Rabbit SLC15A1, SLC7A1 and SLC1A1 genes are affected by site of digestion, stage of development and dietary protein content

Regulation of Paracellular Fluxes of Amino Acids by Claudin-8 in Normal Mouse Intestinal MCE301 Cells

The ingested proteins are catabolized to di/tri-peptides and amino acids (AAs), which are absorbed through various transporters in the small intestinal and colonic epithelial cells. Tight junctions (TJs) are formed between neighboring cells and restrict paracellular fluxes to mineral ions and aqueous molecules. However, it is unknown whether the TJs are implicated in the control of paracellular fluxes to AAs. The paracellular permeability is controlled by claudins (CLDNs), which comprise a family of over 20 members. Here, we found that CLDN8 expression is decreased by AAs deprivation in normal mouse colon-derived MCE301 cells. The reporter activity of CLDN8 was not significantly changed by AAs deprivation, whereas the stability of CLDN8 protein was decreased. MicroRNA analysis showed that AAs deprivation increases the expression of miR-153-5p which targets CLDN8. The AAs deprivation-induced decline of CLDN8 expression was reversed by a miR-153-5p inhibitor. The CLDN8 silencing enhanced the paracellular fluxes to AAs, especially middle molecular size AAs. The expression levels of colonic CLDN8 and miR-153-5p in aged mice were lower and higher than those in young mice, respectively. We suggest that AAs deprivation downregulates CLDN8-dependent barrier function, mediated by the elevation of miR-153-5p expression in the colon, in order to enhance the AAs absorption.

Genome-wide allele and haplotype-sharing patterns suggested one unique Hmong-Mein-related lineage and biological adaptation history in Southwest China

BACKGROUND

Fine-scale genetic structure of ethnolinguistically diverse Chinese populations can fill the gap in the missing diversity and evolutionary landscape of East Asians, particularly for anthropologically informed Chinese minorities. Hmong-Mien (HM) people were one of the most significant indigenous populations in South China and Southeast Asia, which were suggested to be the descendants of the ancient Yangtze rice farmers based on linguistic and archeological evidence. However, their deep population history and biological adaptative features remained to be fully characterized.

OBJECTIVES

To explore the evolutionary and adaptive characteristics of the Miao people, we genotyped genome-wide SNP data in Guizhou HM-speaking populations and merged it with modern and ancient reference populations via a comprehensive population genetic analysis and evolutionary admixture modeling.

RESULTS

The overall genetic admixture landscape of Guizhou Miao showed genetic differentiation between them and other linguistically diverse Guizhou populations. Admixture models further confirmed that Miao people derived their primary ancestry from geographically close Guangxi Gaohuahua people. The estimated identity by descent and effective population size confirmed a plausible population bottleneck, contributing to their unique genetic diversity and population structure patterns. We finally identified several natural selection candidate genes associated with several biological pathways.

CONCLUSIONS

Guizhou Miao possessed a specific genetic structure and harbored a close genetic relationship with geographically close southern Chinese indigenous populations and Guangxi historical people. Miao people derived their major ancestry from geographically close Guangxi Gaohuahua people and experienced a plausible population bottleneck which contributed to the unique pattern of their genetic diversity and structure. Future ancient DNA from Shijiahe and Qujialing will provide new insights into the origin of the Miao people.

Genome-wide evaluation of copy gain and loss variations in three Afghan sheep breeds

Copy number variation (CNV) is one of the main sources of variation between different individuals that has recently attracted much researcher interest as a major source for heritable variation in complex traits. The aim of this study was to identify CNVs in Afghan indigenous sheep consisting of three Arab, Baluchi, and Gadik breeds using genomic arrays containing 53,862 single nucleotide polymorphism (SNP) markers. Data were analyzed using the Hidden Markov Model (HMM) of PennCNV software. In this study, out of 45 sheep studied, 97.8% (44 animals) have shown CNVs. In total, 411 CNVs were observed for autosomal chromosomes and the entire sequence length of around 144 Mb was identified across the genome. The average number of CNVs per each sheep was 9.13. The identified CNVs for Arab, Baluchi, and Gadik breeds were 306, 62, and 43, respectively. After merging overlapped regions, a total of 376 copy number variation regions (CNVR) were identified, which are 286, 50, and 40 for Arab, Baluchi, and Gadik breeds, respectively. Bioinformatics analysis was performed to identify the genes and QTLs reported in these regions and the biochemical pathways involved by these genes. The results showed that many of these CNVRs overlapped with the genes or QTLs that are associated with various pathways such as immune system development, growth, reproduction, and environmental adaptions. Furthermore, to determine a genome-wide pattern of selection signatures in Afghan sheep breeds, the unbiased estimates of FST was calculated and the results indicated that 37 of the 376 CNVRs (~ 10%) have been also under selection signature, most of those overlapped with the genes influencing production, reproduction and immune system. Finally, the statistical methods used in this study was applied in an external dataset including 96 individuals of the Iranian sheep breed. The results indicated that 20 of the 114 CNVRs (18%) identified in Iranian sheep breed were also identified in our study, most of those overlapped with the genes influencing production, reproduction and immune system. Overall, this is the first attempts to develop the genomic map of loss and gain variation in the genome of Afghan indigenous sheep breeds, and may be important to shed some light on the genomic regions associated with some economically important traits in these breeds.

Transcriptomic analysis and transgenerational effects of ZnO nanoparticles on Daphnia magna: Endocrine-disrupting potential and energy metabolism

The widespread application of zinc oxide nanoparticles (ZnO NPs) has raised concerns over the adverse effects on aquatic species. In this study, transcriptomic analysis was applied to evaluate the chronic toxicity of ZnO NPs on the freshwater invertebrate Daphnia magna and the intergenerational effects were then further investigated. Parent daphnia (F0) were exposed to ZnO NPs at 3, 60, and 300 μg L^-1 for 21 days. ZnO NPs significantly inhibited the reproduction (first pregnancy and spawning time, total number of offspring) and growth (molting frequency and body length) of F0. Here, differentially expressed genes (DEGs) involved in lysosomal and phagosome, energy metabolism and endocrine disruption pathways were significantly downregulated. Furthermore, disruption on the transport and catabolic processes probably resulted in the particle accumulation. The inhibited pathways related to energy metabolism may partially account for the body length, molting and reproductive restriction. The suppression of growth and reproduction may attribute to the down-regulation of insulin secretion and ovarian steroidogenesis pathways, respectively. Partial recovery of growth and reproductive inhibition in F1 - F3 descended from the F0 generation exposure did not support constant transgenerational effects. This study unravels the molecular mechanisms and transgenerational consequences of the toxicity of nanoparticles on Daphnia.

The expression of nutrient chemosensing gate molecules in the ileum and colon is altered for goats fed on a high-grain diet

Limited knowledge is clarified about alterations in the related expression of nutrient chemosensors in the distal small intestine and hindgut under a high-grain (HG) diet in small ruminants. Herein, this study was performed to investigate the expression changes related to nutrient sensing and transport in the ileal and colonic epithelium of goats in response to feeding an HG diet. Twelve Liuyang black goats (similar age and weight) were randomly assigned into two groups: an HG diet (concentrate: hay = 90:10) and a CON diet (concentrate: hay = 55:45). Immunohistochemistry was applied to detect morphological changes in the gut epithelium together with altered expression of chemosensors in the ileum and colon. The results showed that feeding an HG diet increased ileal villus height and depth and induced mucosal sloughing in the colon. The expressions of the nutrient transporters GLUT2, GLUT5, SGLT2, CD36, rBAT, EAAT3, and LAT2 and sensing receptors GPR43 and T1R1 were promoted in the ileum under HG conditions. Moreover, feeding an HG diet also enhanced the expression of GLUT2, SGLT2, CD36, and GPR43 in the colon. These findings indicate that adaptation of the gastrointestinal tract to the HG diet promoted the absorption of glucose, fatty acids, and amino acids in goats.

Dietary lysine supplementation improves growth performance and skeletal muscle development in rabbits fed a low protein diet

The purpose of this study was to investigate the effects on growth of Lysine (Lys) supplementation in a low protein diet. We also investigated the gene or protein expression related to skeletal muscle development and intestinal amino acid transporters, and determined the major signalling associated with Lys-regulating skeletal muscle development. 1000 healthy, weights averaging 938.6 ± 6.54 g weaned rabbits were randomly divided into five groups (five replicates in each group and 40 rabbits in each replicate). These groups consisted of the normal protein group (NP group, consuming a diet containing 16.27% protein), the low protein group (LP group, 14.15%-14.19% protein) and the LP group with an addition of 0.15%, 0.3% or 0.45% Lys. The trial included 7 d of pre-feeding and 28 d of exposure to the treatment. Compared with NP diet and LP diet, LP+0.3% Lys group improved growth performance (p < 0.05), full-bore weight and half-bore weight of rabbits (p < 0.05). The LP+0.3% Lys group also resulted in a decrease in the excretion of faecal nitrogen and urinary nitrogen (FN; UN; p < 0.05), and an increase in nitrogen utilisation rate (NUR; p < 0.05). LP diet increased the mRNA expression of MSTN and WWP1, and decreased the mRNA expression of IGF1 (p < 0.05). LP diet decreased the protein expression of P-P70S6K1, P-4EBP1 and P-S6 (p < 0.05). LP+0.3% Lys group attenuated the effects of LP diet on the expression of MSTN, WWP1, IGF1, P-P70S6K1, P-4EBP1 and P-S6 (p < 0.05). LP+0.3% Lys group resulted in an increase in mRNA expression of MyoD and protein expression of P-mTOR relative to the NP and LP groups (p < 0.05). In summary, the addition of Lys to a LP diet provides a theoretical basis for the popularisation and application of Lys in rabbit production.

Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology

The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.

Dusk feeding in laying hens is shifted by light program via involvement of clock genes

Dusk feeding is practised probably to satisfy the energy requirement during night. However, little is known on the changes with clock gene expressions during this feeding behaviour. In our present study, the linkage of clock gene expressions and feeding behaviour in dusk feeding was investigated in laying hens under two lighting programs: the conventional lighting program (Control) with a light period from 05:00 AM to 21:00 PM and a dark period from 21:00 PM to 05:00 AM; or the shifted lighting program group (SLP) with a light period from 02:00 AM to 18:00 PM and a dark period from 18:00 PM to 02:00 AM. The gene expression-related appetite and circadian rhythm were investigated in hypothalamus and proventriculus at 1, 3 and 5 h before scotophase. The results demonstrated that dusk feeding was synchronously shifted with altered lighting program, dusk feeding was observed from 5 h before scotophase in both groups. The expressions of anorexigenic gene proopiomelanocortin (POMC) and cocaine- and amphetamine-regulated transcript (CART) were downregulated (p < 0.05) during dusk feeding and changed in pace with lighting program. The expressions of clock gene period 2 (Per2) and cryptochrome 1 (Cry1) in hypothalamus were downregulated (p < 0.05) during dusk feeding and shifted by lighting program. In the proventriculus, ghrelin expression was decreased (p < 0.05) during dusk feeding by lighting program. In conclusion, the expressions of clock genes Per2 and Cry1 are linked with the downregulated expressions of anorexigenic genes, POMC and CART, and in turn the augmented feed intake at dusk.

Effects of glucocorticoids on the gene expression of nutrient transporters in different rabbit intestinal segments

Glucocorticoids (GCs) are counterregulatory hormones with broad effects on the digestion and absorption of dietary carbohydrates, lipids and proteins, but the underlying molecular mechanisms of these effects remain unclear. The present experiment was conducted to investigate the main expression sites of nutrient transporters and the effects of GCs on the gene expression of these transporters in the rabbit small intestine. The results showed that peptide transporter 1 (PepT1), facultative amino acid transporter (rBAT), neutral amino acid transporter (B0AT), excitatory amino acid transporter 3 (EAAT3), sodium-glucose transporter 1 (SGLT1) and glucose transporter 5 (GLUT5) were mainly expressed in the distal segment, glucose transporter 2 (GLUT2) and fatty-acid-binding protein 4 (FATP4) were mainly expressed in the proximal segment and cationic amino acid transporter 1 (CAT1) was mainly expressed in the middle segment of the rabbit small intestine. In addition, we analysed the effects of 3 h (short-term) or 7 days (long-term) dexamethasone (DEX) treatment on the gene expression of most nutrient transporters. The results showed that short-term DEX treatment significantly decreased PepT1, B0AT, EAAT3, rBAT and SGLT1 expressions in all small intestinal segments, while it significantly decreased GLUT2 in the duodenum and FATP4 in the duodenum and ileum (P < 0.05). Long-term DEX treatment also significantly decreased PepT1, CAT1, B0AT, EAAT3, rBAT and SGLT1 in all small intestinal segments and significantly decreased GLUT2 in the jejunum and FATP4 in the ileum (P < 0.05). In conclusion, DEX could decrease the gene expression of most nutrient transporters (except GLUT5) and affect the transport of intestinal amino acids, monosaccharides and fatty acids.

Characterization of HTATIP2 and its role during hair follicle cycles in Angora rabbit

Hair follicle (HF) growth and cycling is a complex biological process that occurs in most mammals. As HF growth and cycling directly impacts rabbit wool yield, it is important to better understand the potential regulation pattern of HF development. Our previous study demonstrated that HTATIP2 may participate in regulating rabbit HF cycles, but the molecular mechanism of HTATIP2 remained unclear. In this study, the coding sequence of the HTATIP2 gene in Angora rabbit was cloned. The length of the coding region sequence was 840 bp, which could code 279 amino acids, and exhibited high homology in different mammals. Bioinformatics analyses indicated that the HTATIP2 protein is stable, hydrophilic, located around the cytoplasm, and has a putative signal peptide. Moreover, we verified that HTATIP2 is highly expressed during catagen and telogen of the HF cycle. The overexpression vector was constructed and siRNAs were designed. Overexpression and knockdown of HTATIP2 appeared to regulate JAK-STAT pathway genes, such as BCL2, CCND1, c-Myc, and STAT2. It is therefore likely that HTATIP2 promotes cell apoptosis and inhibits cell proliferation. Our results indicate that HTATIP2 is highly expressed during catagen and telogen and may play an important role in JAK-STAT signaling. This study provides a theoretical foundation for investigating HTATIP2 in biological processes.

High doses of cobalt inhibited hair follicle development in Rex Rabbits

<p>An experiment was conducted to investigate the effect of cobalt supplementation on hair follicle development in rabbits. Rex rabbits (30-d-old, n=180) were divided randomly into five equal treatment groups: rabbits fed a basal diet (control, measured cobalt content of 0.27 mg/kg) or rabbits fed a basal diet with an additional 0.1, 0.4, 1.6 or 6.4 mg/kg cobalt (in the form of cobalt sulfate) supplementation (measured cobalt contents of 0.35, 0.60, 1.83 and 6.62 mg/kg, respectively). Treatment with 6.4 mg/kg cobalt significantly decreased hair follicle density (<em>P</em>&lt;0.05), while low levels of cobalt (0.1-1.6 mg/kg) had no effect on hair follicle density (<em>P</em>&gt;0.05). The addition of dietary cobalt at the highest level examined (6.4 mg/kg) significantly increased the gene expression of bone morphogenetic protein (BMP) 2 and BMP4 in skin tissue (<em>P</em>&lt;0.05), while the mRNA levels of versican, alkaline phosphatase, hepatocyte growth factor, and noggin remained unchanged (<em>P</em>&gt;0.05). Compared with their levels in the control group, dietary cobalt treatment significantly suppressed the protein levels of p-mechanistic target of rapamycin (mTOR) and p-ribosomal protein S6 protein kinase (<em>P</em>&lt;0.05) but did not alter the protein levels of p-AMP-activated protein kinase, Wnt10b or p-β-catenin (<em>P</em>&gt;0.05). In conclusion, cobalt at the highest concentration examined inhibited hair follicle development, which may have involved the mTOR-BMP signalling pathway.</p>

The Effect of Low and High Dose Deoxynivalenol on Intestinal Morphology, Distribution, and Expression of Inflammatory Cytokines of Weaning Rabbits

Deoxynivalenol (DON) is a potential pathogenic factor to humans and animals, and intestinal tract is the primary target organ of DON. Data concerning the effects of DON on rabbits are scarce, especially for weaning rabbits. In this study, 45 weaning rabbits (35 d) were randomly and equally assigned into three groups. Group A was fed basic diet, while groups B and C were added DON at 0.5 mg/kg BW/d and 1.5 mg/kg BW/d, respectively, based on the basic diet. The experiment lasted for 24 days and the intestinal morphology, expression, and distribution of several cytokines in intestinal segments have been examined. The results indicated that ADG decreased while F/G increased significantly compared with the control group after DON added at 1.5 mg/kg BW/d. Some of the morphometric parameters (villi length, crypt depth, and goblet cells density) changed after DON was added. Meanwhile, the concentration as well as the expression levels of relative protein and mRNA of IL-1β, IL-2, IL-6, and IL-8 increased significantly. The immunohistochemistry results illustrated that the quantity and distribution of positive cells of inflammatory cytokines were changed after DON was added. In conclusion, the addition of DON damaged the intestinal morphology and changed the distribution and expression of inflammatory cytokines. The toxic effect depended on the dosage of DON.