36 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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    Brithura triprocessa Men & Liu 2019, sp. nov.

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    <i>Brithura triprocessa</i> Men & Liu sp. nov. (Figs 1–31) <p>Diagnosis. Antenna including flagellum yellow. Prescutum brown with three brownish-yellow stripes; pleura generally brown with a white stripe from the lateral region of pronotum to the base of wing. Femora yellow with broadly black tip. Tergite nine with lateral margins straight, shallowly emarginated at hind margin, a pair of horn-shaped processes inserted from the middle region.</p> <p> Description. Adult length. Male body 18.4–22.6 mm (not including antenna, <i>n</i> = 16), wing 19.2–22.6 mm (<i>n</i> = 16), antenna 4.1–4.6 mm (<i>n</i> =16); female body 28.4–30.6 mm (not including antenna, <i>n</i> =32), wing 20.2–25.4 mm (<i>n</i> =32), antenna 4.5–4.8 mm (<i>n</i> = 32).</p> <p>Head. Head brown with rostrum brown in coloration (Figs 1–3). Nasus light brown, cone in shape, densely covered with black setae (Fig. 3). Eye black. Occiput and vertex lacking of marking, mostly dark brown, narrowly margined with yellow along the eyes (Fig. 1). Vertical tubercle cone-shaped, dark brown, black apically (Fig. 1). Antenna 13-segmented, bent backward not reaching the base of haltere; scape brown, elongated, cylindrical, expanded apically; pedicel brown, very short; flagellum entirely yellow with the first flagellomere longest, the remaining segments generally shortened and thinned, base of each flagellomere enlarged with abundant black verticils, the verticils longer than the length of corresponding flagellomere; surface of flagellomere densely covered with short white setae (Fig. 1). Palpus dark brown (Fig. 3).</p> <p>Thorax. Pronotum black medially, dark brown laterally (Fig. 3). Prescutum brown with three brownish-yellow stripes, median one divided by a brown vitta, lateral stripes subequal in length to half of median one, rounded apically (Fig. 2). Scutum with two yellow markings connected to each other, the upper one triangular, the lower one oval, the latter at least two times longer than the former. Scutellum brown with yellow median line (Fig. 2). Postnotum wholly dark brown (Fig. 2). Pleura generally brown with a white stripe from the lateral region of pronotum to the root of wing, laterotergite basally suffused with white (Fig. 3). Leg stout, coxa and trochanter brown, the latter suffused with black apically; femur yellow with broadly black tip; tibia yellow at basal one fifth, the rest region yellowish-brown; tarsi yellowish-brown. Haltere with stem yellow, knob black. Wing light brown, cells c and sc darker than ground color; stigma dark brown, extending to the bases of cells r4, r5 and discal cell; a black spot at the origin of Rs; discal cell transparent, relatively short; wing tip suffused with slightly smoky gray on cells r3 and r4, with five light spots along the outer margin of wing (Fig. 4). Venation: petiole of cell m1 slightly shorter than discal cell, distinctly shorter than the length of cell m1 (Fig. 4).</p> <p>Abdomen. Abdominal tergites brown with lateral margin black, the hind margin suffused with white, extending to the hind corner (Fig. 5). Sternite generally brown with second to fifth segments narrowly suffused with black on lateral margin (Fig. 5). Hypopygoum with tergite nine and sternite nine separated to each other, only fused at base (Figs 6, 9). Tergite nine with lateral margins straight, shallowly emarginated at hind margin, a pair of horn-shaped processes generated from the middle region, which divided by a narrow groove on dorsal surface, a pair of ear-shaped lobes extended from the ventral side (Figs 10–11). Gonocoxite stout, broad basally and shallowly concaved at apex, densely covered with long setae, with two horn-shaped processes black and pointed inward (Figs 9, 12). Sternite nine broad, equipped with a stout process at base, above which with paired finger-shaped processes which directed ventrally (Figs 9, 12). Outer gonostylus complicated, terminated into an obtuse lobe (o ol) and a sharp process (shp) on outer side, between them with a narrow light region, with another obtuse process (i ol) on inner side which connected to the sharp process (Figs 13–18). Inner gonostylus broad basally, squarely turned into a complicated and narrowed apex, a black finger-shaped process generated in the middle region, many long setae covered on dorsal corner (Figs 19–20). Adminiculum cylindrical, broad basally and narrowed to apex, deeply concaved apically (Figs 12, 23).</p> <p>Semen pump. Semen pump with compressor apodeme fan-shaped (Fig. 21). Posterior immovable apodeme being triangular lobe, its dorsal angle sharply acute (Figs 22–23). Anterior immovable apodeme flattened and elongated, roundly expanded in dorsal view (Figs 22–23). Semen pump with a pair of wrinkled lobes which extended posteriorly forming a sheath (Figs 21–22). Aedeagus very short, tubular, narrowed basally, gradually broadened to the distal two third, and then narrowed to end again (Figs 22–23). Compressor apodeme and anterior immovable apodeme both directed ventrally (Fig. 23).</p> <p>Genital bridge. W-shaped basally. Terminated into two narrowed lobes, the dorsal one longer than the ventral one (Fig. 24).</p> <p>Ovipositor. Elongated. Tergite nine very short, dark brown (Figs 25–26). Sternite nine broad basally, narrowed to the median region, and then gradually broadened forming a fusiform part, finally terminated into an acute apex in dorsal view (Figs 7–8, 27–28). Tergite ten yellow. Sternite eight brown, longer than tergite ten (Figs 25–26). Cercus elongated, acinacifoliate, obtuse apically (Fig. 25). Hypogynial valve broad at base, narrowed to apex, distinctly shorter than cercus (Figs 7–8, 25–26). Vaginal apodeme broad basally, narrowed to apex (Fig. 29).</p> <p>Male internal reproductive system. Consisting of a pair of accessory glands generating from the distal end of seminal vesicle which extended posteriorly into ejaculatory duct, a pair of vasa deferentia linking to paired testes anteriorly and converged into a common vas deferens which receiving to seminal vesicle posteriorly (Fig. 30). Ejaculatory duct relatively elongated, longer than the common vas deferens, flexible and spiral (Fig. 30). Seminal vesicle ball-shaped, leading to the proximal end of common vas deferens, running posterior to the apex of ejaculatory duct (Fig. 30). Accessory glands being a pair of elongated tubes, simple and sinuous, arising from base of seminal vesicle, very elongated (Fig. 30). Vas deferens short and stout, slightly shorter than common vas deferens, very smooth (Fig. 30). Testis, an elliptical structure (Fig. 30).</p> <p>Female internal reproductive system. Consisting of a pair of accessory glands connected to bursa copulatrix by a short stem respectively, three spermathecae with responding spermatheca duct (Fig. 31). Bursa copulatrix relatively short and tough, generated from the ventral side of sternite nine, with a strongly sclerotized region near the copulatory opening (Fig. 31). Accessory gland arising from the base of bursa copulatrix, narrowed basally and terminated into an oval and swollen ball, densely covered with small dots (Fig. 31). Spermatheca three, spherical and black, bigger than the expanded end of accessary gland (Fig. 31). Spermathecal duct slender, half the thickness of bursa copulatrix, flexible, arising from the middle of bursa copulatrix and leading to the spermatheca by black internal tube which broadened and strongly sclerotized; the connection points of three spermathecal ducts with bursa copulatrix not at same level (Fig. 28).</p> <p>Material examined. Holotype male, China, Anhui Province, Yuexi, Yaoluoping National Nature Reserve, 12 August 2013, leg. Qiulei Men. Paratypes. 4 females, same data as holotype; 9 males, 8 females, 22 August 2016, others same data as holotype; 6 males, 20 females, 12 August 2018, leg. Qiulei Men, Lei Yang, Weiguang Liu, others same data as holotype. All deposited in ANU.</p> <p>Distribution. China (Anhui).</p> <p> Remarks. The new species is most similar to another Chinese species <i>B. stigmosa</i> Liu & Yang, 2010 in body color, vein pattern and shape of outer gonostylus. It can be separated from the latter by the 9th tergite with two horn-shaped processes (absent in the latter), by the inner gonostylus terminating into a narrowed apex (not changing to a narrowed end in the latter).</p> <p> Etymology. The specific epithet is a noun ‘ <i>processa</i> ’ with Latin prefix ‘ <i>tri</i> ’, referring to the outer gonostylus having three processes.</p> <p> <b>Funding</b> This study is supported by grants from the National Natural Science Foundation of China (41501058, 31300551), the Anhui Outstanding Young Talent Support Program (gxfx2017059) and the Foundation of the Education Department of Anhui Province (KJ2017A360).</p> <p> <b>Acknowledgements</b> We thank to Dr. Pjotr Oosterbroek, University of Amsterdam, Amsterdam, the Netherlands, for his valuable web site, the <i>Catalogue of the Craneflies of the World</i> (http://ccw.naturalis.nl/index.php), which provides much valuable information about distribution and taxonomy.</p>Published as part of <i>Men, Qiulei, Zhang, Zhongxin, Liu, Qifei, Yang, Lei & Liu, Weiguang, 2019, A new species of genus Brithura Edwards from China, with notes on its internal reproductive system (Diptera: Tipulidae), pp. 158-166 in Zoological Systematics 44 (2)</i> on pages 159-165, DOI: 10.11865/zs.201911, <a href="http://zenodo.org/record/5360762">http://zenodo.org/record/5360762</a&gt

    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
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