34 research outputs found

    An atlas of DNA methylomes in porcine adipose and muscle tissues

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    It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level. We generate 1,381 Gb of sequence data from 180 methylated DNA immunoprecipitation libraries, and provide a genome-wide DNA methylation map as well as a gene expression map for adipose and muscle studies. The analysis shows global similarity and difference among breeds, sexes and anatomic locations, and identifies the differentially methylated regions. The differentially methylated regions in promoters are highly associated with obesity development via expression repression of both known obesity-related genes and novel genes. This comprehensive map provides a solid basis for exploring epigenetic mechanisms of adipose deposition and muscle growth

    MicroRNAome of Porcine Pre- and Postnatal Development

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    The domestic pig is of enormous agricultural significance and valuable models for many human diseases. Information concerning the pig microRNAome (miRNAome) has been long overdue and elucidation of this information will permit an atlas of microRNA (miRNA) regulation functions and networks to be constructed. Here we performed a comprehensive search for porcine miRNAs on ten small RNA sequencing libraries prepared from a mixture of tissues obtained during the entire pig lifetime, from the fetal period through adulthood. The sequencing results were analyzed using mammalian miRNAs, the precursor hairpins (pre-miRNAs) and the first release of the high-coverage porcine genome assembly (Sscrofa9, April 2009) and the available expressed sequence tag (EST) sequences. Our results extend the repertoire of pig miRNAome to 867 pre-miRNAs (623 with genomic coordinates) encoding for 1,004 miRNAs, of which 777 are unique. We preformed real-time quantitative PCR (q-PCR) experiments for selected 30 miRNAs in 47 tissue-specific samples and found agreement between the sequencing and q-PCR data. This broad survey provides detailed information about multiple variants of mature sequences, precursors, chromosomal organization, development-specific expression, and conservation patterns. Our data mining produced a broad view of the pig miRNAome, consisting of miRNAs and isomiRs and a wealth of information of pig miRNA characteristics. These results are prelude to the advancement in pig biology as well the use of pigs as model organism for human biological and biomedical studies

    Two-Stream Deep Correlation Network for Frontal Face Recovery

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    Pathogenic Factors and Mechanisms of the Alternaria Leaf Spot Pathogen in Apple

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    Alternaria leaf spot seriously threatens the sustainable development of the global apple industry, causing significant losses and reducing fruit quality and yield. The causal agent Alternaria alternata f. sp. mali (Alternaria mali, ALT) produces various molecules to modulate infection, such as cell wall-degrading enzymes, toxins, and elicitor-like molecules. ALT produces the host-specific AM-toxin, an important pathogenicity factor. ALT also releases effectors into apple cells that modify host defense, but these proteins have not yet been described. Here, we identified the pathogenic fungal types responsible for early defoliation from diseased leaves of Fuji (Malus domestica cv. β€˜Fuji’) apple collected from five districts in Shandong Province, China. The ALT isolates ALT2 to ALT7 were pathogenic to four apple cultivars, with ALT7 being the most aggressive. We extracted mycotoxins (AM-toxin-2 to AM-toxin-7) from each isolate and used them to treat different apple varieties, which led to leaf-spot symptoms and damaged chloroplasts and nuclear membranes, followed by cell death. AM-toxin-7 produced the most severe symptoms, but chloroplasts remained intact when the mycotoxin was inactivated. Mass spectrometry identified 134 secretory proteins in ALT7 exosomes, and three secreted proteins (AltABC, AltAO, and AltPDE) were confirmed to be involved in apple pathogenesis. Therefore, ALT secretes AM-toxin and secretory proteins as an infection strategy to promote fungal invasion and overcome the host defense system

    Quantification of Precipitation Using Polarimetric Radar Measurements during Several Typhoon Events in Southern China

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    Accurate quantitative precipitation estimation (QPE) during typhoon events is critical for flood warning and emergency management. Dual-polarization radar has proven to have better performance for QPE, compared to traditional single-polarization radar. However, polarimetric radar applications have not been extensively investigated in China, especially during extreme events such as typhoons, since the operational dual-polarization system upgrade only happened recently. This paper extends a polarimetric radar rainfall system for local applications during typhoons in southern China and conducts comprehensive studies about QPE and precipitation microphysics. Observations from S-band dual-polarization radar in Guangdong Province during three typhoon events in 2017 are examined to demonstrate the enhanced radar rainfall performance. The microphysical properties of hydrometeors during typhoon events are analyzed through raindrop size distribution (DSD) data and polarimetric radar measurements. The stratiform precipitation in typhoons presents lower mean raindrop diameter and lower raindrop concentration than that of the convection precipitation. The rainfall estimates from the adapted radar rainfall algorithm agree well with rainfall measurements from rain gauges. Using the rain gauge data as references, the maximum normalized mean bias ( N M B ) of the adapted radar rainfall algorithm is 20.27%; the normalized standard error ( N S E ) is less than 40%; and the Pearson’s correlation coefficient ( C C ) is higher than 0.92. For the three typhoon events combined, the N S E and N M B are 36.66% and -15.78%, respectively. Compared with several conventional radar rainfall algorithms, the adapted algorithm based on local rainfall microphysics has the best performance in southern China
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