The microRNA expression profile in porcine skeletal muscle is changed by constant heat stress

A note of caution for using calmodulin antibodies

Calmodulin (CaM) is a ubiquitous intracellular calcium receptor that regulates a plethora of cellular functions through interactions with target proteins. In mammals, an identical Calmodulin protein is expressed by 3 independent genes (CALM1, CALM2, CALM3). Therefore, antibodies generated against either of the three products (CaM1, CaM2, CaM3) of these genes cannot be distinguished, and conclusions based on the supposedly specific CaM antibodies claiming functions of one of the 3 genes may be misleading. In this paper we present 44 articles, using such antibodies for Western blot, ELISA assay, immunohistochemistry or which are based on proteomics and the use of databases with incorrect annotations, all potentially reaching misleading conclusions. This should be taken as a note of caution for researchers working with Calmodulin antibodies and misleading databases.

Heat Stress Induces Alterations in Gene Expression of Actin Cytoskeleton and Filament of Cellular Components Causing Gut Disruption in Growing-Finishing Pigs

We aimed to investigate the impact of heat stress (HS) on the expression of tight junction (TJ) proteins and the interaction between genes affecting intestinal barrier function using transcriptomics in the porcine jejunum. Twenty-four barrows (crossbred Yorkshire × Landrace × Duroc; average initial body weight, 56.71 ± 1.74 kg) were placed in different temperatures (normal temperature [NT]; HS) and reared for 56 days. At the end of the experiment, jejunal samples were collected from three pigs per treatment for transcriptome and reverse-transcription quantitative polymerase chain reaction (RT-qPCR) analyses. We identified 43 differentially expressed genes, involving five Kyoto Encyclopedia of Genes and Genomes pathways, eight molecular functions, seven cellular components (CCs), and nine biological processes, using gene ontology enrichment analysis. Genes associated with the actin cytoskeleton, filament-binding pathways, and TJ proteins were selected and analyzed by RT-qPCR. Significant differences in relative mRNA expression showed that downregulated genes in the HS group included ZO1, CLDN1, OCLN, PCK1, and PCK2, whereas ACTG2, DES, MYL9, MYLK, TPM1, TPM2, CNN1, PDLIM3, and PCP4 were upregulated by HS (p < 0.05). These findings indicate that HS in growing-finishing pigs induces depression in gut integrity, which may be related to genes involved in the actin cytoskeleton and filaments of CC.

High-Temperature-Induced Differential Expression of miRNA Mediates Liver Inflammatory Response in Tsinling Lenok Trout (Brachymystax lenok tsinlingensis)

High-temperature stress poses a significant environmental challenge for aquatic organisms, including tsinling lenok trout (Brachymystax lenok tsinlingensis). This study aimed to investigate the role of microRNAs (miRNAs) in inducing liver inflammation in tsinling lenok trout under high-temperature stress. Tsinling lenok trout were exposed to high-temperature conditions (24 °C) for 8 h, and liver samples were collected for analysis. Through small RNA sequencing, we identified differentially expressed miRNAs in the liver of high-temperature-stressed tsinling lenok trout compared to the control group (maintained at 16 °C). Several miRNAs, including novel-m0105-5p and miR-8159-x, showed significant changes in expression levels. Additionally, we conducted bioinformatics analysis to explore the potential target genes of these differentially expressed miRNAs. Our findings revealed that these miRNA target genes are involved in inflammatory response pathways, such as NFKB1 and MAP3K5. The downregulation of novel-m0105-5p and miR-8159-x in the liver of high-temperature-stressed tsinling lenok trout suggests their role in regulating liver inflammatory responses. To validate this, we performed a dual-luciferase reporter assay to confirm the regulatory relationship between miRNAs and target genes. Our results demonstrated that novel-m0105-5p and miR-8159-x enhance the inflammatory response of hepatocytes by promoting the expression of NFKB1 and MAP3K5, respectively. In conclusion, our study provides evidence that high-temperature stress induces liver inflammation in tsinling lenok trout through dysregulation of miRNAs. Understanding the molecular mechanisms underlying the inflammatory response in tsinling lenok trout under high-temperature stress is crucial for developing strategies to mitigate the negative impacts of environmental stressors on fish health and aquaculture production.

Transcriptomic Analysis of the Porcine Gut in Response to Heat Stress and Dietary Soluble Fiber from Beet Pulp

This study aimed to investigate the impact of heat stress (HS) and the effects of dietary soluble fiber from beet pulp (BP) on gene expression (differentially expressed genes, DEGs) of the porcine jejunum. Out of the 82 DEGs, 47 genes were up-regulated, and 35 genes were downregulated between treatments. The gene ontology (GO) enrichment analysis showed that the DEGs were related mainly to the actin cytoskeleton organization and muscle structure development in biological processes, cytoplasm, stress fibers, Z disc, cytoskeleton, and the extracellular regions in cellular composition, and actin binding, calcium ion binding, actin filament binding, and pyridoxal phosphate binding in the molecular function. The KEGG pathway analysis showed that the DEGs were involved in hypertrophic cardiomyopathy, dilated cardiomyopathy, vascular smooth muscle contraction, regulation of actin cytoskeleton, mucin type O-glycan biosynthesis, and African trypanosomiasis. Several of the genes (HSPB6, HSP70, TPM1, TAGLN, CCL4) in the HS group were involved in cellular oxidative stress, immune responses, and cellular differentiation. In contrast, the DEGs in the dietary BP group were related to intestinal epithelium integrity and immune response to pathogens, including S100A2, GCNT3, LYZ, SCGB1A1, SAA3, and ST3GAL1. These findings might help understand the HS response and the effect of dietary fiber (DF) regarding HS and be a valuable reference for future studies.

Differential regulatory roles of microRNAs during intramuscular adipogenesis in Chinese Guizhou Congjiang Xiang pigs

Intramuscular fat development is regulated by a series of complicated processes, with non-coding RNA (ncRNA) such as microRNA (miRNA) having a critical role during intramuscular preadipocyte proliferation and differentiation in pigs. In the present study, the miRNA expression profiles of intramuscular preadipocytes from the longissimus dorsi muscle of Chinese Guizhou Congjiang Xiang pigs were detected by RNA-seq during various differentiation stages, namely, day 0 (D0), day 4 (D4), and day 8 (D8). A total of 67, 95, and 16 differentially expressed (DE) miRNAs were detected between D4 and D0, D8 and D0, and D8 and D4, respectively. According to gene ontology and Kyoto Encyclopedia of Genes analysis, target genes of DE miRNAs were enriched in categories and pathways related to lipid metabolic process, lipid biosynthetic process, as well as the PI3K-Akt, AMPK, and MAPK signalling pathways. Notably, miR-148a-3p was differentially expressed, with highest expressed abundance in D0, D4, and D8. Overexpression of miR-148a-3p in intramuscular preadipocytes increased cell proliferation and differentiation, and decreased apoptosis, in comparison to the knockdown of miR-148a-3p in intramuscular preadipocytes. Luciferase activity assays, quantitative polymerase-chain reaction, and western blot analysis confirmed that miR-148a-3p regulated adipogenesis by repressing PPARGC1A expression. Accordingly, the effect of miR-148a-3p mimic was attenuated by overexpression of PPARGC1A intramuscular preadipocytes. Furthermore, miR-148a-3p promoted intramuscular preadipocyte differentiation by inhibiting the AMPK/ACC/CPT1C signalling pathway. Taken together, we identified expression profiles of miRNAs in intramuscular preadipocytes and determined that miR-148a-3p acted as a promoter of adipogenesis.

Transcriptome analyses indicate that heat stress-induced inflammation in white adipose tissue and oxidative stress in skeletal muscle is partially moderated by zilpaterol supplementation in beef cattle

Heat stress (HS) triggers oxidative stress, systemic inflammation, and disrupts growth efficiency of livestock. β-adrenergic agonists supplemented to ruminant livestock improve growth performance, increase skeletal muscle mass, and decrease carcass fat. The objective of this study was to understand the independent and interacting effects of HS and zilpaterol hydrochloride (ZH) supplementation on the transcriptome of subcutaneous white adipose tissue and the longissimus dorsi muscle in steers. Twenty-four Red Angus-based steers were assigned to thermoneutral (TN; Temperature Humidity Index [THI] = 68) or HS (THI = 73-85) conditions and were not supplemented or supplemented with ZH (8.33 mg/kg/d) for 21 d in a 2 × 2 factorial. Steers in the TN condition were pair-fed to the average daily feed intake of HS steers. RNA was isolated from adipose tissue and skeletal muscle samples collected via biopsy on 3, 10, and 21 d and sequenced using 3' Tag-Seq to an achieved average depth of 3.6 million reads/sample. Transcripts, mapped to ARS-UCD1.2, were quantified. Differential expression (DE) analyses were performed in DESeq2 with a significance threshold for false discovery rate of 0.05. In adipose, 4 loci (MISP3, APOL6, SLC25A4, and S100A12) were DE due to ZH on day 3, and 2 (RRAD, ALB) were DE due to the interaction of HS and ZH on day 10 (Padj < 0.05). In muscle, 40 loci (including TENM4 and OAZ1) were DE due to ZH on day 10, and 6 loci (HIF1A, LOC101903734, PDZD9, HNRNPU, MTUS1, and TMCO6) were DE due to environment on day 21 (Padj < 0.05). To explore biological pathways altered by environment, supplement, and their interaction, loci with DE (Praw < 0.05) were evaluated in Ingenuity Pathway Analysis. In adipose, 509 pathways were predicted to be altered (P < 0.01): 202 due to HS, 126 due to ZH, and 181 due to the interaction; these included inflammatory pathways predicted to be upregulated due to HS but downregulated due to the interaction of HS and ZH. In muscle, 113 pathways were predicted to be altered (P < 0.01): 23 due to HS, 66 due to ZH, and 24 due to the interaction of HS and ZH. Loci and pathway data in muscle suggest HS induced oxidative stress and that the stress response was moderated by ZH. Metabolic pathways were predicted to be altered due to HS, ZH, and their interaction in both tissues. These data provide evidence that HS and ZH interact to alter expression of genes in metabolic and immune function pathways and that ZH moderates some adverse effects of HS.

How Epigenetics Can Enhance Pig Welfare?

Epigenetics works as an interface between the individual and its environment to provide phenotypic plasticity to increase individual adaptation capabilities. Recently, a wide variety of epi-genetic findings have indicated evidence for its application in the development of putative epi-biomarkers of stress in farm animals. The purpose of this study was to evaluate previously reported stress epi-biomarkers in swine and encourage researchers to investigate potential paths for the development of a robust molecular tool for animal welfare certification. In this literature review, we report on the scientific concerns in the swine production chain, the management carried out on the farms, and the potential implications of these practices for the animals' welfare and their epigenome. To assess reported epi-biomarkers, we identified, from previous studies, potentially stress-related genes surrounding epi-biomarkers. With those genes, we carried out a functional enrichment analysis of differentially methylated regions (DMRs) of the DNA of swine subjected to different stress-related conditions (e.g., heat stress, intrauterine insult, and sanitary challenges). We identified potential epi-biomarkers for target analysis, which could be added to the current guidelines and certification schemes to guarantee and certify animal welfare on farms. We believe that this technology may have the power to increase consumers' trust in animal welfare.

Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs (Sus-scrofa)

RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs. The RNA editing events at the miRNA binding sites were generated. The biological function of the differentially edited gene in skeletal muscle was further characterized in pig muscle-derived satellite cells. RNA editome analysis revealed a total of 171,909 A-to-I RNA editing sites (RESs), and examination of its features showed that these A-to-I editing sites were mainly located in SINE retrotransposons PRE-1/Pre0_SS element. Analysis of differentially edited sites (DESs) revealed a total of 4,552 DESs across tissues between Duroc and Luchuan pigs, and functional category enrichment analysis of differentially edited gene (DEG) sets highlighted a significant association and enrichment of tissue-developmental pathways including TGF-beta, PI3K-Akt, AMPK, and Wnt signaling pathways. Moreover, we found that RNA editing events at the miRNA binding sites in the 3'-UTR of HSPA12B mRNA could prevent the miRNA-mediated mRNA downregulation of HSPA12B in the muscle-derived satellite (MDS) cell, consistent with the results obtained from the Luchuan skeletal muscle. This study represents the most systematic attempt to characterize the significance of RNA editing in regulating gene expression, particularly in skeletal muscle, constituting a new layer of regulation to understand the genetic mechanisms behind phenotype variance in animals.Abbreviations: A-to-I: Adenosine-to-inosine; ADAR: Adenosine deaminase acting on RNA; RES: RNA editing site; DEG: Differentially edited gene; DES: Differentially edited site; FDR: False discovery rate; GO: Gene Ontology; KEGG: Kyoto Encyclopaedia of Genes and Genomes; MDS cell: musclederived satellite cell; RPKM: Reads per kilobase of exon model in a gene per million mapped reads; UTR: Untranslated coding regions.

Evaluation of miRNA as Biomarkers of Emotional Valence in Pigs

Simple Summary

It is widely recognized that the assessment of animal welfare should include measures of positive emotional (affective) state. Existing behavioral and physiological indicators of a positive affective state frequently lack sensitivity, objectivity or are unsuitable in a production environment. Therefore, there is a need to develop new approaches to accurately and objectively measure a positive emotional state in animals, including novel molecular markers such a miRNA. These biomarkers must be measurable in the peripheral circulation and provide an accurate account of the physiological and molecular activity in regions of the brain associated with emotional processing. Further, such markers require validation against established behavioral and physiological indices. Here we investigated the efficacy of circulating miRNA as biomarkers of emotional state in the pig.

Abstract

The ability to assess the welfare of animals is dependent on our ability to accurately determine their emotional (affective) state, with particular emphasis being placed on the identification of positive emotions. The challenge remains that current physiological and behavioral indices are either unable to distinguish between positive and negative emotional states, or they are simply not suitable for a production environment. Therefore, the development of novel measures of animal emotion is a necessity. Here we investigated the efficacy of microRNA (miRNA) in the brain and blood as biomarkers of emotional state in the pig. Female Large White × Landrace pigs (n = 24) were selected at weaning and trained to perform a judgment bias test (JBT), before being exposed for 5 weeks to either enriched (n = 12) or barren housing (n = 12) conditions. Pigs were tested on the JBT once prior to treatment, and immediately following treatment. MiRNA and neurotransmitters were analyzed in blood and brain tissue after euthanasia. Treatment had no effect on the outcomes of the JBT. There was also no effect of treatment on miRNA expression in blood or the brain (FDR p > 0.05). However, pigs exposed to enriched housing had elevated dopamine within the striatum compared to pigs in barren housing (p = 0.02). The results imply that either (a) miRNAs are not likely to be valid biomarkers of a positive affective state, at least under the type of conditions employed in this study, or (b) that the study design used to modify affective state was not able to create differential affective states, and therefore establish the validity of miRNA as biomarkers.

MicroRNA-mediated stress response in bivalve species

Bivalve mollusks are important aquatic organisms, which are used for biological monitoring because of their abundance, ubiquitous nature, and abilities to adapt to different environments. MicroRNAs (miRNAs) are small noncoding RNAs, which typically silence the expression of target genes; however, certain miRNAs directly or indirectly upregulate their target genes. They are rapidly modulated and play an essential role in shaping the response of organisms to stresses. Based on the regulatory function and rapid alteration of miRNAs, they could act as biomarkers for biotic and abiotic stress, including environmental stresses and contaminations. Moreover, mollusk, particularly hemocytes, rapidly respond to environmental changes, such as pollution, salinity changes, and desiccation, which makes them an attractive model for this purpose. Thus, bivalve mollusks could be considered a good animal model to examine a system's response to different environmental conditions and stressors. miRNAs have been reported to adjust the adaptation and physiological functions of bivalves during endogenous and environmental stressors. In this review, we aimed to discuss the potential mechanisms underlying the response of bivalves to stressors and how miRNAs orchestrate this process; however, if necessary, other organisms' response is included to explain specific processes.

MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.

Omics Application in Animal Science-A Special Emphasis on Stress Response and Damaging Behaviour in Pigs

Increasing stress resilience of livestock is important for ethical and profitable meat and dairy production. Susceptibility to stress can entail damaging behaviours, a common problem in pig production. Breeding animals with increased stress resilience is difficult for various reasons. First, studies on neuroendocrine and behavioural stress responses in farm animals are scarce, as it is difficult to record adequate phenotypes under field conditions. Second, damaging behaviours and stress susceptibility are complex traits, and their biology is not yet well understood. Dissecting complex traits into biologically better defined, heritable and easily measurable proxy traits and developing biomarkers will facilitate recording these traits in large numbers. High-throughput molecular technologies (“omics”) study the entirety of molecules and their interactions in a single analysis step. They can help to decipher the contributions of different physiological systems and identify candidate molecules that are representative of different physiological pathways. Here, we provide a general overview of different omics approaches and we give examples of how these techniques could be applied to discover biomarkers. We discuss the genetic dissection of the stress response by different omics techniques and we provide examples and outline potential applications of omics tools to understand and prevent outbreaks of damaging behaviours.

Gga-let-7f-3p promotes apoptosis in selenium deficiency-induced skeletal muscle by targeting selenoprotein K

Selenoprotein K (SELENOK) is primarily observed in the endoplasmic reticulum, and serves to maintain the normal physiological functions of skeletal muscle. Skeletal muscle development and regeneration are associated with significant changes in the expression of specific microRNAs (miRNAs). Downregulated SELENOK expression is observed in chicken muscles deficient of Se. However, the mechanisms of miRNA regulation of SELENOK expression remain elusive. Here, deep sequencing was used to detect the miRNA profiles of muscle in Se deficient (-Se group) and normal (C group) chickens. A dual-luciferase reporter assay was adopted to verify the relationship between SELENOK and gga-let-7f-3p. In addition, gga-let-7f-3p was either overexpressed or knocked-down in chicken myoblasts. Furthermore, the cells were treated with N-acetyl-l-cysteine (NAC) or hydrogen peroxide (H2O2) in order to probe the factors involved in oxidative stress, endoplasmic reticulum stress (ERS) and apoptosis, respectively. Relative to the C group, there were 132 differentially expressed miRNAs (including 57 upregulated and 75 downregulated) in the muscles of the -Se group. The dual-luciferase reporter assay showed that SELENOK was a primary target of gga-let-7f-3p. It was also observed that the overexpression or knock-down of gga-let-7f-3p significantly influenced the SELENOK expression. Moreover, NAC blocked mimics of ga-let-7f-3p, thus inducing oxidative stress, ERS and apoptosis. Simultaneously, gga-let-7f-3p inhibitors blocked the stimulant effects caused by H2O2 in chicken myoblasts. Furthermore, Se deficiency downregulated the SELENOK protein expression and induced oxidative stress, ERS and apoptosis in chicken muscles. In conclusion, the gga-let-7f-3p-SELENOK pathway played a pivotal role in Se deficiency mediated muscle injuries through the induction of oxidative stress and ERS, ultimately promoting apoptosis.

Altered expression of miRNAs and mRNAs reveals the potential regulatory role of miRNAs in the developmental process of early weaned goats

MicroRNAs (miRNAs) play pivotal roles in growth, development, and stress responses. However, the regulatory function of miRNAs in early weaned goats remains unclear. Deep sequencing comparison of mRNA and miRNA expression profiles showed that 18 miRNAs and 373 genes were differentially expressed in pre- and post-weaning Chongming white goats. Bioinformatics analysis indicated that these differentially expressed genes are involved in cellular processes, developmental processes, and growth in terms of biological process analysis. KEGG analysis showed that downregulated genes were enriched in salivary secretion, bile secretion, vascular smooth muscle contraction, and calcium signaling pathways. Additionally, a miRNA-mRNA co-expression network of the 18 dysregulated miRNAs and their 107 target mRNAs was constructed using a combination of Pearson’s correlation analysis and prediction by miRanda software. Among the downregulated miRNAs, two (chi-miR-206 and chi-miR-133a/b) were muscle development-related and the others were cell proliferation associated. Further RT-qPCR analysis confirmed that downregulated miRNAs (chi-miR-99b-3p, chi-miR-224, and chi-miR-10b-5p) were highly expressed in muscle tissues (heart, spleen, or kidney) of the rapid growth period (7-month old) in Chongming white goats. The results of the present study suggested that weaning induced cell proliferation repression in post-weaning goats, providing new insight into the mechanism of muscle development of goats, although additional details remain to be elucidated in the future.

Integrating miRNA and mRNA expression profiles in plasma of laying hens associated with heat stress

High temperature is one of the most common environmental stressors plaguing animal husbandry worldwide. Little is known about the regulatory roles of miRNAs in response to heat stress in laying hens. To systematically identify heat stress-responsive miRNAs and their targets in laying hens, the differential expression of miRNAs and mRNAs was compared under heat stress and normal temperature. We identified 16 miRNAs and 502 genes that were significantly changed in heat-stressed laying hens. By comparing the differentially expressed genes (DEGs) and the putative targets of the altered miRNAs based on bioinformatics prediction, 82 coordinated genes were identified. Gene ontology classification analyses of the 82 putative target genes showed that the biological category 'cellular response to stress' was prominently annotated. Notably, the response-related gene autophagy-related protein 9A was most likely controlled by the upregulated miRNAs gga-miR-92-5p, gga-miR-1618-5p, gga-miR-1737, and gga-miR-6557 in response to heat stress. Analysis of DEGs also revealed an increase in lipid metabolism in heat-stressed laying hens. Some of these genes were negatively correlated with the altered miRNAs, suggesting that they are potential targets of the miRNAs. Taken together, our results advance our understanding of the regulatory mechanism of heat-stress-induced injury in laying hens, specifically with regard to miRNAs.

The critical role of microRNAs in stress response: Therapeutic prospect and limitation

Stress response refers to the systemic nonspecific response upon exposure to strong stimulation or chronic stress, such as severe trauma, shock, infection, burn, major surgery or improper environment, which disturb organisms and damage their physical and psychological health. However, the pathogenesis of stress induced disorder remains complicated and diverse under different stress exposure. Recently, studies have revealed a specific role of microRNAs (miRNAs) in regulating cellular function under different types of stress, suggesting a significant role in the treatment and prevention of stress-related diseases, such as stress ulcer, posttraumatic stress disorder, stress-induced cardiomyopathy and so on. This paper have reviewed the literature on microRNA related stress diseases in different databases including PubMed, Web of Science, and the MiRbase. It considers only peer-reviewed papers published in English between 2004 and 2018. This review summarizes new advances in principles and mechanisms of miRNAs regulating stress signalling pathway and the role of miRNAs in human stress diseases. This comprehensive review is to provide an integrated account of how different stresses affect miRNAs and how stress-miRNA pathways may, in turn, be linked with disease, which offers some potential strategies for stress disorder treatment. Furthermore, the limitation of current studies and challenges for clinical use are discussed.

Proteomic changes of the porcine skeletal muscle in response to chronic heat stress

BACKGROUND

Heat stress (HS) has an adverse effect on meat quality; however, the underlying molecular mechanisms altering meat quality due to muscle responses to stress remain unclear. Sixteen castrated male crossbreeds between Landrace × Yorkshire sows and Duroc boars (79.00 ± 1.50 kg body weight) were exposed to either thermal neutral (22 °C, n = 8) or HS (30 °C, n = 8) conditions for 3 weeks. Subsequently, the longissimus dorsi (LD) muscle of all pigs was assayed for meat quality parameters and proteome analysis.

RESULTS

HS decreased post mortem (24 h) pH and intramuscular fat, changed ultimate L*, a* and b* values and increased drip loss and shear force. Proteome analysis of the LD was conducted by two-dimensional gel electrophoresis and mass spectrometry. A total of 23 differentially expressed proteins were identified, of which three were verified by western blotting analysis. The identified proteins were involved in six types of biological process: carbohydrate metabolism, myofibrillar and cytoskeleton structure, stress response, antioxidant and detoxification, calcium binding and cellular apoptosis. Interestingly, HS induced higher levels of heat shock protein, antioxidants and calcium binding proteins, which are involved in the mechanisms of defense and homeostasis.

CONCLUSION

The results indicate that HS-induced changes in the expression of myofibrillar proteins, glucose and energy metabolism-related proteins, heat shock protein and antioxidant enzymes might, at least partly, contribute to increase in meat tenderness. These findings will provide the foundation for developing future mitigating solutions and preventative therapies to reduce the detrimental effects of chronic HS on muscle function, metabolism and meat quality. © 2017 Society of Chemical Industry.

Transcriptome analysis and identification of significantly differentially expressed genes in Holstein calves subjected to severe thermal stress

RNA-Seq analysis was used to characterize transcriptome response of Holstein calves to thermal stress. A total of eight animals aged between 2 and 3 months were randomly selected and subjected to thermal stress corresponding to a temperature humidity index of 95 in an environmentally controlled house for 12 h consecutively for 3 days. A set of 15,787 unigenes were found to be expressed and after a threshold of threefold change, and a Q value <0.05; 502, 394, and 376 genes were found to be differentially expressed on days 1, 2, and 3 out of which 343, 261 and 256 genes were upregulated and 159, 133, and 120 genes were downregulated. Only 356 genes out of these were expressed on all 3 days, and only they were considered as significantly differentially expressed. KEGG pathway analysis revealed that ten pathways were significantly enriched; the top two among them were protein processing in endoplasmic reticulum and MAPK signaling pathways. These results suggest that thermal stress triggered a complex response in Holstein calves and the animals adjusted their physiological and metabolic processes to survive. Many of the genes identified in this study have not been previously reported to be involved in thermal stress response. The results of this study extend our understanding of the animal's response to thermal stress and some of the identified genes may prove useful in the efforts to breed Holstein cattle with superior thermotolerance, which might help in minimizing production loss due to thermal stress.

Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish

Environmental acclimation is important episode in wildlife occupation of the high-altitude Tibetan Plateau (TP). Transcriptome-wide studies on thermal acclimation mechanism in fish species are rarely revealed in Tibetan Plateau fish at high altitude. Thus, we used mRNA and miRNA transcriptome sequencing to investigate regulation of thermal acclimation in larval Tibetan naked carp, Gymnocypris przewalskii. We first remodeled the regulation network of mRNA and miRNA in thermal acclimation, and then identified differential expression of miRNAs and target mRNAs enriched in metabolic and digestive pathways. Interestingly, we identified two candidate genes contributed to normal skeletal development. The altered expression of these gene groups could potentially be associated with the developmental issues of deformity and induced larval death. Our results have three important implications: first, these findings provide strong evidences to support our hypothesis that G. przewalskii possess ability to build heat-tolerance against the controversial issue. Second, this study shows that transcriptional and post-transcriptional regulations are extensively involved in thermal acclimation. Third, the integrated mRNA and microRNA transcriptome analyses provide a large number of valuable genetic resources for future studies on environmental stress response in G. przewalskii and as a case study in Tibetan Schizothoracine fish.

Genome-wide survey of miRNAs and their evolutionary history in the ascidian, Halocynthia roretzi

BACKGROUND

miRNAs play essential roles in the modulation of cellular functions via degradation and/or translation attenuation of target mRNAs. They have been surveyed in a single ascidian genus, Ciona. Recently, an annotated draft genome sequence for a distantly related ascidian, Halocynthia roretzi, has become available, but miRNAs in H. roretzi have not been previously studied.

RESULTS

We report the prediction of 319 candidate H. roretzi miRNAs, obtained through three complementary methods. Experimental validation suggests that more than half of these candidate miRNAs are expressed during embryogenesis. The majority of predicted H. roretzi miRNAs appear specific to ascidians or tunicates, and only 32 candidates, belonging to 25 families, are widely conserved across metazoans.

CONCLUSION

Our study presents a comprehensive identification of candidate H. roretzi miRNAs. This resource will facilitate the study of the mechanisms for miRNA-controlled gene regulatory networks during ascidian development. Further, our analysis suggests that the majority of Halocynthia miRNAs are specific to ascidian or tunicates, with only a small number of widely conserved miRNAs. This result is consistent with the general notion that animal miRNAs are less conserved between taxa than plant ones.