Transcriptome Analysis and Ultrastructure Observation Reveal that Hawthorn Fruit Softening Is due to Cellulose/Hemicellulose Degradation

Softening, a common phenomenon in many fruits, is a well coordinated and genetically determined process. However, the process of flesh softening during ripening has rarely been described in hawthorn. In this study, we found that ‘Ruanrou Shanlihong 3 Hao’ fruits became softer during ripening, whereas ‘Qiu JinXing’ fruits remained hard. At late developmental stages, the firmness of ‘Ruanrou Shanlihong 3 Hao’ fruits rapidly declined, and that of ‘Qiu JinXing’ fruits remained essentially unchanged. According to transmission electron microscopy (TEM), the middle lamella of ‘Qiu JinXing’ and ‘Ruanrou Shanlihong 3 Hao’ fruit flesh was largely degraded as the fruits matured. Microfilaments in ‘Qiu JinXing’ flesh were arranged close together and were deep in color, whereas those in ‘Ruanrou Shanlihong 3 Hao’ fruit flesh were arranged loosely, partially degraded and light in color. RNA-Seq analysis yielded approximately 46.72 Gb of clean data and 72,837 unigenes. Galactose metabolism and pentose and glucuronate interconversions are involved in cell wall metabolism, play an important role in hawthorn texture. We identified 85 unigenes related to the cell wall between hard- and soft-fleshed hawthorn fruits. Based on data analysis and real-time PCR, we suggest that β-GAL and PE4 have important functions in early fruit softening. The genes Ffase, Gns, α-GAL, PE63, XTH and CWP, which are involved in cell wall degradation, are responsible for the different textures of hawthorn fruits. Thus, we hypothesize that the different textures of ‘Qiu JinXing’ and ‘Ruanrou Shanlihong 3 Hao’ fruits at maturity mainly result from cellulose/hemicelluloses degradation rather than from lamella degradation. Overall, we propose that different types of hydrolytic enzymes in cells interact to degrade the cell wall, resulting in ultramicroscopic Structure changes in the cell wall and, consequently, fruit softening. These results provide fundamental insight regarding the mechanisms by which hawthorn fruits acquire different textures and also lay a solid foundation for further research

Assessment of genome integrity with array CGH in cattle transgenic cell lines produced by homologous recombination and somatic cell cloning

<p>Abstract</p> <p>Background</p> <p>Transgenic cattle carrying multiple genomic modifications have been produced by serial rounds of somatic cell chromatin transfer (cloning) of sequentially genetically targeted somatic cells. However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity or/and introduce epigenetic errors in the resulting cell lines, rendering a decline in cloning. To test these possibilities, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from genetic modification and cloning. Our plan included the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines with either high or low cloning efficiencies.</p> <p>Results</p> <p>We detected similar amounts of differences between the control hybridizations (8, 13 and 39 differences) and the comparative analyses of both "high" and "low" cell lines (ranging from 7 to 57 with a mean of ~20). Almost 75% of the large differences (>10 kb) and about 45% of all differences shared the same type (loss or gain) and were located in nearby genomic regions across hybridizations. Therefore, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents).</p> <p>Conclusions</p> <p>Our findings reveal that large copy number variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning may be responsible for the cloning efficiency decline.</p

The effect of proteoglycans inhibited by RNA interference on metastatic characters of human salivary adenoid cystic carcinoma

<p>Abstract</p> <p>Background</p> <p>Salivary adenoid cystic carcinoma (SACC) is one of the most common malignancies of salivary gland. Recurrence or/and early metastasis is its biological properties. In SACC, neoplastic myoepithelial cells secrete proteoglycans unconventionally full of the cribriform or tubular and glandular structures of SACC. Literatures have demonstrated that extracellular matrix provided an essential microenvironment for the biological behavior of SACC. However, there is rare study of the effect of proteoglycans on the potential metastasis of SACC.</p> <p>In this study, human xylosyltransferase-I (XTLY-I) gene, which catalyzes the rate-limited step of proteoglycans biosynthesis, was knocked down by RNA interference (RNAi) to inhibit the proteoglycans biosynthesis in SACC cell line with high tendency of lung metastasis (SACC-M). The impact of down-regulated proteoglycans on the metastasis characters of SACC-M cells was analyzed and discussed. This research could provide a new idea for the clinical treatment of SACC.</p> <p>Methods</p> <p>The eukaryotic expression vector of short hairpin RNA (shRNA) targeting XTLY-I gene was constructed and transfected into SACC-M cells. A stably transfectant cell line named SACC-M-WJ4 was isolated. The XTLY-I expression was measured by real-time PCR and Western blot; the reduction of proteoglycans was measured. The invasion and metastasis of SACC-M-WJ4 cells were detected; the effect of down-regulated proteoglycans on the potential lung metastasis of nude mice was observed, respectively.</p> <p>Results</p> <p>The shRNA plasmid targeting XTLY-I gene showed powerful efficiency of RNAi. The mRNA level of target gene decreased by 86.81%, the protein level was decreased by 80.10%, respectively. The silence of XTLY-I gene resulted in the reduction of proteoglycans significantly in SACC-M-WJ4 cells. The inhibitory rate of proteoglycans was 58.17% (24 h), 66.06% (48 h), 57.91% (72 h), 59.36% (96 h), and 55.65% (120 h), respectively. The reduction of proteoglycans suppressed the adhesion, invasion and metastasis properties of SACC-M cells, and decreased the lung metastasis of SACC-M cells markedly either.</p> <p>Conclusion</p> <p>The data suggested that the silence of XTLY-I gene in SACC-M cells could suppress proteoglycans biosynthesis and secretion significantly. The reduction of proteoglycans inhibited cell adhesion, invasion and metastasis of SACC-M cells. There is a close relationship between proteoglycans and the biological behavior of SACC.</p

Vortex-induced Shear Polaritons

Hyperbolic shear polaritons (HShPs) emerge with widespread attention as a new class of polariton modes with broken symmetry due to shear lattices. In this letter, we find a new mechanism of generating HShPs. When utilizing vortex waves as excitation sources of hyperbolic materials without off-diagonal elements, HShPs will appear. In addition, this asymmetric HShPs can be recovered as symmetric modes away from the source, with a critical transition mode between the left-skewed and right-skewed HShPs, via tuning the magnitude of the off-diagonal imaginary component and controlling the topological charge of vortex source. It is worth mentioning that we explore the influence of parity of topological charges on the field distribution and demonstrate these exotic phenomena from numerical and analytical perspectives. Our results will promote new opportunities for both HShPs and vortex waves, widening the horizon for various hyperbolic materials based on vortex sources and offering a new degree of freedom to control various kinds of polaritons

CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

General statistics of 487 differential CNVRs between high and low group based on UMD3.1. (XLSX 28 kb

Detection and attribution of nitrogen runoff trend in China's croplands

Reliable detection and attribution of changes in nitrogen (N) runoff from croplands are essential for designing efficient, sustainable N management strategies for future. Despite the recognition that excess N runoff poses a risk of aquatic eutrophication, large-scale, spatially detailed N runoff trends and their drivers remain poorly understood in China. Based on data comprising 535 site-years from 100 sites across China's croplands, we developed a data-driven upscaling model and a new simplified attribution approach to detect and attribute N runoff trends during the period of 1990–2012. Our results show that N runoff has increased by 46% for rice paddy fields and 31% for upland areas since 1990. However, we acknowledge that the upscaling model is subject to large uncertainties (20% and 40% as coefficient of variation of N runoff, respectively). At national scale, increased fertilizer application was identified as the most likely driver of the N runoff trend, while decreased irrigation levels offset to some extent the impact of fertilization increases. In southern China, the increasing trend of upland N runoff can be attributed to the growth in N runoff rates. Our results suggested that increased SOM led to the N runoff rate growth for uplands, but led to a decline for rice paddy fields. In combination, these results imply that improving management approaches for both N fertilizer use and irrigation is urgently required for mitigating agricultural N runoff in China

Single-cell RNA sequencing reveals dynamic changes in A-to-I RNA editome during early human embryogenesis

BACKGROUND: A-to-I RNA-editing mediated by ADAR (adenosine deaminase acting on RNA) enzymes that converts adenosine to inosine in RNA sequence can generate mutations and alter gene regulation in metazoans. Previous studies have shown that A-to-I RNA-editing plays vital roles in mouse embryogenesis. However, the RNA-editing activities in early human embryonic development have not been investigated. RESULTS: Here, we characterized genome-wide A-to-I RNA-editing activities during human early embryogenesis by profiling 68 single cells from 29 human embryos spanning from oocyte to morula stages. We demonstrate dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion. In parallel with ADAR expression level changes, the genome-wide A-to-I RNA-editing levels in cells remained relatively stable until 4-cell stage, but dramatically decreased at 8-cell stage, continually decreased at morula stage. We detected 37 non-synonymously RNA-edited genes, of which 5 were frequently found in cells of multiple embryonic stages. Moreover, we found that A-to-I editings in miRNA-targeted regions of a substantial number of genes preferably occurred in one or two sequential stages. CONCLUSIONS: Our single-cell analysis reveals dynamic changes in genome-wide RNA-editing during early human embryogenesis in a stage-specific fashion, and provides important insights into early human embryogenesis. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-016-3115-2) contains supplementary material, which is available to authorized users

Functional Genomic Analysis of Variation on Beef Tenderness Induced by Acute Stress in Angus Cattle

Beef is one of the leading sources of protein, B vitamins, iron, and zinc in human food. Beef palatability is based on three general criteria: tenderness, juiciness, and flavor, of which tenderness is thought to be the most important factor. In this study, we found that beef tenderness, measured by the Warner-Bratzler shear force (WBSF), was dramatically increased by acute stress. Microarray analysis and qPCR identified a variety of genes that were differentially expressed. Pathway analysis showed that these genes were involved in immune response and regulation of metabolism process as activators or repressors. Further analysis identified that these changes may be related with CpG methylation of several genes. Therefore, the results from this study provide an enhanced understanding of the mechanisms that genetic and epigenetic regulations control meat quality and beef tenderness

Review of molten carbonate-based direct carbon fuel cells

Abstract Direct carbon fuel cell (DCFC) is a promising technology with high energy efficiency and abundant fuel. To date, a variety of DCFC configurations have been investigated, with molten hydroxide, molten carbonate or oxides being used as the electrolyte. Recently, there has been particular interest in DCFC with molten carbonate involved. The molten carbonate is either an electrolyte or a catalyst in different cell structures. In this review, we consider carbonate as the clue to discuss the function of carbonate in DCFCs, and start the paper by outlining the developments in terms of molten carbonate (MC)-based DCFC and its electrochemical oxidation processes. Thereafter, the composite electrolyte merging solid carbonate and mixed ionic–electronic conductors (MIEC) are discussed. Hybrid DCFC (HDCFCs ) combining molten carbonate and solid oxide fuel cell (SOFC) are also touched on. The primary function of carbonate (i.e., facilitating ion transfer and expanding the triple-phase boundaries) in these systems, is then discussed in detail. Finally, some issues are identified and a future outlook outlined, including a corrosion attack of cell components, reactions using inorganic salt from fuel ash, and wetting with carbon fuels

MicroRNA-29b contributes to pre-eclampsia through its effects on apoptosis, invasion and angiogenesis of trophoblast cells,”

Abstract PE (pre-eclampsia), a pregnancy-specific disorder, is characterized by increased trophoblast cell death and deficient trophoblast invasion and reduced trophoblast-mediated remodelling of spiral arteries. The present study was performed to determine the function of miR-29b (microRNA-29b) in trophoblast cells and its underlying role in the pathogenesis of PE. The prediction of miR-29b target genes was performed using computer-based programs, including Targetscan, Pictar and miRBase. The function of these target genes was analysed further by gene ontology (GO). The effects of miR-29b on apoptosis, and invasion and angiogenesis of trophoblast cell lines (HTR-8/SVneo, BeWo and JAR) were examined by flow cytometry and Matrigel assay respectively. We found that miR-29b induced apoptosis and inhibited invasion and angiogenesis of trophoblast cells. Further studies confirmed that miR-29b regulated the expression of MCL1 (myeloid cell leukaemia sequence 1), MMP2 (encoding matrix metallproteinase 2), VEGFA (vascular endothelial growth factor A) and ITGB1 (integrin β1) genes by directly binding to their 3 -UTRs (untranslated regions). Moreover, we identified that there was an inverse correlation between miR-29b and its target genes in subjects with PE. Taken together, these findings support a novel role for miR-29b in invasion, apoptosis and angiogenesis of trophoblast cells, and miR-29b may become a new potential therapeutic target for PE