Association of plasma microRNA expression with age, genetic background and functional traits in dairy cattle

Abstract A number of blood circulating microRNAs (miRNAs) are proven disease biomarkers and have been associated with ageing and longevity in multiple species. However, the role of circulating miRNAs in livestock species has not been fully studied. We hypothesise that plasma miRNA expression profiles are affected by age and genetic background, and associated with health and production traits in dairy cattle. Using PCR arrays, we assessed 306 plasma miRNAs for effects of age (calves vs mature cows) and genetic background (control vs select lines) in 18 animals. We identified miRNAs which were significantly affected by age (26 miRNAs) and genetic line (5 miRNAs). Using RT-qPCR in a larger cow population (n = 73) we successfully validated array data for 12 age-related miRNAs, one genetic line-related miRNA, and utilised expression data to associate their levels in circulation with functional traits in these animals. Plasma miRNA levels were associated with telomere length (ageing/longevity indicator), milk production and composition, milk somatic cell count (mastitis indicator), fertility, lameness, and blood metabolites linked with body energy balance and metabolic stress. In conclusion, circulating miRNAs could provide useful selection markers for dairy cows to help improve health, welfare and production performance

Striated muscle activator of Rho signalling (STARS) is reduced in ageing human skeletal muscle and targeted by miR-628-5p

Aim: The striated muscle activator of Rho signalling (STARS) is a muscle-specific actin-binding protein. The STARS signalling pathway is activated by resistance exercise and is anticipated to play a role in signal mechan-otransduction. Animal studies have reported a negative regulation of STARS signalling with age, but such regulation has not been investigated in humans. Methods: Ten young (18–30 years) and 10 older (60–75 years) subjects completed an acute bout of resistance exercise. Gene and protein expres-sion of members of the STARS signalling pathway and miRNA expression of a subset of miRNAs, predicted or known to target members of STARS signalling pathway, were measured in muscle biopsies collected pre-exer-cise and 2 h post-exercise. Results: For the first time, we report a significant downregulation of the STARS protein in older subjects. However, there was no effect of age on the magnitude of STARS activation in response to an acute bout of exer-cise. Finally, we established that miR-628-5p, a miRNA regulated by age and exercise, binds to the STARS 3’UTR to directly downregulate its tran-scription. Conclusion: This study describes for the first time the resistance exercise-induced regulation of STARS signalling in skeletal muscle from older humans and identifies a new miRNA involved in the transcriptional con-trol of STARS

MicroRNA Predictors of Longevity in Caenorhabditis elegans

Neither genetic nor environmental factors fully account for variability in individual longevity: genetically identical invertebrates in homogenous environments often experience no less variability in lifespan than outbred human populations. Such variability is often assumed to result from stochasticity in damage accumulation over time; however, the identification of early-life gene expression states that predict future longevity would suggest that lifespan is least in part epigenetically determined. Such “biomarkers of aging,” genetic or otherwise, nevertheless remain rare. In this work, we sought early-life differences in organismal robustness in unperturbed individuals and examined the utility of microRNAs, known regulators of lifespan, development, and robustness, as aging biomarkers. We quantitatively examined Caenorhabditis elegans reared individually in a novel apparatus and observed throughout their lives. Early-to-mid–adulthood measures of homeostatic ability jointly predict 62% of longevity variability. Though correlated, markers of growth/muscle maintenance and of metabolic by-products (“age pigments”) report independently on lifespan, suggesting that graceful aging is not a single process. We further identified three microRNAs in which early-adulthood expression patterns individually predict up to 47% of lifespan differences. Though expression of each increases throughout this time, mir-71 and mir-246 correlate with lifespan, while mir-239 anti-correlates. Two of these three microRNA “biomarkers of aging” act upstream in insulin/IGF-1–like signaling (IIS) and other known longevity pathways, thus we infer that these microRNAs not only report on but also likely determine longevity. Thus, fluctuations in early-life IIS, due to variation in these microRNAs and from other causes, may determine individual lifespan

High-throughput profiling of caenorhabditis elegans starvation-responsive microRNAs

MicroRNAs (miRNAs) are non-coding RNAs of ~22 nucleotides in length that regulate gene expression by interfering with the stability and translation of mRNAs. Their expression is regulated during development, under a wide variety of stress conditions and in several pathological processes. In nature, animals often face feast or famine conditions. We observed that subjecting early L4 larvae from Caenorhabditis elegans to a 12-hr starvation period produced worms that are thinner and shorter than well-fed animals, with a decreased lipid accumulation, diminished progeny, reduced gonad size, and an increased lifespan. Our objective was to identify which of the 302 known miRNAs of C. elegans changed their expression under starvation conditions as compared to well-fed worms by means of deep sequencing in early L4 larvae. Our results indicate that 13 miRNAs (miR-34-3p, the family of miR-35-3p to miR-41-3p, miR-39-5p, miR-41-5p, miR-240-5p, miR-246-3p and miR-4813-5p) were upregulated, while 2 miRNAs (let-7-3p and miR-85-5p) were downregulated in 12-hr starved vs. well-fed early L4 larvae. Some of the predicted targets of the miRNAs that changed their expression in starvation conditions are involved in metabolic or developmental process. In particular, miRNAs of the miR-35 family were upregulated 6-20 fold upon starvation. Additionally, we showed that the expression of gld-1, important in oogenesis, a validated target of miR-35-3p, was downregulated when the expression of miR-35-3p was upregulated. The expression of another reported target, the cell cycle regulator lin-23, was unchanged during starvation. This study represents a starting point for a more comprehensive understanding of the role of miRNAs during starvation in C. elegans

Modelling the molecular mechanisms of ageing

This document is the Accepted Manuscript version of a published work that appeared in final form in Bioscience reports. To access the final edited and published work see http://www.bioscirep.org/content/37/1/BSR20160177.The ageing process is driven at the cellular level by random molecular damage which slowly accumulates with age. Although cells possess mechanisms to repair or remove damage, they are not 100% efficient and their efficiency declines with age. There are many molecular mechanisms involved and exogenous factors such as stress also contribute to the ageing process. The complexity of the ageing process has stimulated the use of computational modelling in order to increase our understanding of the system, test hypotheses and make testable predictions. As many different mechanisms are involved, a wide range of models have been developed. This paper gives an overview of the types of models that have been developed, the range of tools used, modelling standards, and discusses many specific examples of models which have been grouped according to the main mechanisms that they address. We conclude by discussing the opportunities and challenges for future modelling in this field

A New Narnavirus that Infects the Late Blight Pathogen, Phytophthora infestans, with a Supergroup 2 RNA-dependent RNA Polymerase

Phytophthora infestans (Mont.) de Bary is the oomycete that caused the historic Irish potato famine of 1845-1850 and beyond, and it continues to cause worldwide devastation of the modern potato and tomato industries. Double-stranded RNAs (dsRNAs) have been discovered in P. infestans but have never been further investigated. Our lab has discovered several dsRNAs that are effectively viral genomes. One of these viruses has been characterized and is tentatively named Phytophthora infestans RNA virus 4 (PiRV-4). PiRV-4 has a 3.00 kb genome with one open reading frame (ORF) coding for a supergroup 2 RNA-dependent RNA polymerase (RdRp). Based on sequence and phylogenetic comparisons, PiRV-4 is most similar to a linear 20S RNA (2.5 kb) narnavirus found in Saccharomyces cerevisiae. No virus sequence was found in the P. infestans genome. PiRV-4 could not be cured from the P. infestans host after three generations of growth on antiviral media; it is still not clear if the virus is affecting the pathogenicity of its host. PiRV-4 is designated as a new member of the genus Narnavirus in the family Narnaviridae