Time Learning and Anticipatory Activity in Groups of Arctic Charr

Time learning and anticipatory activity were studied in five groups of 16–17 Arctic charr (Salvelinus alpinus) using self‐feeding devices with individual recognition (PIT (Passive Integrated Transponders)‐tags). The fish were kept under a LD 12:12 h cycle and periods of free access to the food were alternated with periods of time‐limited (2 h) access to food. Self‐feeding activity was significantly related to the light period in unrestricted conditions while related to the feeding periods during time‐limited access to food. The fish learned to concentrate their feeding activity to the restricted mealtime (>50% of the daily self‐feeding activity) within 10 d. The food anticipatory activity, measured as an increased self‐feeding activity before the feeding time and as aggressive interactions close to the trigger, was significant in both cases. The dominant individuals increased the trigger activity in advance of the time‐restricted reward period and subdominant individuals approached the trigger also in advance, inducing aggressive interactions. Thus, anticipating and learning a temporally predictable food source was pronounced in groups of self‐feeding Arctic charr.     

Adjustments of Protein Metabolism in Fasting Arctic Charr,Salvelinus alpinus

Protein metabolism, including the interrelated processes of synthesis and degradation, mediates the growth of an animal. In ectothermic animals, protein metabolism is responsive to changes in both biotic and abiotic conditions. This study aimed to characterise responses of protein metabolism to food deprivation that occur in the coldwater salmonid, Arctic charr, Salvelinus alpinus. We compared two groups of Arctic charr: one fed continuously and the other deprived of food for 36 days. We measured the fractional rate of protein synthesis (K_S) in individuals from the fed and fasted groups using a flooding dose technique modified for the use of deuterium-labelled phenylalanine. The enzyme activities of the three major protein degradation pathways (ubiquitin proteasome, lysosomal cathepsins and the calpain systems) were measured in the same fish. This study is the first to measure both K_S and the enzymatic activity of protein degradation in the same fish, allowing us to examine the apparent contribution of different protein degradation pathways to protein turnover in various tissues (red and white muscle, liver, heart and gills). K_S was lower in the white muscle and in liver of the fasted fish compared to the fed fish. There were no observable effects of food deprivation on the protease activities in any of the tissues with the exception of liver, where the ubiquitin proteasome pathway seemed to be activated during fasting conditions. Lysosomal proteolysis appears to be the primary degradation pathway for muscle protein, while the ubiquitin proteasome pathway seems to predominate in the liver. We speculate that Arctic charr regulate protein metabolism during food deprivation to conserve proteins.     

Effects of Partially Anadromous Arctic Charr (Salvelinus alpinus) Populations on Ecology of Coastal Arctic Lakes

Little research has been conducted on effects of iteroparous anadromous fishes on Arctic lakes. We investigated trophic ecology, fish growth, and food web structure in six lakes located in Nunavut, Canada; three lakes contained anadromous Arctic charr (Salvelinus alpinus) whereas three lakes did not contain Arctic charr. All lakes contained forage fishes and lake trout (Salvelinus namaycush; top predator). Isotope ratios (δ¹³C, δ¹⁵N) of fishes and invertebrates did not differ between lakes with and without anadromous Arctic charr; if anadromous Arctic charr deliver marine-derived nutrients and/or organic matter to freshwater lakes, these inputs could not be detected with δ¹³C and/or δ¹⁵N. Lake trout carbon (C):nitrogen (N) and condition were significantly higher in lakes with Arctic charr (C:N = 3.42, K = 1.1) than in lakes without Arctic charr (C:N = 3.17, K = 0.99), however, and ninespine stickleback (Pungitius pungitius) condition was significantly lower in lakes with Arctic charr (K = 0.58) than in lakes without Arctic charr (K = 0.64). Isotope data indicated that pre-smolt and resident Arctic charr may be prey for lake trout and compete with ninespine stickleback. Linear distance metrics applied to isotope data showed that food webs were more compact and isotopically redundant in lakes where Arctic charr were present. Despite this, lake trout populations in lakes with Arctic charr occupied a larger isotope space and showed greater inter-individual isotope differences. Anadromous Arctic charr appear to affect ecology and feeding of sympatric freshwater species, but effects are more subtle than those seen for semelparous anadromous species.     

The Importance of Egg Size and Social Effects for Behaviour of Arctic Charr Juveniles

Early behaviour can determine food intake and growth rate with important consequences for life history and survival in fishes. Egg size is known to affect growth rate of young Arctic charr but its influence on the development of behaviour is poorly documented. It is believed that egg size influence on growth and potentially on the behaviour of young fish decreases over time, minimized by the effects of social factors. Shortly after first feeding, we examined differences in mobility and foraging of Arctic charr in relation to egg size and social environment. The behaviour of juveniles from small and large eggs was compared five times over the course of development and in three different experimental settings: long‐term isolation (isolation before hatching), short‐term isolation vs. group rearing and mixed size group vs. homogeneous size groups. Egg size affected foraging behaviour and mobility of fish: fish coming from large eggs were more mobile and foraged more than fish coming from small eggs. Social environment affected foraging behaviour, mobility and space use: fish in a group were more mobile, foraged more and responded faster to food delivery than isolated fish. The interaction of egg size and social effects was seen primarily in foraging activities but did not affect mobility or space use. Large fish in groups foraged more than the three other groups: large fish in isolation, small fish in groups and small fish in isolation. Agonistic behaviour was rarely observed and there was no significant effect of group composition on agonistic behaviour. We discuss the importance of egg size and social effects at early stages of development with a focus on the evolutionary ecology of Arctic charr.     

Genetic Variability and Structuring of Arctic Charr (Salvelinus alpinus) Populations in Northern Fennoscandia

Variation in presumably neutral genetic markers can inform us about evolvability, historical effective population sizes and phylogeographic history of contemporary populations. We studied genetic variability in 15 microsatellite loci in six native landlocked Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia, where this species is considered near threatened. We discovered that all populations were genetically highly (mean F _ST ≈ 0.26) differentiated and isolated from each other. Evidence was found for historical, but not for recent population size bottlenecks. Estimates of contemporary effective population size (N _e) ranged from seven to 228 and were significantly correlated with those of historical N _e but not with lake size. A census size (N _C) was estimated to be approximately 300 individuals in a pond (0.14 ha), which exhibited the smallest N _e (i.e. N _e/N _C = 0.02). Genetic variability in this pond and a connected lake is severely reduced, and both genetic and empirical estimates of migration rates indicate a lack of gene flow between them. Hence, albeit currently thriving, some northern Fennoscandian populations appear to be vulnerable to further loss of genetic variability and are likely to have limited capacity to adapt if selection pressures change.     

Reproductive Investment and Energy Allocation in an Alpine Arctic Charr, Salvelinus alpinus, Population

Reproductive investment was determined in a population of stunted Arctic charr, Salvelinus alpinus, living in an ultra-oligotrophic alpine lake (altitude 1100m) in central Norway (62°51W). No reductions in somatic energy content (carcass and intestines) were detected during the spawning period. Post-spawning somatic lipid, protein and total energy content did not differ between male spawners, female spawners and immatures. The recorded reproductive output consisted of gonad tissue equivalent to 13% of total pre-spawning energy in females and 4% in males, respectively. Mean stored somatic lipid reserves were as low as 2.8% and did not change significantly from pre- (30 June) to post-spawning (1% October) samples. Female fecundity varied between 41 and 84 (mean 60) eggs, with a corresponding body length varying between 110 to 160mm (mean 13%). Mean yearly survival rate after maturation was 70% for females and 64% for males, respectively. This particularly low reproductive investment is discussed in relation to environmental conditions and low resource availability.     

miRNA异构体：miRNA序列多样性

微RNA（microRNA,miRNA)是一类抑制基因表达的调控分子,在多种生物学进程中扮演重要角色。近来,基于新一代测序技术获得的小RNA测序数据发现,对于某一miRNA来说,它并不是单一的序列,而是由一系列长度/序列及表达不同的异构微RNA (isomicroRNA, isomiRNA/isomiR)所组成。这些isomiR表达多样且序列多样,甚至引入多样的5′端及种子区域。特定miRNA位点在疾病组织中可具有异常的表达模式,现已证实,部分isomiR具有重要的生物学功能。所关注的经典miRNA序列,其实仅是多重isomiR序列中的1条特殊序列,仅从miRNA角度的研究已不足以揭示小RNA的奥秘,全面的研究应同时在miRNA和isomiR中开展,由此可进一步拓宽miRNA的研究思路。本文主要从isomiR的生物学特点、表达及功能等方面进行介绍。     

Ensemble Methods for MiRNA Target Prediction from Expression Data

Background

microRNAs (miRNAs) are short regulatory RNAs that are involved in several diseases, including cancers. Identifying miRNA functions is very important in understanding disease mechanisms and determining the efficacy of drugs. An increasing number of computational methods have been developed to explore miRNA functions by inferring the miRNA-mRNA regulatory relationships from data. Each of the methods is developed based on some assumptions and constraints, for instance, assuming linear relationships between variables. For such reasons, computational methods are often subject to the problem of inconsistent performance across different datasets. On the other hand, ensemble methods integrate the results from individual methods and have been proved to outperform each of their individual component methods in theory.

Results

In this paper, we investigate the performance of some ensemble methods over the commonly used miRNA target prediction methods. We apply eight different popular miRNA target prediction methods to three cancer datasets, and compare their performance with the ensemble methods which integrate the results from each combination of the individual methods. The validation results using experimentally confirmed databases show that the results of the ensemble methods complement those obtained by the individual methods and the ensemble methods perform better than the individual methods across different datasets. The ensemble method, Pearson+IDA+Lasso, which combines methods in different approaches, including a correlation method, a causal inference method, and a regression method, is the best performed ensemble method in this study. Further analysis of the results of this ensemble method shows that the ensemble method can obtain more targets which could not be found by any of the single methods, and the discovered targets are more statistically significant and functionally enriched. The source codes, datasets, miRNA target predictions by all methods, and the ground truth for validation are available in the Supplementary materials.     

The Relevance of Individual Size to Management of Arctic Charr, Salvelinus Alpinus, Populations

Arctic charr, Salvelinus alpinus, tend to form stunted populations presumably due to competition for limited resources. In this context a long-term intensive fishery programme aiming at reducing charr density, and thereby increasing growth and harvestable sizes, was initiated in the early 1980s in a Norwegian alpine lake. Here we present long-term data on catch statistics and changes in mean weights of charr caught with gill nets on spawning grounds, as well as changes in mean weight of juvenile charr caught with funnel traps during the 1990s. Furthermore, we present results from shorter-term studies on growth, size- and age-distribution, and size-related habitat and resource utilisation of Arctic charr and brown trout, Salmo trutta, in this lake. Mean weight (± SD) of charr caught on the spawning grounds increased significantly from 129.8g (±11.9) in the years 1982–1990 to 213.1g (±37.8) in the years 1996–1999, whereas catch per unit of effort decreased significantly. Mean weight of juveniles caught in funnel traps increased significantly from 21.2g (±6.9) in 1993 to 41.9g (±14.8) in 1999. Apparently the increase in weight of spawning charr coincided with the onset of trap fishing for juvenile charr. Compared to generally shallow dwelling trout, charr grew rapidly and were generally found in deeper areas of the lake. Charr went through a distinct size-related niche shift from mainly consuming small zooplankton in the pelagic to consuming large benthic prey in shallower waters. Resource and habitat utilisation in different size-groups of charr and trout are discussed with respect to possible competitive and predatory intra- and interspecific interactions, and with regard to management of charr populations.     

Next-Generation Sequencing Analysis of MiRNA Expression in Control and FSHD Myogenesis

Emerging evidence has demonstrated that miRNA sequences can regulate skeletal myogenesis by controlling the process of myoblast proliferation and differentiation. However, at present a deep analysis of miRNA expression in control and FSHD myoblasts during differentiation has not yet been derived. To close this gap, we used a next-generation sequencing (NGS) approach applied to in vitro myogenesis. Furthermore, to minimize sample genetic heterogeneity and muscle-type specific patterns of gene expression, miRNA profiling from NGS data was filtered with FC≥4 (log₂FC≥2) and p-value<0.05, and its validation was derived by qRT-PCR on myoblasts from seven muscle districts. In particular, control myogenesis showed the modulation of 38 miRNAs, the majority of which (34 out 38) were up-regulated, including myomiRs (miR-1, -133a, -133b and -206). Approximately one third of the modulated miRNAs were not previously reported to be involved in muscle differentiation, and interestingly some of these (i.e. miR-874, -1290, -95 and -146a) were previously shown to regulate cell proliferation and differentiation. FSHD myogenesis evidenced a reduced number of modulated miRNAs than healthy muscle cells. The two processes shared nine miRNAs, including myomiRs, although with FC values lower in FSHD than in control cells. In addition, FSHD cells showed the modulation of six miRNAs (miR-1268, -1268b, -1908, 4258, -4508- and -4516) not evidenced in control cells and that therefore could be considered FSHD-specific, likewise three novel miRNAs that seem to be specifically expressed in FSHD myotubes. These data further clarify the impact of miRNA regulation during control myogenesis and strongly suggest that a complex dysregulation of miRNA expression characterizes FSHD, impairing two important features of myogenesis: cell cycle and muscle development. The derived miRNA profiling could represent a novel molecular signature for FSHD that includes diagnostic biomarkers and possibly therapeutic targets.     

Spatial and Temporal Variability in the Diet of Anadromous Arctic Charr, Salvelinus Alpinus, In Northern Labrador

Spatial and temporal variation in the diet of anadromous Arctic charr, Salvelinus alpinus, was determined from over 2500 prey-containing stomachs collected from three stock complex areas in northern Labrador. Based on the percent wet mass, sand lance, Ammodytes spp., capelin, Mallotus villosus, and sculpins, Triglops spp. and Myoxocephalus spp., were the most important components of the diet in the Voisey stock complex, with capelin, sand lance, and hyperiid amphipods, Parathemisto spp., dominating in the Nain region. In contrast, hyperiid amphipods and sculpins were the main prey items in the more northern Hebron–Saglek complex indicating that diet differs among stocks, and at times over limited spatial scales. The relative importance of prey varied with size of predator. Mean weight of charr has declined over time (p < 0.01), and for one stock complex, is highly correlated with the average quantity of capelin found in the stomachs (r = 0.66, p < 0.001). Dietary shifts observed in anadromous charr in some areas of northern Labrador could be associated, in part, with changes in the distribution of capelin in the northwest Atlantic Ocean, possibly as a result of anomalous ocean climate conditions.     

The Effect of Carlin Tags on Survival and Growth of Anadromous Arctic Charr, Salvelinus Alpinus

Fish tagging methods are important tools in the research and management of salmonids; the Carlin tag is widely used, especially in anadromous salmonids. However, this tagging method may interfere with fish behaviour and increase post-smolt mortality. To estimate Carlin-tag-inflicted mortality in Arctic charr, we used jet injection of alcian blue (colour tags) as a control. Recapture rates were higher for the colour-tagged fish than for the Carlin-tagged fish for both one- and two-year-old smolts. For one-year-old smolts in 1992, the recapture rate was 18.9% for colour-tagged fish and 10.0% for Carlin-tagged ones. For two-year-old smolts in the same year, 34.0% of colour- and 28.6% of Carlin-tagged fish were recaptured; in 1993, recapture rates were 17.2% and 6.3% for colour- and Carlin-tagged fish, respectively. Colour-tagged one-year-old Arctic charr also grew faster than their Carlin-tagged counterparts. No differences in growth rates were found between tagging methods in two-year-olds. These results imply that for hatchery-reared Arctic charr, survival rates using Carlin tagging may be half to one third that of colour tagging. Growth was also higher among colour-tagged fish, indicating that Carlin tags alter the behaviour of fish in the sea.     

Diversification, Sympatric Speciation, and Trophic Polymorphism of Arctic Charr, Salvelinus Alpinus Complex, in Transbaikalia

In northern Transbaikalia, independently evolving landlocked populations of Arctic charr are found in mountain lakes. To assess the diversity of charr in this region, speciation modes involved in the evolution of charr forms, and the role of trophic polymorphism in their divergence, we studied the morphology and feeding of dwarf, small, and large forms of Arctic charr from a number of Transbaikalian lakes. Meristic data on charr from five lakes support the earlier conclusion that the three forms do not represent separate lineages but have independently diverged in sympatry in each of the lakes. In 10 lakes, the dwarf form showed varying degrees of differentiation from normal (small and large) charr in meristic characters (up to morphologically distinct and presumably reproductively isolated groupings), which is viewed as various levels of sympatric divergence. Indexes of gill raker length in fish from 20 lakes vary among populations of both dwarf and normal charr, with forms having short and long rakers being sympatric in some of these lakes. However, the index can be used only for comparing charr of different forms up to about 32cm fork length (FL) because it is strongly negatively correlated with size in larger fish. The study of charr diets in 21 lakes indicates that large charr are piscivorous whereas dwarf and small charr feed on a wide range of invertebrates, partitioning these resources in different ways. Planktivores, including very specialized ones, and non-planktivores (benthic feeders, insectivores) can be identified within the small and dwarf forms. The proportion of plankton in the diets of dwarf and small charr is positively correlated with the number and length of gill rakers while the proportion of benthos is negatively correlated. Allopatric planktivorous and non-planktivorous small charr differ in body proportions; parallel emergence of such morphotypes in different parts of the range is a characteristic feature of the Salvelinus alpinus complex.     

MiRNA Expression Profile of Human Subcutaneous Adipose and during Adipocyte Differentiation

Background

Potential regulators of adipogenesis include microRNAs (miRNAs), small non-coding RNAs that have been recently shown related to adiposity and differentially expressed in fat depots. However, to date no study is available, to our knowledge, regarding miRNAs expression profile during human adipogenesis. Thereby, the aim of this study was to investigate whether miRNA pattern in human fat cells and subcutaneous adipose tissue is associated to obesity and co-morbidities and whether miRNA expression profile in adipocytes is linked to adipogenesis.

Methodology/Principal Findings

We performed a global miRNA expression microarray of 723 human and 76 viral mature miRNAs in human adipocytes during differentiation and in subcutaneous fat samples from non-obese (n = 6) and obese with (n = 9) and without (n = 13) Type-2 Diabetes Mellitus (DM-2) women. Changes in adipogenesis-related miRNAs were then validated by RT-PCR. Fifty of 799 miRNAs (6.2%) significantly differed between fat cells from lean and obese subjects. Seventy miRNAs (8.8%) were highly and significantly up or down-regulated in mature adipocytes as compared to pre-adipocytes. Otherwise, 17 of these 799 miRNAs (2.1%) were correlated with anthropometrical (BMI) and/or metabolic (fasting glucose and/or triglycerides) parameters. We identified 11 miRNAs (1.4%) significantly deregulated in subcutaneous fat from obese subjects with and without DM-2. Interestingly, most of these changes were associated with miRNAs also significantly deregulated during adipocyte differentiation.

Conclusions/Significance

The remarkable inverse miRNA profile revealed for human pre-adipocytes and mature adipocytes hints at a closely crosstalk between miRNAs and adipogenesis. Such candidates may represent biomarkers and therapeutic targets for obesity and obesity-related complications.     

Diplostomiasis (Trematoda: Strigeidae) in Arctic charr (Salvelinus alpinus) from Charr Lake, northern Labrador

The eyes of 273 Arctic charr (Salvelinus alpinus) taken from Charr Lake, the Ikarut River, and Hebron Fiord in northern Labrador were examined for diplostomula. All anadromous charr taken from the Ikarut river and Hebron Fiord were uninfected. The resident fish from Charr Lake were parasitized with large numbers of diplostomula and intensity of infection increased with age and length. Infections of up to 2,852 diplostomula in one fish are the highest recorded. Such infections did not appear to affect the vision of the charr.