Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana

Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA) is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of ∼24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler) could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC), a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col) with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of ∼24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes

Transcriptome profiling analysis of uterus during chicken laying periods

Abstract The avian eggshell is formed in the uterus. Changes in uterine function may have a significant effect on eggshell quality. To identify the vital genes impacting uterine functional maintenance in the chicken, uteri in three different periods (22W, 31W, 51W) were selected for RNA sequencing and bioinformatics analysis. In our study, 520, 706 and 736 differentially expressed genes (DEGs) were respectively detected in the W31 vs W22 group, W51 vs W31 group and W51 vs W22 group. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated DEGs were enriched in the extracellular matrix, extracellular region part, extracellular region, extracellular matrix structural constituent, ECM receptor interaction, collagen-containing extracellular matrix and collagen trimer in the uterus (P < 0.05). Protein–protein interaction analysis revealed that FN1, LOX, THBS2, COL1A1, COL1A2, COL5A1, COL5A2, POSTN, MMP13, VANGL2, RAD54B, SPP1, SDC1, BTC, ANGPTL3 might be key candidate genes for uterine functional maintenance in chicken. This study discovered dominant genes and pathways which enhanced our knowledge of chicken uterine functional maintenance

An UWB/Vision Fusion Scheme for Determining Pedestrians’ Indoor Location

This paper proposes a method for determining a pedestrian&rsquo;s indoor location based on an UWB (ultra-wideband) and vison fusion algorithm. Firstly, an UWB localization algorithm based on EKF (extended Kalman filter) is proposed, which can achieve indoor positioning accuracy of 0.3 m. Secondly, a method to solve scale ambiguity and repositioning of the monocular ORB-SLAM (oriented fast and rotated brief-simultaneous localization and mapping) algorithm based on EKF is proposed, which can calculate the ambiguity in real time and can quickly reposition when the vision track fails. Lastly, two experiments were carried out, one in a corridor with sparse texture and the other with the light brightness changing frequently. The results show that the proposed scheme can reliably achieve positioning accuracy on the order of 0.2 m; with the combination of algorithms, the scale ambiguity of monocular ORB-Slam can be solved, with the failed vision trace repositioned by UWB, and the positioning accuracy of UWB can be improved, making it suitable for pedestrian location in indoor environments with sparse texture and frequent light brightness changes

An Emergency Seamless Positioning Technique Based on ad hoc UWB Networking Using Robust EKF

In this paper, a new emergency positioning technique is proposed based on ad hoc GNSS/UWB (Global Navigation Satellite System/Ultra-Wideband) network. The main innovations of the program are reflected in two aspects. First of all, a unified coordinate frame for indoor and outdoor environments is constructed dynamically with GNSS/UWB integration. In the outdoor environments, the high accuracy positioning can be achieved with GNSS/UWB equipment. The high-accuracy indoor coordinate is obtained by measuring the range observations between adjacent network nodes and outdoor GNSS/UWB nodes, and the range information of the UWB network is transmitted to the cloud server center. A network adjustment algorithm is proposed to improve the positioning accuracy of the UWB network. Secondly, a UWB indoor location algorithm based on robust EKF (Extended Kalman Filter) is proposed. By analyzing the transfer characteristics of gross error in EKF model, a new robust EKF model is established. The model is constructed based on the statistical characteristics of redundant observation components and prediction residual. The robust equivalent gain matrix is constructed, and the robust positioning solution of UWB is obtained with iteration. The global test is carried out first to further improve the real-time operation efficiency. Finally, a field indoor and outdoor seamless positioning experiment was carried out to verify the effectiveness of the proposed algorithm. The results show that the positioning accuracy of UWB emergency network nodes (anchors) can reach 0.35 m. Based on the network, the positioning accuracy of the tag can reach 0.38 m by applying the improved robust EKF positioning algorithm, which is improved by 20.83% and 73.43% compared with standard EKF and least square method, respectively

Inhibition of Viability, Proliferation, Cytokines Secretion, Surface Antigen Expression, and Adipogenic and Osteogenic Differentiation of Adipose-Derived Stem Cells by Seven-Day Exposure to 0.5 T Static Magnetic Fields

After seven-day exposure to 0.5-Tesla Static Magnetic Field (SMF), Adipose-derived Stem Cells (ASCs) and those labeled by superparamagnetic iron oxide (SPIO) nanoparticles were examined for viability by methyl thiazol tetrazolium (MTT) assay, proliferation by cell counting and bromodeoxyuridine (BrdU) incorporation, DNA integrity by single cell gel electrophoresis, surface antigen by flow cytometry analysis, and the expression of cytokines and genetic markers by reverse transcription-PCR and underwent adipogenic and osteogenic differentiation assessed by quantifying related specific genes expression. The SMF slightly reduced cell viability and proliferation and inhibited the expression of CD49d, CD54, and CD73 but did not damage DNA integrity. The SMF slightly downregulated the expression of cytokines including Vascular Endothelial Growth Factor (VEGF), Insulin-like Growth Factor-1 (IGF-1), Transforming Growth Factor Beta 1 (TGF-β1), genetic markers comprising Stem Cell Antigen-1 (Sca1), Octamer-4 (Oct-4), ATP-binding Cassette Subfamily B Member 1 (ABCB1), adipogenic marker genes containing Lipoprotein Lipase (LPL), Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ), and osteogenic marker genes including Secreted Phosphor-protein 1 (SPP1) and Osterix (OSX). Exposure to 0.5 T SMF for seven days inhibited viability, proliferation, surface antigen expression, cytokine secretion, stem cell genetic marker expression, and adipogenic and osteogenic differentiation but did not affect the DNA integrity in ASCs with or without SPIO labeling

Short-Term Effect of the Addition of Rice Husk Gasification Slag on the Movement and Transformation of Phosphorus in Different Soil Types

Rice husk gasification slag (RS) is a type of biochar that is one of the main by-products generated from the production of biomass power with rice husk as the feed. This study aimed to explore the short-term effect of the application of RS on the movement and transformation of fertilizer P in two different soil types through an incubation experiment. The results showed that the RS addition had a significant influence on the diffusive movement of P in soil microsites close to fertilizer placements both in latosolic red soil and fluvo-aquic soil. After 50 d of incubation, most of the WE-P (water-extractable P), AE-P (acid-extractable P), and Olsen-P (available P) were concentrated within 0&ndash;5 mm from the fertilization site. WE-P, Olsen-P, and the movement amount of the P in the 0&ndash;5 mm soil section were significantly increased at all levels of the RS application in the fertilizer P both in the two soil types. The application of the RS reduced the sorption and precipitation of the fertilizer P in the soil and improved the efficiency of the fertilizer P. The findings presented in this study may be used as references in developing RS applications that reduce losses of fertilizer P and reduce environmental risks

Preservation of Myocardial Perfusion and Function by Keeping Hypertrophied Heart Empty and Beating for Valve Surgery: An In Vivo MR Study of Pig Hearts

Objectives. Normothermic hyperkalemic cardioplegia arrest (NHCA) may not effectively preserve hypertrophied myocardium during open-heart surgery. Normothermic normokalemic beating perfusion (NNBP), keeping hearts empty-beating, was utilized as an alternative to evaluate its cardioprotective role. Materials and Methods. Twelve hypertrophied pig hearts at 58.6 ± 7.2 days after ascending aorta banding underwent NNBP and NHCA, respectively. Near infrared myocardial perfusion imaging with indocyanine green (ICG) was conducted to assess myocardial perfusion. Left ventricular (LV) contractile function was assessed by cine MRI. TUNEL staining and western blotting for caspase-3 cleavage and cardiac troponin I (cTnI) degradation were conducted in LV tissue samples. Results. Ascending aortic diameter was reduced by 52.7%±0.4% at approximately fifty-eight days after banding. LV wall thickness was significantly higher in aorta banding than in sham operation. Myocardial blood flow reflected by maximum ICG absorbance value was markedly higher in NNBP than in NHCA. The amount of apoptotic cardiomyocyte was significantly lower in NNBP than in NHCA. NNBP alleviated caspase-3 cleavage and cTnI degradation associated with NHCA. NNBP displayed a substantially increased postoperative ejection fraction relative to NHCA. Conclusions. NNBP was better than NHCA in enhancing myocardial perfusion, inhibiting cardiomyocyte apoptosis, and preserving LV contractile function for hypertrophied hearts

Analysis of Population Structure and Differentially Selected Regions in Guangxi Native Breeds by Restriction Site Associated with DNA Sequencing

Guangxi indigenous chicken breeds play a very important role in promoting the high-quality development of the broiler industry in China. However, studies on genomic information of Guangxi indigenous chicken to date remain poorly explored. To decipher the population genetic structure and differentially selected regions (DSRs) in Guangxi indigenous chickens, we dug into numerous SNPs from seven Guangxi native chickens (GX) by employing the restriction site associated with DNA sequencing (RAD-seq) technology. Another three breeds, Cobb, White Leghorn, and Chahua (CH) chicken, were used as a control. After quality control, a total of 185,117 autosomal SNPs were kept for further analysis. The results showed a significant difference in population structure, and the control breeds were distinctly separate from the Guangxi native breeds, which was also strongly supported by the phylogenetic tree. Distribution of FST indicated that there were three SNPs with big genetic differentiation (FST value all reach to 0. 9427) in GX vs. CH group, which were located on chr1-96,859,720,chr4-86,139,601, and chr12-8,128,322, respectively. Besides, we identified 717 DSRs associated with 882 genes in GX vs. Cobb group, 769 DSRs with 476 genes in GX vs. Leghorn group, and 556 DSRs with 779 genes in GX vs. CH group. GO enrichment showed that there were two significant terms, namely GPI-linked ephrin receptor activity and BMP receptor binding, which were enriched in GX vs. Leghorn group. In conclusion, this study suggests that Guangxi native chickens have a great differentiation with Cobb and Leghorn. Our findings would be beneficial to fully evaluate the genomic information on Guangxi native chicken and facilitate the application of these resources in chicken breeding