Effects of fulvic acid on broiler performance, blood biochemistry, and intestinal microflora.

To study the effects of mineral fulvic acid (FuA) on broiler performance, slaughter performance, blood biochemistry index, antioxidant function, immune performance, and intestinal microflora, 360 Arbor Acres (AA) broiler chickens with similar body weights were randomly divided into 5 groups with 6 replicates in each group and 12 chickens in each replicate in the current study. Chickens in the control group (C) were fed with the basal diet, and chickens in the test groups (I, II, III, and IV) were fed with the diet supplemented with 0.05%, 0.1%, 0.2%, and 0.3% mineral FuA, respectively. The indicators were measured on the hatching day, d 21 and d 35. From the whole experimental period, FuA supplement significantly increased average body weight (ABW) (P < 0.05), average daily gain (ADG) of broilers (P < 0.05), and thymus weight (P < 0.05) in II and IV groups, but bascially reduced the pH value of thigh meat. FuA supplement significantly improved aspartate aminotransferase (AST) activity in the group III on d 35 (P < 0.05) and the serum levels of IgA and IgG on d 21 and d 35 (P < 0.05), but reduced glutathione peroxidase (GSH-Px) level on d 21 (P < 0.05) and malondialdehyde (MDA) level in serum on d 35 (P < 0.05). FuA supplement significantly affected the abundance of Barnesiella, Lachnospiraceae, Alistipes, Lactobacillus, and Christensenellaceae on genus level. Differences between group III and other groups were significant in the genera microflora composition on d 21 and d 35. Functional analysis showed that the cecum microbiota were mainly enriched in carbohydrate metabolism, amino acid metabolism, and energy metabolism. In conclusion, FuA may potentially have significant positive effects on the growth performance and immune function of AA chickens through the modulation of the gut microbiota, and the 0.1% FuA was the best in broiler diet based on the present study.

Symbiotic bacteria stabilize the intestinal environment by producing phenylpropanoids.

Salmonella enterica serovar Enteritidis (S. Enteritidis) can colonize in the intestinal tract of chickens and transmit to humans. In order to decrypt the mechanism of avian resistance to S. Enteritidis, we utilized two China local chicken breeds to generate the reciprocal crosses (the Cross and the Reverse-cross). The two lines of hybrids were orally inoculated with S. Enteritidis at 2-day old and sampled at 3 days post-inoculation. Along the analysis direction of multi-omics, differential metabolites, functional pathways and correlated microbes, we found that 12 species of microbes thrived upon S. Enteritidis challenge and probably contributed to the intestinal stability in the Cross by enhancing the production of phenylpropanoids. Our findings can help to understand the symbiotic and resistant mechanisms derived from the intestinal microbiota.

Regulation of mRNA and miRNA in the response to Salmonella enterica serovar Enteritidis infection in chicken cecum.

BACKGROUND: Salmonella enterica, serovar Enteritidis (SE) is a food-borne pathogen, which can cause great threat to human health through consumption of the contaminated poultry products. Chicken is the main host of SE. The mRNA and microRNA (miRNA) expression profiles were analyzed on cecum of Shouguang chicken via next-generation sequencing and bioinformatics approaches. The treated group was inoculated SE, and the control group was inoculated with phosphate buffer saline (PBS). RESULTS: There were 1760 differentially expressed mRNAs in the SE-infected group, of which 1046 were up-regulated mRNA, and 714 were down-regulated mRNA. In addition, a total of 821 miRNAs were identified, and 174 miRNAs were differentially expressed, of which 100 were up-regulated and 74 were down-regulated. Functional enrichment of differentially expressed mRNAs was similar to miRNA target genes. The functional analysis results of differentially expressed mRNAs and miRNAs were performed. Immune-related processes and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were enriched by up-regulated mRNA. The down-regulated mRNAs were enriched in tissue development and metabolic-related KEGG pathways. The functional analysis of up-regulated miRNA target genes was similar to the down-regulated mRNAs. The down-regulated miRNA target genes were enriched in metabolic-related GO (Gene Ontology) -BP (Biological process) terms and KEGG pathways. The overlap of the up-regulated mRNA and the up-regulated miRNA target genes (class I) was 325, and the overlap of the down-regulated miRNA target genes (class II) was 169. The class I enriched in the immune-related GO-BP terms and KEGG pathways. The class II mainly enriched in metabolic-related GO-BP terms and KEGG pathways. Then we detected the expression of mRNA and miRNA through qRT-PCR. The results shown that the expression of HHIP, PGM1, HTR2B, ITGB5, RELN, SFRP1, TCF7L2, SCNN1A, NEK7, miR-20b-5p, miR-1662, miR-15a, miR-16-1-3p was significantly different between two groups. Dual-luciferase reporter assay was used to detect the relationship between miR-20b-5p and SCNN1A. The result indicated that miR-20b-5p regulate immune or metabolic responses after SE infection in Shouguang chickens by directly targeting SCNN1A. CONCLUSIONS: The findings here contribute to the further analysis of the mechanism of mRNA and miRNA defense against SE infection, and provide a theoretical foundation for the molecular disease-resistant breeding of chickens.

The response of cecal microbiota to inflammatory state induced by Salmonella enterica serovar Enteritidis.

By combining the experiments of reciprocal crosses of chicken infected with Salmonella enterica serovar Enteritidis (S. Enteritidis), we focused on the common response of cecal microbiota to an inflammatory state in respect of transcriptome and microbiome. The inoculation of S. Enteritidis improved the microbial diversity and promoted the microbiota evolution in our infection model. Correlation analysis between bacteria and inflammation-related genes showed that some intestinal microorganisms were "inflammophile" and thrived in an inflamed environment. The global function of cecal microbiome was to maintain the homeostasis likely by the up-regulation of microbial metabolism pathway in bacitracin, putrescine, and flavonoids production, although the bacitracin may affect the symbiotic bacteria Enterococcus. The action of S. Enteritidis had close relationships with multiple inflammation-related genes, including the genes PTAFR, LY96, and ACOD1 which proteins are related to the binding and tolerance of LPS, and the genes IL-18, IL-18R1 and IL-18RAP which products can form a functional complex and transmit IL-18 pro-inflammatory signal. Additionally, the infection of S. Enteritidis aroused the transcription of EXFABP, which protein has a potential to sequestrate the siderophore and might cause the decline of Escherichia-Shigella and Enterococcus. S. Enteritidis can escape from the sequestrating through the salmochelin, another kind of siderophore which cannot be recognized by EXFABP. Probably by this way, S. Enteritidis competed with the symbiotic bacteria and edged out the niches. Our research can help to understand the interplay between host, pathogen, and symbiotic bacteria.

Research Note: IsomiRs of chicken miR-146b-5p are activated upon Salmonella enterica serovar Enteritidis infection.

In order to enrich the knowledge of chicken transcriptomic response to Salmonella enterica serovar Enteritidis infection, 2-day-old chicks were orally inoculated with this bacteria (1.0 × 108 cfu/mL), and then the cecum tissues of 3 days post-inoculation were utilized for RNA sequencing (6 replicates each for treatment group and control group). After analysis, we found a variety of inflammatory genes were triggered at the mRNA level upon infection. Notably, the expression profiles at the miRNA level and the isomiR level were heterogeneous. Certain isomiRs of chicken miR-146b-5p were significantly increased by more than 2 times compared to control (Padj < 0.05). Combining the bioinformatics prediction, transcriptome data and RT-qPCR results, we deduced that the isomiRs of chicken miR-146b-5p might act to sustain the RIG-I-like receptor signaling and type I interferon induction by repressing USP3 transcript. Our findings provide a new perspective on the regulatory function of miR-146b-5p and facilitate the study of isomiRs.

Coupled effects of fly ash and calcium formate on strength development of cemented tailings backfill.

Cemented tailings backfill (CTB) is widely adopted to ensure the safety of underground goafs and mitigate environmental risks. Fly ash (FA) and calcium formate (CF) are common industrial by-products that improve the mechanical performance of CTB. How the coupling of the two components affects the strength development is not yet well-understood. Neural network modelling was conducted to predict the strength development, including the static indicator of uniaxial compressive strength (UCS) and the dynamic indicator of ultrasonic pulse velocity (UPV). Sobol' sensitivity analysis was carried out to reveal the contributions of FA, CF and curing time to CTB strength. SEM microstructure investigation on CTB samples was implemented to reveal the mechanism of strength development and justify the predictions by neural network modelling and sensitivity analysis. Results show that the combination of FA content, CF content and curing time can be used to predict both UCS and UPV while providing adequate accuracy. The maximum of UCS of 6.1215 MPa is achieved at (FA content, CF content, curing time) = (13.78 w%, 3.76 w%, 28 days), and the maximum of UPV of 2.9887 km/s is arrived at (FA content, CF content, curing time) = (11.67 w%, 3.08 w%, 10 days). It is also implicated that prediction of UCS using UPV alone, although common in field application is not recommended. However, UPV measurement, in combination with the information of FA dosage, CF dosage and curing time, could be used to improve UCS prediction. The rank of variable significance for UCS is curing time > FA content > CF content, and for UPV is FA content > curing time > CF content; variable interaction is strongest for FA with CF for UCS development, and for FA with curing time for UPV evolution. Influence of FA on CTB strength development is due to improved polymerisation and consumption of Ca(OH)2. Influence of CF on strength development is a result of accelerated hydration and increased combined-water content in calcium silicate hydrate (CSH). Effect of curing time is attributed to the evolution of CSH product and pore-water content during cement hydration.

Phosphoproteomics Profile of Chicken Cecum in the Response to Salmonella enterica Serovar Enteritidis Inoculation.

Salmonella enterica serovar Enteritidis (S. Enteritidis) is a foodborne pathogen, which can cause great threats to human health through the consumption of contaminated poultry products. This research combines TMT labeling, HPLC and mass-spectrometry-based phosphoproteomics on cecum of the F1 cross of Guangxi Yao chicken and Jining Bairi chicken. The treated group was inoculated with 0.3 mL inoculum S. Enteritidis, and the control group was inoculated with 0.3 mL phosphate-buffered saline (PBS). A total of 338 differentially phosphorylated modification sites in 243 differentially phosphorylated proteins (DPPs) were chosen for downstream analyses. A total of 213 sites in 146 DPPs were up-regulated and 125 sites in 97 DPPs were down-regulated. Functional analysis was performed for DPPs based on gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and the protein domain. The DPPs were mainly enriched in immune- and metabolic-related GO-BP (biological process) and KEGG pathways. We predicted and classified the subcellular structure and COG/KOG of DPPs. Furthermore, protein-protein interaction network analyses were performed by using multiple algorithms. We identified 71 motifs of the phosphorylated modification sites and selected 18 sites randomly to detect the expression level through parallel reaction monitoring (PRM). S. Enteritidis inoculation caused phosphorylation alteration in immune- and metabolic-related proteins. The invasion of S. Enteritidis may be actualized by inducing cecum cell apoptosis through the endoplasmic reticulum pathway, and chickens could resist the invasion of S. Enteritidis by affecting the function of ECM receptors. The findings herein provide a crucial theoretical foundation to understand the molecular mechanism and epigenetic regulation in response to S. Enteritidis inoculation in chickens.

X-ray computed tomography images and network data of sands under compression.

Ottawa sand and Angular sand consist of particles with distinct shapes. The x-ray computed tomography (XCT) image stacks of their in-situ confined compressive testings are provided in this paper. For each image stack, a contact network, a thermal network and a network feature - edge betweenness centrality - of each edge in the networks are also provided. The readers can use the image data to construct digital sands with applications of (1) extracting microstructural parameters such as particle size, particle shape, coordination number and more network features; (2) analysing mechanical behaviour and transport processes such as fluid flow, heat transfer and electrical conduction using either traditional simulation tools such as finite element method and discrete element method or newly network models which could be built based on the network files available here.

The correlated expression of immune and energy metabolism related genes in the response to Salmonella enterica serovar Enteritidis inoculation in chicken.

BACKGROUND: Salmonella enterica serovar Enteritidis (SE) is one of the food-borne pathogenic bacteria, which affects poultry production and poses severe threat to human health. The correlation of immune system and metabolism in chicken after SE inoculation is important but not clear. In the current study, we identified the expression of immune and energy metabolism related genes using quantitative PCR to evaluate the correlation between immune system and energy metabolism against SE inoculation in Jining Bairi chicken. RESULTS: ATP5G1, ATP5G3 and ND2 were significantly up-regulated at 1 dpi (day post inoculation), and ATP5E, ATP5G1, ATP5G3 were significantly down-regulated at 7 dpi (P < 0.05). IL-8 and IL-1ß were significantly down-regulated at 1 dpi, IL-8 and IL-18 were significantly down-regulated at 3 dpi, IL-8 and BCL10 were significantly up-regulated at 7 dpi (P < 0.05). CONCLUSIONS: These findings indicate that the correlation between immune and energy metabolism related genes gradually change with time points post SE inoculation, from one homeostasis to an opposite homeostasis with 3 dpi as a turning point. These results will pave the foundation for the relationship between immune system and energy metabolism in the response to SE inoculation in chicken.

Improved Vinegar & Wellington calibration for estimation of fluid saturation and porosity from CT images for a core flooding test under geologic carbon storage conditions.

X-ray computed tomography (CT) of fluid flow in formation rocks is an important characterization technique in geologic carbon sequestration research to provide insight into the migration and capillary trapping of CO2 under reservoir conditions. An improved calibration method adapted from traditional Vinegar & Wellington calibration is proposed to map the 3D pore and fluid distributions from the CT images of CO2/brine displacement flooding. Similar to Vinegar & Wellington calibration, the proposed method adopts the linear scaling law of CT number transformation to mass density. However, different from Vinegar & Wellington calibration that uses a 100% brine-saturated core image and a 100% CO2-saturated core image as references to calculate CO2 and brine saturations at all time steps, the proposed method uses the CT numbers of CO2 and brine to calculate the incremental of CO2 and brine saturations from time step i to time step i +1. The method is intended for cases in which the two 100% brine saturation and 100% CO2 saturation images can not be successfully obtained. Overall, the improved calibration proposed by this study presents more reasonable results of CO2 and brine distribution in a Berea sandstone core, as compared to traditional Vinegar & Wellington calibration. The reconstructed porosity image agrees with the laminated structure of the Berea sandstone core, and the average porosity evaluated over the entire core (0.176) is comparable to the physical porosity (0.165). Furthermore, the reconstructed saturation images using the improved calibration reveal a flat piston-like flooding front from a homogeneous longitudinal-section of the 3D orthogonal view and preferential fingerings from another non-homogeneous longitudinal-section, which are not present in the reconstructed saturation images using traditional Vinegar & Wellington calibration. Concerns and causes with respect to the uncertainty of linear CT number calibration are also explained, and approaches to alleviate the uncertainty are suggested.

Identification of Prognostic Dosage-Sensitive Genes in Colorectal Cancer Based on Multi-Omics.

Several studies have already identified the prognostic markers in colorectal cancer (CRC) based on somatic copy number alteration (SCNA). However, very little information is available regarding their value as a prognostic marker. Gene dosage effect is one important mechanism of copy number and dosage-sensitive genes are more likely to behave like driver genes. In this work, we propose a new pipeline to identify the dosage-sensitive prognostic genes in CRC. The RNAseq data, the somatic copy number of CRC from TCGA were assayed to screen out the SCNAs. Wilcoxon rank-sum test was used to identify the differentially expressed genes in alteration samples with |SCNA| > 0.3. Cox-regression was used to find the candidate prognostic genes. An iterative algorithm was built to identify the stable prognostic genes. Finally, the Pearson correlation coefficient was calculated between gene expression and SCNA as the dosage effect score. The cell line data from CCLE was used to test the consistency of the dosage effect. The differential co-expression network was built to discover their function in CRC. A total of six amplified genes (NDUFB4, WDR5B, IQCB1, KPNA1, GTF2E1, and SEC22A) were found to be associated with poor prognosis. They demonstrate a stable prognostic classification in more than 50% threshold of SCNA. The average dosage effect score was 0.5918 ± 0.066, 0.5978 ± 0.082 in TCGA and CCLE, respectively. They also show great stability in different data sets. In the differential co-expression network, these six genes have the top degree and are connected to the driver and tumor suppressor genes. Function enrichment analysis revealed that gene NDUFB4 and GTF2E1 affect cancer-related functions such as transmembrane transport and transformation factors. In conclusion, the pipeline for identifying the prognostic dosage-sensitive genes in CRC was proved to be stable and reliable.