Deep sequencing of the microRNA expression in fall dormant and non-dormant alfalfa

AbstractMicroRNAs (miRNAs) play a critical role in post-transcriptional gene regulation that down-regulates target genes by mRNA degradation or translational repression. Evidence is increasing for their crucial roles during plant development. Identification of miRNAs at the global genome-level by high-throughput sequencing is essential to functionally characterize miRNAs in plants. Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial forage legumes worldwide. Fall dormancy is an adaptive character related to the biomass production and winter survival in alfalfa. However, little is known about miRNA-mediated developmental regulation of fall dormancy in alfalfa. Here, we provide detailed experimental methods and analysis pipeline in our study to identify miRNAs that were responsive to fall dormancy (Fan W et al., Genome-wide identification of different dormant Medicago sativa L. microRNAs in response to fall dormancy, submitted for publication) for reproducible research. The data generated in our work provide meaningful information for understanding the roles of miRNAs in response to seasonal change and growth regulation in alfalfa

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets

Dietary fiber (DF) is increasingly thought to regulate diversity of piglet gut microbiota to alleviate weaning stress in piglets. This study was conducted to investigate the effects of DF on growth performance of piglets and composition of their gut microbiota, as well as the interaction between gut microbiota and short-chain fatty acids (SCFAs) in piglets. A total of 840 piglets were allocated to three dietary treatments consisting of a control group (CG), an alfalfa meal group (AG), and a commodity concentrated fiber group (OG) in a 30-day feeding trial. Gut mucosa and feces samples were used to determine bacterial community diversity by 16S rRNA gene amplicon sequencing. Fiber treatment had a positive effect on growth performance and metabolism of SCFAs in piglets, in particular, compared with CG, the diarrhea rate was significantly decreased, and the content of propionic acid (PA) in the cecum was markedly increased in AG. The Shannon indices of the jejunum microbiota in AG were higher than CG. At the genus level, compared to CG, in the duodenum, the relative abundance of Paenibacillus in AG and OG was higher; in the jejunum, the relative abundances of Bacillus, Oceanobacillus, Paenibacillus, Lactococcus, Enterococcus, and Exiguobacterium were higher, whereas the relative abundance of Mycoplasma was lower in AG; in the cecum, there was also lower relative abundance of Helicobacter in AG and OG, and furthermore, the relative abundance of Faecalibacterium in OG was higher than in CG and AG. Spearman correlation analysis showed that Pseudobutyrivibrio was positively correlated with acetic acid, PA, and butyric acid (BA), while Bacteroides and Anaerotruncus were negatively correlated with PA and BA. In addition, microbiota analyses among different intestine segments showed distinct differences in microbiota between the proximal and distal intestines. Bacteria in the proximal segments were mainly Firmicutes, while bacteria in the distal segments were mainly Bacteroidetes and Firmicutes. Overall, these findings suggested that DF treatment could reduce the diarrhea rate of piglets and had beneficial effects on gut health, which might be attributed to the alteration in gut microbiota induced by DF and the interaction of the gut microbiota with SCFAs

Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall

Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level

3D FACE CORRESPONDENCE BASED ON UNIFORM MESH RESAMPLING COMBINED WITH MESH SIMPLIFICATION

This present study, proposes a new 3D face correspondence method. A uniform mesh re-sampling algorithm is combined with mesh simplification algorithm to make correspondence between vertices of prototypical 3D faces. Uniform mesh re-sampling algorithm is developed to obtain the same topology between 3D faces with different structures. A global error metrics is proposed and mesh simplification is implemented on 3D faces with same topologies simultaneously. The new method overcomes the limitation of conventional uniform mesh re-sampling and optical flow algorithm, decreases the vertices, and triangles that need to represent 3D face while preserving correspondence between vertices of the prototypes. The experimental results show the new method gives good performance on computing 3D face correspondence

Effects of alfalfa saponin extract on the performance and cholesterol metabolism of 1 laying hens 2

Abstract 31 The experiment was performed to determine the effects of alfalfa saponin extract (ASE

Digital gene-expression of alfalfa saponin extract on laying hens

Cardiovascular disease is a major cause of death worldwide, so people are advised to limit their intake of dietary cholesterol [1]. Egg consumption has been seriously reduced because of the high levels of cholesterol [2]. The objective of this study was to evaluate the cholesterol metabolism effects of alfalfa saponin extract (ASE) in liver and ovary tissues using digital gene-expression (DGE) profiling analysis. The liver and ovary tissues were isolated from laying hens fed with ASE for RNA sequencing. Here, we provide detailed experimental methods and analysis pipeline in our study to identify digital gene expression of alfalfa saponin extract on laying hens and analysis pipeline published by Singh and colleagues in the PLOS ONE [3]. The data generated in our work provide meaningful information for understanding the molecular mechanisms underlying the cholesterol-lowering effects of ASE

The regulation of alfalfa saponin extract on key genes involved in hepatic cholesterol metabolism in hyperlipidemic rats.

To investigate the cholesterol-lowering effects of alfalfa saponin extract (ASE) and its regulation mechanism on some key genes involved in cholesterol metabolism, 40 healthy 7 weeks old male Sprague Dawley (SD) rats were randomly divided into four groups with 10 rats in each group: control group, hyperlipidemic group, ASE treatment group, ASE prevention group. The body weight gain, relative liver weight and serum lipid 1evels of rats were determined. Total cholesterol (TC) and total bile acids (TBA) levels in liver and feces were also measured. Furthermore, the activity and mRNA expressions of Hmgcr, Acat2, Cyp7a1 and Ldlr were investigated. The results showed the following: (1) The abnormal serum lipid levels in hyperlipidemic rats were ameliorated by ASE administration (both ASE prevention group and treatment group) (P<0.05). (2) Both ASE administration to hyperlipidemic rats significantly reduced liver TC and increased liver TBA level (P<0.05). TC and TBA levels in feces of hyperlipidemic rats were remarkably elevated by both ASE administration (P<0.05). (3) mRNA expressions of Hmgcr and Acat2 in the liver of hyperlipidemic rats were remarkably down-regulated (P<0.05), as well as mRNA expressions of Cyp7a1 and Ldlr were dramatically up-regulated by both ASE administration (P<0.05). The activities of these enzymes also paralleled the observed changes in mRNA levels. (4) There was no significant difference between ASE treatment and ASE prevention group for most parameters evaluated. Our present study indicated that ASE had cholesterol-lowering effects. The possible mechanism could be attributed to (1) the down-regulation of Hmgcr and Acat2, as well as up-regulation of Cyp7a1 and Ldlr in the liver of hyperlipidemic rats, which was involved in cholesterol biosynthesis, uptake, and efflux pathway; (2) the increase in excretion of cholesterol. The findings in our study suggested ASE had great potential usefulness as a natural agent for treating hyperlipidemia

Multi-Channel Metabolomics Analysis Identifies Novel Metabolite Biomarkers for the Early Detection of Fatty Liver Disease in Dairy Cows

Fatty liver disease, a type of metabolic disorder, frequently occurs in dairy cows during the parturition period, causing a high culling rate and, therefore, considerable economic losses in the dairy industry owing to the lack of effective diagnostic methods. Here, metabolite biomarkers were identified and validated for the diagnosis of metabolic disorders. A total of 58 participant cows, including severe fatty liver disease and normal control groups, in the discovery set (liver biopsy tested, n = 18), test set (suspected, n = 20) and verification set (liver biopsy tested, n = 20), were strictly recruited and a sample collected for their feces, urine, and serum. Non-targeted GC-MS-based metabolomics methods were used to characterize the metabolite profiles and to screen in the discovery set. Eventually, ten novel biomarkers involved in bile acid, amino acid, and fatty acid were identified and validated in the test set. Each of them had a higher diagnostic ability than the traditional serum biochemical indicators, with an average area under the receiver operating characteristic curve of 0.830 &plusmn; 0.0439 (n = 10) versus 0.377 &plusmn; 0.182 (n = 9). Especially, combined biomarker panels via different metabolic pipelines had much better diagnostic sensitivity and specificity than every single biomarker, suggesting their powerful utilization potentiality for the early detection of fatty liver disease. Intriguingly, the serum biomarkers were confirmed perfectly in the verification set. Moreover, common biological pathways were found to be underlying the pathogenesis of fatty liver syndrome in cattle via different metabolic pipelines. These newly-discovered and non-invasive metabolic biomarkers are meaningful in reducing the high culling rate of cows and, therefore, benefit the sustainable development of the dairy industry

Digital Gene-Expression Profiling Analysis of the Cholesterol-Lowering Effects of Alfalfa Saponin Extract on Laying Hens

<div><p>Background</p><p>To prevent cardiovascular disease, people are advised to limit their intake of dietary cholesterol to less than 300 mg/day. Egg consumption has been seriously reduced because of the high levels of cholesterol. The purpose of the present study was to evaluate the cholesterol-lowering effects of alfalfa saponin extract (ASE) in yolk and the molecular mechanisms underlying these effects using digital gene-expression profiling analysis. Liver and ovary tissues were isolated from laying hens fed with ASE for RNA sequencing.</p><p>Results</p><p>The cholesterol content of the yolks of eggs from hens fed 120 mg/kg ASE declined considerably on day 60. Other groups (60, 240, 480 mg/kg ASE group) also showed decreases, but they were not significant. Digital gene expression generated over nine million reads per sample, producing expression data for least 12,384 genes. Among these genes, 110 genes showed greater than normal expression in the liver and 107 genes showed greater than normal expression in the ovary. Cholesterol 7 alpha-hydroxylase (<i>Cyp7a1</i>) and apolipoprotein H (<i>Apoh</i>), which act in the synthesis of bile acid and cholesterol efflux, showed more expression in the livers of hens given dietary ASE supplementation. In the ovary, levels of very low density lipoprotein receptor (<i>Vldlr</i>), apolipoprotein B (<i>Apob</i>), apovitellenin 1 (<i>ApovldlII</i>) and vitellogenin (<i>VtgI</i>, <i>VtgII</i> and <i>VtgIII</i>) in ovary decreased with dietary ASE supplementation.</p><p>Conclusion</p><p>Transcriptome analysis revealed that the molecular mechanisms underlying the cholesterol-lowering effects of ASE were partially mediated by enhancement of cholesterol efflux in the liver and this reduced of cholesterol deposition in the ovary.</p></div

Ectopic recurrence craniopharyngioma: series report and literature review

Abstract Background Craniopharyngioma is a common intracranial tumor located in the sellar-suprasellar region. Due to the involvement of adjacent structures, it can lead to increased intracranial pressure, visual impairment, and endocrine deficiencies. Surgical resection is the primary treatment, but it is a tough challenge to achieve total resection, which will led to the frequency of recurrences and progressions. Among them, distant spread is extremely rare, but important complication, identifying and providing proper therapy, is crucial. Methods We report two cases of ectopic recurrence craniopharyngioma and make a literature review for the published similar case reports. Results Our literature review revealed 63 cases (including our patient). The onset age in children group and adult group ranges from 2–14 years old (6.70 ± 3.33) to 17–73 years old (40.63 ± 15.58), while the interval year between tumor initiation and ectopic recurrence ranges from 0.17–20 (7.28 ± 6.76) years to 0.3–34 (6.85 ± 7.29). Achieving gross total resection seems not to prevent the ectopic recurrence. The major pathology of ectopic recurrence craniopharyngioma is adamantinomatous type. The most common site of ectopic recurrence is frontal lobe. According to the pathogenesis, 35 cases were seeding along the surgical approach, and 28 cases were seeding via the CSF pathway. Conclusion Ectopic recurrence craniopharyngioma is rare, but it can lead to serious symptoms. Delicate surgical procedure can help to reduce the risk of ectopic recurrence, and standardized follow-up can provide valuable information for treatment