Strengths and limitations of reduced representation bisulfite sequencing (RRBS) in the perspective of DNA methylation analysis in fish: a case-study on rainbow trout spermatozoa

DNA methylation in CpG dinucleotides is an important epigenetic mark in fish spermatozoa since it has been shown that some sperm methylome features are transmitted to the offspring. Reduced representation bisulfite sequencing (RRBS) is one genome-scale methods developed to assess DNA methylation at CpG sites. It allows the sequencing of a reduced fraction of the genome expected to be enriched in CpGs. The aim of this study is to characterize the extent of the CpG sites that can be identified in the RRBS-reduced sequenced fraction of rainbow trout spermatozoa, in order to evaluate the potential of RRBS for sperm DNA methylation studies. We observed that RRBS did provide a reduced amount of genomic data, the sum of the CpGs analyzed on 12 males spanning 9% of the total genomic CpGs. CpGs were only slightly enriched in the RRBS data (×1.7 times the sequenced nucleotides), the possible causes being linked to trout genome structure and sequenced fragments size. All genomic functional features were represented in our CpG dataset, with a noticeable enrichment in exons but, strikingly, not in promoters. The number of CpGs shared between biological replicates was low, but this proportion reached workable values from six biological replicates (46% of the analyzed cytosines) on. The choices that are to be made regarding fragment size selection and the options during bioinformatic data processing are discussed. In all, RRBS is a relevant first-approach method to scan the CpG DNA methylation status of spermatozoa along rainbow trout genome, although in a very reduced pattern among biological replicates.

Artificial light at night disrupts male dominance relationships and reproductive success in a model fish species

Environmental light is perceived and anticipated by organisms to synchronize their biological cycles. Therefore, artificial light at night (ALAN) disrupts both diurnal and seasonal biological rhythms. Reproduction is a complex physiological process involving integration of environmental signals by the brain, and release of endocrine signals by the pituitary that regulate gametogenesis and spawning. In addition, males from many species form a dominance hierarchy that, through a combination of aggressive and protective behavior, influences their reproductive success. In this study, we investigated the effect of ALAN and continuous daylight on the behavior and fitness of male fish within a dominance hierarchy using a model fish, the Japanese medaka. In normal light/dark cycles, male medaka establish a hierarchy with the dominant males being more aggressive and remaining closer to the female thus limiting the access of subordinate males to females during spawning. However, determination of the paternity of the progeny revealed that even though subordinate males spend less time with the females, they are, in normal light conditions, equally successful at producing progeny due to an efficient sneaking behavior. Continuous daylight completely inhibited the establishment of male hierarchy, whereas ALAN did not affect it. Nonetheless, when exposed to ALAN, subordinate males fertilize far fewer eggs. Furthermore, we found that when exposed to ALAN, subordinate males produced lower quality sperm than dominant males. Surprisingly, we found no differences in circulating sex steroid levels, pituitary gonadotropin levels, or gonadosomatic index between dominant and subordinate males, neither in control nor ALAN condition. This study is the first to report an effect of ALAN on sperm quality leading to a modification of male fertilization success in any vertebrate. While this work was performed in a model fish species, our results suggest that in urban areas ALAN may impact the genetic diversity of species displaying dominance behavior.

Cryopreservation effect on DNA methylation profile in rainbow trout spermatozoa

Spermatozoa are the cells that are most commonly used for cryopreservation of valuable genetic resources in aquaculture. It is known that fish spermatozoa transmit to the embryo not only their genetic but also their epigenetic profile, especially DNA methylation. Therefore, any alteration of the DNA methylation profile in spermatozoa induces the risk of transmitting epigenetic alterations to the offspring. The aim of this study was to assess the effect of cryopreservation on DNA methylation in rainbow trout spermatozoa. To trigger variable cellular response after freezing-thawing, spermatozoa from mature males were cryopreserved with dimethyl sulfoxide, methanol or glycerol as cryoprotectant. We observed that dimethyl sulfoxide was the best to preserve thawed spermatozoa functions. Methanol only slightly preserved all the cellular parameters, while glycerol failed to protect motility and fertilization ability. The consequences on DNA methylation were assessed using Reduced Representation Bisulfite Sequencing (RRBS). Sperm cryopreservation did not thoroughly impact DNA methylation, although 335-564 differentially methylated cytosines were characterized depending on the cryoprotectant. Very few of them were shared between cryoprotectants, and no correlation with the extent of cellular damage was found. Our study showed that DNA methylation was only slightly altered after sperm cryopreservation, and this may render further analysis of the risk for the progeny very challenging.

A Proposed Role for Pro-Inflammatory Cytokines in Damaging Behavior in Pigs

Sickness can change our mood for the worse, leaving us sad, lethargic, grumpy and less socially inclined. This mood change is part of a set of behavioral symptoms called sickness behavior and has features in common with core symptoms of depression. Therefore, the physiological changes induced by immune activation, for example following infection, are in the spotlight for explaining mechanisms behind mental health challenges such as depression. While humans may take a day off and isolate themselves until they feel better, farm animals housed in groups have only limited possibilities for social withdrawal. We suggest that immune activation could be a major factor influencing social interactions in pigs, with outbreaks of damaging behavior such as tail biting as a possible result. The hypothesis presented here is that the effects of several known risk factors for tail biting are mediated by pro-inflammatory cytokines, proteins produced by the immune system, and their effect on neurotransmitter systems. We describe the background for and implications of this hypothesis.

Increased number of regulatory T cells in esophageal tissue of patients with eosinophilic esophagitis in comparison to gastro esophageal reflux disease and control groups

BACKGROUND

Eosinophilic esophagitis (EoE) is a primarily polygenic allergic disorder. Although most patients have IgE sensitization, it seems that non-IgE mediated responses mainly contribute to the pathogenesis of EoE. Regulatory T cells (Tregs) may have an important role in allergies. There are limited data on the association of Tregs and EoE. In this study, we enumerated and compared T lymphocytes and Tregs in esophageal tissue of patients with EoE, gastroesophageal reflux disease (GERD) and normal controls.

METHODS

Ten patients with EoE, ten patients with GERD and eight normal controls were included. Immunohistochemistry staining was used to enumerate T lymphocytes and Tregs. CD3+ cells were considered as T cells and FOXP3+, CD3+ cells were considered as Tregs. T cells and Tregs were counted in 10 high power fields (HPF) (×400) for each patient and the average of 10 HPFs was recorded.

RESULTS

The mean±SEM of Tregs in esophageal tissue of patients with EoE (10.90±2.14cells/HPF) was significantly higher than the GERD (2.77±0.66cells/HPF) and control groups (0.37±0.08cells/HPF) (P<0.001). Additionally, the mean±SEM of T lymphocytes in esophageal tissue of patients with EoE (24.39±3.86cells/HPF) were increased in comparison to the GERD (10.07±2.65cells/HPF) and control groups (3.17±0.93cells/HPF) (P<0.001).

CONCLUSION

There is an increase in the number of esophageal T lymphocytes and regulatory T cells in patients with EoE compared to the GERD and control groups.

Transfer of Deoxynivalenol (DON) through Placenta, Colostrum and Milk from Sows to Their Offspring during Late Gestation and Lactation

Deoxynivalenol (DON) contamination of feed may result in reduced growth, feed refusal, immunosuppression, and health problems in swine. Piglets can be exposed to DON via placenta before birth and via milk during lactation. The extent of early-life exposure of piglets to DON is, however, not fully known. This study was therefore aimed at investigating DON uptake in sows fed with naturally contaminated diets, DON transfer across placenta during late gestation, and transfer of DON to piglets via colostrum and milk. Forty-four crossbred sows were evaluated from day 93 ± 1 of gestation until weaning of piglets and fed with feed made from naturally DON-contaminated oats at three concentration levels: (1) control (DON < 0.2 mg/kg), (2) DON level 1 (1.4 mg DON/kg), and (3) DON level 2 (1.7 mg DON/kg). The transfer of DON to the piglets was evaluated in 15 sows, with repeated sampling of blood and milk from the sows and blood samples from five piglets of each litter. The piglet/sow plasma DON ratio and milk/plasma (M/P) DON ratio in sows were calculated to estimate the degree of transfer. Piglet/sow plasma ratios were 2.14 at birth, 2.30 within 12–36 h after parturition, 0.08 on day 7, 0.16 on day 21, and 0.20 at weaning. M/P ratios were 0.92, 1.11, 0.94, 1.21, and 0.90, respectively. The results indicate that DON is efficiently transferred across placenta and into milk. However, the low piglet/sow plasma ratios at mid-lactation to weaning indicate that the piglets were most strongly exposed to DON in early life, despite the high M/P ratios and efficient secretion of DON in milk throughout the entire lactation.

Effects of feeding naturally contaminated deoxynivalenol diets to sows during late gestation and lactation in a high-yield specific pathogen-free herd

Background

The most prevalent Fusarium mycotoxin in grains is deoxynivalenol (DON). Contamination of swine feed with DON can result in reduced consumption and poor growth performance. Gestating and lactating sows need sufficient feed intake for fetus development during late gestation and milk production and body maintenance during lactation. Therefore, there is considerable concern in modern piglet production about the effects of DON contamination in sow feed. Most previous studies in sows have been done under experimental conditions, with DON levels ≥2.8 mg/kg feed. The aim of the current field trial was to investigate the effects of feeding grains that are naturally contaminated with more realistic levels of DON on sows during late gestation and lactation.

Methods

In a commercial, high-yield specific pathogen-free piglet production unit, 45 Norwegian Landrace × Yorkshire sows were fed three diets from 93 ± 1 days of gestation until weaning of the piglets, and average daily feed intake (ADFI), body weight (BW), production and reproduction performance, as well as sow blood parameters were recorded. Diets were made from naturally contaminated oats, with three concentration levels: 1) control (DON < 0.2 mg/kg), 2) DON level 1 (1.4 mg DON/kg), and 3) DON level 2 (1.7 mg DON/kg).

Results

Sows that were fed DON level 1 and 2 diets showed a 4–10% reduction in feed consumption during lactation, compared with sows in the control group. However, the DON-contaminated diets did not significantly affect sow BW or backfat thickness. Similarly, there were neither effects on production or reproduction performance, nor on blood parameters in the sows. The effects on skin temperature were variable.

Conclusion

Naturally contaminated diets with realistic, moderately increased DON levels, fed during late gestation and lactation in a modern high-yield piglet production farm, had limited effects on sow health and production.

Electronic supplementary material

The online version of this article (10.1186/s40813-018-0102-9) contains supplementary material, which is available to authorized users.

Effects and biotransformation of the mycotoxin deoxynivalenol in growing pigs fed with naturally contaminated pelleted grains with and without the addition of Coriobacteriaceum DSM 11798

Deoxynivalenol (DON) is one of the most prevalent Fusarium mycotoxins in grain and can cause economic losses in pig farming due to reduced feed consumption and lower weight gains. Biodetoxification of mycotoxins using bacterial strains has been a focus of research for many years. However, only a few in vivo studies have been conducted on the effectiveness of microbial detoxification of fusariotoxins. This study was therefore aimed at investigating the effect of a feed additive containing the bacterial strain Coriobacteriaceum DSM 11798 (the active ingredient in Biomin® BBSH 797) on growth performance and blood parameters, as well as uptake and metabolism of DON, in growing pigs. Forty-eight crossbred (Landrace-Yorkshire/Duroc-Duroc) weaning pigs were fed with pelleted feed made from naturally contaminated oats, with DON at four concentration levels: (1) control diet (DON < 0.2 mg kg^-1), (2) low-contaminated diet (DON = 0.92 mg kg^-1), (3) medium-contaminated diet (DON = 2.2 mg kg^-1) and (4) high-contaminated diet (DON = 5.0 mg kg^-1) and equivalent diets containing DSM 11798 as feed additive. During the first 7 days of exposure, pigs in the highest-dose group showed a 20-28% reduction in feed intake and a 24-34% reduction in weight gain compared with pigs in the control and low-dose groups. These differences were levelled out by study completion. Towards the end of the experiment, dose-dependent reductions in serum albumin, globulin and total serum protein were noted in the groups fed with DON-contaminated feed compared with the controls. The addition of DSM 11798 had no effect on the DON-related clinical effects or on the plasma concentrations of DON. The ineffectiveness of the feed additive in the present study could be a consequence of its use in pelleted feed, which might have hindered its rapid release, accessibility or detoxification efficiency in the pig's gastrointestinal tract.