scholarly journals Rumen epithelial transcriptome and microbiome profiles of rumen epithelium and contents of beef cattle with and without liver abscesses

2020 ◽  
Vol 98 (12) ◽  
Author(s):  
Waseem Abbas ◽  
Brittney N Keel ◽  
Stephan D Kachman ◽  
Samodha C Fernando ◽  
James E Wells ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Bacterial Communities ◽  
Differentially Expressed Gene ◽  
Fusobacterium Necrophorum ◽  
Differentially Expressed ◽  
Rumen Content ◽  
Epithelial Tissue ◽  
Beef Industry ◽  
Rumen Epithelium ◽  
Liver Abscesses

Abstract Abscess is the highest cause of liver condemnation and is estimated to cost the beef industry US$64 million annually. Fusobacterium necrophorum, commonly found in the bovine rumen, is the primary bacteria associated with liver abscess in cattle. Theoretically, damage to the rumen wall allows F. necrophorum to invade the bloodstream and colonize the liver. The objective of this study was to determine the changes in gene expression in the rumen epithelium and microbial populations adherent to the rumen epithelium and in the rumen contents of beef cattle with liver abscesses compared with those with no liver abscesses. Rumen epithelial tissue and rumen content were collected from 31 steers and heifers with liver abscesses and 30 animals with no liver abscesses. Ribonucleic acid (RNA) sequencing was performed on the rumen epithelium, and a total of 221 genes were identified as differentially expressed in the animals with liver abscesses compared with animals with no abscesses, after removal of genes that were identified as a result of interaction with sex. The nuclear factor kappa-light-chain enhancer of activated B cells signaling and interferon signaling pathways were significantly enriched in the differentially expressed gene (DEG) set. The majority of the genes in these pathways were downregulated in animals with liver abscesses. In addition, RNA translation and protein processing genes were also downregulated, suggesting that protein synthesis may be compromised in animals with liver abscesses. The rumen content bacterial communities were significantly different from the rumen wall epimural bacterial communities. Permutational multivariate analysis of variance (PERMANOVA) analysis did not identify global differences in the microbiome of the rumen contents but did identify differences in the epimural bacterial communities on the rumen wall of animals without and with liver abscesses. In addition, associations between DEG and specific bacterial amplicon sequence variants of epimural bacteria were observed. The DEG and bacterial profile on the rumen papillae identified in this study may serve as a method to monitor animals with existing liver abscesses or to predict those that are more likely to develop liver abscesses.

scholarly journals Differentially expressed extracellular vesicle, exosome and non-exosome miRNA profile in high and low tick-resistant beef cattle

2021 ◽  
Author(s):  
Pevindu Abeysinghe ◽  
Natalie Turner ◽  
Hassendrini Peiris ◽  
Kanchan Vaswani ◽  
Nick Cameron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Blood Plasma ◽  
Noncoding Rna ◽  
Extracellular Vesicle ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Transcriptional Level ◽  
Beef Industry ◽  
Tick Resistance

Abstract Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance.A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR < 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

scholarly journals Differentially Expressed Extracellular Vesicle, Exosome and Non-Exosome miRNA Profile in High and Low Tick-Resistant Beef Cattle

2021 ◽  
Vol 11 ◽  
Author(s):  
Pevindu Abeysinghe ◽  
Natalie Turner ◽  
Hassendrini Peiris ◽  
Kanchan Vaswani ◽  
Nick Cameron ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Blood Plasma ◽  
Noncoding Rna ◽  
Extracellular Vesicle ◽  
Micro Rna ◽  
Differentially Expressed ◽  
Economic Losses ◽  
Transcriptional Level ◽  
Beef Industry ◽  
Tick Resistance

Heavy tick burden on beef cattle account for huge economic losses globally, with an estimated value of US$22-30 billion per annum. In Australia, ticks cost the northern beef industry approximately A$170-200 million. Methods to evaluate and predict tick resistance would therefore be of great value to the global cattle trade. Exosomes (EX) are small extracellular vesicles (EVs) of ~30-150nm diameter and have gained popularity for their diagnostic and prognostic potential. EX contain, among other biomolecules, various types of RNA including micro-RNA (miRNA) and long noncoding RNA (lncRNA). MiRNA specifically have been validated as therapeutic biomarkers as they perform regulatory functions at the post-transcriptional level and are differentially expressed between divergent groups. The objective of the present study was to evaluate the miRNA profiles of EV and fractionated exosomal samples of high and low tick-resistant beef cattle to highlight potential miRNA biomarkers of tick resistance. Cows (n = 3/group) were classified into high or low tick resistant groups according to a novel scoring system. EVs and EX were isolated and fractionated from the blood plasma of high and low tick resistant cattle using established isolation and enrichment protocols. The resultant EX and non-EX samples were processed for next generation miRNA sequencing. Offspring of the cows in each high and low tick resistant group underwent the same processing for blood plasma EX, non-EX and miRNA analysis to evaluate the heritability of miRNA associated with tick resistance. A total of 2631 miRNAs were identified in EX and non-EX fractionated samples from high and low tick-resistant beef cattle. MiR-449a was highly expressed in maternal high tick-resistant EX samples. Of these, 174 were novel miRNAs, and 10 were differentially expressed (DE) (FDR &lt; 0.05). These 10 DE miRNAs were also present in EVs, and three miRNAs were highly expressed: miR-2419-3p, miR-7861-3p and miR-2372-5p. Although 196 novel miRNAs were identified in fractionated samples of offspring, no miRNA were differentially expressed in these animals.

PSIV-6 Effect of a Direct Fed Microbial Feed Additive on Finishing Beef Cattle Performance and Liver Abscess Rate

2021 ◽  
Vol 99 (Supplement_1) ◽  
pp. 212-212
Author(s):  
Kelton Adair ◽  
Samodha Fernando ◽  
Galen E Erickson ◽  
Alison Bartenslager ◽  
Zachary E Carlson
Keyword(s):  
Beef Cattle ◽  
Liver Abscess ◽  
Average Daily Gain ◽  
Fusobacterium Necrophorum ◽  
Feed Additive ◽  
Bacterial Cells ◽  
Liver Abscesses ◽  
Significant Difference ◽  
Gate System ◽  
Finishing Beef Cattle

Abstract A feedlot study was conducted comparing the effects of a direct-fed microbial feed additive (DFM) to no feed additive (CON) on performance and liver abscess rates in finishing beef cattle. The study utilized 60 crossbred steers (initial BW 274 kg ± 2.23) individually fed using a Calan gate system. Steers were housed in separate pens by treatment to avoid DFM cross-contamination, with pen (barn of 30 steers) assigned randomly to each treatment. Cattle were fed a diet consisting of 15% corn silage, 36.5% high moisture corn, 24.5% dry rolled corn, 20% modified distillers grains, and 4% supplement for 189 days. The DFM counts were estimated using cell cytometry and was top dressed at a concentration of approximately 81 billion bacterial cells/head/day. The DFM additive used in this study was developed to reduce the abundance of Fusobacterium necrophorum and Streptococcus bovis in the rumen. No effect of treatment on hot carcass weight (HCW), average daily gain (ADG), dry matter intake (DMI), feed efficiency (G:F), or carcass traits (Table 1) were observed. No significant difference in the occurrence of liver abscesses between treatment groups were observed with 4 steers having abscessed livers in the CON group and 3 steers in the DFM group. Additionally, there were no differences in the severity of liver abscesses; all observed liver abscesses received the score of A. The DFM utilized in this study did not significantly affect performance, liver abscess rate, or the severity of liver abscesses in finishing beef cattle.

scholarly journals 224 Epimural microbiota and rumen epithelial gene expression in healthy and liver-abscessed animals

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 135-135
Author(s):  
Waseem Abbas ◽  
Amanda K Lindholm-Perry ◽  
Brittney N Keel ◽  
James E Wells ◽  
Kristin Hales ◽  
...  
Keyword(s):  
Gene Expression ◽  
Bacterial Community ◽  
Differentially Expressed Genes ◽  
Feedlot Cattle ◽  
Differentially Expressed ◽  
Feed Additive ◽  
Rumen Content ◽  
Liver Abscesses ◽  
Rdna Sequencing ◽  
Wide Range

Abstract Different dietary and feed additive strategies have been developed to reduce the liver abscess in feedlot cattle, but liver abscesses are still a major problem in beef production. We have limited knowledge about how rumen microbial communities interact with host epithelial gene expression in healthy and liver-abscessed animals. The objective of this study was to investigate the associations between the rumen content associated and rumen epimural microbiome and epithelial gene expression in liver-abscessed and healthy animals. To this end, we collected the ruminal contents and tissue samples from healthy (N=30; score=0, steers n=19 and heifers n=11) and liver-abscessed (N=30; score=A+, steers n=21 and heifers n=9) feedlot cattle at harvest. The bacterial community compositions in the ruminal contents and papillae were evaluated via 16S rDNA sequencing of the V4 region using the Illumina MiSeq platform. Additionally, total RNA was extracted from rumen epithelial tissues and sequenced using the Illumina NextSeq platform. The permutational analysis (PERMANOVA) on Bray Curtis distances matrices showed the microbial community in the ruminal contents was significantly different (P&lt; 0.001) from the bacterial community observed in rumen papillae. The ruminal contents contained a higher abundance of Bacteroidetes and Proteobacteria while papillae contained higher abundance of Firmicutes. The epimural microbiota was different (P&lt; 0.01) between healthy and liver abscessed animals while ruminal contents microbiome was not different between the two groups. The DeSeq2 algorithm identified differentially expressed genes (221) related to MAPK, NF-kappa B signaling pathway, immune and inflammatory response in liver-abscessed animals. Additionally, a wide range of epimural bacterial taxa were correlated (-0.52 to 0.67) with differentially expressed genes. These data demonstrate the interaction between epimural microbiota and the host and its effect on liver abscesses, and indicate the need to study the epimural microbiome for its impact on liver abscesses in feedlot cattle. USDA is an equal opportunity provider and employer.

Decoding Psoriasis: Integrated Bioinformatics Approach to Understand Hub Genes and Involved Pathways

2020 ◽  
Vol 26 (29) ◽  
pp. 3619-3630
Author(s):  
Saumya Choudhary ◽  
Dibyabhaba Pradhan ◽  
Noor S. Khan ◽  
Harpreet Singh ◽  
George Thomas ◽  
...  
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Gene ◽  
Therapeutic Targets ◽  
Interaction Network ◽  
Gene Expression Omnibus ◽  
Differentially Expressed ◽  
Keratinocyte Differentiation ◽  
Hub Genes ◽  
Lesional Skin ◽  
Ncbi Gene Expression Omnibus

Background: Psoriasis is a chronic immune mediated skin disorder with global prevalence of 0.2- 11.4%. Despite rare mortality, the severity of the disease could be understood by the accompanying comorbidities, that has even led to psychological problems among several patients. The cause and the disease mechanism still remain elusive. Objective: To identify potential therapeutic targets and affecting pathways for better insight of the disease pathogenesis. Method: The gene expression profile GSE13355 and GSE14905 were retrieved from NCBI, Gene Expression Omnibus database. The GEO profiles were integrated and the DEGs of lesional and non-lesional psoriasis skin were identified using the affy package in R software. The Kyoto Encyclopaedia of Genes and Genomes pathways of the DEGs were analyzed using clusterProfiler. Cytoscape, V3.7.1 was utilized to construct protein interaction network and analyze the interactome map of candidate proteins encoded in DEGs. Functionally relevant clusters were detected through Cytohubba and MCODE. Results: A total of 1013 genes were differentially expressed in lesional skin of which 557 were upregulated and 456 were downregulated. Seven dysregulated genes were extracted in non-lesional skin. The disease gene network of these DEGs revealed 75 newly identified differentially expressed gene that might have a role in development and progression of the disease. GO analysis revealed keratinocyte differentiation and positive regulation of cytokine production to be the most enriched biological process and molecular function. Cytokines -cytokine receptor was the most enriched pathways. Among 1013 identified DEGs in lesional group, 36 DEGs were found to have altered genetic signature including IL1B and STAT3 which are also reported as hub genes. CCNB1, CCNA2, CDK1, IL1B, CXCL8, MKI 67, ESR1, UBE2C, STAT1 and STAT3 were top 10 hub gene. Conclusion: The hub genes, genomic altered DEGs and other newly identified differentially dysregulated genes would improve our understanding of psoriasis pathogenesis, moreover, the hub genes could be explored as potential therapeutic targets for psoriasis.

Identification of the Differentially Expressed Genes Involved in the Synergistic Neurotoxicity of an HIV Protease Inhibitor and Methamphetamine

2019 ◽  
Vol 17 (4) ◽  
pp. 290-303
Author(s):  
Sangsang Li ◽  
Yanfei Li ◽  
Bingpeng Deng ◽  
Jie Yan ◽  
Yong Wang
Keyword(s):  
Protease Inhibitor ◽  
Growth Inhibition ◽  
Quantitative Polymerase Chain Reaction ◽  
Differentially Expressed Gene ◽  
Antiretroviral Drugs ◽  
Differentially Expressed ◽  
Hiv Protease ◽  
Hiv Protease Inhibitor ◽  
Dopaminergic Cells ◽  
Immunodeficiency Syndrome

Background: The abuse of psychostimulants such as methamphetamine (METH) is common in human immunodeficiency virus (HIV)-infected individuals. Acquired immunodeficiency syndrome (AIDS) patients taking METH and antiretroviral drugs could suffer severe neurologic damage and cognitive impairment. Objective: To reveal the underlying neuropathologic mechanisms of an HIV protease inhibitor (PI) combined with METH, growth-inhibition tests of dopaminergic cells and RNA sequencing were performed. Methods: A combination of METH and PI caused more growth inhibition of dopaminergic cells than METH alone or a PI alone. Furthermore, we identified differentially expressed gene (DEG) patterns in the METH vs. untreated cells (1161 genes), PI vs. untreated cells (16 genes), METH-PI vs. PI (3959 genes), and METH-PI vs. METH groups (14 genes). Results: The DEGs in the METH-PI co-treatment group were verified in the brains of a mouse model using quantitative polymerase chain reaction and were involved mostly in the regulatory functions of cell proliferation and inflammation. Conclusion: Such identification of key regulatory genes could facilitate the study of their neuroprotective potential in the users of METH and PIs.

Gene Set Correlation Analysis and Visualization Using Gene Expression Data

2020 ◽  
Vol 15 ◽  
Author(s):  
Chen-An Tsai ◽  
James J. Chen
Keyword(s):  
Gene Expression ◽  
Correlation Analysis ◽  
Gene Expression Data ◽  
Differentially Expressed Gene ◽  
Differentially Expressed ◽  
Superior Performance ◽  
Expression Data ◽  
Gene Set ◽  
Gene Sets ◽  
Set Correlation

Background: Gene set enrichment analyses (GSEA) provide a useful and powerful approach to identify differentially expressed gene sets with prior biological knowledge. Several GSEA algorithms have been proposed to perform enrichment analyses on groups of genes. However, many of these algorithms have focused on identification of differentially expressed gene sets in a given phenotype. Objective: In this paper, we propose a gene set analytic framework, Gene Set Correlation Analysis (GSCoA), that simultaneously measures within and between gene sets variation to identify sets of genes enriched for differential expression and highly co-related pathways. Methods: We apply co-inertia analysis to the comparisons of cross-gene sets in gene expression data to measure the costructure of expression profiles in pairs of gene sets. Co-inertia analysis (CIA) is one multivariate method to identify trends or co-relationships in multiple datasets, which contain the same samples. The objective of CIA is to seek ordinations (dimension reduction diagrams) of two gene sets such that the square covariance between the projections of the gene sets on successive axes is maximized. Simulation studies illustrate that CIA offers superior performance in identifying corelationships between gene sets in all simulation settings when compared to correlation-based gene set methods. Result and Conclusion: We also combine between-gene set CIA and GSEA to discover the relationships between gene sets significantly associated with phenotypes. In addition, we provide a graphical technique for visualizing and simultaneously exploring the associations of between and within gene sets and their interaction and network. We then demonstrate integration of within and between gene sets variation using CIA and GSEA, applied to the p53 gene expression data using the c2 curated gene sets. Ultimately, the GSCoA approach provides an attractive tool for identification and visualization of novel associations between pairs of gene sets by integrating co-relationships between gene sets into gene set analysis.

scholarly journals Alteration of protein expression and spliceosome pathway activity during Barrett’s carcinogenesis

2021 ◽  
Author(s):  
Christoph Stingl ◽  
Angela Bureo Gonzalez ◽  
Coşkun Güzel ◽  
Kai Yi Nadine Phoa ◽  
Michail Doukas ◽  
...  
Keyword(s):  
Micro Rna ◽  
Differentially Expressed ◽  
Epithelial Tissue ◽  
Label Free ◽  
Tissue Samples ◽  
Damage Repair ◽  
Inter Observer Variability ◽  
Stromal Tissue ◽  
The Face ◽  
Abundance And Diversity

Abstract Background Barrett’s esophagus (BE) is a known precursor lesion and the strongest risk factor for esophageal adenocarcinoma (EAC), a common and lethal type of cancer. Prediction of risk, the basis for efficient intervention, is commonly solely based on histologic examination. This approach is challenged by problems such as inter-observer variability in the face of the high heterogeneity of dysplastic tissue. Molecular markers might offer an additional way to understand the carcinogenesis and improve the diagnosis—and eventually treatment. In this study, we probed significant proteomic changes during dysplastic progression from BE into EAC. Methods During endoscopic mucosa resection, epithelial and stromal tissue samples were collected by laser capture microdissection from 10 patients with normal BE and 13 patients with high-grade dysplastic/EAC. Samples were analyzed by mass spectrometry-based proteomic analysis. Expressed proteins were determined by label-free quantitation, and gene set enrichment was used to find differentially expressed pathways. The results were validated by immunohistochemistry for two selected key proteins (MSH6 and XPO5). Results Comparing dysplastic/EAC to non-dysplastic BE, we found in equal volumes of epithelial tissue an overall up-regulation in terms of protein abundance and diversity, and determined a set of 226 differentially expressed proteins. Significantly higher expressions of MSH6 and XPO5 were validated orthogonally and confirmed by immunohistochemistry. Conclusions Our results demonstrate that disease-related proteomic alterations can be determined by analyzing minute amounts of cell-type-specific collected tissue. Further analysis indicated that alterations of certain pathways associated with carcinogenesis, such as micro-RNA trafficking, DNA damage repair, and spliceosome activity, exist in dysplastic/EAC.

Gill microbiome structure and function in the chemosymbiotic coastal lucinid Stewartia floridana

2021 ◽  
Author(s):  
Shen Jean Lim ◽  
Brenton Davis ◽  
Danielle Gill ◽  
John Swetenburg ◽  
Laurie C Anderson ◽  
...  
Keyword(s):  
Amino Acids ◽  
Nutrient Cycling ◽  
Bacterial Communities ◽  
Structure And Function ◽  
Differentially Expressed ◽  
Seagrass Species ◽  
Bare Sand ◽  
And Function

Abstract Lucinid bivalves harbor environmentally acquired, chemosynthetic, gammaproteobacterial gill endosymbionts. Lucinid gill microbiomes, which may contain other gammaproteobacterial and/or spirochete taxa, remain under-sampled. To understand inter-host variability of the lucinid gill microbiome, specifically in the bacterial communities, we analyzed the microbiome content of Stewartia floridana collected from Florida. Sampled gills contained a monospecific gammaproteobacterial endosymbiont expressing lithoautotrophic, mixotrophic, diazotrophic, and C1 compound oxidation-related functions previously characterized in similar lucinid species. Another low-abundance Spirochaeta-like species in ∼72% of the sampled gills was most closely related to Spirochaeta-like species in another lucinid Phacoides pectinatus and formed a clade with known marine Spirochaeta symbionts. The spirochete expressed genes were involved in heterotrophy and the transport of sugars, amino acids, peptides, and other substrates. Few muscular and neurofilament genes from the host and none from the gammaproteobacterial and spirochete symbionts were differentially expressed among quadrats predominantly covered with seagrass species or 80% bare sand. Our results suggest that spirochetes are facultatively associated with S. floridana, with potential scavenging and nutrient cycling roles. Expressed stress- and defense-related functions in the host and symbionts also suggest species-species communications, which highlight the need for further study of the interactions among lucinid hosts, their microbiomes, and their environment.

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