scholarly journals The synergistic interaction of thermal stress coupled with overstocking strongly modulates the transcriptomic activity and immune capacity of rainbow trout (Oncorhynchus mykiss)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexander Rebl ◽  
Tomáš Korytář ◽  
Andreas Borchel ◽  
Ralf Bochert ◽  
Joanna Ewa Strzelczyk ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
High Temperature ◽  
Critical Temperature ◽  
Differentially Expressed Genes ◽  
Reference Group ◽  
Synergistic Effects ◽  
Stocking Density ◽  
Transcript Abundance ◽  
Condition Index ◽  
Differentially Expressed

Abstract The objective of the present study is to identify and evaluate informative indicators for the welfare of rainbow trout exposed to (A) a water temperature of 27 °C and (B) a stocking density of 100 kg/m3 combined with a temperature of 27 °C. The spleen-somatic and condition index, haematocrit and the concentrations of haemoglobin, plasma cortisol and glucose revealed non-significant differences between the two stress groups and the reference group 8 days after the onset of the experiments. The transcript abundance of almost 1,500 genes was modulated at least twofold in in the spleen of rainbow trout exposed to a critical temperature alone or a critical temperature combined with crowding as compared to the reference fish. The number of differentially expressed genes was four times higher in trout that were simultaneously challenged with high temperature and crowding, compared to trout challenged with high temperature alone. Based on these sets of differentially expressed genes, we identified unique and common tissue- and stress type-specific pathways. Furthermore, our subsequent immunologic analyses revealed reduced bactericidal and inflammatory activity and a significantly altered blood-cell composition in challenged versus non-challenged rainbow trout. Altogether, our data demonstrate that heat and overstocking exert synergistic effects on the rainbow trout’s physiology, especially on the immune system.

scholarly journals Comparisons among rainbow trout, Oncorhynchus mykiss, populations of maternal transcript profile associated with egg viability

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gregory M. Weber ◽  
Jill Birkett ◽  
Kyle Martin ◽  
Doug Dixon ◽  
Guangtu Gao ◽  
...  
Keyword(s):  
Rainbow Trout ◽  
Egg Quality ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Rainbow Trout Oncorhynchus Mykiss ◽  
Analysis Group ◽  
Maternal Transcripts ◽  
Single Batch ◽  
Insight Into

Abstract Background Transcription is arrested in the late stage oocyte and therefore the maternal transcriptome stored in the oocyte provides nearly all the mRNA required for oocyte maturation, fertilization, and early cleavage of the embryo. The transcriptome of the unfertilized egg, therefore, has potential to provide markers for predictors of egg quality and diagnosing problems with embryo production encountered by fish hatcheries. Although levels of specific transcripts have been shown to associate with measures of egg quality, these differentially expressed genes (DEGs) have not been consistent among studies. The present study compares differences in select transcripts among unfertilized rainbow trout eggs of different quality based on eyeing rate, among 2 year classes of the same line (A1, A2) and a population from a different hatchery (B). The study compared 65 transcripts previously reported to be differentially expressed with egg quality in rainbow trout. Results There were 32 transcripts identified as DEGs among the three groups by regression analysis. Group A1 had the most DEGs, 26; A2 had 15, 14 of which were shared with A1; and B had 12, 7 of which overlapped with A1 or A2. Six transcripts were found in all three groups, dcaf11, impa2, mrpl39_like, senp7, tfip11 and uchl1. Conclusions Our results confirmed maternal transcripts found to be differentially expressed between low- and high-quality eggs in one population of rainbow trout can often be found to overlap with DEGs in other populations. The transcripts differentially expressed with egg quality remain consistent among year classes of the same line. Greater similarity in dysregulated transcripts within year classes of the same line than among lines suggests patterns of transcriptome dysregulation may provide insight into causes of decreased viability within a hatchery population. Although many DEGs were identified, for each of the genes there is considerable variability in transcript abundance among eggs of similar quality and low correlations between transcript abundance and eyeing rate, making it highly improbable to predict the quality of a single batch of eggs based on transcript abundance of just a few genes.

scholarly journals A red herring in zebrafish genetics: allele-specific gene expression can underlie altered transcript abundance in zebrafish mutants

2021 ◽  
Author(s):  
Richard J White ◽  
Eirinn Mackay ◽  
Stephen W Wilson ◽  
Elisabeth M Busch-Nentwich
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed Gene ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Model Organisms ◽  
Specific Gene ◽  
Wild Type ◽  
Specific Expression ◽  
Genomic Location ◽  
Allele Specific

In model organisms, RNA sequencing is frequently used to assess the effect of genetic mutations on cellular and developmental processes. Typically, animals heterozygous for a mutation are crossed to produce offspring with different genotypes. Resultant embryos are grouped by genotype to compare homozygous mutant embryos to heterozygous and wild-type siblings. Genes that are differentially expressed between the groups are assumed to reveal insights into the pathways affected by the mutation. Here we show that in zebrafish, differentially expressed genes are often overrepresented on the same chromosome as the mutation due to different levels of expression of alleles from different genetic backgrounds. Using an incross of haplotype-resolved wild-type fish, we found evidence of widespread allele-specific expression, which appears as differential expression when comparing embryos homozygous for a region of the genome to their siblings. When analysing mutant transcriptomes, this means that differentially expressed genes on the same chromosome as a mutation of interest may not be caused by that mutation. Typically, the genomic location of a differentially expressed gene is not considered when interpreting its importance with respect to the phenotype. This could lead to pathways being erroneously implicated or overlooked due to the noise of spurious differentially expressed genes on the same chromosome as the mutation. These observations have implications for the interpretation of RNA-seq experiments involving outbred animals and non-inbred model organisms.

A novel method to prioritize RNAseq data for post-hoc analysis based on absolute changes in transcript abundance

2015 ◽  
Vol 14 (3) ◽  
Author(s):  
Patrick McNutt ◽  
Ian Gut ◽  
Kyle Hubbard ◽  
Phil Beske
Keyword(s):  
Differentially Expressed Genes ◽  
Transcript Abundance ◽  
Fold Change ◽  
Differentially Expressed ◽  
Post Hoc Analysis ◽  
Rnaseq Data ◽  
Novel Method ◽  
Post Hoc

AbstractThe use of fold-change (FC) to prioritize differentially expressed genes (DEGs) for

scholarly journals Explicating anti-amyloidogenic role of curcumin and piperine via amyloid beta (Aβ) explicit pathway: recovery and reversal paradigm effects

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10003
Author(s):  
Aimi Syamima Abdul Manap ◽  
Priya Madhavan ◽  
Shantini Vijayabalan ◽  
Adeline Chia ◽  
Koji Fukui
Keyword(s):  
Differentially Expressed Genes ◽  
Cell Model ◽  
Synergistic Effects ◽  
Expression Profiles ◽  
Combined Treatment ◽  
Neuronal Cell ◽  
Treated Group ◽  
Fold Change ◽  
Differentially Expressed ◽  
Microarray Profiling

Previously, we reported the synergistic effects of curcumin and piperine in cell cultures as potential anti-cholinesterase and anti-amyloidogenic agents. Due to limited findings on the enrolment of these compounds on epigenetic events in AD, we aimed at elucidating the expression profiles of Aβ42-induced SH-SY5Y cells using microarray profiling. In this study, an optimized concentration of 35 µM of curcumin and piperine in combination was used to treat Aβ42 fibril and high-throughput microarray profiling was performed on the extracted RNA. This was then compared to curcumin and piperine used singularly at 49.11 µM and 25 µM, respectively. Our results demonstrated that in the curcumin treated group, from the top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ −2), there were five upregulated and three downregulated genes involved in the amyloidogenic pathway. While from top 10 upregulated and top 10 downregulated significantly differentially expressed genes (p < 0.05; fold change ≥ 2 or ≤ − 2) in the piperine treated group, there were four upregulated and three downregulated genes involved in the same pathway, whereas there were five upregulated and two downregulated genes involved (p < 0.05; fold change ≥ 2 or ≤ − 2) in the curcumin-piperine combined group. Four genes namely GABARAPL1, CTSB, RAB5 and AK5 were expressed significantly in all groups. Other genes such as ITPR1, GSK3B, PPP3CC, ERN1, APH1A, CYCS and CALM2 were novel putative genes that are involved in the pathogenesis of AD. We revealed that curcumin and piperine have displayed their actions against Aβ via the modulation of various mechanistic pathways. Alterations in expression profiles of genes in the neuronal cell model may explain Aβ pathology post-treatment and provide new insights for remedial approaches of a combined treatment using curcumin and piperine.

scholarly journals Revealing Differentially Expressed Genes and Identifying Effector Proteins of Puccinia striiformis f. sp. tritici in Response to High-Temperature Seedling Plant Resistance of Wheat Based on Transcriptome Sequencing

mSphere ◽  
2020 ◽  
Vol 5 (3) ◽  
Author(s):  
Fei Tao ◽  
Yangshan Hu ◽  
Chang Su ◽  
Juan Li ◽  
Lili Guo ◽  
...  
Keyword(s):  
High Temperature ◽  
Differentially Expressed Genes ◽  
Puccinia Striiformis ◽  
Effector Proteins ◽  
Differentially Expressed ◽  
Content Type ◽  
Molecular Pattern ◽  
Seedling Plant ◽  
Effector Triggered Immunity ◽  
Pathogen Associated Molecular Pattern

ABSTRACT Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum L.) globally. Recently, more aggressive Pst races have evolved to acquire new virulence profiles and are adapted better to high temperature than most of the previous races. Breeding cultivars with durable high-temperature seedling-plant (HTSP) resistance is an important strategy for controlling stripe rust. Understanding the mechanism of wheat HTSP resistance against Pst is important for more efficient breeding to improve host resistance. In the present study, transcriptomic analysis identified 25 Pst differentially expressed genes (DEGs) that were involved in the HTSP resistance in wheat cultivar Xiaoyan6 (XY6). Functional annotation indicated that these DEGs are related to membrane proteins, mRNA binding proteins, cell membrane transporters, and synthesis of cell nitrogen compounds. Among these DEGs, a candidate effector, PstCEP1 (PSTG_13342), was identified and cloned, and its function was verified. Barley stripe mosaic virus (BSMV)-mediated host-induced gene silencing (HIGS) of PstCEP1 reduced Pst virulence. Signal peptide verification and functional testing in Nicotiana benthamiana indicated that PstCEP1 is a secreted protein and has the function of suppressing programmed cell death (PCD). PstCEP1 as a candidate effector was further supported by type three secretion system (TTSS)-mediated overexpression responding to wheat HTSP resistance via affecting the pathogen-associated molecular pattern (PAMP)-triggered immunity (PTI) and effector-triggered immunity (ETI). IMPORTANCE In the present study, we performed transcriptomic analysis to identify differentially expressed genes and effector proteins of Puccinia striiformis f. sp. tritici (Pst) in response to the high-temperature seedling-plant (HTSP) resistance in wheat. Experimental validation confirmed the function of the highest upregulated effector protein, PstCEP1. This study provides a key resource for understanding the biology and molecular basis of Pst responses to wheat HTSP resistance, and PstCEP1 may be used in future studies to understand pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity processes in the Pst-wheat interaction system.

scholarly journals Selection and Evaluation of Reference Genes for ddPCR-Based Transcript Abundance Studies in Oidiodendron Maius Across Varying Carbon Sources

2021 ◽  
Author(s):  
Erin Feldman ◽  
Elena Martino ◽  
Annegret Kohler ◽  
Daniel Durall ◽  
Melanie Jones
Keyword(s):  
Stability Analysis ◽  
Differentially Expressed Genes ◽  
Reference Genes ◽  
Geometric Mean ◽  
Mycorrhizal Fungus ◽  
Carbon Sources ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Transcriptional Responses ◽  
Oidiodendron Maius

Abstract Background When identifying transcript abundance in response to treatment, accurate quantification is critical, especially when examining subtle differences in expression. In particular, data normalization is necessary to account for differences among samples including those associated with RNA quantity and quality. Due to the capacity of droplet digital PCR to absolutely quantify the copy number of the target gene in a given sample, normalization, such as the use of an internal control gene, has not customarily been considered obligatory. Decades of quantitative PCR research have shown, however, that the use of endogenous controls undoubtedly aid in correcting sample variability. With our limited knowledge of gene function in many fungi, typical ‘housekeeping genes’ commonly used as internal references may not be relevant in these organisms. This study aimed to identify and validate suitable reference genes for transcript abundance studies in Oidiodendron maius, a globally distributed, model ericoid mycorrhizal fungus. Results A shortlist of 251 non-differentially expressed genes was generated from RNA-Seq analyses of O. maius grown on three different carbon sources or in symbiosis with Vaccinium myrtillus. Subsequently, a set of criteria (stable expression, valid annotation and relatively high expression) was applied to select three candidate reference genes. These three genes were validated across a further eleven carbon sources using ddPCR and the application of geNorm and NormFinder stability analysis algorithms. Expression stability analysis of three genes - EfTu, vma, and sar - confirmed their reliability as internal references; the geometric mean of their expression values demonstrated the highest stability as a normalization factor.Conclusions We propose the use of the geometric mean of O. maius genes EfTu, vma and sar as a reference tool to normalize RNA expression in ddPCR assays. These newly selected and validated reference genes will increase reliability and reproducibility when studying transcriptional responses of O. maius at different developmental stages and/or under a range of physiological conditions. In addition, the list of 251 non-differentially expressed genes can serve as a valuable resource for selecting reference genes for related experiments and enhances the limited information available on O. maius.

scholarly journals A Sense of Place: Transcriptomics Identifies Environmental Signatures in Cabernet Sauvignon Berry Skins in the Late Stages of Ripening

2019 ◽  
Author(s):  
Grant R. Cramer ◽  
Noé Cochetel ◽  
Ryan Ghan ◽  
Agnès Destrac-Irvine ◽  
Serge Delrot
Keyword(s):  
Gene Ontology ◽  
Differentially Expressed Genes ◽  
Transcript Abundance ◽  
Differentially Expressed ◽  
Cabernet Sauvignon ◽  
Rna Seq ◽  
Cold Response ◽  
Berry Ripening ◽  
Berry Skins ◽  
Late Stages

AbstractBackgroundGrape berry ripening is influenced by climate, the main component of the “terroir” of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.ResultsTo better understand the effect of “place” on transcript abundance during the late stages of berry ripening, Cabernet Sauvignon berries grown in Bordeaux and Reno were compared at similar sugar levels (19 to 26 °Brix (total soluble solids)). Day temperatures were warmer and night temperatures were cooler in Reno. °Brix was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-Seq analysis identified 5528 differentially expressed genes between Bordeaux and Reno grape skins at 22°Brix. Weighted Gene Coexpression Network Analysis for all expressed transcripts for all four °Brix levels measured indicated that the majority (75%) of transcript expression differed significantly between the two locations. Top gene ontology categories for the common transcript sets were translation, photosynthesis, DNA metabolism and catabolism. Top gene ontology categories for the differentially expressed genes at 22°Brix involved response to stimulus, biosynthesis and response to stress. Some differentially expressed genes encoded terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. Bordeaux berries had higher transcript abundance with differentially expressed genes associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with differentially expressed genes involved in water deprivation, cold response, ABA signaling and iron homeostasis.ConclusionsTranscript abundance profiles in the berry skins at maturity were highly dynamic. RNA-Seq analysis identified a smaller (25% of total) common core set of ripening genes that appear not to depend on rootstock, vineyard management, plant age, soil and climatic conditions. Much of the gene expression differed between the two locations and could be associated with multiple differences in environmental conditions that may have affected the berries in the two locations; some of these genes may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result.

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