD were reduced after hydrogen treatment. These results provide a theoretical framework for exploring new metabolic pathways of S. meliloti.

scholarly journals Mechanisms for the adverse effects of late gestational increases in maternal cortisol on the heart revealed by transcriptomic analyses of the fetal septum

2014 ◽  
Vol 46 (15) ◽  
pp. 547-559 ◽  
Author(s):  
Elaine M. Richards ◽  
Charles E. Wood ◽  
Maria Belen Rabaglino ◽  
Andrew Antolic ◽  
Maureen Keller-Wood
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Cell Apoptosis ◽  
Metabolic Pathways ◽  
Fetal Heart ◽  
Pathway Inference ◽  
Apoptosis Pathways ◽  
Altered Metabolism ◽  
Mitochondrial Number ◽  
Muscle Cell Apoptosis

We have previously shown in sheep that 10 days of modest chronic increase in maternal cortisol resulting from maternal infusion of cortisol (1 mg/kg/day) caused fetal heart enlargement and Purkinje cell apoptosis. In subsequent studies we extended the cortisol infusion to term, finding a dramatic incidence of stillbirth in the pregnancies with chronically increased cortisol. To investigate effects of maternal cortisol on the heart, we performed transcriptomic analyses on the septa using ovine microarrays and Webgestalt and Cytoscape programs for pathway inference. Analyses of the transcriptomic effects of maternal cortisol infusion for 10 days (130 day cortisol vs 130 day control), or ∼25 days (140 day cortisol vs 140 day control) and of normal maturation (140 day control vs 130 day control) were performed. Gene ontology terms related to immune function and cytokine actions were significantly overrepresented as genes altered by both cortisol and maturation in the septa. After 10 days of cortisol, growth factor and muscle cell apoptosis pathways were significantly overrepresented, consistent with our previous histologic findings. In the term fetuses (∼25 days of cortisol) nutrient pathways were significantly overrepresented, consistent with altered metabolism and reduced mitochondria. Analysis of mitochondrial number by mitochondrial DNA expression confirmed a significant decrease in mitochondria. The metabolic pathways modeled as altered by cortisol treatment to term were different from those modeled during maturation of the heart to term, and thus changes in gene expression in these metabolic pathways may be indicative of the fetal heart pathophysiologies seen in pregnancies complicated by stillbirth, including gestational diabetes, Cushing's disease and chronic stress.

scholarly journals Effect of short term diet restriction on gene expression in the bovine hypothalamus using next generation RNA sequencing technology

BMC Genomics ◽  
2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Daragh Matthews ◽  
Michael G. Diskin ◽  
David A. Kenny ◽  
Christopher J. Creevey ◽  
Kate Keogh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Next Generation ◽  
Diet Restriction ◽  
Sequencing Technology ◽  
Short Term

scholarly journals Transfer of clinically relevant gene expression signatures in breast cancer: from Affymetrix microarray to Illumina RNA-Sequencing technology

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 1008 ◽  
Author(s):  
Debora Fumagalli ◽  
Alexis Blanchet-Cohen ◽  
David Brown ◽  
Christine Desmedt ◽  
David Gacquer ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Rna Sequencing ◽  
Sequencing Technology ◽  
Affymetrix Microarray ◽  
Gene Expression Signatures ◽  
Relevant Gene

123 Effect of heat stress on oocyte developmental competence and global gene expression dynamics in Bos taurus crossbred beef cows

2019 ◽  
Vol 31 (1) ◽  
pp. 187 ◽  
Author(s):  
Z. Jiang ◽  
F. A. Diaz ◽  
E. J. Gutierrez ◽  
B. A. Foster ◽  
P. T. Hardin ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Heat Stress ◽  
Rna Sequencing ◽  
Molecular Mechanisms ◽  
Global Gene Expression ◽  
Developmental Competence ◽  
Differentially Expressed ◽  
Regulation Of Transcription

It is known that animals under the effect of heat stress present reduced fertility. We aimed to investigate the effect of heat stress on the developmental competence and global gene expression profile of oocytes through the transition from spring to summer under Louisiana conditions. Oocytes were collected from 6 crossbred, non-lactating cows once a month from May to July. Temperature and humidity indexes for May and July were 72.48 and 78.06, respectively. An index above 75 indicates that cows are under heat stress. All cows underwent dominant follicle removal, and then 7 days later, ovum pickup was performed to aspirate germinal vesicle (GV) oocytes. Half of the oocytes were processed for RNA-seq as GV, and half were matured in vitro to metaphase II (MII). Smart-seq protocol was followed to prepare RNA sequencing libraries from a pool of 4 oocytes (GV n=6; MII n=6). Sequencing reads were pre-filtered and aligned to the bovine genome, and gene expression values were calculated as transcripts per million. Genes were deemed differentially expressed between different conditions if they showed a false discovery rate P-value<0.05 using DESEqn 2 package. DAVID (https://david.ncifcrf.gov) and IPA (ingenuity pathway analysis) were used to reveal the gene ontology and pathways, respectively. The RNA sequencing showed that a total of 212 genes were differentially expressed as a result of heat stress at the GV stage, with 94 and 118 genes up- and down-regulated, respectively. Gene ontology analysis indicated significant over-representation of elements involved in steroid biosynthetic process, oxidation reduction, and mitophagy in response to mitochondrial depolarization. Several pathways were influenced by heat stress, including glucocorticoid biosynthesis, apoptosis signalling, and HIPPO signalling. At the MII oocyte stage, only 93 genes (19 up-regulated and 74 down-regulated) were significantly differentially expressed in oocytes between July and May groups. Oocytes retrieved on different collection days, from the same cows under the same treatments, showed no difference on maturation rates, suggesting that the in vitro maturation process equalizes the expression of several genes. The primary biological processes significantly affected in MII oocytes were regulation of MAPK cascade, melanosome organisation, and negative regulation of transcription. In addition, we found that UBE2I, a gene involved in phosphorylation-dependent sumoylation of heat shock factor 1 (HSF1), was significantly up-regulated in July compared with May in MII oocytes. Interestingly, only 5 common genes were significantly affected by heat in both GV and MII oocytes: E2F8, GATAD2B, BHLHE41, FBXO44, and RAB39B. Our findings provide new insight into the molecular mechanisms of detrimental conditions (heat stress) on bovine oocytes, which may help to reveal master regulators controlling oocyte competence.

scholarly journals Early Detection of Neurological Dysfunction Using Blood Cell Transcript Profiles

2018 ◽  
Author(s):  
Mohammad Ali Moni ◽  
Humayan Kabir Rana ◽  
M. Babul Islam ◽  
Md Bashir Ahmed ◽  
Pietro Liò ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Blood Cell ◽  
Blood Cells ◽  
Neurological Dysfunction ◽  
Transcriptional Analysis ◽  
Genetic Associations ◽  
Regulation Of Expression ◽  
Significant Gene ◽  
Pathway Analyses

AbstractIdentification of genes whose regulation of expression is similar in both brain and blood cells could enable monitoring of significant neurological traits and disorders by analysis of blood samples. We thus employed transcriptional analysis of pathologically affected tissues, using agnostic approaches to identify overlapping gene functions and integrating this transcriptomic information with expression quantitative trait loci (eQTL) data. Here, we estimate the correlation of genetic expression in the top-associated cis-eQTLs of brain tissue and blood cells in Parkinson’s (PD).We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors in PD, a neurodegenerative disease. We examined gene expression microarray and RNA-Seq datasets from human brain and blood tissues from PD-affected and control individuals. Differentially expressed genes (DEG) were identified for both brain and blood cells to determine common DEG overlaps. Based on neighborhood-based benchmarking and multilayer network topology aproaches we then developed genetic associations of factors with PD.Overlapping DEG sets underwent gene enrichment using pathway analysis and gene ontology methods, which identified candidate common genes and pathways. We identified 12 significantly dysregulated genes shared by brain and blood cells, which were validated using dbGaP (gene SNP-disease linkage) database for gold-standard benchmarking of their significance in disease processes. Ontological and pathway analyses identified significant gene ontology and molecular pathways that indicate PD progression.In sum, we found possible novel links between pathological processes in brain and blood cells by examining cell path-way commonalities, corroborating these associations using well validated datasets. This demonstrates that for brain-related pathologies combining gene expression analysis and blood cell cis-eQTL is a potentially powerful analytical approach. Thus, our methodologies facilitate data-driven approaches that can advance knowledge of disease mechanisms and may enable prediction of neurological dysfunction using blood cell transcript profiling.

Overexpression of miR-340-5p Inhibits Skin Fibroblast Proliferation by Targeting Kruppel-like Factor 2

2019 ◽  
Vol 20 (13) ◽  
pp. 1147-1154 ◽  
Author(s):  
Ling Chen ◽  
Qian Li ◽  
Xun Lu ◽  
Xiaohua Dong ◽  
Jingyun Li
Keyword(s):  
Gene Ontology ◽  
Skin Fibroblast ◽  
Kegg Pathway ◽  
Normal Skin ◽  
Skin Fibroblasts ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Fibroblast Proliferation ◽  
Pathway Analyses ◽  
Normal Skin Fibroblast

<P>Objective: MicroRNA (miR)-340-5p has been identified to play a key role in several cancers. However, the function of miR-340-5p in skin fibroblasts remains largely unknown. </P><P> Methods: Gain of function experiments were performed by infecting normal skin fibroblast cells with a lentivirus carrying 22-bp miR-340-5p. Cell proliferation was detected by Cell Counting Kit-8 (CCK-8) assay. To uncover the mechanisms, mRNA-seq was used. Differentially expressed mRNAs were further determined by Gene Ontology and KEGG pathway analyses. The protein levels were analysed by Western blotting. A dual-luciferase reporter assay was used to detect the direct binding of miR-340-5p with the 3&#039;UTR of Kruppel-like factor 2 (KLF2). </P><P> Results: MiR-340-5p lentivirus infection suppressed normal skin fibroblast proliferation. The mRNAseq data revealed that 41 mRNAs were differentially expressed, including 22 upregulated and 19 downregulated transcripts in the miR-340-5p overexpression group compared with those in the control group. Gene Ontology and KEGG pathway analyses revealed that miR-340-5p overexpression correlated with the macromolecule biosynthetic process, cellular macromolecule biosynthetic process, membrane, and MAPK signalling pathway. Bioinformatics analysis and luciferase reporter assays showed that miR-340-5p binds to the 3&#039;UTR of KLF2. Forced expression of miR-340-5p decreased the expression of KLF2 in normal skin fibroblasts. Overexpression of KLF2 restored skin fibroblast proliferation in the miR-340-5p overexpression group. </P><P> Conclusion: This study demonstrates that miR-340-5p may suppress skin fibroblast proliferation, possibly through targeting KLF2. These findings could help us understand the function of miR-340-5p in skin fibroblasts. miR-340-5p could be a therapeutic target for preventing scarring.</P>

scholarly journals Endolysosomal Cation Channels and MITF in Melanocytes and Melanoma

Biomolecules ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1021
Author(s):  
Carla Abrahamian ◽  
Christian Grimm
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Transcription Factor ◽  
Convincing Evidence ◽  
Signaling Cascades ◽  
Cation Channels ◽  
Pore Channel ◽  
Different Types ◽  
Canonical Wnt ◽  
The Relationship

Microphthalmia-associated transcription factor (MITF) is the principal transcription factor regulating pivotal processes in melanoma cell development, growth, survival, proliferation, differentiation and invasion. In recent years, convincing evidence has been provided attesting key roles of endolysosomal cation channels, specifically TPCs and TRPMLs, in cancer, including breast cancer, glioblastoma, bladder cancer, hepatocellular carcinoma and melanoma. In this review, we provide a gene expression profile of these channels in different types of cancers and decipher their roles, in particular the roles of two-pore channel 2 (TPC2) and TRPML1 in melanocytes and melanoma. We specifically discuss the signaling cascades regulating MITF and the relationship between endolysosomal cation channels, MAPK, canonical Wnt/GSK3 pathways and MITF.

scholarly journals Mitochondrial Sirtuins in Reproduction

Antioxidants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1047
Author(s):  
Giovanna Di Emidio ◽  
Stefano Falone ◽  
Paolo Giovanni Artini ◽  
Fernanda Amicarelli ◽  
Anna Maria D’Alessandro ◽  
...  
Keyword(s):  
Stress Responses ◽  
Metabolic Pathways ◽  
Redox Balance ◽  
Antioxidant Defenses ◽  
Metabolic Abnormalities ◽  
Female Reproduction ◽  
Mitochondrial Dysfunctions ◽  
Early Embryos ◽  
The Relationship

Mitochondria act as hubs of numerous metabolic pathways. Mitochondrial dysfunctions contribute to altering the redox balance and predispose to aging and metabolic alterations. The sirtuin family is composed of seven members and three of them, SIRT3-5, are housed in mitochondria. They catalyze NAD+-dependent deacylation and the ADP-ribosylation of mitochondrial proteins, thereby modulating gene expression and activities of enzymes involved in oxidative metabolism and stress responses. In this context, mitochondrial sirtuins (mtSIRTs) act in synergistic or antagonistic manners to protect from aging and aging-related metabolic abnormalities. In this review, we focus on the role of mtSIRTs in the biological competence of reproductive cells, organs, and embryos. Most studies are focused on SIRT3 in female reproduction, providing evidence that SIRT3 improves the competence of oocytes in humans and animal models. Moreover, SIRT3 protects oocytes, early embryos, and ovaries against stress conditions. The relationship between derangement of SIRT3 signaling and the imbalance of ROS and antioxidant defenses in testes has also been demonstrated. Very little is known about SIRT4 and SIRT5 functions in the reproductive system. The final goal of this work is to understand whether sirtuin-based signaling may be taken into account as potential targets for therapeutic applications in female and male infertility.

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