Evaluating the performance of genomic prediction accounting for effects of single nucleotide polymorphism markers in reproductive traits of Japanese Black cattle

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Abstract

We examined the prediction accuracies of genomic best linear unbiased prediction (GBLUP), various weighted GBLUP according to the degrees of marker effects (WGBLUP) and machine learning (ML) methods, and compared them with traditional BLUP for age at first calving (AFC), calving difficulty (CD), and gestation length in Japanese Black cattle. For WGBLUP, firstly, BayesC and FarmCPU were used to estimate marker effects. Then, we constructed three weighted genomic relationship matrices from information of estimated marker effects in the first step: absolute value of the estimated marker-effect WGBLUP, estimated marker-variance WGBLUP, and genomic-feature WGBLUP. For ML, we applied Gaussian kernel, random forest, extreme gradient boost, and support vector regression. We collected a total of 2583 animals having both phenotypic records and genotypes with 30,105 markers and 16,406 pedigree records. For AFC, prediction accuracies of WGBLUP methods using FarmCPU exceeded BLUP by 25.7%–39.5%. For CD, estimated marker-variance WGBLUP using BayesC achieved the highest prediction accuracy. Among ML methods, extreme gradient boost, support vector regression, and Gaussian kernel increased prediction accuracies by 28.4%, 19.0%, and 36.4% for AFC, CD, and gestation length compared with BLUP, respectively. Thus, prediction performance could be improved using suitable WGBLUP and ML methods according to target reproductive traits for the population used.

Mean age at menarche and climate variables on a global scale

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Abstract

Objectives

Cross-population variation in age at menarche is related to many factors. The purpose of this study was to examine climate variables in relation to mean age at menarche among 87 modern human populations. We hypothesized a later age at menarche among populations living in areas with high precipitation variability, heavy seasonal rainfall, and high temperatures year-round due to water-borne diseases and periods of resource scarcity.

Methods

Using a comparative dataset, we examined geospatial distribution and climate variables in relation to age at menarche for 87 modern human populations.

Results

We found the strongest predictor of a later age at menarche was higher fertility followed by a later mean age at death. In addition, higher annual rainfall, higher precipitation seasonality, and lower annual mean temperature were moderate predictors of age at menarche.

Conclusions

We propose that later ages at menarche in countries with high fertility may be a life-history strategy developed in response to climatic conditions that have resulted in higher immunological load. In these conditions, females may prioritize growth rather than reproduction. Shifts in climate and global population growth may change the future biological landscape of age at menarche.

Differences in thermal energetics of the cave myotis (Myotis velifer) from a cool and a warm environment of central Mexico

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Canadian Journal of Zoology, Ahead of Print.
Endotherm homeotherms deal with the energetic cost of maintaining a stable body temperature (Tb) in ecosystems differing in ambient temperature (Ta). In response, animals adjust some of their thermal energetics to meet the energy requirements of thermoregulation. Bats are small mammals with a geographical distribution that may include environments with different Ta. Therefore, these animals should adjust their thermal energetics depending on the environmental characteristics of the habitats where they live. Using open-flow respirometry, we measured basal metabolic rate (BMR), thermal conductance (C’), lower and upper critical temperatures (TLC and TUC), and breadth of the thermoneutral zone (TNZb) of the cave myotis (Myotis velifer (J.A. Allen, 1890)) living in a coniferous forest versus a tropical deciduous forest in central Mexico. To our knowledge, this is the first attempt to measure thermal energetics at the intraspecific level in populations measured at the same time. Bats from the coniferous forest had lower BMR, C’, TLC, TUC, and a wider TNZb than bats from the tropical deciduous forest. The results we found here are likely the consequence of the differences between the energy demands imposed by Ta, where the animals roost, and the Ta and prey availability of their foraging areas. These differences may help individuals regulate their heat production and dissipation to maintain low thermoregulatory costs in the places they inhabit.

The m6A modification of Il17a in CD4+ T cells promotes inflammation in psoriasis

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The m6A modification of Il17a in CD4+ T cells promotes inflammation in psoriasis

Molecular mechanism of m6A in CD4+ T cells in psoriasis.


Abstract

Psoriasis is a chronic inflammatory skin disorder. The mechanism of psoriasis pathogenesis is not entirely clear. Here, we reported that the level of the N6-methyladenosine (m6A) modification was increased in psoriatic CD4+ T cells compared with healthy controls. In the psoriasis mouse model, depletion of the RNA demethylase, Alkbh5, from CD4+ T cells promoted the psoriasis-like phenotype and inflammation. Intriguingly, this phenotype and inflammation were alleviated by the ablation of the m6A methyltransferase Mettl3 in CD4+ T cells. Mechanistically, we found that the m6A modification of IL17A mRNA increased the expression of IL-17A (an important pro-inflammatory factor in psoriasis) and promoted psoriasis. Thus, our study provided evidence that the m6A modification of IL17A in CD4+ T cells regulates inflammation in psoriasis.

Physiology of lipid digestion and absorption in poultry: An updated review on the supplementation of exogenous emulsifiers in broiler diets

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Abstract

Lipids are a concentrated source of energy with at least twice as much energy as the same amount of carbohydrates and protein. Dietary lipids provide a practical alternative toward increasing the dietary energy density of feeds for high-performing modern broilers. However, the digestion and absorption of dietary lipids are much more complex than that of the other macronutrients. In addition, young birds are physiologically limited in their capacity to utilise dietary fats and oils effectively. The use of dietary emulsifiers as one of the strategies aimed at improving fat utilisation has been reported to elicit several physiological responses including improved fat digestibility and growth performance. In practical terms, this allows for the incorporation of lipids into lower-energy diets without compromising broiler performance. Such an approach may potentially lower feed costs and raise revenue gains. The current review revisits lipids and the different roles that they perform in diets and whole-body metabolism. Additional information on the process of dietary lipid digestion and absorption in poultry; and the physiological limitation brought about by age on lipid utilisation in the avian gastrointestinal tract have been discussed. Subsequently, the physiological responses resulting from the dietary supplementation of exogenous emulsifiers as a strategy for improved lipid utilisation in broiler nutrition are appraised. Suggestions of nascent areas for a better understanding of exogenous emulsifiers have been highlighted.

Label‐free proteomic analysis reveals an estrous cycle transition between the follicular phase and the luteal phase in yak ovary

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Abstract

In order to further study the physiological mechanism about yak reproduction for the improvement of its fertility, differentially expressed proteins (DEGs) of the ovary were screened during the follicular and luteal phases of yak based on label-free quantitative proteomics. The main research results were as follows: it discovered 2867 proteins during the follicular phase and 2180 proteins during the luteal phase, among which there were 2011 proteins of expression during both phases, 856 during the follicular phase, and 169 during the luteal phase. According to the bioinformatics and Gene Ontology analysis, the screened differentially expressed proteins were mostly located in the cell membrane and extracellular region and primarily acted on the activity of laminin. Kyoto Encyclopedia of Genes and Genomes analysis indicated that the main involvement of differentially expressed proteins included steroid biosynthesis, chemokine signaling pathway, protein processing in the endoplasmic reticulum, glycerol phospholipid metabolism, carbon metabolism, PI3K-Akt signaling pathways, PPAR signaling pathways, nucleotide oligomerization domain (NOD) receptor signaling pathways, and purine metabolic pathways. Screened proteins related to reproductive function, so as to lay a theoretical foundation for the in-depth study of the regulation mechanism of yak reproduction and improve its fertility.

Heat enhances the inhibitory effect of lipopolysaccharide on duck granulosa cell proliferation and steroid biosynthesis in vitro

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Abstract

Lipopolysaccharide (LPS) reduces the reproductive performance of laying ducks, especially during the hot summer months. To study the underlying mechanisms, we investigated the effects of different LPS concentrations and heat on duck granulosa cell (GC) proliferation and steroid biosynthesis in vitro. We investigated GC proliferation, secretion, and activation of the MAPK pathway. The cell cycle results showed that LPS treatment alone did not significantly affect cell proliferation, whereas the mRNA expression levels of IGF2, IGFBP2, and CyclinD1 were downregulated and p27kip1 was significantly upregulated after 2000 ng/mL LPS treatment when compared to untreated cells. In steroid hormone synthesis, although LPS increased the expression of most steroid biosynthesis genes, it inhibited the expression of CYP11A1 at high LPS concentrations. High temperatures enhanced the inhibitory effect of LPS on the expression of proliferation-promoting genes. Heat significantly reduced CYP11A1 and CYP19A1 expression. In addition, the phosphorylation of P38 was significantly upregulated by high temperatures combined with LPS, whereas the phosphorylation of ERK1/2 and JNK was downregulated. The relative protein expression of Bax/BCL-2 was upregulated at high temperatures in combination with LPS. Heat treatment enhanced the inhibitory effects of LPS on the proliferation and hormone biosynthesis of duck GCs in vitro.

The effects of dietary microbial 6‐phytase on growth parameters, intestinal morphometric properties and selected intestinal genes expression in rainbow trout (Oncorhynchus mykiss, Walbaum 1876)

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Abstract

This study investigated the effects of dietary 6-phytase, produced by a genetically modified Komagataella phaffii, on growth performance, feed utilisation, flesh quality, villus morphometric properties, and intestinal mRNA expression in rainbow trout. Six iso-nitrogenous, iso-lipidic, and iso-caloric diets were formulated and fed to triplicate groups of juvenile rainbow trout weighing 32.57 ± 0.36 g (mean ± SD) for 90 days. The dietary treatments included two positive controls (PC), one formulated with 400 g/kg of fish meal named T1, and the other formulated with 170 g/kg of fish meal plus 1% avP derived from monocalcium phosphate named T2. The remaining dietary treatments consisted of a negative control (NC) formulated with 170 g/kg of fish meal (T3), NC+ 750, NC+ 1500, and NC+ 3000 OTU/kg levels of phytase designated as T4, T5, and T6 diets respectively. Compared to T1, weight gain (WG) increased by 16.29, 13.71 and 11.66% in T4, T5 and T6, respectively (p < 0.05). Feed conversion ratio (FCR) was lowered by 3.2 and 0.8% in T4 and T5 compared to T1 (p < 0.05). WG, feed intake (FI), FCR, final body length, bone ash, bone ash P, and intestinal morphometry were negatively affected in T3 fed fish (p < 0.05). Whole-body fish nutrient, bone ash, bone ash phosphorus (P) compositions and mucosal villus morphometric properties improved in rainbow trout fed diets supplemented with phytase dose ranging from 750–3000 OTU. Bone ash increased by 6.12% in T5 compared to T1 (p < 0.05). Phytase inclusion enhanced the profitability of feeding juvenile rainbow trout such diets as it reduced the feed price and economic conversion rate. Dietary inclusion of phytase down-regulated mRNA expression of genes responsible for fatty acid synthesis and lipogenesis in juvenile rainbow trout. Dietary phytase up-regulated the mRNA expression of genes (SLC4A11 and ATP1A3A) responsible for nutrient uptake and down-regulated intestinal expression of MUCIN 5AC—like genes (mucus secreting genes) in juvenile rainbow trout. Along with improving performance parameters, the inclusion of phytase in rainbow trout diet containing plant-based protein sources, can preserve intestinal morphology by regulating the mRNA expression of genes responsible for fatty acid synthesis, lipogenesis and nutrient uptake and transport.

A novel lncRNA LOC105613571 binding with BDNF in pituitary promotes gonadotropin secretion by AKT/ERK‐mTOR pathway in sheep associated with prolificacy

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A novel lncRNA LOC105613571 binding with BDNF in pituitary promotes gonadotropin secretion by AKT/ERK-mTOR pathway in sheep associated with prolificacy

Candidate lncRNA LOC105613571 targeted BDNF via trans-regulated relationships was characterized by pituitary transcriptome from Hu sheep with high and low fecundity. GnRH stimulation increased BDNF and lncRNA LOC105613571 expression in pituitary cells. BDNF-binding lncRNA LOC105613571 promotes pituitary gonadotropin secretion by activating AKT/ERK-mTOR pathway in pituitary cells.


Abstract

The pituitary is a vital endocrine organ for synthesis and secretion of gonadotropic hormones (FSH and LH), and the gonadotropin showed fluctuations in animals with different fecundity. Long non-coding RNAs (lncRNAs) have been identified as regulatory factors for the reproductive process. However, the profiles of lncRNAs and their roles involved in sheep fecundity remains unclear. In this study, we performed RNA-sequencing for the sheep pituitary gland associated with different fecundity, and identified a novel candidate lncRNA LOC105613571 targeting BDNF related to gonadotropin secretion. Our results showed that expression of lncRNA LOC105613571 and BDNF could be significantly upregulated by GnRH stimulation in sheep pituitary cells in vitro. Notably, either lncRNA LOC105613571 or BDNF silencing inhibited cell proliferation while promoted cell apoptosis. Moreover, lncRNA LOC105613571 knockdown could also downregulate gonadotropin secretion via inactivation AKT, ERK and mTOR pathway. In addition, co-treatment with GnRH stimulation and lncRNA LOC105613571 or BDNF knockdown showed the opposite effect on sheep pituitary cells in vitro. In summary, BDNF-binding lncRNA LOC105613571 in sheep regulates pituitary cell proliferation and gonadotropin secretion via the AKT/ERK-mTOR pathway, providing new ideas for the molecular mechanisms of pituitary functions.