Plasma concentrations of branched-chain amino acids differ with Holstein genetic strain in pasture-based dairy systems

In pasture-based systems, there are nutritional and climatic challenges exacerbated across lactation; thus, dairy cows require an enhanced adaptive capacity compared with cows in confined systems. We aimed to evaluate the effect of lactation stage (21 vs. 180 days in milk, DIM) and Holstein genetic strain (North American Holstein, NAH, n = 8; New Zealand Holstein, NZH, n = 8) on metabolic adaptations of grazing dairy cows through plasma metabolomic profiling and its association with classical metabolites. Although 67 metabolites were affected (FDR < 0.05) by DIM, no metabolite was observed to differ between genetic strains while only alanine was affected (FDR = 0.02) by the interaction between genetic strain and DIM. However, complementary tools for time-series analysis (ASCA analysis, MEBA ranking) indicated that alanine and the branched-chain amino acids (BCAA) differed between genetic strains in a lactation-stage dependent manner. Indeed, NZH cows had lower (P-Tukey < 0.05) plasma concentrations of leucine, isoleucine and valine than NAH cows at 21 DIM, probably signaling for greater insulin sensitivity. Metabolic pathway analysis also revealed that, independently of genetic strains, AA metabolism might be structurally involved in homeorhetic changes as 40% (19/46) of metabolic pathways differentially expressed (FDR < 0.05) between 21 and 180 DIM belonged to AA metabolism.

Age, Sex and Strain Respond Differently to Acute Ritalin (Methylphenidate) Exposure

The dose-dependent response to variable methylphenidate (MPD) doses on the behavior of male and female adolescent (post-natal day 39) and adult (post-natal day 60) rats of three different genetic strains was studied to examine whether there are sex, age and strain dependent differences in response to MPD. Twenty-four male and twenty-four female groups were used. The 48 groups each had an N=8. The results show that female adolescents and adult rats of Sprague-Dawley (SD) and Spontaneous Hyperactive Rat (SHR) strains were more sensitive to the acute exposure of MPD. Furthermore, female adult rats of the SD, SHR and Wistar-Kyoto (WKY) strains generally responded with greater increase in locomotor activity than the adolescent females of these strains. In the WKY strain, adolescent males tended to experience a greater increase in activity than adult males. Lastly, significant differences in response to MPD also were observed among the three genetic strains. These variable responses to the acute dose of MPD reinforce the need to study the effects of this psychostimulant across the various sexes, ages and strains.

Sarcoptic mange in wild ruminants in Spain: solving the epidemiological enigma using microsatellite markers

Background In Spain, sarcoptic mange was first described in native wildlife in 1987 in Cazorla Natural Park, causing the death of nearly 95% of the local native population of Iberian ibex (Capra pyrenaica). Since then, additional outbreaks have been identified in several populations of ibex and other wild ungulate species throughout the country. Although the first epizootic outbreak in wildlife was attributed to the introduction of an infected herd of domestic goats, the origin and the cause of its persistence remain unclear. The main aims of this study are to understand (i) the number of Sarcoptes scabiei “strains” circulating in wild ruminant populations in Spain, and (ii) the molecular epidemiological relationships between S. scabiei and its hosts. Methods Ten Sarcoptes microsatellite markers were used to characterize the genetic structure of 266 mites obtained from skin scrapings of 121 mangy wild ruminants between 2011 and 2019 from 11 areas in Spain. Results Seventy-three different alleles and 37 private alleles were detected. The results of this study show the existence of three genetic strains of S. scabiei in the wild ruminant populations investigated. While two genetic clusters of S. scabiei were host- and geography-related, one cluster included multi-host mites deriving from geographically distant populations. Conclusions The molecular epidemiological study of S. scabiei in wild ruminants in Spain indicates that the spreading and persistence of the parasite may be conditioned by host species community composition and the permissiveness of each host population/community to the circulation of individual “strains,” among other factors. Wildlife–livestock interactions and the role of human-driven introduction or trade of wild and domestic animals should be better investigated to prevent further spread of sarcoptic mange in as yet unaffected natural areas of the Iberian Peninsula.

An Expanded Gene Catalog of Mouse Gut Metagenomes

ABSTRACT High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice. IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.

Emerging SARS-CoV-2 Lineages in Middle Eastern Jordan with Increasing Mutations Near Antibody Recognition Sites

The genomic analysis of the 556 viral sequences from Jordan uncovered three dominant genetic SARS-CoV-2 lineages that are currently circulating in Jordan: B.1.1.312 (76%), B.1.36.10 (11%), and B.1.1.7 (6%), replacing the genetic strains that were dominant before sustained community transmission in Jordan. This raises speculations about these new genetic lineages and their relationship to the severity of disease symptoms in Jordan.

A hotspot of Toxoplasma gondii Africa 1 lineage in Benin: How new genotypes from West Africa contribute to understand the parasite genetic diversity worldwide

Through international trades, Europe, Africa and South America share a long history of exchanges, potentially of pathogens. We used the worldwide parasite Toxoplasma gondii to test the hypothesis of a historical influence on pathogen genetic diversity in Benin, a West African country with a longstanding sea trade history. In Africa, T. gondii spatial structure is still non-uniformly studied and very few articles have reported strain genetic diversity in fauna and clinical forms of human toxoplasmosis so far, even in African diaspora. Sera from 758 domestic animals (mainly poultry) in two coastal areas (Cotonou and Ouidah) and two inland areas (Parakou and Natitingou) were tested for T. gondii antibodies using a Modified Agglutination Test (MAT). The hearts and brains of 69 seropositive animals were collected for parasite isolation in a mouse bioassay. Forty-five strains were obtained and 39 genotypes could be described via 15-microsatellite genotyping, with a predominance of the autochthonous African lineage Africa 1 (36/39). The remaining genotypes were Africa 4 variant TUB2 (1/39) and two identical isolates (clone) of Type III (2/39). No difference in terms of genotype distribution between inland and coastal sampling sites was found. In particular, contrarily to what has been described in Senegal, no type II (mostly present in Europe) was isolated in poultry from coastal cities. This result seems to refute a possible role of European maritime trade in Benin despite it was one of the most important hubs during the slave trade period. However, the presence of the Africa 1 genotype in Brazil, predominant in Benin, and genetic analyses suggest that the triangular trade was a route for the intercontinental dissemination of genetic strains from Africa to South America. This supports the possibility of contamination in humans and animals with potentially imported virulent strains.

Commercial vaccines do not confer protection against two genetic strains of Piscirickettsia salmonis, LF-89-like and EM-90-like, in Atlantic salmon.

In Atlantic salmon, vaccines have failed to control and prevent Piscirickettsiosis, for reasons that remain elusive. In this study, we report the efficacy of a commercial vaccine developed with the Piscirickettsia salmonis isolate AL100005 against other two isolates which are considered highly and ubiquitously prevalent in Chile: LF-89-like and EM-90-like. Two cohabitation trials were performed to mimic real-life conditions and vaccine performance: 1) post smolt fish were challenged with a single infection of LF-89-like, 2) adults were coinfected with EM-90-like and a low coinfection of sea lice. In the first trial, the vaccine delayed smolt mortalities by two days; however, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 60.3%, vaccinated: 56.7%; p = 0.28). In the second trial, mortality started three days later for vaccinated fish than unvaccinated fish. However, unvaccinated and vaccinated fish did not show significant differences in survival (unvaccinated: 64.6%, vaccinated: 60.2%, p= 0.58). Thus, we found no evidence that the evaluated vaccines confer effective protection against of LF-89-like or EM-90-like with estimated relative survival proportions (RPSs) of -9% and -12%, respectively. More studies are necessary to evaluate whether pathogen heterogeneity is a key determinant of the vaccine efficacy against P. salmonis.

Reestablishing a stepping-stone population of the threatened elkhorn coral Acropora palmata to aid regional recovery

Recovery of the elkhorn coral Acropora palmata is critical to reversing coral reef ecosystem collapse in the western Atlantic, but the species is severely threatened. To gauge potential for the species’ restoration in Florida, USA, we conducted an assisted migration experiment where 50 coral fragments of 5 nursery-raised genetic strains (genets) from the upper Florida Keys were moved to 5 sites across 350 km of the offshore reef. Additionally, 4 fragments from the 1 remaining colony of A. palmata in Dry Tortugas National Park (DRTO) were added to the 2 DRTO experimental sites to test for local adaptation. To measure coral performance, we tracked coral survival, calcification, growth, and condition from May 2018 to October 2019. All 24 corals relocated to the DRTO sites survived and calcified ~85% faster than the fewer surviving corals transplanted to the 2 upper Keys sites. While coral survival across the entire experiment did not depend on genet, there was a weak but statistically significant genetic effect on calcification rate among the corals relocated to DRTO. The DRTO native genet was among the fastest growing genets, but it was not the fastest, suggesting a lack of local adaptation at this scale. Our results indicate that DRTO, a remote reef system inhabited by the species during the Holocene and located at the nexus of major ocean currents, may be a prime location for reestablishing A. palmata. Assisted migration of A. palmata to DRTO could restore a sexually reproducing population in <10 yr, thereby promoting the species’ regional recovery.

Muscle Atrophy: Different Strains of Mice Respond Differently to Single Limb Immobilization

To examine whether genetic variability plays a role in muscle adaption to its mechanical environment, we examined hind limb immobilization in five different strains of mice: CAST/EiJ, NOD/ShiLtJ, NZO/HILtJ, 129S1/SvImJ and A/J. Mice had one limb immobilized by a cast for three weeks. The response to immobilization was dependent on the strain of mice examined. A/J mice lost the most body weight following immobilization and displayed a significant decrease in physical activity. None of the other strains displayed a significant decrease in activity. Food consumption was significantly increased in NOD/ShiLtJ mice. All other strains had non-significant changes in food consumption. Muscle mass/body weight was decreased by immobilization, to varying degrees, in all strains except 1291/SvImJ. Casting decreased absolute muscle mass in both quadriceps and gastrocnemius in NOD/ShiltJ and NZO/HILtJ mice, two strains that can develop diabetes, but not in the other strains. Three weeks of immobilization caused a significant increase in quadriceps levels of atrogenes in CAST/EiJ mice but not in other strains. Immobilization caused a significant increase in quadriceps and gastrocnemius levels of Myh4 in CAST/EiJ mice but not in any other strain. A similar trend was observed for Myh7 in gastrocnemius muscle. Immobilization resulted in a decrease the p-p70S6K1/total p706SK1 ratio in quadriceps of NOD/ShiLtJ mice and the gastrocnemius of A/J mice, but not in other strains. Immobilization did not affect the p-4EBP1/total 4EBP1 ratio in quadriceps of any of the strains examined. However, the p-4EBP1/total 4EBP1 ratio in gastrocnemius was greater in immobilized, relative to control, limbs in CAST/EiJ mice. Muscle mass normalized to body weight in both gastrocnemius and quadriceps displayed the greatest degree of heritability. These results reveal remarkable variability in responsiveness to immobilization across five different genetic strains of mice.