MicroRNA regulation below zero: differential expression of miRNA-21 and miRNA-16 during freezing in wood frogs

Ice in the intertidal: patterns and processes of freeze tolerance in intertidal invertebrates

Many intertidal invertebrates are freeze tolerant, meaning that they can survive ice formation within their body cavity. Freeze tolerance is a fascinating trait, and understanding its mechanisms is important for predicting the survival of intertidal animals during extreme cold weather events. In this Review, we bring together current research on the ecology, biochemistry and physiology of this group of freeze-tolerant organisms. We first introduce the ecology of the intertidal zone, then highlight the strong geographic and taxonomic biases within the current body of literature on this topic. Next, we detail current knowledge on the mechanisms of freeze tolerance used by intertidal invertebrates. Although the mechanisms of freeze tolerance in terrestrial arthropods have been well-explored, marine invertebrate freeze tolerance is less well understood and does not appear to work similarly because of the osmotic differences that come with living in seawater. Freeze tolerance mechanisms thought to be utilized by intertidal invertebrates include: (1) low molecular weight cryoprotectants, such as compatible osmolytes and anaerobic by-products; (2) high molecular weight cryoprotectants, such as ice-binding proteins; as well as (3) other molecular mechanisms involving heat shock proteins and aquaporins. Lastly, we describe untested hypotheses, methods and approaches that researchers can use to fill current knowledge gaps. Understanding the mechanisms and consequences of freeze tolerance in the intertidal zone has many important ecological implications, but also provides an opportunity to broaden our understanding of the mechanisms of freeze tolerance more generally.

Differential Mitochondrial Genome Expression of Four Hylid Frog Species under Low-Temperature Stress and Its Relationship with Amphibian Temperature Adaptation

Extreme weather poses huge challenges for animals that must adapt to wide variations in environmental temperature and, in many cases, it can lead to the local extirpation of populations or even the extinction of an entire species. Previous studies have found that one element of amphibian adaptation to environmental stress involves changes in mitochondrial gene expression at low temperatures. However, to date, comparative studies of gene expression in organisms living at extreme temperatures have focused mainly on nuclear genes. This study sequenced the complete mitochondrial genomes of five Asian hylid frog species: Dryophytes japonicus, D. immaculata, Hyla annectans, H. chinensis and H. zhaopingensis. It compared the phylogenetic relationships within the Hylidae family and explored the association between mitochondrial gene expression and evolutionary adaptations to cold stress. The present results showed that in D. immaculata, transcript levels of 12 out of 13 mitochondria genes were significantly reduced under cold exposure (p < 0.05); hence, we put forward the conjecture that D. immaculata adapts by entering a hibernation state at low temperature. In H. annectans, the transcripts of 10 genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, COX1, COX2 and ATP8) were significantly reduced in response to cold exposure, and five mitochondrial genes in H. chinensis (ND1, ND2, ND3, ND4L and ATP6) also showed significantly reduced expression and transcript levels under cold conditions. By contrast, transcript levels of ND2 and ATP6 in H. zhaopingensis were significantly increased at low temperatures, possibly related to the narrow distribution of this species primarily at low latitudes. Indeed, H. zhaopingensis has little ability to adapt to low temperature (4 °C), or maybe to enter into hibernation, and it shows metabolic disorder in the cold. The present study demonstrates that the regulatory trend of mitochondrial gene expression in amphibians is correlated with their ability to adapt to variable climates in extreme environments. These results can predict which species are more likely to undergo extirpation or extinction with climate change and, thereby, provide new ideas for the study of species extinction in highly variable winter climates.

Sperm Cryopreservation Today: Approaches, Efficiency, and Pitfalls

The cryopreservation of human spermatozoa has been an option for patients undergoing chemo or radiotherapies since the late 1950s. Presently, there are different techniques for the cryopreservation of spermatozoa. The most commonly used techniques are programmable slow freezing and freezing on liquid nitrogen vapors, while the use of vitrification is still not accepted as clinically relevant. Although there have been many improvements, the ideal technique for achieving better post-thaw sperm quality continues to be a mystery. A major obstacle during cryopreservation is the formation of intracellular ice crystals. Cryodamage generated by cryopreservation causes structural and molecular alterations in spermatozoa. Injuries can happen because of oxidative stress, temperature stress, and osmotic stress, which then result in changes in the plasma membrane fluidity, motility, viability, and DNA integrity of the spermatozoa. To prevent cryodamage as much as possible, cryoprotectants are added, and in some clinical trial cases, even antioxidants that may improve post-thaw sperm quality are added. This review discusses cryopreservation techniques, cryodamage on molecular and structural levels, and cryoprotectants. It provides a comparison of cryopreservation techniques and describes recent advances in those techniques.

Hepatic citrate synthase suppression in the freeze-tolerant wood frog (Rana sylvatica)

The wood frog, Rana sylvatica endures whole body freezing for weeks/months while overwintering at subzero temperatures. Survival of long-term freezing requires not only cryoprotectants but also strong metabolic rate depression (MRD) and reorganization of essential processes in order to maintain a balance between ATP-producing and ATP-consuming processes. Citrate synthase (CS) (E.C. 2.3.3.1) is an important irreversible enzyme of the tricarboxylic acid (TCA) cycle and forms a crucial checkpoint for many metabolic processes. Present study investigated the regulation of CS from wood frog liver during freezing. CS was purified to homogeneity by a two-step chromatographic process. Kinetic and regulatory parameters of the enzyme were investigated and, notably, demonstrated a significant decrease in the V_max of the purified form of CS from frozen frogs as compared to controls when assayed at both 22 °C and 5 °C. This was further supported by a decrease in the maximum activity of CS from liver of frozen frogs. Immunoblotting also showed changes in posttranslational modifications with a significant decrease in threonine phosphorylation (by 49 %) for CS from frozen frogs. Taken together, these results suggest that CS is suppressed and TCA flux is inhibited during freezing, likely to support MRD survival of harsh winters.

Hayvanlarda Soğuğa Dayanıklılık: Çift Yaşarların Kriyobiyolojisi

Organizmalar yaşamlarını devam ettirebilmek için abiyotik çevresel koşullara uyum sağlarlar. Özellikle ortam sıcaklığındaki değişimler; canlıların beslenme, üreme, gelişim ve morfolojileri üzerinde etkilidir. Sıra dışı sıcaklık değişimleri özellikle ektotermik hayvanlar için ölümcül olabilir. Karasal ektotermler. doğada donma noktasının altındaki sıcaklıklarda hayatta kalabilmek için davranışsal, fizyolojik ve biyokimyasal bazı özel stratejiler geliştirmişlerdir. Bazı türler göç ederek su ya da toprak altında kış uykusuna yatmak suretiyle dondurucu sıcaklıklardan kaçınırlar. Bazıları ise donma koşullarına maruz kalarak kışı geçirmek zorundadırlar. Genel olarak dondurucu soğuğa dayanıklılık donmadan kaçınma (süper soğuma) ve donma toleransı stratejilerine bağlıdır. Donmadan kaçınma durumunda vücut sıvılarının donma noktasının altındaki sıcaklıklarda sıvı formu korunurken donma toleransı stratejisini kullanan canlılarda ise vücutlarındaki toplam suyun %50’sinden fazlasının donması tolere edilebilir. Karasal hibernatör hayvanlardan bazı amfibi ve sürüngen gruplarında da tespit edilen donma toleransı stratejisi onların dondurucu kış koşullarında hayatta kalmalarını sağlamaktadır. Bu özel türler kriyoprotektif mekanizmaları ile donmanın ölümcül etkilerinden korunurlar. Donma süresince yaşamsal faaliyetleri tamamen duran bu hayvanlar çözündükten sonra kısa bir süre içerisinde de normal yaşama dönerler. Bu mucizevi mekanizmanın araştırılması yalnızca hayvanların karmaşık adaptasyonunu açıklamakla kalmaz, aynı zamanda doku ve hücre kriyoprezervasyon teknolojisine de kaynak sağlar. Bu derleme amfibilerin donma toleransı stratejilerine dair bilgiler sunarak henüz yeterince çalışılmamış bu konuda araştırma yapmak isteyenlere katkı sağlayacaktır.

Lessons from nature: Leveraging the freeze-tolerant wood frog as a model to improve organ cryopreservation and biobanking

The freeze-tolerant wood frog, Rana sylvatica, is one of the very few vertebrate species known to endure full body freezing in winter and thaw in early spring without any significant sign of damage. Once frozen, wood frogs show no cardiac or lung activity, brain function, or physical movement yet resume full physiological and biochemical functions within hours after thawing. The miraculous ability to tolerate such extreme stresses makes wood frogs an attractive model for identifying the molecular mechanisms that can promote freeze/thaw endurance. Recapitulating these pro-survival strategies in transplantable human cells and organs could improve viability post-thaw leading to better post-transplant outcomes, in addition to providing more time for adequate distribution of these transplantable materials across larger geographical areas. Indeed, several laboratories are beginning to mimic the pro-survival responses observed in wood frogs to preservation of human cells, tissues and organs and, to date, a few trials have been successful in extending preservation time prior to transplantation. In this review, we discuss the biology of the freeze-tolerant wood frog, current advances in biobanking based on these animals, and extend our discussion to future prospects for cryopreservation as an aid to regenerative medicine.

Regulation of Apoptosis and Autophagy During Anoxia in the Freshwater Crayfish, Faxonius virilis

The ability of an animal to survive prolonged periods of oxygen deprivation is a critical area of study, both in terms of its importance to better understanding the physiology of these incredible animals and to its potential applicability to medical fields. The freshwater crayfish, Faxonius virilis, is one such animal capable of resisting anoxia, but it remains understudied and much of the metabolic mechanisms underlying this anoxia tolerance remain largely unprofiled. This study examines the activity and regulation of apoptosis and autophagy in F. virilis in response to 20-h anoxia. Apoptosis signaling was assessed through pro- and anti-apoptosis targets, whereas autophagy was assessed via expression response of multiple autophagy proteins. An anoxia-triggered, tissue-specific result arose, potentially based on the importance of individual organ integrity through hypometabolism. Tail muscle, which showed increased expression profiles of all three target groups, contrasted with hepatopancreas, which appeared to not be susceptible to either apoptotic or autophagic signaling during anoxia. This is likely due to the importance of the hepatopancreas, given that apoptosis or autophagy of this organ at any significant level could be fatal to the organism. The data provides a comprehensive overview of the responses and integration of multiple stress-responsive signaling pathways in F. virilis that provide a novel contribution to our understanding of pro-survival mechanisms supporting invertebrate anoxia resistance.

Mitochondrial gene expression in different organs of Hoplobatrachus rugulosus from China and Thailand under low-temperature stress

Background

Hoplobatrachus rugulosus (Anura: Dicroglossidae) is distributed in China and Thailand and the former can survive substantially lower temperatures than the latter. The mitochondrial genomes of the two subspecies also differ: Chinese tiger frogs (CT frogs) display two identical ND5 genes whereas Thai tiger frogs (TT frogs) have two different ND5 genes. Metabolism of ectotherms is very sensitive to temperature change and different organs have different demands on energy metabolism at low temperatures. Therefore, we conducted studies to understand: (1) the differences in mitochondrial gene expression of tiger frogs from China (CT frogs) versus Thailand (TT frogs); (2) the differences in mitochondrial gene expression of tiger frogs (CT and TT frogs) under short term 24 h hypothermia exposure at 25 °C and 8 °C; (3) the differences in mitochondrial gene expression in three organs (brain, liver and kidney) of CT and TT frogs.

Results

Utilizing RT-qPCR and comparing control groups at 25 °C with low temperature groups at 8 °C, we came to the following results. (1) At the same temperature, mitochondrial gene expression was significantly different in two subspecies. The transcript levels of two identical ND5 of CT frogs were observed to decrease significantly at low temperatures (P < 0.05) whereas the two different copies of ND5 in TT frogs were not. (2) Under low temperature stress, most of the genes in the brain, liver and kidney were down-regulated (except for COI and ATP6 measured in brain and COI measured in liver of CT frogs). (3) For both CT and TT frogs, the changes in overall pattern of mitochondrial gene expression in different organs under low temperature and normal temperature was brain > liver > kidney.

Conclusions

We mainly drew the following conclusions: (1) The differences in the structure and expression of the ND5 gene between CT and TT frogs could result in the different tolerances to low temperature stress. (2) At low temperatures, the transcript levels of most of mitochondrial protein-encoding genes were down-regulated, which could have a significant effect in reducing metabolic rate and supporting long term survival at low temperatures. (3) The expression pattern of mitochondrial genes in different organs was related to mitochondrial activity and mtDNA replication in different organs.

Pro- and anti-apoptotic microRNAs are differentially regulated during estivation in Xenopus laevis

Xenopus laevis, the African clawed frog, undergoes seasonal estivation to survive periods of drought when its lake-bed habitats dry up. The frog can lose ∼30% of its total body water, leading to conditions of impaired blood flow and ischemia which risk cellular survival under these harsh conditions. MicroRNAs are short, noncoding, single-stranded RNAs 21-24 nt long that have been widely implicated in hypometabolic responses, and serve functions including apoptosis survival. The levels of three pro-apoptotic and four anti-apoptotic miRNAs were measured in liver and skeletal muscle of estivating X. laevis, and bioinformatic analysis was performed to verify potential mRNA targets of these miRNAs. Members of pro-apoptotic miRNAs miR-15a, miR-16, and miR-101 showed upregulation as a result of dehydration stress, while anti-apoptotic miRNAs miR-19b, miR-21, miR-92a, and miR-155 showed differential regulation between the two tissues. Together, these miRNAs act in a more diverse fashion than arbitrarily pro- or anti-apoptotic, and encompass functions ranging from the inhibition of cell proliferation through cell cycle arrest to the prevention of skeletal muscle atrophy.

Role of MicroRNAs in Extreme Animal Survival Strategies

The critical role microRNAs play in modulating global functions is emerging, both in the maintenance of homeostatic mechanisms and in the adaptation to diverse environmental stresses. When stressed, cells must divert metabolic requirements toward immediate survival and eventual recovery and the unique features of miRNAs, such as their relatively ATP-inexpensive biogenesis costs, and the quick and reversible nature of their action, renders them excellent "master controllers" for rapid responses. Many animal survival strategies for dealing with extreme environmental pressures involve prolonged retreats into states of suspended animation to extend the time that they can survive on their limited internal fuel reserves until conditions improve. The ability to retreat into such hypometabolic states is only possible by coupling the global suppression of nonessential energy-expensive functions with an activation of prosurvival networks, a process in which miRNAs are now known to play a major role. In this chapter, we discuss the activation, expression, biogenesis, and unique attributes of miRNA regulation required to facilitate profound metabolic rate depression and implement stress-specific metabolic adaptations. We examine the role of miRNA in strategies of biochemical adaptation including mammalian hibernation, freeze tolerance, freeze avoidance, anoxia and hypoxia survival, estivation, and dehydration tolerance. By comparing these seemingly different adaptive programs in traditional and exotic animal models, we highlight both unique and conserved miRNA-meditated mechanisms for survival. Additional topics discussed include transcription factor networks, temperature dependent miRNA-targeting, and novel species-specific and stress-specific miRNAs.

MicroRNA Cues from Nature: A Roadmap to Decipher and Combat Challenges in Human Health and Disease?

MicroRNAs are small non-coding RNA (18–24 nt long) that fine-tune gene expression at the post-transcriptional level. With the advent of “multi-omics” analysis and sequencing approaches, they have now been implicated in every facet of basic molecular networks, including metabolism, homeostasis, and cell survival to aid cellular machinery in adapting to changing environmental cues. Many animals must endure harsh environmental conditions in nature, including cold/freezing temperatures, oxygen limitation (anoxia/hypoxia), and food or water scarcity, often requiring them to revamp their metabolic organization, frequently on a seasonal or life stage basis. MicroRNAs are important regulatory molecules in such processes, just as they are now well-known to be involved in many human responses to stress or disease. The present review outlines the role of miRNAs in natural animal models of environmental stress and adaptation including torpor/hibernation, anoxia/hypoxia tolerance, and freeze tolerance. We also discuss putative medical applications of advances in miRNA biology including organ preservation for transplant, inflammation, ageing, metabolic disorders (e.g., obesity), mitochondrial dysfunction (mitoMirs) as well as specialized miRNA subgroups respective to low temperature (CryomiRs) and low oxygen (OxymiRs). The review also covers differential regulation of conserved and novel miRNAs involved at cell, tissue, and stress specific levels across multiple species and their roles in survival. Ultimately, the species-specific comparison and conserved miRNA responses seen in evolutionarily disparate animal species can help us to understand the complex miRNA network involved in regulating and reorganizing metabolism to achieve diverse outcomes, not just in nature, but in human health and disease.

Implications of cryopreservation on structural and functional attributes of bovine spermatozoa: An overview

Sperm cryopreservation is an important adjunct to assisted reproduction techniques (ART) for improving the reproductive efficiency of dairy cattle and buffaloes. Improved understanding of mechanisms and challenges of bovine semen cryopreservation is vital for artificial insemination on a commercial basis. Although cryopreservation of bovine spermatozoa is widely practiced and advanced beyond that of other species, there are still major gaps in the knowledge and technology. Upon cryopreservation, disruption of spermatozoal plasma membrane configuration due to alterations in metabolic pathways, enzymes and antioxidants activity add to lower efficiency with loss of sperm longevity and fertilising ability. Therefore, the effective amalgamation of cryo-variables like ambient temperature, cooling and thawing rates, nucleation temperature, type and concentration of the cryoprotectant, seminal plasma composition, free radicals and antioxidant status are required to optimise cryopreservation. Novel strategies like supplementation of cholesterol-loaded cyclodextrins (CLC), nanovesicles, osteopontin, antioxidants, etc., in an extender and recent techniques like nano-purification and modified packaging have to be optimised to ameliorate the cryodamage. This article is intended to describe the basic facts about the sperm cryopreservation process in bovine and the associated biochemical, biophysical, ultra-structural, molecular and functional alterations.

Molecular mechanism of Chinese alligator (Alligator sinensis) adapting to hibernation

Hibernation is a physiological state for Chinese alligators to cope with cold weather. In mammals, gene expression changes during hibernation and their regulatory mechanisms have been extensively studied, however, these studies in reptiles are still rare. Here, integrated analysis of messenger RNA (mRNA), microRNA (miRNA), and long noncoding RNA (lncRNA) reveals the molecular mechanisms of the hypothalamus, liver, and skeletal muscle in hibernating and active individuals. During hibernation, the number of genes increased in the hypothalamus, liver, and skeletal muscle was 585, 282, and 297, while the number of genes decreased was 215, 561, and 627, respectively, as compared with active individuals. Through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, the differential expressed genes were mainly enriched in DNA damage repair, biological rhythm, energy metabolism, myoprotein degradation, and other related items and pathways. Besides, 4740 miRNAs were identified in three tissues. Through the comprehensive analysis of miRNA and mRNA abundance profiles, 12,291, 6997, and 8232 miRNA-mRNA pairs all showed a negative correlation in the hypothalamus, liver, and skeletal muscle, respectively. Some miRNA target genes were related tobiological rhythm and energy metabolism, suggesting that miRNA may play an important role in the physiological metabolism of the hibernating adaptability of Chinese alligators. Moreover, 402, 230, and 130 differentially expressed lncRNAs were identified in the hypothalamus, liver, and skeletal muscle, respectively. The targeting relationship of four lncRNA-mRNA pairs were predicted, with the main function of target genes involved in the amino acid transportation. These results are helpful to further understand the molecular regulatory basis of the hibernation adaptation in Chinese alligators.

Mitochondria, metabolic control and microRNA: Advances in understanding amphibian freeze tolerance

Winter survival for many animal species depends freeze tolerance, a capacity to endure the conversion of as much as 65-70% of total body water into extracellular ice while reorganizing metabolism to provide cells with cryoprotection against insults that include prolonged ischemia and hyperosmotic stress. Natural freeze tolerance involves not just de novo preservation mechanisms such as synthesis of high levels of cryoprotectants or novel proteins that manage ice formation, but also requires attention to and co-ordination of many cellular processes. The present review examines recent studies of the freeze-tolerant wood frog (Rana sylvatica) that probed previously unexplored areas of metabolic adaptation for freezing survival, with a particular emphasis on mitochondria. Post-translational controls on enzyme function play a prominent role in resculpting metabolic responses of the wood frog to freezing including reversible phosphorylation control over fuel processing at the pyruvate dehydrogenase locus and modulation of antioxidant defense enzymes (Mn-SOD, catalase). Enzymes involved in mitochondrial nitrogen metabolism (glutamate dehydrogenase, carbamoyl phosphate synthetase) are also differentially regulated during freezing but by different post-translational modifications including ADP-ribosylation, lysine acetylation or glutarylation. The action of microRNAs in mediating post-translational controls on gene expression aid the suppression of energy-expensive (cell cycle) or destructive (apoptosis) processes in the frozen state while also providing storage of transcripts that will be immediately available for repair or reactivation of metabolic processes after thawing. The effects of low temperature in strengthening mRNA-microRNA interactions can also provide a passive mechanism of metabolic suppression in the frozen state.

Functional impact of microRNA regulation in models of extreme stress adaptation

When confronted with severe environmental stress, some animals are able to undergo a substantial reorganization of their cellular environment that enables long-term survival. One molecular mechanism of adaptation that has received considerable attention in recent years has been the action of reversible transcriptome regulation by microRNA. The implementation of new computational and high-throughput experimental approaches has started to uncover the vital contributions of microRNA towards stress adaptation. Indeed, recent studies have suggested that microRNA may have a major regulatory influence over a number of cellular processes that are essential to prolonged environmental stress survival. To date, a number of studies have highlighted the role of microRNA in the regulation of a metabolically depressed state, documenting stress-responsive microRNA expression during mammalian hibernation, frog and insect freeze tolerance, and turtle and marine snail anoxia tolerance. These studies collectively indicate a conserved principle of microRNA stress response across phylogeny. As we are on the verge of dissecting the role of microRNA in environmental stress adaptation, this review summarizes recent research advances and the hallmark expression patterns that facilitate stress survival.

The potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber

The sea cucumber (Apostichopus japonicus) has become a good model organism for studying environmentally-induced aestivation by a marine invertebrate more recently. In the present study, we hypothesized that miRNA-200-3p may contribute to establish rapid biological control to regulate fatty acid metabolism during a estivation. The peroxisomal bi-functional enzyme (EHHADH) is a crucial participant of the classical peroxisomal fatty acid β-oxidation pathway, the relative mRNA transcripts and protein expressions of EHHADH were analyzed in intestine from sea cucumbers experienced long-term aestivation. Both mRNA transcripts and protein expressions of EHHADH in intestine decreased significantly during deep-aestivation as compared with non-aestivation controls. Analysis of the 3′ UTR of AjEHHADH showed the presence of a conserved binding site for miR-200-3p. Level of miR-200-3p showed an inverse correlation with EHHADH mRNA transcripts and protein levels in intestine, implicating miR-200-3p may directly targeted AjEHHADH by inducing the degradation of AjEHHADH mRNA in the aestivating sea cucumber, further dual-luciferase reporter assay validated the predicted role of miRNA-200-3p in regulating AjEHHADH. In order to further understand their regulatory mechanism, we conducted the functional experiment in vivo. The overexpression of miR-200-3p in sea cucumber significantly decreased mRNA and protein expression levels of AjEHHADH. Taken together, these findings suggested the potential contribution of miRNA-200-3p to the fatty acid metabolism by regulating AjEHHADH during aestivation in sea cucumber.

Micromanaging freeze tolerance: the biogenesis and regulation of neuroprotective microRNAs in frozen brains

When temperatures plummet below 0 °C, wood frogs (Rana sylvatica) can endure the freezing of up to ~ 65% of their body water in extracellular ice masses, displaying no measurable brain activity, no breathing, no movement, and a flat-lined heart. To aid survival, frogs retreat into a state of suspended animation characterized by global suppression of metabolic functions and reprioritization of energy usage to essential survival processes that is elicited, in part, by the regulatory controls of microRNAs. The present study is the first to investigate miRNA biogenesis and regulation in the brain of a freeze tolerant vertebrate. Indeed, proper brain function and adaptations to environmental stimuli play a crucial role in coordinating stress responses. Immunoblotting of miRNA biogenesis factors illustrated an overall reduction in the majority of these processing proteins suggesting a potential suppression of miRNA maturation over the freeze-thaw cycle. This was coupled with a large-scale RT-qPCR analysis of relative expression levels of 113 microRNA species in the brains of control, 24 h frozen, and 8 h thawed R. sylvatica. Of the 41 microRNAs differentially regulated during freezing and thawing, only two were significantly upregulated. Bioinformatic target enrichment of the downregulated miRNAs, performed at the low temperatures experienced during freezing and thawing, predicted their involvement in the potential activation of various neuroprotective processes such as synaptic signaling, intracellular signal transduction, and anoxia/ischemia injury protection. The predominantly downregulated microRNA fingerprint identified herein suggests a microRNA-mediated cryoprotective mechanism responsible for maintaining neuronal functions and facilitating successful whole brain freezing and thawing.

MicroRNAs regulate survival in oxygen-deprived environments

Some animals must endure prolonged periods of oxygen deprivation to survive. One such extreme model is the Northern Crayfish (Orconectes virilis), that regularly survives year-round hypoxic and anoxic stresses in its warm stagnant summer waters and in its cold, ice-locked winter waters. To elucidate the molecular underpinnings of anoxia-resistance in this natural model, we surveyed the expression profiles of 76 highly-conserved microRNAs in crayfish hepatopancreas and tail muscle from normoxic, acute 2hr anoxia, and chronic 20hr anoxia exposures. MicroRNAs are known to regulate a diverse array of cellular functions required for environmental stress adaptations, and here we explore their role in anoxia tolerance. The tissue-specific anoxia responses observed herein, with 22 anoxia-responsive microRNAs in hepatopancreas and only 4 changing microRNAs in muscle, suggest that microRNAs facilitate a reprioritization of resources to preserve crucial organ functions. Bioinformatic microRNA target enrichment analysis predicted that the anoxia-downregulated microRNAs in hepatopancreas targeted hippo-signalling, suggesting that cell proliferation and apoptotic signalling are highly regulated in this liver-like organ during anoxia. Compellingly, miR-125-5p, miR-33-5p, and miR-190-5p, all known to target the master regulator of oxygen deprivation responses HIF1 (Hypoxia Inducible Factor-1), were anoxia-downregulated in hepatopancreas. The anoxia-increased transcript levels of the oxygen dependent subunit HIF1α, highlight a potential critical role for miRNA-HIF targeting in facilitating a successful anoxia response. Studying the cytoprotective mechanisms in place to protect against the challenges associated with surviving in oxygen-poor environments is critical to elucidating microRNAs’ vast and substantial role in the regulation of metabolism and stress in aquatic invertebrates.

The role of MEF2 transcription factors in dehydration and anoxia survival in Rana sylvatica skeletal muscle

The wood frog (Rana sylvatica) can endure freezing of up to 65% of total body water during winter. When frozen, wood frogs enter a dormant state characterized by a cessation of vital functions (i.e., no heartbeat, blood circulation, breathing, brain activity, or movement). Wood frogs utilize various behavioural and biochemical adaptations to survive extreme freezing and component anoxia and dehydration stresses, including a global suppression of metabolic functions and gene expression. The stress-responsive myocyte enhancer factor-2 (MEF2) transcription factor family regulates the selective expression of genes involved in glucose transport, protein quality control, and phosphagen homeostasis. This study examined the role of MEF2A and MEF2C proteins as well as select downstream targets (glucose transporter-4, calreticulin, and muscle and brain creatine kinase isozymes) in 40% dehydration and 24 h anoxia exposure at the transcriptional, translational, and post-translational levels using qRT-PCR, immunoblotting, and subcellular localization. Mef2a/c transcript levels remained constant during dehydration and anoxia. Total, cytoplasmic, and nuclear MEF2A/C and phospho-MEF2A/C protein levels remained constant during dehydration, whereas a decrease in total MEF2C levels was observed during rehydration. Total and phospho-MEF2A levels remained constant during anoxia, whereas total MEF2C levels decreased during 24 h anoxia and P-MEF2C levels increased during 4 h anoxia. In contrast, cytoplasmic MEF2A levels and nuclear phospho-MEF2A/C levels were upregulated during anoxia. MEF2 downstream targets remained constant during dehydration and anoxia, with the exception of glut4 which was upregulated during anoxia. These results suggest that the upregulated MEF2 response reported in wood frogs during freezing may in part stem from their cellular responses to surviving prolonged anoxia, rather than dehydration, leading to an increase in GLUT4 expression which may have an important role during anoxia survival.

Small noncoding RNA expression during extreme anoxia tolerance of annual killifish (Austrofundulus limnaeus) embryos

Small noncoding RNAs (sncRNA) have recently emerged as specific and rapid regulators of gene expression, involved in a myriad of cellular and organismal processes. MicroRNAs, a class of sncRNAs, are differentially expressed in diverse taxa in response to environmental stress, including anoxia. In most vertebrates, a brief period of oxygen deprivation results in severe tissue damage or death. Studies on sncRNA and anoxia have focused on these anoxia-sensitive species. Studying sncRNAs in anoxia-tolerant organisms may provide insight into adaptive mechanisms supporting anoxia tolerance. Embryos of the annual killifish Austrofundulus limnaeus are the most anoxia-tolerant vertebrates known, surviving over 100 days at their peak tolerance at 25°C. Their anoxia tolerance and physiology vary over development, such that both anoxia-tolerant and anoxia-sensitive phenotypes comprise the species. This allows for a robust comparison to identify sncRNAs essential to anoxia-tolerance. For this study, RNA sequencing was used to identify and quantify expression of sncRNAs in four embryonic stages of A. limnaeus in response to an exposure to anoxia and subsequent aerobic recovery. Unique stage-specific patterns of expression were identified that correlate with anoxia tolerance. In addition, embryos of A. limnaeus appear to constitutively express stress-responsive miRNAs. Most differentially expressed sncRNAs were expressed at higher levels during recovery. Many novel groups of sncRNAs with expression profiles suggesting a key role in anoxia tolerance were identified, including sncRNAs derived from mitochondrial tRNAs. This global analysis has revealed groups of candidate sncRNAs that we hypothesize support anoxia tolerance.

Stress-responsive microRNAs are involved in re-programming of metabolic functions in hibernators

Mammalian hibernation includes re-programing of metabolic capacities, partially, encouraged by microRNAs (miRNAs). Albeit much is known about the functions of miRNAs, we need learning on low temperature miRNAs target determination. As hibernators can withstand low body temperatures (TB) for a long time without anguish tissue damage, understanding the means and mechanisms that empower them to do as such are of restorative intrigue. Nonetheless, these mechanisms by which miRNAs and the hibernators react to stressful conditions are not much clear. It is evident from recent data that the gene expression and the translation of mRNA to protein are controlled by miRNAs. The miRNAs also influence regulation of major cellular processes. As the significance of miRNAs in stress conditions adaptation are getting clearer, this audit article abridges the key alterations in miRNA expression and the mechanism that facilitates stress survival.

Transiently expressed pattern during myogenesis and candidate miRNAs of Tmem8C in goose

Transmembrane protein 8C (Tmem8C) is a muscle-specific membrane protein that controls myoblast fusion, which is essential for the formation of multinucleated muscle fibres. As most of the birds can fly, they have enormous requirement for the muscle, but there are only a few studies of Tmem8C in birds. In this study, we obtained the coding sequence (CDS) of Tmem8C in goose, predicted miRNAs that can act on the 3'UTR, analysed expression profiles of this gene in breast and leg muscles (BM and LM) during the embryonic period and neonatal stages, and identified miRNAs that might affect the targeted gene. The results revealed a high homology between Tmem8C in goose and other animals (indicated by sequence comparisons and phylogenetic trees), some conservative characteristics (e.g., six transmembrane domains and two E-boxes in the 5'UTR might be the potential binding sites of muscle regulatory factors (MRFs)), and the d_N/d_S ratio indicated purifying selection acting on this gene, facilitating conservatism in vertebrates. Q-PCR indicated Tmem8C had a peak expression pattern, reaching its highest expression levels in stage E15 in LM and E19 in BM, and then dropping transiently in E23 (P < 0.05). We examined 13 candidate miRNAs, and negative relationships were detected both in BM and LM (mir-125b-5p, mir-15a, mir-16-1 and mir-n23). Notably, mir-16-1 significantly decreased luciferase activity in dual luciferase reporter gene (LRG) assay, suggesting that it can be identified as potential factors affecting Tmem8C. This study investigated Tmem8C in water bird for the first time, and provided useful information about this gene and its candidate miRNAs in goose.

Molecular Physiology of Freeze Tolerance in Vertebrates

Freeze tolerance is an amazing winter survival strategy used by various amphibians and reptiles living in seasonally cold environments. These animals may spend weeks or months with up to ∼65% of their total body water frozen as extracellular ice and no physiological vital signs, and yet after thawing they return to normal life within a few hours. Two main principles of animal freeze tolerance have received much attention: the production of high concentrations of organic osmolytes (glucose, glycerol, urea among amphibians) that protect the intracellular environment, and the control of ice within the body (the first putative ice-binding protein in a frog was recently identified), but many other strategies of biochemical adaptation also contribute to freezing survival. Discussed herein are recent advances in our understanding of amphibian and reptile freeze tolerance with a focus on cell preservation strategies (chaperones, antioxidants, damage defense mechanisms), membrane transporters for water and cryoprotectants, energy metabolism, gene/protein adaptations, and the regulatory control of freeze-responsive hypometabolism at multiple levels (epigenetic regulation of DNA, microRNA action, cell signaling and transcription factor regulation, cell cycle control, and anti-apoptosis). All are providing a much more complete picture of life in the frozen state.

Identification of cold-responsive miRNAs in rats by deep sequencing

miRNA is an endogenously noncoding sRNA, which is involved in post-transcription gene expression regulation of growth, tumor development and stress survival. As a biological marker, miRNA has been used for the early diagnosis of diseases and the evaluation of some physiological state. We constructed two small RNA libraries with the serums of rats treated or not with cold conditions (4℃ for 12h) by deep sequencing, in order to understand the miRNAs' expressions of cold-exposed rats and find new cold-responsive biological markers. 485 conserved miRNAs and 287 novel miRNAs were identified in the two libraries by comparing to the known miRNAs of rat in miRBase 21.0 Differential expression analysis showed that 56 conserved miRNAs and 3 novel miRNAs were expressed differentially in low ambient temperature. The qRT-PCR results confirmed that rno-miR-151-3p, rno-miR-210-3p, rno-miR-425-5p, rno-miR-383-5p, rno-miR-92a-3p, rno-miR-98-5p and rno-miR-328a-3p decreased significantly in rats serums treated with cold exposure. The expressions of the 7 miRNAs changed significantly in cold-exposed rats' livers too. rno-miR-383-5p decreased significantly, but all the others increased significantly. Thus, the 7 miRNAs were considered as cold-responsive miRNAs of rat. 670 target genes of the 7 cold-responsive miRNAs were predicted. KEGG analysis showed that they were enriched in 28 pathways and most of them were enriched by metabolic pathway. Overall, the results of this study suggest an important role for selected miRNA's in the response to cold stress.

Lessons from mammalian hibernators: molecular insights into striated muscle plasticity and remodeling

Striated muscle shows an amazing ability to adapt its structural apparatus based on contractile activity, loading conditions, fuel supply, or environmental factors. Studies with mammalian hibernators have identified a variety of molecular pathways which are strategically regulated and allow animals to endure multiple stresses associated with the hibernating season. Of particular interest is the observation that hibernators show little skeletal muscle atrophy despite the profound metabolic rate depression and mechanical unloading that they experience during long weeks of torpor. Additionally, the cardiac muscle of hibernators must adjust to low temperature and reduced perfusion, while the strength of contraction increases in order to pump cold, viscous blood. Consequently, hibernators hold a wealth of knowledge as it pertains to understanding the natural capacity of myocytes to alter structural, contractile and metabolic properties in response to environmental stimuli. The present review outlines the molecular and biochemical mechanisms which play a role in muscular atrophy, hypertrophy, and remodeling. In this capacity, four main networks are highlighted: (1) antioxidant defenses, (2) the regulation of structural, contractile and metabolic proteins, (3) ubiquitin proteosomal machinery, and (4) macroautophagy pathways. Subsequently, we discuss the role of transcription factors nuclear factor (erythroid-derived 2)-like 2 (Nrf2), Myocyte enhancer factor 2 (MEF2), and Forkhead box (FOXO) and their associated posttranslational modifications as it pertains to regulating each of these networks. Finally, we propose that comparing and contrasting these concepts to data collected from model organisms able to withstand dramatic changes in muscular function without injury will allow researchers to delineate physiological versus pathological responses.

Up-regulation of Long Non-coding RNA TUG1 in Hibernating Thirteen-lined Ground Squirrels

Mammalian hibernation is associated with multiple physiological, biochemical, and molecular changes that allow animals to endure colder temperatures. We hypothesize that long non-coding RNAs (lncRNAs), a group of non-coding transcripts with diverse functions, are differentially expressed during hibernation. In this study, expression levels of lncRNAsH19 and TUG1 were assessed via qRT-PCR in liver, heart, and skeletal muscle tissues of the hibernating thirteen-lined ground squirrels (Ictidomys tridecemlineatus). TUG1 transcript levels were significantly elevated 1.94-fold in skeletal muscle of hibernating animals when compared with euthermic animals. Furthermore, transcript levels of HSF2 also increased 2.44-fold in the skeletal muscle in hibernating animals. HSF2 encodes a transcription factor that can be negatively regulated by TUG1 levels and that influences heat shock protein expression. Thus, these observations support the differential expression of the TUG1–HSF2 axis during hibernation. To our knowledge, this study provides the first evidence for differential expression of lncRNAs in torpid ground squirrels, adding lncRNAs as another group of transcripts modulated in this mammalian species during hibernation.

Analysis of microRNA expression during the torpor-arousal cycle of a mammalian hibernator, the 13-lined ground squirrel

Hibernation is a highly regulated stress response that is utilized by some mammals to survive harsh winter conditions and involves a complex metabolic reprogramming at the cellular level to maintain tissue protections at low temperature. In this study, we profiled the expression of 117 conserved microRNAs in the heart, muscle, and liver of the 13-lined ground squirrel (Ictidomys tridecemlineatus) across four stages of the torpor-arousal cycle (euthermia, early torpor, late torpor, and interbout arousal) by real-time PCR. We found significant differential regulation of numerous microRNAs that were both tissue specific and torpor stage specific. Among the most significant regulated microRNAs was miR-208b, a positive regulator of muscle development that was found to be upregulated by fivefold in the heart during late torpor (13-fold during arousal), while decreased by 3.7-fold in the skeletal muscle, implicating a potential regulatory role in the development of cardiac hypertrophy and skeletal muscle atrophy in the ground squirrels during torpor. In addition, the insulin resistance marker miR-181a was upregulated by 5.7-fold in the liver during early torpor, which supports previous suggestions of hyperinsulinemia in hibernators during the early stages of the hibernation cycle. Although microRNA expression profiles were largely unique between the three tissues, GO annotation analysis revealed that the putative targets of upregulated microRNAs tend to enrich toward suppression of progrowth-related processes in all three tissues. These findings implicate microRNAs in the regulation of both tissue-specific processes and general suppression of cell growth during hibernation.

Mammalian hibernation and regulation of lipid metabolism: a focus on non-coding RNAs

Numerous species will confront severe environmental conditions by undergoing significant metabolic rate reduction. Mammalian hibernation is one such natural model of hypometabolism. Hibernators experience considerable physiological, metabolic, and molecular changes to survive the harsh challenges associated with winter. Whether as fuel source or as key signaling molecules, lipids are of primary importance for a successful bout of hibernation and their careful regulation throughout this process is essential. In recent years, a plethora of non-coding RNAs has emerged as potential regulators of targets implicated in lipid metabolism in diverse models. In this review, we introduce the general characteristics associated with mammalian hibernation, present the importance of lipid metabolism prior to and during hibernation, as well as discuss the potential relevance of non-coding RNAs such as miRNAs and lncRNAs during this process.

Expression of miRNAs in response to freezing and anoxia stresses in the freeze tolerant fly Eurosta solidaginis

Insect cold hardiness is associated with substantial metabolic rate suppression, often including developmental diapause as well as metabolic suppression imposed by freezing and freeze-associated oxygen limitation. MicroRNAs, small non-coding transcripts that bind to mRNA, are known modulators of hypometabolism in freeze tolerant insects. To further contribute to the growing signature of stress-responsive miRNAs, this study amplified and quantified changes in the expression levels of four microRNA species, miR-8, miR-9, miR-92b and miR-277, in response to freezing or anoxia exposures of freeze tolerant gall fly larvae, Eurosta solidaginis. MiR-92b levels were significantly elevated by 1.57-fold in frozen E. solidaginis at -15°C as compared with 5°C controls, whereas miR-92b levels were significantly reduced in anoxic E. solidaginis to levels that were 0.77-fold as compared with larvae held under normoxic conditions. The other miRNAs investigated showed no significant changes in stressed larvae. These data demonstrate differential miR-92b expression in frozen/anoxic versus control insect larvae and position this miRNA as a stress responsive marker in this model insect.

Insight into post-transcriptional gene regulation: stress-responsive microRNAs and their role in the environmental stress survival of tolerant animals

Living animals are constantly faced with various environmental stresses that challenge normal life, including: oxygen limitation, very low or high temperature, as well as restriction of water and food. It has been well established that in response to these stresses, tolerant organisms regularly respond with a distinct suite of cellular modifications that involve transcriptional, translational and post-translational modification. In recent years, a new mechanism of rapid and reversible transcriptome regulation, via the action of non-coding RNA molecules, has emerged into post-transcriptional regulation and has since been shown to be part of the survival response. However, these RNA-based mechanisms by which tolerant organisms respond to stressed conditions are not well understood. Recent studies have begun to show that non-coding RNAs control gene expression and translation of mRNA to protein, and can also have regulatory influence over major cellular processes. For example, select microRNAs have been shown to have regulatory influence over the cell cycle, apoptosis, signal transduction, muscle atrophy and fatty acid metabolism during periods of environmental stress. As we are on the verge of dissecting the roles of non-coding RNA in environmental stress adaptation, this Commentary summarizes the hallmark alterations in microRNA expression that facilitate stress survival.

MicroRNA profiling of the intestine during hypothermic circulatory arrest in swine

AIM: To perform a profiling analysis of changes in intestinal microRNA (miRNA) expression during hypothermic circulatory arrest (HCA).

METHODS: A total of eight piglets were randomly divided into HCA and sham operation (SO) groups. Under general anesthesia, swine in the HCA group were subjected to hypothermic cardiopulmonary bypass at 24 °C followed by 80 min of circulatory arrest, and the reperfusion lasted for 180 min after cross-clamp removal. The counterparts in the SO group were only subjected to median sternotomy. Histopathological analysis was used to detect mucosal injury, and Pick-and-Mix custom miRNA real-time polymerase chain reaction (PCR) panels containing 306 unique primer sets were utilized to assay unpooled intestinal samples harvested from the two groups.

RESULTS: The intestinal mucosa of the animals that were subjected to 24 °C HCA exhibited representative ischemic reperfusion injury of grade 2 or 3 according to the Chiu score. Such intestinal mucosal injuries, with the subepithelial space and epithelial layer lifting away from the lamina propria, were accompanied by shortened and irregular villi. On the contrary, the intestinal mucosa remained normal in the sham-operated animals. In total, twenty-five miRNAs were differentially expressed between the two groups (15 upregulated and 10 downregulated in the HCA group). Among these, eight miRNAs (miR-122, miR-221-5p, miR-31, miR-421-5p, miR-4333, miR-499-3p, miR-542 and let-7d-3p) were significantly dysregulated (four higher and four lower). The expression of miR-122 was significantly (5.37-fold) increased in the HCA group vs the SO group, indicating that it may play a key role in HCA-induced mucosal injury.

CONCLUSION: Exposure to HCA caused intestinal miRNA dysregulation and barrier dysfunction in swine. These altered miRNAs might be related to the protection or destruction of the intestinal barrier.

Regulation of hypometabolism: insights into epigenetic controls

For many animals, survival of severe environmental stress (e.g. to extremes of heat or cold, drought, oxygen limitation, food deprivation) is aided by entry into a hypometabolic state. Strong depression of metabolic rate, often to only 1–20% of normal resting rate, is a core survival strategy of multiple forms of hypometabolism across the animal kingdom, including hibernation, anaerobiosis, aestivation and freeze tolerance. Global biochemical controls are needed to suppress and reprioritize energy use; one such well-studied control is reversible protein phosphorylation. Recently, we turned our attention to the idea that mechanisms previously associated mainly with epigenetic regulation can also contribute to reversible suppression of gene expression in hypometabolic states. Indeed, situations as diverse as mammalian hibernation and turtle anoxia tolerance show coordinated changes in histone post-translational modifications (acetylation, phosphorylation) and activities of histone deacetylases, consistent with their use as mechanisms for suppressing gene expression during hypometabolism. Other potential mechanisms of gene silencing in hypometabolic states include altered expression of miRNAs that can provide post-transcriptional suppression of mRNA translation and the formation of ribonuclear protein bodies in the nucleus and cytoplasm to allow storage of mRNA transcripts until animals rouse themselves again. Furthermore, mechanisms first identified in epigenetic regulation (e.g. protein acetylation) are now proving to apply to many central metabolic enzymes (e.g. lactate dehydrogenase), suggesting a new layer of regulatory control that can contribute to coordinating the depression of metabolic rate.

Forensic miRNA: potential biomarker for body fluids?

In forensic investigation, body fluids represent an important support to professionals when detected, collected and correctly identified. Through many years, various approaches were used, namely serology-based methodologies however, their lack of sensitivity and specificity became difficult to set aside. In order to sidetrack the problem, miRNA profiling surged with a real potential to be used to identify evidences like urine, blood, menstrual blood, saliva, semen and vaginal secretions. MiRNAs are small RNA structures with 20-25 nt whose proprieties makes them less prone to degradation processes when compared to mRNA which is extremely important once, in a crime scene, biological evidences might be exposed to several unfavorable environmental factors. Recently, published studies were able to identify some specific miRNAs, however their results were not always reproducible by others which can possibly be the reflection of different workflow strategies for their profiling studies. Given the current blast of interest in miRNAs, it is important to acknowledge potential limitations of miRNA profiling, yet, the lack of such studies are evident. This review pretends to gather all the information to date and assessed a multitude of factors that have a potential aptitude to discrediting miRNA profiling, such as: methodological approaches, environmental factors, physiological conditions, gender, pathologies and samples storage. It can be asserted that much has yet to be made, but we pretend to highlight a potential answer for the ultimate question: Can miRNA profiling be used as the forensic biomarker for body fluids identification?

New Approaches to Comparative and Animal Stress Biology Research in the Post-genomic Era: A Contextual Overview

Although much is known about the physiological responses of many environmental stresses in tolerant animals, studies evaluating the regulation of stress-induced mechanisms that regulate the transitions to and from this state are beginning to explore new and fascinating areas of molecular research. Current findings have developed a general, but refined, view of the important molecular pathways contributing to stress-survival. However, studies utilizing newly developed technologies that broadly focus on genomic and proteomic screening are beginning to identify many new targets for future study. This minireview will provide a contextual overview on the use of DNA/RNA sequencing, microRNA annotation and prediction software, protein structure and function prediction tools, as well as methods of high-throughput protein expression analysis. We will also use select examples to highlight the existing use of these technologies in stress biology research. Such tools can be used in comparative stress biology in the characterization of animal responses to environmental challenges. Although there are many areas of study left to be explored, research in comparative stress biology will always be continuing as new technologies allow the further analysis of cell function, and new paradigms in gene regulation and regulatory molecules (such as microRNAs) are continuing to be discovered. Building upon the findings of past research, while utilizing new technologies in the appropriate manner, future studies can be carried out in new and exciting areas still unexplored. Proper use of rapidly developing technologies will help to create a complete understanding of the animal stress response and survival mechanisms utilized by many diverse organisms.

MicroRNA-133 inhibits behavioral aggregation by controlling dopamine synthesis in locusts

Phenotypic plasticity is ubiquitous and primarily controlled by interactions between environmental and genetic factors. The migratory locust, a worldwide pest, exhibits pronounced phenotypic plasticity, which is a population density-dependent transition that occurs between the gregarious and solitary phases. Genes involved in dopamine synthesis have been shown to regulate the phase transition of locusts. However, the function of microRNAs in this process remains unknown. In this study, we report the participation of miR-133 in dopamine production and the behavioral transition by negatively regulating two critical genes, henna and pale, in the dopamine pathway. miR-133 participated in the post-transcriptional regulation of henna and pale by binding to their coding region and 3′ untranslated region, respectively. miR-133 displayed cellular co-localization with henna/pale in the protocerebrum, and its expression in the protocerebrum was negatively correlated with henna and pale expression. Moreover, miR-133 agomir delivery suppressed henna and pale expression, which consequently decreased dopamine production, thus resulting in the behavioral shift of the locusts from the gregarious phase to the solitary phase. Increasing the dopamine content could rescue the solitary phenotype, which was induced by miR-133 agomir delivery. Conversely, miR-133 inhibition increased the expression of henna and pale, resulting in the gregarious-like behavior of solitary locusts; this gregarious phenotype could be rescued by RNA interference of henna and pale. This study shows the novel function and modulation pattern of a miRNA in phenotypic plasticity and provides insight into the underlying molecular mechanisms of the phase transition of locusts.

Phenotypic plasticity refers to the ability of an organism to alter its phenotypes in response to environmental changes. Genetic factors, such as coding and non-coding RNAs, contribute to phenotypic variation. MicroRNAs (miRNAs), which are non-coding RNAs, function as post-transcriptional repressors of gene expression. Migratory locusts show remarkable phenotypic plasticity, referred to as phase transition, which is dependent on population density changes. In the present study, we elucidated the miRNA-133-mediated post-transcriptional mechanisms involved in dopamine production that result in behavioral phase changes. We found that miR-133 directly represses two genes, henna and pale, in the dopamine pathway. Administration of the miR-133 agomir decreased dopamine production and induced a behavioral shift from the gregarious to the solitary phase. Additionally, miR-133 targeted henna in the coding region and pale in the 3′ untranslated region, possibly indicating that different mechanisms of post-transcriptional regulation by miR-133 occur in the dopamine pathway. Moreover, the rescue experiments significantly eliminated the effects of miR-133 overexpression and inhibition on the behavioral phase changes of locusts. Our results demonstrate the role of miR-133 in phenotypic plasticity in locusts, in which the miR-133 regulates behavioral changes by controlling dopamine synthesis.

Identification and profiling of microRNAs in the embryonic breast muscle of pekin duck

MicroRNAs (miRNAs) regulate gene expression by fully or partially binding to complementary sequences and play important roles in skeletal muscle development. However, the roles of miRNAs in embryonic breast muscle of duck are unclear. In this study, we analyzed the miRNAs profiling in embryonic breast muscle of Pekin duck at E13 (the 13(th) day of hatching), E19, and E27 by high-throughput sequencing. A total of 382 miRNAs including 359 preciously identified miRNAs 23 novel miRNA candidates were obtained. The nucleotide bias analysis of identified miRNAs showed that the miRNAs in Pekin duck was high conserved. The expression of identified miRNAs were significantly different between E13 and E19 as well as between E27 and E19. Fifteen identified miRNAs validated using stem-loop qRT-PCR can be divided into three groups: those with peak expression at E19, those with minimal expression at E19, and those with continuous increase from E11 to E27. Considering that E19 is the fastest growth stage of embryonic Pekin duck breast muscle, these three groups of miRNAs might be the potential promoters, the potential inhibitors, and the potential sustainer for breast muscle growth. Among the 23 novel miRNAs, novel-miRNA-8 and novel-miRNA-14 had maximal expression at some stages. The stem-loop qRT-PCR analysis of the two novel miRNAs and their two targets (MAP2K1 and PPARα) showed that the expression of novel-mir-8 and PPARα reached the lowest points at E19, while that of novel-mir-14 and MAP2K1 peaked at E19, suggesting novel-miRNA-8 and novel-miRNA-14 may be a potential inhibitor and a potential promoter for embryonic breast muscle development of duck. In summary, these results not only provided an overall insight into the miRNAs landscape in embryonic breast muscle of duck, but also a basis for the further investigation of the miRNAs roles in duck skeletal muscle development.

Large-scale identification and comparative analysis of miRNA expression profile in the respiratory tree of the sea cucumber Apostichopus japonicus during aestivation

The sea cucumber Apostichopus japonicus withstands high water temperatures in the summer by suppressing its metabolic rate and entering a state of aestivation. We hypothesized that changes in the expression of miRNAs could provide important post-transcriptional regulation of gene expression during hypometabolism via control over mRNA translation. The present study analyzed profiles of miRNA expression in the sea cucumber respiratory tree using Solexa deep sequencing technology. We identified 279 sea cucumber miRNAs, including 15 novel miRNAs specific to sea cucumber. Animals sampled during deep aestivation (DA; after at least 15 days of continuous torpor) were compared with animals from a non-aestivation (NA) state (animals that had passed through aestivation and returned to an active state). We identified 30 differentially expressed miRNAs ([RPM (reads per million) >10, |FC| (|fold change|)≥1, FDR (false discovery rate)<0.01]) during aestivation, which were validated by two other miRNA profiling methods: miRNA microarray and real-time PCR. Among the most prominent miRNA species, miR-124, miR-124-3p, miR-79, miR-9 and miR-2010 were significantly over-expressed during deep aestivation compared with non-aestivation animals, suggesting that these miRNAs may play important roles in metabolic rate suppression during aestivation. High-throughput sequencing data and microarray data have been submitted to the GEO database with accession number: 16902695.