scholarly journals Potential Functional Variants in Innate Immune Response Genes Associated with Feed Efficiency in Beef Cattle

2020 ◽  
Author(s):  
Gabriela Ribeiro ◽  
Aline Silva Mello Cesar ◽  
Pâmela Almeida Alexandre ◽  
José Bento Sterman Ferraz ◽  
Heidge Fukumasu
Keyword(s):  
Immune Response ◽  
Beef Cattle ◽  
Innate Immune Response ◽  
Feed Efficiency ◽  
Factor H ◽  
Innate Immune ◽  
Functional Enrichment ◽  
Rna Seq ◽  
Immune Response Genes ◽  
Functional Variants

Abstract Background: Identifying and selecting animals for feed efficiency (FE) is extremely important for the beef production chain. Currently, the most common parameter to access the FE animals is residual feed intake (RFI), which is the residual of the linear regression that estimates DMI based on average daily gain and mid-test metabolic body weight. However, it relies on costly and time-consuming data collection, creating a growing demand for alternative approaches to identify genetically superior animals for FE. This study aimed to detect potential liver-specific functional variants from RNA-seq data of 16 Nellore bulls divergently selected for FE. Results: The variant call analysis detected 247 missense SNPs and nine insertion-deletions (INDELs) that alter the protein functions. These variants were found within 190 genes differentially found (P < 0.05) in liver tissue between high FE (HFE) and low FE (LFE) animals. To better understand the role of these variants in biological pathways, we performed a functional enrichment analysis, which highlighted six genes involved in complement cascade and cascade complement regulation pathways, and 20 genes involved in the regulation of the innate immune system. They had four different significant variants in the complement factor H (CFH) family genes, and all were homozygous in HFE animals rather than some degree of heterozygous in LFE animals. Conclusion: We developed a pipeline to detect potential liver-specific functional variants from RNA-seq data from animals divergently selected for feed efficiency. With this approach, we found potential functional variants in innate immune response genes associated with feed efficiency in beef cattle.

scholarly journals Expression of Innate Immune Response Genes in Liver and Three Types of Adipose Tissue in Cloned Pigs

2012 ◽  
Vol 14 (5) ◽  
pp. 407-417 ◽  
Author(s):  
Tina Rødgaard ◽  
Kerstin Skovgaard ◽  
Jan Stagsted ◽  
Peter M.H. Heegaard
Keyword(s):  
Immune Response ◽  
Adipose Tissue ◽  
Innate Immune Response ◽  
Innate Immune ◽  
Immune Response Genes

scholarly journals Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish

Genetics ◽  
2020 ◽  
Vol 216 (4) ◽  
pp. 1117-1136 ◽  
Author(s):  
Laura C. Swanson ◽  
Edna A. Trujillo ◽  
Gene H. Thiede ◽  
Rebeccah J. Katzenberger ◽  
Evgenia Shishkova ◽  
...  
Keyword(s):  
Traumatic Brain Injury ◽  
Immune Response ◽  
Brain Injury ◽  
Innate Immune Response ◽  
Genetic Background ◽  
Cellular Response ◽  
Expression Profiles ◽  
Innate Immune ◽  
Immune Response Genes ◽  
Secondary Injuries

Traumatic brain injury (TBI) pathologies are caused by primary and secondary injuries. Primary injuries result from physical damage to the brain, and secondary injuries arise from cellular responses to primary injuries. A characteristic cellular response is sustained activation of inflammatory pathways commonly mediated by nuclear factor-κB (NF-κB) transcription factors. Using a Drosophila melanogaster TBI model, we previously found that the main proximal transcriptional response to primary injuries is triggered by activation of Toll and Imd innate immune response pathways that engage NF-κB factors Dif and Relish (Rel), respectively. Here, we found by mass spectrometry that Rel protein level increased in fly heads at 4–8 hr after TBI. To investigate the necessity of Rel for secondary injuries, we generated a null allele, Reldel, by CRISPR/Cas9 editing. When heterozygous but not homozygous, the Reldel mutation reduced mortality at 24 hr after TBI and increased the lifespan of injured flies. Additionally, the effect of heterozygosity for Reldel on mortality was modulated by genetic background and diet. To identify genes that facilitate effects of Reldel on TBI outcomes, we compared genome-wide mRNA expression profiles of uninjured and injured +/+, +/Reldel, and Reldel/Reldel flies at 4 hr following TBI. Only a few genes changed expression more than twofold in +/Reldel flies relative to +/+ and Reldel/Reldel flies, and they were not canonical innate immune response genes. Therefore, Rel is necessary for TBI-induced secondary injuries but in complex ways involving Rel gene dose, genetic background, diet, and possibly small changes in expression of innate immune response genes.

scholarly journals ELF18-INDUCED LONG-NONCODING RNA Associates with Mediator to Enhance Expression of Innate Immune Response Genes in Arabidopsis

2017 ◽  
Vol 29 (5) ◽  
pp. 1024-1038 ◽  
Author(s):  
Jun Sung Seo ◽  
Hai-Xi Sun ◽  
Bong Soo Park ◽  
Chung-Hao Huang ◽  
Shyi-Dong Yeh ◽  
...  
Keyword(s):  
Immune Response ◽  
Innate Immune Response ◽  
Long Noncoding Rna ◽  
Noncoding Rna ◽  
Innate Immune ◽  
Immune Response Genes

scholarly journals Analysis of the basal colonic innate immune response of pigs divergent in feed efficiency and following an ex vivo lipopolysaccharide challenge

2019 ◽  
Vol 51 (9) ◽  
pp. 443-448 ◽  
Author(s):  
Stafford Vigors ◽  
John V. O’ Doherty ◽  
Marion Ryan ◽  
Torres Sweeney
Keyword(s):  
Immune Response ◽  
Innate Immune Response ◽  
Feed Efficiency ◽  
Ex Vivo ◽  
Innate Immune ◽  
Colonic Tissue ◽  
Experimental Conditions ◽  
Defense Proteins ◽  
Lps Challenge ◽  
Genes Encoding

While feed efficiency is influenced by multiple physiological processes, it is not known how efficient and inefficient pigs differ in relation to their basal immune response, and particularly their innate immune response to a microbial challenge. Hence, the objective was to examine the expression of genes encoding innate immune response markers in basal colonic tissue and colonic tissue following an ex vivo lipopolysaccharide (LPS) challenge from pigs divergent in residual feed intake (RFI). Pigs that differed in RFI were selected from two different farms of origin. Colonic tissue was harvested from high RFI (HRFI) and low (LRFI) pigs, and two experimental conditions were explored: the first was basal unchallenged tissue and the second was colonic tissue following an ex vivo LPS challenge. RNA was extracted and tested on a Nanostring panel of 72 genes coding for barrier defense proteins, transmembrane receptors, kinases, transcription regulators, cytokines, and cytokine regulators. In the basal unchallenged tissue, the LRFI pigs had increased expression of AOAH, AP1, and TRAM and the cytokines TNF, IL10, and CXCL8, compared with the HRFI pigs ( P < 0.05), with a significant effect of farm of origin on 31 genes ( P < 0.05). In the LPS-challenged tissues, the LRFI group had higher expression of TLR1, TLR7, TLR8, GPR43/FFAR2, JAK2, and NFAM1 compared with the HRFI group ( P < 0.05). In conclusion, these data suggest that LRFI pigs have an upregulated basal colonic inflammatory state and a heightened response to an LPS challenge compared with the inefficient HRFI pigs. This immune profile potentially enhances their capacity to respond to an infectious challenge.

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