scholarly journals Identification of differentially expressed genes for fescue toxicosis in high and low tolerant Angus cows

2019 ◽  
Author(s):  
Piush Khanal ◽  
Leticia P Sanglard ◽  
Kyle Mayberry ◽  
Jeffery Sommer ◽  
Matthew H Poore ◽  
...  
Keyword(s):  
Immune Response ◽  
Differentially Expressed Genes ◽  
Gene Networks ◽  
Cardiovascular Function ◽  
Cellular Growth ◽  
Differentially Expressed ◽  
Fescue Toxicosis ◽  
Biological Processes ◽  
Q Value ◽  
Beef Industry

Abstract Background Fescue toxicosis (FT) is the multifaceted syndrome that causes the major loss of revenue in beef industry. Management of FT has been substantial challenge for the beef industry. Little research has been conducted to identify host genetic variation for FT response. Therefore, the objectives of this study were 1) to identify differentially expressed genes (DEG) in animals with contrasting response to fescue toxicosis, 2) to assess the biological relevance of DEG and 3) to investigate the relationships of DEG through gene networks in Angus cows. Results Genotype-by-location-by-time interaction was evident, with one location (2,296) having much greater number of DEG (q-value < 0.1) between HT and LT animals than the other (554). In addition, there was a greater number of DEG (q-value < 0.1) between HT and LT animals on week 5 (3,892) than on weeks 1(1,413), 9 (1,384), and 13 (573). So, further analyses focused on DEG between HT and LT animals on week 5 at the most toxic location. The most significant DEG between HT and LT animals had relevant functions associated with FT: cellular growth (SPDYC, HEYL, ANXA13), cardiovascular function (FGB, HBA, WNT11, BPIFB4, MESP2), protein metabolism (ENPP6, MMP8), and immune response (CTBS, SDC2, CXCL13, IL-13, JAKMIP2). The strongest positive partial correlation (0.99) was between CTBS and CXCL13, where CTBS is involved in carbohydrate metabolism and immune function, and CXCL13 is involved in immune, inflammatory, and defense response, and G-protein coupled pathway. The regulation of the most significant DEG between HT and LT animals on week 5 are highly correlated, indicating a complex interaction between. When all DEG were analyzed, the enriched biological processes associated with fescue toxicosis included immune response, cardiovascular function and development, metabolic, cellular and biological processes, and fertilization. Conclusions These findings provide potential biomarkers that should be evaluated for selection of cattle with greater tolerance to fescue toxicosis which will help to establish the herd with fescue tolerant cows in regions where high endophyte infected pasture is present.

scholarly journals PSVII-2 Differentially expressed genes and their biological function in skeletal muscle of calves born from cows with or without protein supplementation during mid-gestation

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 165-166
Author(s):  
Elisa B Carvalho ◽  
Letícia P Sanglard ◽  
Karolina B Nascimento ◽  
Javier M Meneses ◽  
Daniel R Casagrande ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Differentially Expressed Genes ◽  
Muscle Development ◽  
Negative Binomial ◽  
Muscle Protein ◽  
Basal Diet ◽  
Protein Supplementation ◽  
Differentially Expressed ◽  
Control Group ◽  
Q Value

Abstract Gestating cows have an increased nutrient demand to meet the needs of developing the fetus and the mid-gestation is a critical period for the fetal skeletal muscle development. The aim of this study was to evaluate the skeletal muscle transcriptome in the progeny as a function of the maternal protein nutrition during mid-gestation. Eleven Tabapuã cows and their male calves were used in this study. In the first third of gestation (0 to 100 days of gestation; dg), all cows were kept on pasture. From 100 to 200 dg, the control group (CTRL; 7 animals) received a basal diet achieving 5.5% crude protein (CP), whereas the supplemented group (SUPPL; 4 animals) received a basal diet plus protein supplementation (40% CP). After 200 dg, all animals received the same diet. Weaning was performed at 205 ± 7.5 days of age and animals were kept on pasture until reaching 240 days of age, when they were transferred to a feedlot. Muscle samples were collected at 260 days of age and RNA was extracted for RNA-seq analysis. Gene expression data was analyzed with a negative binomial model to identify (q-value ≤ 0.05) differentially expressed genes (DEG) between treatments. A total of 716 DEG were identified (289 DEG up-regulated and 427 down-regulated in SUPPL group; q-value ≤ 0.05). From the 10 most significant down-regulated DEG in the SUPPL group, two genes associated with apoptotic process were identified: MAPK8IP1 and GRINA, with log2 Fold-Changes (log2FC) of 1.04 and 0.49, respectively. From the 10 most significant up-regulated DEG in the SUPPL group, mTOR was identified, with log2FC=0.31. This is a well-known gene involved in muscle protein synthesis. In conclusion, maternal protein supplementation during mid-gestation affects the expression of genes related to energy metabolism and muscle development, which can lead to long-term impacts on production efficiency.

scholarly journals Integrative Analysis of the Genes Induced by the Intestine Microbiota of Infant Born to Term and Breastfed

2020 ◽  
Vol 14 ◽  
pp. 117793222090616
Author(s):  
Badreddine Nouadi ◽  
Yousra Sbaoui ◽  
Mariame El Messal ◽  
Faiza Bennis ◽  
Fatima Chegdani
Keyword(s):  
Gene Expression ◽  
Breast Milk ◽  
Differentially Expressed Genes ◽  
Bacterial Colonization ◽  
Biological Data ◽  
Integrative Analysis ◽  
Differentially Expressed ◽  
Epithelial Tissue ◽  
Biological Processes

Nowadays, the integration of biological data is a major challenge for bioinformatics. Many studies have examined gene expression in the epithelial tissue in the intestines of infants born to term and breastfed, generating a large amount of data. The integration of these data is important to understand the biological processes involved during bacterial colonization of the newborns intestine, particularly through breast milk. This work aims to exploit the bioinformatics approaches, to provide a new representation and interpretation of the interactions between differentially expressed genes in the host intestine induced by the microbiota.

scholarly journals Transcriptomic analysis of PPARα-dependent alterations during cardiac hypertrophy

2008 ◽  
Vol 36 (1) ◽  
pp. 15-23 ◽  
Author(s):  
Pascal J. H. Smeets ◽  
Heleen M. de Vogel-van den Bosch ◽  
Peter H. M. Willemsen ◽  
Alphons P. Stassen ◽  
Torik Ayoubi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Immune Response ◽  
Lipid Metabolism ◽  
Cardiac Hypertrophy ◽  
Signaling Pathways ◽  
Differentially Expressed Genes ◽  
Left Ventricular ◽  
Transcriptomic Analysis ◽  
Differentially Expressed ◽  
Wild Type

Peroxisome proliferator-activated receptor (PPAR)α regulates lipid metabolism at the transcriptional level and modulates the expression of genes involved in inflammation, cell proliferation, and differentiation. Although PPARα has been shown to mitigate cardiac hypertrophy, knowledge about underlying mechanisms and the nature of signaling pathways involved is fragmentary and incomplete. The aim of this study was to identify the processes and signaling pathways regulated by PPARα in hearts challenged by a chronic pressure overload by means of whole genome transcriptomic analysis. PPARα−/− and wild-type mice were subjected to transverse aortic constriction (TAC) for 28 days, and left ventricular gene expression profile was determined with Affymetrix GeneChip Mouse Genome 430 2.0 arrays containing >45,000 probe sets. In unchallenged hearts, the mere lack of PPARα resulted in 821 differentially expressed genes, many of which are related to lipid metabolism and immune response. TAC resulted in a more pronounced cardiac hypertrophy and more extensive changes in gene expression (1,910 and 312 differentially expressed genes, respectively) in PPARα−/− mice than in wild-type mice. Many of the hypertrophy-related genes were related to development, signal transduction, actin filament organization, and collagen synthesis. Compared with wild-type hypertrophied hearts, PPARα−/− hypertrophied hearts revealed enrichment of gene clusters related to extracellular matrix remodeling, immune response, oxidative stress, and inflammatory signaling pathways. The present study therefore demonstrates that, in addition to lipid metabolism, PPARα is an important modulator of immune and inflammatory response in cardiac muscle.

scholarly journals Transcriptomic and Proteomic Profiling of Anabaena sp. Strain 90 under Inorganic Phosphorus Stress

2015 ◽  
Vol 81 (15) ◽  
pp. 5212-5222 ◽  
Author(s):  
Jonna Teikari ◽  
Julia Österholm ◽  
Matthias Kopf ◽  
Natalia Battchikova ◽  
Matti Wahlsten ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Cyanobacterial Bloom ◽  
Inorganic Phosphorus ◽  
Cellular Growth ◽  
Differentially Expressed ◽  
Cyanobacterial Blooms ◽  
Limiting Factors ◽  
Transport Systems ◽  
Phosphorus Starvation ◽  
Phosphorus Stress

ABSTRACTInorganic phosphorus (Pi) is one of the main growth-limiting factors of diazotrophic cyanobacteria. Due to human activity, the availability of Pihas increased in water bodies, resulting in eutrophication and the formation of massive cyanobacterial blooms. In this study, we examined the molecular responses of the cyanobacteriumAnabaenasp. strain 90 to phosphorus deprivation, aiming at the identification of candidate genes to monitor the Pistatus in cyanobacteria. Furthermore, this study increased the basic understanding of how phosphorus affects diazotrophic and bloom-forming cyanobacteria as a major growth-limiting factor. Based on RNA sequencing data, we identified 246 differentially expressed genes after phosphorus starvation and 823 differentially expressed genes after prolonged Pilimitation, most of them related to central metabolism and cellular growth. The transcripts of the genes related to phosphorus transport and assimilation (phoregulon) were most upregulated during phosphorus depletion. One of the most increased transcripts encodes a giant protein of 1,869 amino acid residues, which contains, among others, a phytase-like domain. Our findings predict its crucial role in phosphorus starvation, but future studies are still needed. Using two-dimensional difference in gel electrophoresis (2D-DIGE) and liquid chromatography-tandem mass spectrometry (LC-MS/MS), we found 43 proteins that were differentially expressed after prolonged phosphorus stress. However, correlation analysis unraveled an association only to some extent between the transcriptomic and proteomic abundances. Based on the present results, we suggest that the method used for monitoring the Pistatus in cyanobacterial bloom should contain wider combinations ofphoregulon genes (e.g., PstABCS transport systems) in addition to the commonly used alkaline phosphatase gene alone.

scholarly journals Fecal Host Transcriptomics for Non-invasive Human Mucosal Immune Profiling: Proof of Concept in Clostridium difficile Infection

2018 ◽  
Vol 3 (2) ◽  
pp. 164
Author(s):  
Robert Schlaberg ◽  
Amanda Barrett ◽  
Kornelia Edes ◽  
Michael Graves ◽  
Litty Paul ◽  
...  
Keyword(s):  
Immune Response ◽  
Clostridium Difficile ◽  
Differentially Expressed Genes ◽  
Clostridium Difficile Infection ◽  
Expression Profiles ◽  
Principal Component ◽  
Mucosal Immune Response ◽  
Differentially Expressed ◽  
Proof Of Concept ◽  
Non Invasive

Background: Host factors play an important role in pathogenesis and disease outcome in Clostridium difficile infection (CDI), and characterization of these responses could uncover potential host biomarkers to complement existing microbe-based diagnostics.Methods: We extracted RNA from fecal samples of patients with CDI and profiled human mRNA using amplicon-based next-generation sequencing (NGS). We compared the fecal host mRNA transcript expression profiles of patients with CDI to controls with non-CDI diarrhea.Results: We found that the ratio of human actin gamma 1 (ACTG1) to 16S ribosomal RNA (rRNA) was highly correlated with NGS quality as measured by percentage of reads on target. Patients with CDI could be differentiated from those with non-CDI diarrhea based on their fecal mRNA expression profiles using principal component analysis. Among the most differentially expressed genes were ones related to immune response (IL23A, IL34) and actin-cytoskeleton function (TNNT1, MYL4, SMTN, MYBPC3, all adjusted P-values <1×10-3).Conclusions: In this proof-of-concept study, we used host fecal transcriptomics for non-invasive profiling of the mucosal immune response in CDI. We identified differentially expressed genes with biological plausibility based on animal and cell culture models. This demonstrates the potential of fecal transcriptomics to uncover host-based biomarkers for enteric infections.

Identification of aberrantly methylated differentially expressed genes in melanoma

2020 ◽  
Author(s):  
Wei Han ◽  
Guo-liang Shen
Keyword(s):  
Gene Expression ◽  
Cell Proliferation ◽  
Differentially Expressed Genes ◽  
Enrichment Analysis ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Biological Processes ◽  
Hub Genes ◽  
Positive Regulation ◽  
Upregulated Genes

Abstract Background: Skin Cutaneous Melanoma (SKCM) is known as an aggressive malignant cancer, which could be directly derived from melanocytic nevi. However, the molecular mechanisms underlying malignant transformation of melanocytes and melanoma tumor progression still remain unclear. Increasing researches showed significant roles of epigenetic modifications, especially DNA methylation, in melanoma. This study focused on identification and analysis of methylation-regulated differentially expressed genes (MeDEGs) between melanocytic nevus and malignant melanoma in genome-wide profiles. Methods: The gene expression profiling datasets (GSE3189 and GSE114445) and gene methylation profiling datasets (GSE86355 and GSE120878) were downloaded from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) were identified via GEO2R. MeDEGs were obtained by integrating the DEGs and DMGs. Then, functional enrichment analysis of MeDEGs were performed. STRING and Cytoscape were used to describe protein-protein interaction(PPI) network. Furthermore, survival analysis was implemented to select the prognostic hub genes. Finally, we conducted gene set enrichment analysis (GSEA) of hub genes. Results: We identified 237 hypomethylated, upregulated genes and 182 hypermethylated, downregulated genes. Hypomethylation-upregulated genes were enriched in biological processes of the oxidation-reduction process, cell proliferation, cell division, phosphorylation, extracellular matrix disassembly and protein sumoylation. Pathway enrichment showed selenocompound metabolism, small cell lung cancer and lysosome. Hypermethylation-downregulated genes were enriched in biological processes of positive regulation of transcription from RNA polymerase II promoter, cell adhesion, cell proliferation, positive regulation of transcription, DNA-templated and angiogenesis. The most significantly enriched pathways involved the transcriptional misregulation in cancer, circadian rhythm, tight junction, protein digestion and absorption and Hippo signaling pathway. After PPI establishment and survival analysis, seven prognostic hub genes were CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2 and FBL. Moreover, the most involved hallmarks obtained by GSEA were E2F targets, G2M checkpoint and mitotic spindle. Conclusions: Our study identified potential aberrantly methylated-differentially expressed genes participating in the process of malignant transformation from nevus to melanoma tissues based on comprehensive genomic profiles. Transcription profiles of CKS2, DTL, KIF2C, KPNA2, MYBL2, TPX2 and FBL provided clues of aberrantly methylation-based biomarkers, which might improve the development of precise medicine.

scholarly journals Evaluation of Combining Several Statistical Methods with a Flexible Cutoff for Identifying Differentially Expressed Genes in Pairwise Comparison of EST Sets

2008 ◽  
Vol 2 ◽  
pp. BBI.S431 ◽  
Author(s):  
Angelica Lindlöf ◽  
Marcus Bräutigam ◽  
Aakash Chawade ◽  
Olof Olsson ◽  
Björn Olsson
Keyword(s):  
Statistical Methods ◽  
Differentially Expressed Genes ◽  
Relative Frequency ◽  
Large Scale ◽  
Pairwise Comparison ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Exact Test ◽  
The Difference ◽  
Derived Data

The detection of differentially expressed genes from EST data is of importance for the discovery of potential biological or pharmaceutical targets, especially when studying biological processes in less characterized organisms and where large-scale microarrays are not an option. We present a comparison of five different statistical methods for identifying up-regulated genes through pairwise comparison of EST sets, where one of the sets is generated from a treatment and the other one serves as a control. In addition, we specifically address situations where the sets are relatively small (~2,000– 10,000 ESTs) and may differ in size. The methods were tested on both simulated and experimentally derived data, and compared to a collection of cold stress induced genes identified by microarrays. We found that combining the method proposed by Audic and Claverie with Fisher's exact test and a method based on calculating the difference in relative frequency was the best combination for maximizing the detection of up-regulated genes. We also introduced the use of a flexible cutoff, which takes the size of the EST sets into consideration. This could be considered as an alternative to a static cutoff. Finally, the detected genes showed a low overlap with those identified by microarrays, which indicates, as in previous studies, low overall concordance between the two platforms.

The impact of a moderate chronic temperature increase on spleen immune-relevant gene transcription depends on whether Atlantic cod (Gadus morhua) are stimulated with bacterial versus viral antigens

Genome ◽  
2013 ◽  
Vol 56 (10) ◽  
pp. 567-576 ◽  
Author(s):  
Tiago S. Hori ◽  
A. Kurt Gamperl ◽  
Gord Nash ◽  
Marije Booman ◽  
Ashoktaru Barat ◽  
...  
Keyword(s):  
Immune Response ◽  
Elevated Temperature ◽  
Differentially Expressed Genes ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Aeromonas Salmonicida ◽  
Differentially Expressed ◽  
Important Species ◽  
Transcriptome Response ◽  
The Impact

Exposure to elevated temperature is an inherent feature of Atlantic cod (Gadus morhua) sea-cage culture in some regions (e.g., Newfoundland) and may also become an increasingly prevalent challenge for wild fish populations because of accelerated climate change. Therefore, understanding how elevated temperatures impacts the immune response of this commercially important species may help to reduce the potential negative impacts of such challenges. Previously, we investigated the impacts of moderately elevated temperature on the antiviral responses of Atlantic cod (Hori et al. 2012) and reported that elevated temperature modulated the spleen transcriptome response to polyriboinosinic polyribocytidylic acid (pIC, a viral mimic). Herein, we report a complementary microarray study that investigated the impact of the same elevated temperature regime on the Atlantic cod spleen transcriptome response to intraperitoneal (IP) injection of formalin-killed Aeromonas salmonicida (ASAL). Fish were held at two different temperatures (10 °C and 16 °C) prior to immune stimulation and sampled 6 and 24 h post-injection (HPI). In this experiment, we identified 711 and 666 nonredundant ASAL-responsive genes at 6HPI and 24HPI, respectively. These included several known antibacterial genes, including hepcidin, cathelicidin, ferritin heavy subunit, and interleukin 8. However, we only identified 15 differentially expressed genes at 6HPI and 2 at 24HPI (FDR 1%) when comparing ASAL-injected fish held at 10 °C versus 16 °C. In contrast, the same comparisons with pIC-injected fish yielded 290 and 339 differentially expressed genes (FDR 1%) at 6HPI and 24HPI, respectively. These results suggest that moderately elevated temperature has a lesser effect on the Atlantic cod spleen transcriptome response to ASAL (i.e., the antibacterial response) than to pIC (i.e., antiviral response). Thus, the impacts of high temperatures on the cod’s immune response may be pathogen dependent.

scholarly journals Early Transcriptional Changes Induced by Wnt/β-Catenin Signaling in Hippocampal Neurons

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
Eduardo Pérez-Palma ◽  
Víctor Andrade ◽  
Mario O. Caracci ◽  
Bernabé I. Bustos ◽  
Camilo Villaman ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Hippocampal Neurons ◽  
Target Genes ◽  
Primary Cultures ◽  
Stem Cell Differentiation ◽  
Differentially Expressed ◽  
Molecular Networks ◽  
Biological Processes ◽  
Neuronal Structure ◽  
Transcriptional Changes

Wnt/β-catenin signaling modulates brain development and function and its deregulation underlies pathological changes occurring in neurodegenerative and neurodevelopmental disorders. Since one of the main effects of Wnt/β-catenin signaling is the modulation of target genes, in the present work we examined global transcriptional changes induced by short-term Wnt3a treatment (4 h) in primary cultures of rat hippocampal neurons. RNAseq experiments allowed the identification of 170 differentially expressed genes, including known Wnt/β-catenin target genes such as Notum, Axin2, and Lef1, as well as novel potential candidates Fam84a, Stk32a, and Itga9. Main biological processes enriched with differentially expressed genes included neural precursor (GO:0061364,p-adjusted = 2.5 × 10−7), forebrain development (GO:0030900,p-adjusted = 7.3 × 10−7), and stem cell differentiation (GO:0048863p-adjusted = 7.3 × 10−7). Likewise, following activation of the signaling cascade, the expression of a significant number of genes with transcription factor activity (GO:0043565,p-adjusted = 4.1 × 10−6) was induced. We also studied molecular networks enriched upon Wnt3a activation and detected three highly significant expression modules involved in glycerolipid metabolic process (GO:0046486,p-adjusted = 4.5 × 10−19), learning or memory (GO:0007611,p-adjusted = 4.0 × 10−5), and neurotransmitter secretion (GO:0007269,p-adjusted = 5.3 × 10−12). Our results indicate that Wnt/β-catenin mediated transcription controls multiple biological processes related to neuronal structure and activity that are affected in synaptic dysfunction disorders.

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