Comparative analysis of whole blood transcriptomics between European and local Caribbean pigs in response to feed restriction in a tropical climate.

BACKGROUND: Feed restriction occurs frequently during pig growth, either due to economic reasons or stressful environmental conditions. Local breeds are suggested to have better tolerance to periods of feed restriction. However, the mechanisms underlying the response to feed restriction in different breeds is largely unknown. The aims of the present study were (1) to compare the blood transcriptome profile in response to feed restriction and refeeding of two contrasted breeds, Large White (LW), which has been selected for high performance, and Creole (CR), which is adapted to tropical conditions, and (2) to investigate the effect of a moderate feed restriction and refeeding on whole blood transcriptome. Analysis of blood transcriptome allows to study the response to feed restriction and refeeding in a dynamic way. RNAseq was performed on blood samples of growing LW and CR pigs at two time points: after 3 weeks of feed restriction and after 3 weeks of refeeding. The data was compared with samples from control animals offered the same diet on an ad libitum basis throughout the whole experiment. RESULTS: In terms of performance (body weight and feed efficiency), CR pigs were less impacted by feed restriction than LW. The transcriptional response to feed restriction and refeeding between CR and LW was contrasted both in terms of number of DEGs and enriched pathways. CR demonstrated a stronger transcriptional response to feed restriction whereas LW had a stronger response to refeeding. Differences in the transcriptional response to feed restriction between CR and LW were related to cell stress response (Aldosterone Signalling, Protein ubiquitination, Unfolded Protein Signalling) whereas after refeeding, differences were linked to thermogenesis, metabolic pathways and cell proliferation (p38 MAPK, ERK/MAPK pathway). In both breeds, transcriptional changes related to the immune response were found after restriction and refeeding. CONCLUSIONS: Altogether, the present study indicates that blood transcriptomics can be a useful tool to study differential genetic response to feed restriction in a dynamic way. The results indicate a differential response of blood gene expression to feed restriction and refeeding between breeds, affecting biological pathways that are in accordance with performance and thermoregulatory results.

Isolating Caenorhabditis elegans from the Natural Habitat.

Wild populations of the model organism C. elegans represent a valuable resource, allowing for genetic characterization underlying natural phenotypic variation. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes, and mating tests. This protocol uses standard laboratory equipment and requires little prior knowledge of C. elegans biology.

Plasticity of feeding behaviour traits in response to production environment (temperate vs. tropical) in group-housed growing pigs.

Heat stress affects pig metabolism, health and welfare, resulting in reduced growth and important economic losses. The present experiment aimed to evaluate the effects of two climatic environments [temperate (TEMP) vs. tropical humid (TROP)] on feeding behaviour in growing pigs. The feeding behaviour traits were measured with automated feeders and included: daily feed intake, daily eating time, feeding rate, daily number of meals, feed intake per meal, and feeding time per meal. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. The same 10 F1 LW × CR boars (sire families [SF]) were mated with related LW sows in each environment. Feeding behaviour was recorded for a total of 1,296 pigs (n = 634 pigs for TEMP and n = 662 pigs for TROP) between 11 and 23 weeks of age. Growth performance and thermoregulatory responses (rectal and skin temperatures) were also measured. Results show that TROP conditions affect feeding behaviour traits: animals had more meals per day but these meals were smaller both in duration and in size, resulting in lower daily feed intake and less time eating per day. Significant SF by environment (GxE) interactions were found for all feeding behaviour traits. When SF were distributed into robust and sensitive groups (previously defined according to performance and thermoregulatory traits), results showed group by environment interactions for all feeding traits, except meal frequency. Moreover, a significant difference in feeding rate between robust and sensitive group was detected in TEMP, suggesting that feeding rate may be a good candidate to evaluate heat tolerance.

KaruBioNet: a network and discussion group for a better collaboration and structuring of bioinformatics in Guadeloupe (French West Indies).

Summary: Sequencing and other biological data are now more frequently available and at a lower price. Mutual tools and strategies are needed to analyze the huge amount of heterogeneous data generated by several research teams and devices. Bioinformatics represents a growing field in the scientific community globally. This multidisciplinary field provides a great amount of tools and methods that can be used to conduct scientific studies in a more strategic way. Coordinated actions and collaborations are needed to find more innovative and accurate methods for a better understanding of real-life data. A wide variety of organizations are contributing to KaruBioNet in Guadeloupe (French West Indies), a Caribbean archipelago. The purpose of this group is to foster collaboration and mutual aid among people from different disciplines using a 'one health' approach, for a better comprehension and surveillance of humans, plants or animals' health and diseases. The KaruBioNet network particularly aims to help researchers in their studies related to 'omics' data, but also more general aspects concerning biological data analysis. This transdisciplinary network is a platform for discussion, sharing, training and support between scientists interested in bioinformatics and related fields. Starting from a little archipelago in the Caribbean, we envision to facilitate exchange between other Caribbean partners in the future, knowing that the Caribbean is a region with non-negligible biodiversity which should be preserved and protected. Joining forces with other Caribbean countries or territories would strengthen scientific collaborative impact in the region. Information related to this network can be found at: http://www.pasteur-guadeloupe.fr/karubionet.html. Furthermore, a dedicated 'Galaxy KaruBioNet' platform is available at: http://calamar.univ-ag.fr/c3i/galaxy_karubionet.html. Availability and implementation Information about KaruBioNet is availabe at: http://www.pasteur-guadeloupe.fr/karubionet.html. Contact: dcouvin@pasteur-guadeloupe.fr. Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Germ cell apoptosis is critical to maintain Caenorhabditis elegans offspring viability in stressful environments.

Maintaining reproduction in highly variable, often stressful, environments is an essential challenge for all organisms. Even transient exposure to mild environmental stress may directly damage germ cells or simply tax the physiology of an individual, making it difficult to produce quality gametes. In Caenorhabditis elegans, a large fraction of germ cells acts as nurse cells, supporting developing oocytes before eventually undergoing so-called physiological germ cell apoptosis. Although C. elegans apoptosis has been extensively studied, little is known about how germline apoptosis is influenced by ecologically relevant environmental stress. Moreover, it remains unclear to what extent germline apoptosis contributes to maintaining oocyte quality, and thus offspring viability, in such conditions. Here we show that exposure to diverse environmental stressors, likely occurring in the natural C. elegans habitat (starvation, ethanol, acid, and mild oxidative stress), increases germline apoptosis, consistent with previous reports on stress-induced apoptosis. Using loss-of-function mutant alleles of ced-3 and ced-4, we demonstrate that eliminating the core apoptotic machinery strongly reduces embryonic survival when mothers are exposed to such environmental stressors during early adult life. In contrast, mutations in ced-9 and egl-1 that primarily block apoptosis in the soma but not in the germline, did not exhibit such reduced embryonic survival under environmental stress. Therefore, C. elegans germ cell apoptosis plays an essential role in maintaining offspring fitness in adverse environments. Finally, we show that ced-3 and ced-4 mutants exhibit concomitant decreases in embryo size and changes in embryo shape when mothers are exposed to environmental stress. These observations may indicate inadequate oocyte provisioning due to the absence of germ cell apoptosis. Taken together, our results show that the central genes of the apoptosis pathway play a key role in maintaining gamete quality, and thus offspring fitness, under ecologically relevant environmental conditions.

The Genetics of Thermoregulation in Pigs: A Review.

Heat stress (HS) affects pig performance, health and welfare, resulting in a financial burden to the pig industry. Pigs have a limited number of functional sweat glands and their thermoregulatory mechanisms used to maintain body temperature, are challenged by HS to maintain body temperature. The genetic selection of genotypes tolerant to HS is a promising long-term (adaptation) option that could be combined with other measures at the production system level. This review summarizes the current knowledge on the genetics of thermoregulation in pigs. It also discusses the different phenotypes that can be used in genetic studies, as well as the variability in thermoregulation between pig breeds and the inheritance of traits related to thermoregulation. This review also considers on-going challenges to face for improving heat tolerance in pigs.

Systematic Review of the Interaction between Nutrition and Immunity in Livestock: Effect of Dietary Supplementation with Synthetic Amino Acids.

Infectious diseases represent one of the most critical threats to animal production worldwide. Due to the rise of pathogen resistance and consumer concern about chemical-free and environmentally friendly productions, the use of antimicrobials drugs is no longer desirable. The close relationship between nutrition and infection has led to numerous studies about livestock. The impact of feeding strategies, including synthetic amino acid supplementation, on host response to various infections has been investigated in different livestock animals. This systematic review provides a synthesis of the experimental studies on the interactions between synthetic amino acid supplementation and immune response to infectious diseases in livestock. Following PRISMA guidelines, quantitative research was conducted using two literature databases, PubMed and Web of Science. The eligibility criteria for the research articles were: (1) the host is a livestock animal; (2) the supplementation with at least one synthetic amino acid; (3) at least one mediator of immunity is measured; (4) at least one production trait is measured. Data were extracted from 58 selected studies. Articles on poultry were the most numerous; few contained experiments using ruminants and pigs. Most of the authors hypothesized that synthetic amino acid supplementation would particularly improve the animals' immune response against intracellular pathogens. An increase in T and natural killer lymphocytes and macrophages activation, intracellular redox state, lymphocytes proliferation and antibodies production were the most described immune mechanisms associated with synthetic amino acid supplementation. Most of the selected studies focused on three amino acids (methionine, threonine and arginine), all of which are associated with a significant improvement of the host immune response. The use of synthetic amino acid supplementation appears as an encouraging perspective for livestock infectious disease management, and research must concentrate on more analytical studies using these three amino acids.

Mechanical instabilities of aorta drive blood stem cell production: a live study.

During embryogenesis of all vertebrates, haematopoietic stem/progenitor cells (HSPCs) extrude from the aorta by a complex process named endothelial-to-haematopoietic transition (EHT). HSPCs will then colonize haematopoietic organs allowing haematopoiesis throughout adult life. The mechanism underlying EHT including the role of each aortic endothelial cell (EC) within the global aorta dynamics remains unknown. In the present study, we show for the first time that EHT involves the remodelling of individual cells within a collective migration of ECs which is tightly orchestrated, resulting in HSPCs extrusion in the sub-aortic space without compromising aorta integrity. By performing a cross-disciplinary study which combines high-resolution 4D imaging and theoretical analysis based on the concepts of classical mechanics, we propose that this complex developmental process is dependent on mechanical instabilities of the aorta preparing and facilitating the extrusion of HSPCs.

Genotype by environment interactions for performance and thermoregulation responses in growing pigs1,2.

Heat stress affects pig health, welfare, and production, and thus the economic viability of the pig sector in many countries. Breeding for heat tolerance is a complex issue, increasingly important due to climate change and the development of pig production in tropical areas. Characterizing genetic determinism of heat tolerance would help building selection schemes dedicated to high performance in tropical areas. The main objective of our study was to estimate the genetic parameters for production and thermoregulation traits in two highly related growing pig populations reared in temperate (TEMP) or tropical humid (TROP) environment. Pigs came from a backcross population between Large White (LW, heat sensitive) and Creole (CR, heat tolerant) pigs. Phenotypic data were obtained on a total of 1,297 pigs using the same procedures in both environments, for body weight (BW, at weeks 11 and 23), daily feed intake (ADFI), backfat thickness (BFT, at weeks 19 and 23), cutaneous temperature (CT, at weeks 19 and 23), and rectal temperature (RT, at weeks 19, 21, and 23). Feed conversion ratio (FCR) and residual feed intake (RFI) were computed for the whole test period (11 to 23 wk). Criteria comparing the fits to the data revealed genotype × environment (G × E) interactions for most traits but not for FCR. The variance components were obtained using two different methods, a restricted maximum likelihood method and a Bayesian Markov chain Monte Carlo method, considering that traits are either similar or different in each environment. Regardless of the method, heritability estimates for production traits were moderate to high, except for FCR (lower than 0.18). Heritability estimates for RT were low to moderate, ranging from 0.04 to 0.34. The genetic correlations of each trait between environments generally differed from 1, except for FCR and ADG. For most thermoregulation traits, they also did not differ significantly from zero, suggesting that the main genetic bases of heat tolerance may vary in different environment. Within environments, the unfavorable genetic correlations between production traits and RT suggest an antagonism between the ability to maintain inner temperature and the ability to increase ADFI and ADG. However, greater RT were also associated to leaner pigs and better feed efficiency. Nevertheless, due to large inaccuracies of these estimations, larger cohorts would be needed to decide about the best breeding schemes to choose for tropical pig production.

Effect of feed restriction and refeeding on performance and metabolism of European and Caribbean growing pigs in a tropical climate.

Reduction in feed intake is a common physiological response of growing pigs facing stressful environmental conditions. The present experiment aims to study (1) the effects of a short-term feed restriction and refeeding on pig performance and metabolism and (2) the differential response between two breeds, Large White (LW), which has been selected for high performance, and Creole (CR), which is adapted to tropical conditions. A trial of 36 castrated male pigs (18 LW and 18 CR) was carried out. For each breed, half of the animals were restrictively fed at 50% of the standard feed allowance for 6 days and then fed normally for the next 14 days. Growth performance, thermoregulatory responses, plasma hormones and metabolites were measured. Results showed that, for all traits, the difference in response between the two breeds was small and rarely significant, which may be due to the short duration of the feed restriction. Irrespective of breed, feed restriction induced a reduction of growth rate and feed efficiency that was rapidly compensated for upon refeeding. Feed restriction also reduced skin temperature, rectal temperature and respiratory rate, as well as blood urea and cholesterol, which are of interest as potential biomarkers for feed restriction.

Complex heterochrony underlies the evolution of Caenorhabditis elegans hermaphrodite sex allocation.

Hermaphroditic organisms are key models in sex allocation research, yet the developmental processes by which hermaphrodite sex allocation can evolve remain largely unknown. Here we use experimental evolution of hermaphrodite-male (androdioecious) Caenorhabditis elegans populations to quantify the developmental changes underlying adaptive shifts in hermaphrodite sex allocation. We show that the experimental evolution of increased early-life self-fertility occurred through modification of a suite of developmental traits: increased self-sperm production, accelerated oogenesis and ovulation, and increased embryo retention. The experimental evolution of increased self-sperm production delayed entry into oogenesis-as expected, given the sequentially coupled production of self-spermatogenesis and oogenesis. Surprisingly, however, delayed oogenesis onset did not delay reproductive maturity, nor did it trade-off with gamete or embryo size. Comparing developmental time dynamics of germline and soma indicates that the evolution of increased sperm production did not delay reproductive maturity due to a globally accelerated larval development during the period of self-spermatogenesis. Overall, heterochrony in gametogenesis and soma can explain adaptive shifts in hermaphrodite sex allocation.

Convergent evolution of sperm gigantism and the developmental origins of sperm size variability in Caenorhabditis nematodes.

Sperm cells provide essential, if usually diminutive, ingredients to successful sexual reproduction. Despite this conserved function, sperm competition and coevolution with female traits can drive spectacular morphological change in these cells. Here, we characterize four repeated instances of convergent evolution of sperm gigantism in Caenorhabditis nematodes using phylogenetic comparative methods on 26 species. Species at the extreme end of the 50-fold range of sperm-cell volumes across the genus have sperm capable of comprising up to 5% of egg-cell volume, representing severe attenuation of the magnitude of anisogamy. Furthermore, we uncover significant differences in mean and variance of sperm size among genotypes, between sexes, and within and between individuals of identical genotypes. We demonstrate that the developmental basis of sperm size variation, both within and between species, becomes established during an early stage of sperm development at the formation of primary spermatocytes, while subsequent meiotic divisions contribute little further sperm size variability. These findings provide first insights into the developmental determinants of inter- and intraspecific sperm size differences in Caenorhabditis. We hypothesize that life history and ecological differences among species favored the evolution of alternative sperm competition strategies toward either many smaller sperm or fewer larger sperm.

Evolutionarily divergent thermal sensitivity of germline development and fertility in hermaphroditic Caenorhabditis nematodes.

Thermal developmental plasticity represents a key organismal adaptation to maintain reproductive capacity in contrasting and fluctuating temperature niches. Although extensively studied, research on thermal plasticity has mainly focused on phenotypic outcomes, such as adult life history, rather than directly measuring plasticity of underlying developmental processes. How thermal plasticity of developmental phenotypes maps into plasticity of resulting final phenotypes, and how such mapping relationships evolve, thus remain poorly understood. Here we address these questions by quantifying thermal plasticity of Caenorhabditis hermaphrodite germline development. We integrate measurements of germline development and fertility at the upper thermal range in isolates of C. briggsae, C. elegans, and C. tropicalis. First, we compare intra- and interspecific variation in thermal germline plasticity with plasticity in reproductive output. Second, we ask whether the developmental errors leading to fertility break-down at upper thermal limits are evolutionarily conserved. We find that temperature variation modulates spermatogenesis, oogenesis and germ cell progenitor pools, yet the thermal sensitivity of these processes varies among isolates and species, consistent with evolutionary variation in upper thermal limits of hermaphrodite fertility. Although defective sperm function is a major contributor to heat-induced fertility break-down, high temperature also significantly perturbs oogenesis, germline integrity, and mitosis-meiosis progression. Remarkably, the occurrence and frequency of specific errors are strongly species- and genotype-dependent, indicative of evolutionary divergence in thermal sensitivity of distinct processes in germline development. Therefore, the Caenorhabditis reproductive system displays complex genotype-by-temperature interactions at the developmental level, which may remain masked when studying thermal plasticity exclusively at the life history level.

Sampling and Isolation of C. elegans from the Natural Habitat.

Wild populations of the model organism C. elegans allow characterization of natural genetic variation underlying diverse phenotypic traits. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes and/or mating tests. This protocol uses standard laboratory equipment and requires no prior knowledge of C. elegans biology.

The role of eIF1 in translation initiation codon selection in Caenorhabditis elegans.

The selection of a proper AUG start codon requires the base-pairing interactions between the codon on the mRNA and the anticodon of the initiator tRNA. This selection process occurs in a pre-initiation complex that includes multiple translation initiation factors and the small ribosomal subunit. To study how these initiation factors are involved in start codon recognition in multicellular organisms, we isolated mutants that allow the expression of a GFP reporter containing a non-AUG start codon. Here we describe the characterization of mutations in eif-1, which encodes the Caenorhabditis elegans translation initiation factor 1 (eIF1). Two mutations were identified, both of which are substitutions of amino acid residues that are identical in all eukaryotic eIF1 proteins. These residues are located in a structural region where the amino acid residues affected by the Saccharomyces cerevisiae eIF1 mutations are also localized. Both C. elegans mutations are dominant in conferring a non-AUG translation initiation phenotype and lead to growth arrest defects in homozygous animals. By assaying reporter constructs that have base changes at the AUG start codon, these mutants are found to allow expression from most reporters that carry single base changes within the AUG codon. This trend of non-AUG mediated initiation was also observed previously for C. elegans eIF2ß mutants, indicating that these two factors play a similar role. These results support that eIF1 functions in ensuring the fidelity of AUG start codon recognition in a multicellular organism.