Tea is one of the most popular beverages across the world and is made exclusively from cultivars of Camellia sinensis. Many wild relatives of the genus Camellia that are closely related to C. ...sinensis are native to Southwest China. In this study, we first identified the distinct genetic divergence between C. sinensis and its wild relatives and provided a glimpse into the artificial selection of tea plants at a genome-wide level by analyzing 15,444 genomic SNPs that were identified from 18 cultivated and wild tea accessions using a high-throughput genome-wide restriction site-associated DNA sequencing (RAD-Seq) approach. Six distinct clusters were detected by phylogeny inferrence and principal component and genetic structural analyses, and these clusters corresponded to six Camellia species/varieties. Genetic divergence apparently indicated that C. taliensis var. bangwei is a semi-wild or transient landrace occupying a phylogenetic position between those wild and cultivated tea plants. Cultivated accessions exhibited greater heterozygosity than wild accessions, with the exception of C. taliensis var. bangwei. Thirteen genes with non-synonymous SNPs exhibited strong selective signals that were suggestive of putative artificial selective footprints for tea plants during domestication. The genome-wide SNPs provide a fundamental data resource for assessing genetic relationships, characterizing complex traits, comparing heterozygosity and analyzing putatitve artificial selection in tea plants.
Senescence and altered differentiation potential of bone marrow stromal cells (BMSCs) lead to age‐related bone loss. As an important posttranscriptional regulatory pathway, alternative splicing (AS) ...regulates the diversity of gene expression and has been linked to induction of cellular senescence. However, the role of splicing factors in BMSCs during aging remains poorly defined. Herein, we found that the expression of the splicing factor Y‐box binding protein 1 (YBX1) in BMSCs decreased with aging in mice and humans. YBX1 deficiency resulted in mis‐splicing in genes linked to BMSC osteogenic differentiation and senescence, such as Fn1, Nrp2, Sirt2, Sp7, and Spp1, thus contributing to BMSC senescence and differentiation shift during aging. Deletion of Ybx1 in BMSCs accelerated bone loss in mice, while its overexpression stimulated bone formation. Finally, we identified a small compound, sciadopitysin, which attenuated the degradation of YBX1 and bone loss in old mice. Our study demonstrated that YBX1 governs cell fate of BMSCs via fine control of RNA splicing and provides a potential therapeutic target for age‐related osteoporosis.
Synopsis
Alternative splicing has been shown to regulate cellular senescence and differentiation. This study links the reduced expression of the splicing regulator YBX1 in aging bone marrow stromal cells to senescence and aging‐related bone loss.
The expression level of YBX1 in BMSCs decreases during aging.
Ybx1 overexpression in BMSCs stimulates bone formation, while its deletion accelerates bone loss.
YBX1 suppresses BMSC senescence and modulates BMSC differentiation by controlling RNA splicing.
The small compound sciadopitysin attenuates YBX1 degradation and bone loss in old mice.
Reduced expression of YBX1 in aging bone marrow stromal cells induces their senescence and bone loss due to mRNA mis‐splicing.
Tea is one of the most popular non-alcoholic beverages worldwide. However, the tea plant, Camellia sinensis, is difficult to culture in vitro, to transform, and has a large genome, rendering little ...genomic information available. Recent advances in large-scale RNA sequencing (RNA-seq) provide a fast, cost-effective, and reliable approach to generate large expression datasets for functional genomic analysis, which is especially suitable for non-model species with un-sequenced genomes.
Using high-throughput Illumina RNA-seq, the transcriptome from poly (A)+ RNA of C. sinensis was analyzed at an unprecedented depth (2.59 gigabase pairs). Approximate 34.5 million reads were obtained, trimmed, and assembled into 127,094 unigenes, with an average length of 355 bp and an N50 of 506 bp, which consisted of 788 contig clusters and 126,306 singletons. This number of unigenes was 10-fold higher than existing C. sinensis sequences deposited in GenBank (as of August 2010). Sequence similarity analyses against six public databases (Uniprot, NR and COGs at NCBI, Pfam, InterPro and KEGG) found 55,088 unigenes that could be annotated with gene descriptions, conserved protein domains, or gene ontology terms. Some of the unigenes were assigned to putative metabolic pathways. Targeted searches using these annotations identified the majority of genes associated with several primary metabolic pathways and natural product pathways that are important to tea quality, such as flavonoid, theanine and caffeine biosynthesis pathways. Novel candidate genes of these secondary pathways were discovered. Comparisons with four previously prepared cDNA libraries revealed that this transcriptome dataset has both a high degree of consistency with previous EST data and an approximate 20 times increase in coverage. Thirteen unigenes related to theanine and flavonoid synthesis were validated. Their expression patterns in different organs of the tea plant were analyzed by RT-PCR and quantitative real time PCR (qRT-PCR).
An extensive transcriptome dataset has been obtained from the deep sequencing of tea plant. The coverage of the transcriptome is comprehensive enough to discover all known genes of several major metabolic pathways. This transcriptome dataset can serve as an important public information platform for gene expression, genomics, and functional genomic studies in C. sinensis.
Summary
This paper presents a numerical approach for the design sensitivity analysis of modal frequencies of elastic structures submerged in an unbounded heavy fluid domain. Because the feedback of ...sound pressure onto the fluid‐loaded structures has to be taken into account in this case, a fully coupled scheme which combines the structural finite element method (FEM) and the acoustic boundary element method (BEM) is employed in the numerical simulation. The resulting nonlinear eigenvalue problem created by the coupled finite element and boundary element (FE‐BE) method is converted into a generalized eigenvalue problem (GEP) of reduced dimension by using a contour integral method. The design sensitivity formulation for non‐repeated eigenvalues is derived based on an adjoint method which uses both the left and right eigenvectors, and a small GEP is formed to calculate the gradients of repeated eigenvalues. The Burton‐Miller formulation is employed to shift the fictitious eigenfrequencies and their derivatives, and the parameter setting which is beneficial to the filtering of fictitious eigenfrequencies is investigated. Numerical examples are given to verify the accuracy and effectiveness of the developed method.
•Withered tea leaves were subjected to transcriptome and metabolite profiling.•Tea leaves were intact, alive and showed active gene-expression during withering.•Dehydration triggered changes in ...transcription and content of tea flavor compounds.
Withering is an indispensable process for improving flavors in green, black and white teas during their manufacturing. The effects of the withering process on the formation of tea flavors were investigated using transcriptome and metabolite profiling in withered tea leaves. A total of 3268, 23,282 and 25,185 differentially expressed genes (DEGs) were identified at 3 h (68%, water content), 12 h (61%) and 24 h (48%) of the withering process, respectively. The DEGs, involved in flavonoid biosynthesis were significantly downregulated, which could be correlated with the reduction of catechins. Enhancement of terpenoids and alpha-linolenic acid metabolism could trigger an increase in the total content and number of volatiles. The increase in free amino acid-content could be related to 261 DEGs. Our study suggests that dehydration stress during withering induced significant changes in the gene transcription and content of the tea flavor compounds, which promoted the special flavors in various teas.
A total of 64 acute gastroenteritis outbreaks with 2,953 patients starting in December of 2016 and occurring mostly in the late spring of 2017 were reported in Jiangsu, China. A recombinant ...GII.P16-GII.2 norovirus variant was associated with 47 outbreaks (73.4%) for the gastroenteritis epidemic, predominantly occurring in February and March of 2017. Sequence analysis of the RNA-dependent RNA polymerase (RdRp) and capsid protein of the viral isolates from these outbreaks confirmed that this GII.P16-GII.2 strain was the GII.P16-GII.2 variant with the intergenotypic recombination, identified in Taiwan, Hong Kong, and other cities in China in 2016. This GII.P16-GII.2 recombinant variant appeared to a re-emerging strain, firstly identified in 2011-2012 from Japan and USA but might be independently originated from other GII.P16-GII.2 variants for sporadic and outbreaks of gastroenteritis in Japan and China before 2016. Further identification of unique amino acid mutations in both VP1 and RdRp of NoV strain as shown in this report may provide insight in explaining its structural and antigenic changes, potentially critical for the variant recombinant to gain its predominance in causing regional and worldwide epidemics.
An accurate numerical solver is developed in this paper for eigenproblems governed by the Helmholtz equation and formulated through the boundary element method. A contour integral method is used to ...convert the nonlinear eigenproblem into an ordinary eigenproblem, so that eigenvalues can be extracted accurately by solving a set of standard boundary element systems of equations. In order to accelerate the solution procedure, the parameters affecting the accuracy and efficiency of the method are studied and two contour paths are compared. Moreover, a wideband fast multipole method is implemented with a block IDR(s) solver to reduce the overall solution cost of the boundary element systems of equations with multiple right-hand sides. The Burton–Miller formulation is employed to identify the fictitious eigenfrequencies of the interior acoustic problems with multiply connected domains. The actual effect of the Burton–Miller formulation on tackling the fictitious eigenfrequency problem is investigated and the optimal choice of the coupling parameter as α=i/k is confirmed through exterior sphere examples. Furthermore, the numerical eigenvalues obtained by the developed method are compared with the results obtained by the finite element method to show the accuracy and efficiency of the developed method.
Gastric cancer continues to be the second most frequent cause of cancer deaths worldwide. However, the exact molecular mechanisms are still unclear. Further research to find potential targets for ...therapy is critical and urgent. In this study, we found that ARPC2 promoted cell proliferation and invasion in the human cancer cell line MKN-28 using a cell total number assay, MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide) assay, cell colony formation assay, migration assay, invasion assay, and wound healing assay. For downstream pathways, CTNND1, EZH2, BCL2L2, CDH2, VIM, and EGFR were upregulated by ARPC2, whereas PTEN, BAK, and CDH1 were downregulated by ARPC2. In a clinical study, we examined the expression of ARPC2 in 110 cases of normal human gastric tissues and 110 cases of human gastric cancer tissues. ARPC2 showed higher expression in gastric cancer tissues than in normal gastric tissues. In the association analysis of 110 gastric cancer tissues, ARPC2 showed significant associations with large tumor size, lymph node invasion, and high tumor stage. In addition, ARPC2-positive patients exhibited lower RFS and OS rates compared with ARPC2-negative patients. We thus identify that ARPC2 plays an aneretic role in human gastric cancer and provided a new target for gastric cancer therapy.
The diamond/ZnSe/ITO composite film (DZSCF) electroluminescence (EL) device was deposited on n-type heavily doped silicon substrate by microwave plasma chemical vapor deposition technique and vacuum ...electron beam vapor deposition technique. Its composition, microstructure, current-voltage characteristic and EL characteristic were characterized with a series of corresponding detection equipment. The experimental results show that the device can emit strong white light at a forward applied voltage of 240 V, and its CIE coordinates (0.361,0.334) show that its white light purity is higher and its corresponding color temperature is lower(4271 K). The EL spectra of the device show two broad peaks in the blue-green region (central wavelength at 496 nm) and the red region (central wavelength at 660 nm), respectively. In addition, the device also exhibits obvious rectification characteristics. The corresponding experimental results are explained reasonably.
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•A diamond/ZnSe composite film EL device was made. The device can emit strong white light visible to the naked eye.•The electron acceleration effect of diamond layer effectively improve the EL intensity of ZnSe layer.•This study provides a new possible way to achieve high luminance white electroluminescent based on diamond thin film.
Osteoarthritis is a common type of degenerative joint disease. Inflammation-related chondrocyte senescence plays a major role in the pathogenesis of osteoarthritis. Omentin-1 is a newly identified ...anti-inflammatory adipokine involved in lipid metabolism. In this study, we examined the biological function of omentin-1 in cultured chondrocytes. The presence of omentin-1 potently suppresses IL-1β-induced cellular senescence as revealed by staining with senescence-associated beta-galactosidase (SA-β-Gal). At the cellular level, omentin-1 attenuates IL-1β-induced G1 phase cell-cycle arrest. Mechanistically, we demonstrate that omentin-1 reduced IL-1β-induced expression of senescent factors including caveolin-1, p21, and PAI-1 as well as p53 acetylation through ameliorating SIRT1 reduction. Notably, silencing of SIRT1 abolishes IL-1β-induced senescence along with the induction of p21 and PAI-1, suggesting that the action of omentin-1 in chondrocytes is dependent on SIRT1. Collectively, our results revealed the molecular mechanism through which the adipokine omentin-1 exerts a beneficial effect, thereby protecting chondrocytes from senescence. Thus, omentin-1 could have clinical implication in the treatment of osteoarthritis.
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