Host evolution shapes gut microbiome composition in Astyanax mexicanus.

The ecological and genetic changes that underlie the evolution of host-microbe interactions remain elusive, primarily due to challenges in disentangling the variables that alter microbiome composition. To understand the impact of host habitat, host genetics, and evolutionary history on microbial community structure, we examined gut microbiomes of river- and three cave-adapted morphotypes of the Mexican tetra, Astyanax mexicanus, in their natural environments and under controlled laboratory conditions. Field-collected samples were dominated by very few taxa and showed considerable interindividual variation. We found that lab-reared fish exhibited increased microbiome richness and distinct composition compared to their wild counterparts, underscoring the significant influence of habitat. Most notably, however, we found that morphotypes reared on the same diet throughout life developed distinct microbiomes suggesting that genetic loci resulting from cavefish evolution shape microbiome composition. We observed stable differences in Fusobacteriota abundance between morphotypes and demonstrated that this could be used as a trait for quantitative trait loci mapping to uncover the genetic basis of microbial community structure.

Effects of genotype × environment interaction on the estimation of genetic parameters and gains in Nile tilapia.

Nile tilapia (Oreochromis niloticus) is the major fish species produced in Brazil, a country with a vast territory and great climate diversity. This study assessed the effects of the genotype × environment interaction on heritability estimates and selection responses in Nile tilapia (Tilamax strain) cultivated in earthen ponds and net cages. The weight at harvest, trunk length, and head percentage of 4400 individuals were determined. Trait heritabilities were higher in pond fish (0.27-0.52) than in caged fish (0.09-0.33). Genetic correlations between farming systems were lower than 0.5 for the three traits. The rank position of the top 10 families differed according to the environment, as did the response to direct and indirect selection. The results revealed significant genotype × environment effects on the heritability of Nile tilapia farmed under different systems.

TMEM176A and TMEM176B Are Candidate Regulators of Inhibition of Dendritic Cell Maturation and Function after Chronic Spinal Cord Injury.

Inhibition of dendritic cell maturation and activation, together with abnormal functioning of cell-mediated immunity, has been reported in chronic spinal cord injury (SCI). The development of immune-based therapies could: 1) prevent or slow down limit further tissue damage in chronic SCI, and 2) promote tissue regeneration. To identify novel candidate molecular pathways mediating SCI-induced immune changes, we performed whole-genome microarray and molecular pathway analyses. Subjects with motor complete chronic SCI (> 2 years post-injury) and uninjured controls were selected from an ongoing study. Microarray analysis was performed with RNA extracted from circulating monocytes. Partek Genomic Suite (PGS) software was used to limit the 54,000 gene list to only those genes up-regulated or down-regulated by 2-fold or more in SCI compared with control. Pathway analyses were performed with Ingenuity Systems IPA software to identify biological pathways of interest involving differentially expressed genes. Genes of interest were then confirmed by quantitative PCR (qPCR). Six SCI subjects and five uninjured controls were included in the final analyses. A molecular pathway related to immune cell trafficking was identified as being significantly upregulated in the SCI subjects. Two genes in that network, transmembrane domain protein (TMEM)176A and TMEM176B, were notable for the magnitude of overexpression. Dendritic cells have been shown to mediate recovery and/or protective autoimmunity in central nervous system injuries and have the capacity to induce neuroprotection and neurogenesis in stroke patients. High TMEM176A and TMEM176B levels have been shown to prevent dendritic cell maturation and inhibit dendritic cell activity in the general population. Here, we report overexpression of both genes in SCI compared with control subjects. Thus, we propose that TMEM176A and TMEM176B are candidate genes involved in inhibiting protective immune responses in SCI. This study may support future research aimed at developing new targets for therapies to promote immune system-mediated neuroprotection and recovery in SCI.

Correlated changes in body shape after five generations of selection to improve growth rate in a breeding program for Nile tilapia Oreochromis niloticus in Brazil.

Body shape is a commercial trait of great interest as it impacts profit and productivity of aquaculture enterprises. In the present study, we examined correlated changes in two measures of body shape (depth to length ratio, DL-R and ellipticity of mid sagittal plane, EL-H) from a selection program for high daily weight gain in a Nile tilapia population reared in freshwater cages in Brazil. Genetic parameters for body shape and its genetic association with growth traits (body weight and daily gain) were also estimated from 8,725 individuals with growth performance recorded over five generations from 2008 to 2013. Mixed model analysis showed that the selection program resulted in substantial improvement in growth performance (about 4 % genetic gain per generation or per year) and also brought about trivial changes in body shape. The heritabilities ranged from 0.470 to 0.564 for growth traits and 0.180 to 0.289 for body shape. The common family effects were low for all traits studied, accounting for only 3-11 % of total phenotypic variance. The genetic correlations between body shape and growth traits were weak, i.e., -0.385 between EL-H and growth traits and 0.28 between DL-R and body weight or daily gain. Strong and negative genetic association was found between the two body shape traits (rg = --0.955). Harvest body weight and daily gain are essentially the same traits, as indicated by the close to one genetic correlations between the two characters. Our results demonstrated that the selection process to increase growth rate had small, but slowly constant effect in body shape traits; and in the long term, the fish would have become rotund.