scholarly journals Parallel epigenetic modifications induced by hatchery rearing in a Pacific Salmon

2017 ◽  
Author(s):  
Jérémy Le Luyer ◽  
Martin Laporte ◽  
Terry D. Beacham ◽  
Karia H. Kaukinen ◽  
Ruth E. Withler ◽  
...  
Keyword(s):  
Early Development ◽  
Rapid Change ◽  
Epigenetic Modifications ◽  
Phenotypic Traits ◽  
Past Century ◽  
Rearing Environment ◽  
Single Generation ◽  
Natural Origin ◽  
Domestication Selection ◽  
Explanatory Mechanism

Highlights- First study to highlight parallel epigenetic modifications induced by hatchery rearing as a potential explanatory mechanism for rapid change in fitnessSummaryA puzzling question in conservation biology is how to maintain overall fitness of individuals bred in captive environment upon release into the wild, especially for rehabilitating declining or threatened species [1,2]. For salmonid species, a heritable change in fitness related traits and gene expression has been reported to occur in a single generation of captivity in hatchery environment [3–5]. Such rapid changes are congruent with models of inadvertent domestication selection which may lead to maladaptation in the natural environment [4]. Arguably, the underlying mechanism by which captivity may induce fitness difference between wild and captive congeners is still poorly understood. Short-term selection on complex phenotypic traits is expected to induce subtle changes in allele frequency over multiple loci [7–9]. Yet, most studies investigating the molecular basis for rapid change in fitness related traits occurring in hatchery have concentrated their effort on finding evidence for selection at the genome level by identifying loci with large effect.Numerous wild stocks of Pacific anadromous salmon and trout (genus Oncorhynchus and Salmo) have experienced fluctuating abundance over the past century, with a series of sharp declines [6–8]. With the objectives of preserving ecosystem integrity, enhancing declining populations and sustaining fisheries, conservation hatcheries have been flourishing. This is particularly true along the North American Pacific coast where billions of salmonids, all species included, are released each year. Despite substantial improvement of production management, the beneficial ecological role of hatcheries in enhancing and restoring wild stocks is still debated, mainly because of the reduced fitness and maladaptation of hatchery-fish when released in the wild [3,5,9]. Although previous studies showed that domestication selection was involved in such fitness impairment, they also observed that different environmental conditions (e.g. reduced fish density) significantly modulated the physiological acclimation to hatchery environment [4].Environmental stimuli are especially relevant during early embryonic development, which also correspond to a sensitive methylation reprogramming window in vertebrates [10,11]. It is therefore plausible that differences in rearing environment during early development may result in epigenetic modifications that could in turn impact on fitness. However, the only epigenetic study to date pertaining to captive rearing in salmonids and performed using methylation-sensitive amplified fragments (MSAP) failed to identify significant changes in methylation profile associated with hatchery rearing [12]Here, we used a higher resolution approach to compare the genome-wide pattern of methylation in hatchery-reared juvenile (smolt) Coho Salmon with that of their wild counterparts in two geographically distant rivers in British Columbia, Canada. Using a reduced representation bisulfite sequencing (RRBS) approach covering an average per individual of about 70 million cytosines in CpG context, we identified 100 methylated regions (DMRs) that differed in parallel between hatchery and natural origin salmon in both rivers. The total variance of epigenetic variation among individuals explained by river or origin and rearing environment in a RDA model was 16% (adj.R2=0.16), and both variables equally explained about 8% of the variance after controlling for each other. The gene ontology analysis revealed that regions with different methylation levels between hatchery and natural origin salmon showed enrichment for ion homeostasis, synaptic and neuromuscular regulation, immune and stress response, and control of locomotion functions. We further identified 15,044 SNPs that allowed detection of significant differences between either rivers or sexes. However, no effect of rearing environment was observed, confirming that hatchery and natural origin fish of a given river belong to the same panmictic population, as expected based on the hatchery programs applied in these rivers (see Supplementary experimental procedures). Moreover, neither a standard genome-scan approach nor a polygenic statistical framework allowed detection of selective effects within a single generation between hatchery and natural origin salmon. Therefore, this is the first study to demonstrate that parallel epigenetic modifications induced by hatchery rearing during early development may represent a potential explanatory mechanism for rapid change in fitness-related traits previously reported in salmonids.

scholarly journals From the Eurasian Steppes to the Roman Circuses: A Review of Early Development of Horse Breeding and Management

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1859
Author(s):  
Weronika Klecel ◽  
Elżbieta Martyniuk
Keyword(s):  
Social Status ◽  
Early Development ◽  
Iron Age ◽  
Ancient World ◽  
Phenotypic Traits ◽  
Striking Resemblance ◽  
Training Systems ◽  
Horse Breeding ◽  
Breeding Practices

The domestication of the horse began about 5500 years ago in the Eurasian steppes. In the following millennia horses spread across the ancient world, and their role in transportation and warfare affected every ancient culture. Ownership of horses became an indicator of wealth and social status. The importance of horses led to a growing interest in their breeding and management. Many phenotypic traits, such as height, behavior, and speed potential, have been proven to be a subject of selection; however, the details of ancient breeding practices remain mostly unknown. From the fourth millennium BP, through the Iron Age, many literature sources thoroughly describe horse training systems, as well as various aspects of husbandry, many of which are still in use today. The striking resemblance of ancient and modern equine practices leaves us wondering how much was accomplished through four thousand years of horse breeding.

scholarly journals Spontaneous HTLV-1 transcription is accompanied by distinct epigenetic changes in the 5′ and 3′ long terminal repeats

2018 ◽  
Vol 3 ◽  
pp. 105 ◽  
Author(s):  
Michi Miura ◽  
Paola Miyazato ◽  
Yorifumi Satou ◽  
Yuetsu Tanaka ◽  
Charles R.M. Bangham
Keyword(s):  
Histone Modifications ◽  
Insertion Site ◽  
Rapid Change ◽  
Epigenetic Modifications ◽  
The Body ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
Long Terminal Repeats ◽  
Terminal Repeats ◽  
The Impact

Background:The human retrovirus HTLV-1 inserts the viral complementary DNA of 9 kb into the host genome. Both plus- and minus-strands of the provirus are transcribed, respectively from the 5′ and 3′ long terminal repeats (LTR). Plus-strand expression is rapid and intense once activated, whereas the minus-strand is transcribed at a lower, more constant level. To identify how HTLV-1 transcription is regulated, we investigated the epigenetic modifications associated with the onset of spontaneous plus-strand expression and the potential impact of the host factor CTCF.Methods:Patient-derived peripheral blood mononuclear cells (PBMCs) and in vitro HTLV-1-infected T cell clones were examined. Cells were stained for the plus-strand-encoded viral protein Tax, and sorted into Tax+and Tax–populations. Chromatin immunoprecipitation and methylated DNA immunoprecipitation were performed to identify epigenetic modifications in the provirus. Bisulfite-treated DNA fragments from the HTLV-1 LTRs were sequenced. Single-molecule RNA-FISH was performed, targeting HTLV-1 transcripts, for the estimation of transcription kinetics. The CRISPR/Cas9 technique was applied to alter the CTCF-binding site in the provirus, to test the impact of CTCF on the epigenetic modifications.Results:Changes in the histone modifications H3K4me3, H3K9Ac and H3K27Ac were strongly correlated with plus-strand expression. DNA in the body of the provirus was largely methylated except for the pX and 3′ LTR regions, regardless of Tax expression. The plus-strand promoter was hypomethylated when Tax was expressed. Removal of CTCF had no discernible impact on the viral transcription or epigenetic modifications.Conclusions:The histone modifications H3K4me3, H3K9Ac and H3K27Ac are highly dynamic in the HTLV-1 provirus: they show rapid change with the onset of Tax expression, and are reversible. The HTLV-1 provirus has an intrinsic pattern of epigenetic modifications that is independent of both the provirus insertion site and the chromatin architectural protein CTCF which binds to the HTLV-1 provirus.

scholarly journals Microalgae as Sources of High-Quality Protein for Human Food and Protein Supplements

Foods ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3002
Author(s):  
Yanwen Wang ◽  
Sean M. Tibbetts ◽  
Patrick J. McGinn
Keyword(s):  
Product Development ◽  
Biological Diversity ◽  
Rapid Change ◽  
Food Sources ◽  
Phenotypic Traits ◽  
Market Demand ◽  
High Quality ◽  
Protein Supplements ◽  
Human Food ◽  
High Quality Protein

As a result of population growth, an emerging middle-class, and a more health-conscious society concerned with overconsumption of fats and carbohydrates, dietary protein intake is on the rise. To address this rapid change in the food market, and the subsequent high demand for protein products, agriculture, aquaculture, and the food industry have been working actively in recent years to increase protein product output from both production and processing aspects. Dietary proteins derived from animal sources are of the highest quality, containing well-balanced profiles of essential amino acids that generally exceed those of other food sources. However, as a result of studies highlighting low production efficiency (e.g., feed to food conversion) and significant environmental impacts, together with the negative health impacts associated with the dietary intake of some animal products, especially red meats, the consumption of animal proteins has been remaining steady or even declining over the past few decades. To fill this gap, researchers and product development specialists at all levels have been working closely to discover new sources of protein, such as plant-based ingredients. In this regard, microalgae have been recognized as strategic crops, which, due to their vast biological diversity, have distinctive phenotypic traits and interactions with the environment in the production of biomass and protein, offering possibilities of production of large quantities of microalgal protein through manipulating growing systems and conditions and bioengineering technologies. Despite this, microalgae remain underexploited crops and research into their nutritional values and health benefits is in its infancy. In fact, only a small handful of microalgal species are being produced at a commercial scale for use as human food or protein supplements. This review is intended to provide an overview on microalgal protein content, its impact by environmental factors, its protein quality, and its associated evaluation methods. We also attempt to present the current challenges and future research directions, with a hope to enhance the research, product development, and commercialization, and ultimately meet the rapidly increasing market demand for high-quality protein products.

scholarly journals "Jangarri": economics, environment, society

2003 ◽  
Vol 9 (1) ◽  
pp. 36
Author(s):  
Garry English
Keyword(s):  
Early Development ◽  
Good Life ◽  
Rapid Change ◽  
Eucalyptus Marginata ◽  
Southwestern Australia ◽  
Life Values ◽  
Guiding Principles ◽  
Best Teachers ◽  
Extensive Agriculture

A BRIEF description of my formative years and the location of my early development provides clues to my philosophy about life which influences my approach to farming. I was fortunate to have had the experience of an upbringing on the land during the 1940s, at Kukerin in the wheatbelt, and 19S0s, in the Mount Barker region, in southwestern Australia. It was a period of rapid change when mechanization brought about development that far outstripped long-term planning. Huge areas of the Jarrah Eucalyptus marginata forest were cleared and burnt to make way for agriculture. The sandplains rich in flora and fauna were easily cleared for extensive agriculture. These changes left me with a feeling of regret and those who follow my generation will never know what we have lost. This period was a time when education taught the basics of life and when good "life" values were inculcated with sayings, morals and mottoes. Two of these I have never forgotten: "waste not, want not"; and "good, better, best, never let it rest, till your good is better, and your better best". They have been guiding principles for me. I also hold to the sentiment that nature and experience are the best teachers and that nothing is more certain than change.

scholarly journals Parallel epigenetic modifications induced by hatchery rearing in a Pacific salmon

2017 ◽  
Vol 114 (49) ◽  
pp. 12964-12969 ◽  
Author(s):  
Jérémy Le Luyer ◽  
Martin Laporte ◽  
Terry D. Beacham ◽  
Karia H. Kaukinen ◽  
Ruth E. Withler ◽  
...  
Keyword(s):  
Coho Salmon ◽  
Pacific Salmon ◽  
Alternative Hypothesis ◽  
Management Practice ◽  
Significant Proportion ◽  
Epigenetic Modifications ◽  
Past Century ◽  
Epigenetic Variation ◽  
In The Wild ◽  
Captive Rearing

Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatchery-born smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.

Social Change and Women’s Work and Family Experience in Ireland and the United States

1986 ◽  
Vol 10 (2) ◽  
pp. 171-193
Author(s):  
Edward L. Kain ◽  
Niall Bolger
Keyword(s):  
United States ◽  
Labor Force ◽  
Labor Force Participation ◽  
Economic Activity ◽  
Rapid Change ◽  
The United States ◽  
Work And Family ◽  
Married Women ◽  
Late Nineteenth Century ◽  
Past Century

This paper examines the changing nature of the female labor force in Ireland and the United States. Data from the two countries are used to illustrate both similarities and variations in the Western experience of women during the period of rapid change in work and family life since the late nineteenth century.A central facet of how Western families have been transformed during the past century has involved the increased participation of women in the paid labor force, and in the most recent decades, a dramatic rise in the labor force participation of married women. In his classic work, World Revolution and Family Patterns, Goode suggests that the increase in female participation in the non-agricultural labor force was clearly evident in Western countries but was not dramatic during the first half of this century (1963: 59-60). Since 1950, however, increases in the economic activity of women have occurred throughout the West. For example, using data from Scandinavian countries, Haavio-Mannila and Kari (1980) document the increased economic activity of women throughout this century, the transformation of the economies of Scandinavia from an agricultural to an industrial base, and the rapid increase in labor force participation of married women since 1950.

scholarly journals THE POPULATION GENETICS OF PARTHENOGENETIC STRAINS OF DROSOPHILA MERCATORUM. II. THE CAPACITY FOR PARTHENOGENESIS IN A NATURAL, BISEXUAL POPULATION

Genetics ◽  
1976 ◽  
Vol 82 (3) ◽  
pp. 527-542
Author(s):  
Alan R Templeton ◽  
Hampton L Carson ◽  
Charles F Sing
Keyword(s):  
Virgin Female ◽  
Radical Change ◽  
Phenotypic Traits ◽  
Bisexual Species ◽  
Single Generation ◽  
Drosophila Mercatorum ◽  
Bisexual Population ◽  
Parthenogenetic Reproduction ◽  
And Behavior ◽  
Low Rate

ABSTRACT Drosophila mercatorum is a bisexual species, but certain strains are capable of parthenogenetic reproduction in the laboratory. We investigated the parthenogenetic capacity of the virgin daughters of females captured from a natural, bisexual population in Hawaii. An isozyme survey indicated the natural population is polymorphic at about 50% of its loci, and its individuals heterozygous at 18% of their loci. The predominant mode of parthenogenesis in D. mercatorum causes homozygosity for all loci in a single generation. Despite this radical change in genetic state, 23% of the virgin female lines produced adult parthenogenetic progeny, and 16% produced parthenogenetic progeny themselves capable of parthenogenetic reproduction. The parthenogenetic rate as measured by the number of parthenogenetic progeny themselves capable of parthenogenesis divided by the number of eggs laid is around 10-5 for the virgin female lines. We argue that one of the major reasons for this low rate is that very few of the impaternate zygotes have a genotype that can survive and reproduce under the genetic conditions imposed by parthenogenetic reproduction. This intense selective bottleneck can be passed in a single generation if enough unfertilized eggs are laid, and once passed is accompanied by a large (perhaps a thousandfold) increase in the rate of parthenogenesis and by modifications in many phenotypic traits such as morphology and behavior.

scholarly journals Meteotsunami occurrence in the Gulf of Finland over the past century

2020 ◽  
Vol 20 (9) ◽  
pp. 2535-2546
Author(s):  
Havu Pellikka ◽  
Terhi K. Laurila ◽  
Hanna Boman ◽  
Anu Karjalainen ◽  
Jan-Victor Björkqvist ◽  
...  
Keyword(s):  
Sea Level ◽  
Meteorological Data ◽  
Convective Available Potential Energy ◽  
Rapid Change ◽  
Air Pressure ◽  
Gulf Of Finland ◽  
Past Century ◽  
Data Set ◽  
The Past ◽  
The Gulf Of Finland

Abstract. We analyse changes in meteotsunami occurrence over the past century (1922–2014) in the Gulf of Finland, Baltic Sea. A major challenge for studying these short-lived and local events is the limited temporal and spatial resolution of digital sea level and meteorological data. To overcome this challenge, we examine archived paper recordings from two tide gauges, Hanko for 1922–1989 and Hamina for 1928–1989, from the summer months of May–October. We visually inspect the recordings to detect rapid sea level variations, which are then digitised and compared to air pressure observations from nearby stations. The data set is complemented with events detected from digital sea level data 1990–2014 by an automated algorithm. In total, we identify 121 potential meteotsunami events. Over 70 % of the events could be confirmed to have a rapid change in air pressure occurring shortly before or simultaneously with the sea level oscillations. The occurrence of meteotsunamis is strongly connected with lightning over the region: the number of cloud-to-ground (CG) flashes over the Gulf of Finland were on average over 10 times higher during the days when a meteotsunami was recorded compared to days with no meteotsunamis in May–October. On a monthly level, statistically significant differences between meteotsunami months and other months were found in the number of CG flashes, convective available potential energy (CAPE), and temperature. Meteotsunami occurrence over the past century shows a statistically significant increasing trend in Hamina, but not in Hanko.

scholarly journals Epigenetic changes around the pX region and spontaneous HTLV-1 transcription are CTCF-independent

2018 ◽  
Vol 3 ◽  
pp. 105 ◽  
Author(s):  
Michi Miura ◽  
Paola Miyazato ◽  
Yorifumi Satou ◽  
Yuetsu Tanaka ◽  
Charles R.M. Bangham
Keyword(s):  
Histone Modifications ◽  
Single Molecule ◽  
Mononuclear Cells ◽  
Insertion Site ◽  
Rapid Change ◽  
Epigenetic Modifications ◽  
The Body ◽  
Ctcf Binding ◽  
Ctcf Binding Site ◽  
The Impact

Background:The human retrovirus HTLV-1 inserts the viral complementary DNA of 9 kb into the host genome. Both plus- and minus-strands of the provirus are transcribed, respectively from the 5′ and 3′ long terminal repeats (LTR). Plus-strand expression is rapid and intense once activated, whereas the minus-strand is transcribed at a lower, more constant level. To identify how HTLV-1 transcription is regulated, we investigated the epigenetic modifications associated with the onset of spontaneous plus-strand expression and the potential impact of the host factor CTCF.Methods:Patient-derived peripheral blood mononuclear cells (PBMCs) and in vitro HTLV-1-infected T cell clones were examined. Cells were stained for the plus-strand-encoded viral protein Tax, and sorted into Tax+and Tax–populations. Chromatin immunoprecipitation and methylated DNA immunoprecipitation were performed to identify epigenetic modifications in the provirus. Bisulfite-treated DNA fragments from the HTLV-1 LTRs were sequenced. Single-molecule RNA-FISH was performed, targeting HTLV-1 transcripts, for the estimation of transcription kinetics. The CRISPR/Cas9 technique was applied to alter the CTCF-binding site in the provirus, to test the impact of CTCF on the epigenetic modifications.Results:Changes in the histone modifications H3K4me3, H3K9Ac and H3K27Ac were strongly correlated with plus-strand expression. DNA in the body of the provirus was largely methylated except for the pX and 3′ LTR regions, regardless of Tax expression. The plus-strand promoter was hypomethylated when Tax was expressed. Removal of CTCF had no discernible impact on the viral transcription or epigenetic modifications.Conclusions:The histone modifications H3K4me3, H3K9Ac and H3K27Ac are highly dynamic in the HTLV-1 provirus: they show rapid change with the onset of Tax expression, and are reversible. The HTLV-1 provirus has an intrinsic pattern of epigenetic modifications that is independent of both the provirus insertion site and the chromatin architectural protein CTCF which binds to the HTLV-1 provirus.

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