湖北省极小种群野生植物在原生群落中的竞争地位及保护建议

极小种群野生植物是亟需保护、最为濒危的植物, 研究极小种群野生植物物种重要值和竞争格局对保护与恢复具有重要实践意义。本文通过野外群落调查, 研究了湖北省分布的7种极小种群野生植物大别山五针松(Pinus fenzeliana var. dabeshanensis)、水杉(Metasequoia glyptostroboides)、峨眉含笑(Michelia wilsonii)、小勾儿茶(Berchemiella wilsonii)、长果秤锤树(Sinojackia dolichocarpa)、黄梅秤锤树(S. huangmeiensis)和庙台槭(Acer miaotaiense)的重要值及改进后的Hegyi竞争指数。结果表明: 从重要值来看, 水杉、长果秤锤树在各自所属的群落中具有较高的重要值及较低的变异系数, 为群落中的优势种; 庙台槭和黄梅秤锤树重要值较高, 为群落中的亚优势种; 大别山五针松、峨眉含笑、小勾儿茶重要值较低, 为群落伴生种。从改进后的Hegyi竞争指数来看, 湖北省7种极小种群野生植物受到的竞争压力的来源和强度存在较大差异, 大别山五针松、峨眉含笑、小勾儿茶、黄梅秤锤树主要受到种间竞争, 而水杉、长果秤锤树、庙台槭主要受到种内竞争, 因此在制定保护措施前要充分考虑物种间的竞争情况, 才能采取更有针对性的保护措施。     

基于红外相机技术对广东鼎湖山及其周边林地的鸟兽调查

本研究采用公里网格抽样方案, 在广东鼎湖山国家级自然保护区及其周边林地(烂柯山省级自然保护区和小湘林区)选取3个监测样地, 共设置60个红外相机监测位点, 对区域内大中型兽类和地面活动鸟类开展物种编目清查与评估。2017年1月至2018年12月, 红外相机累计工作34,212个相机日, 共获得独立有效照片11,725份。共记录到75种野生动物, 隶属于13目32科63属, 包括兽类12种、鸟类63种, 其中国家一级重点保护动物有1种, 即中华穿山甲(Manis pentadactyla), 国家二级重点保护动物有9种。兽类中相对多度指数排前三的依次为野猪(Sus scrofa)、鼬獾(Melogale moschata)和赤麂(Muntiacus vaginalis); 鸟类依次为白鹇(Lophura nycthemera)、橙头地鸫(Geokichla citrina)和紫啸鸫(Myophonus caeruleus)。三个监测样地的相对多度指数排前三的物种基本一致, 其中鼎湖山的白鹇相对多度指数最高; 小湘的豹猫(Prionailurus bengalensis)相对多度指数位列第三, 仅次于野猪和鼬獾; 烂柯山相对多度指数排前三的鸟类则依次为画眉(Garrulax canorus)、灰胸竹鸡(Bambusicola thoracicus)和红嘴相思鸟(Leiothrix lutea)。本研究为广东鼎湖山及其周边林地生物多样性监测与评估提供了数据参考。     

DDX17 induces epithelial-mesenchymal transition and metastasis through the miR-149-3p/CYBRD1 pathway in colorectal cancer

DEAD box helicase 17 (DDX17) has been reported to be involved in the initiation and development of several cancers. However, the functional role and mechanisms of DDX17 in colorectal cancer (CRC) malignant progression and metastasis remain unclear. Here, we reported that DDX17 expression was increased in CRC tissues compared with noncancerous mucosa tissues and further upregulated in CRC liver metastasis compared with patient-paired primary tumors. High levels of DDX17 were significantly correlated with aggressive phenotypes and worse clinical outcomes in CRC patients. Ectopic expression of DDX17 promoted cell migration and invasion in vitro and in vivo, while the opposite results were obtained in DDX17-deficient CRC cells. We identified miR-149-3p as a potential downstream miRNA of DDX17 through RNA sequencing analysis, and miR-149-3p displayed a suppressive effect on the metastatic potential of CRC cells. We demonstrated that CYBRD1 (a ferric reductase that contributes to dietary iron absorption) was a direct target of miR-149-3p and that miR-149-3p was required for DDX17-mediated regulation of CYBRD1 expression. Moreover, DDX17 contributed to the metastasis and epithelial to mesenchymal transition (EMT) of CRC cells via downregulation of miR-149-3p, which resulted in increased CYBRD1 expression. In conclusion, our findings not only highlight the significance of DDX17 in the aggressive development and prognosis of CRC patients, but also reveal a novel mechanism underlying DDX17-mediated CRC cell metastasis and EMT progression through manipulation of the miR-149-3p/CYBRD1 pathway.Subject terms: Cell migration, Metastasis     

PACAP ameliorates fertility in obese male mice via PKA/CREB pathway-dependent Sirt1 activation and p53 deacetylation

Obesity is strongly linked to male infertility. Testicular spermatogenic cell apoptosis plays an important role in obesity-related male infertility. Pituitary adenylate cyclase-activating peptide (PACAP) has been recently shown to exhibit antiapoptotic and antidiabetic effects. However, the effects of PACAP on obesity-related male infertility remain unknown. The purpose of the current study is to explore the role of PACAP in obesity-related male infertility. Here, C57BL/6 male mice were fed with a high-fat diet to induce obesity and then treated with PACAP. PACAP treatment ameliorated obesity characteristics, including body weight, epididymal adipose weight, testes/body weight, serum lipids levels, and reproductive hormone levels in vivo. Additionally, PACAP was shown to improve the reproductive function of the obese mice, which was characterized by improved testis morphology, sperm parameters, acrosome reaction, and embryo quality after in vitro fertilization via silent information regulator 1 (Sirt1) activation and p53 deacetylation. These beneficial effects of PACAP were abolished in obese mice with testis-specific knockdown of Sirt1. The mechanism studies showed that PACAP selectively binds to the PAC1 receptor to attenuate palmitic acid-induced mouse spermatogenic cell (GC-1) apoptosis via the PKA/CREB/Sirt1/p53 pathway. However, this mechanism was inhibited in GC-1 cells lacking Sirt1. Finally, human semen studies showed that the decline in sperm quality in obese infertile men was partly due to Sirt1 downregulation and p53 acetylation. Our data suggest that PACAP could ameliorate fertility in obese male mice and may be a promising candidate drug for obesity-induced male infertility.     

High-throughput mass spectrometric discovery of protein post-translational modifications.

The availability of genome sequences, affordable mass spectrometers and high-resolution two-dimensional gels has made possible the identification of hundreds of proteins from many organisms by peptide mass fingerprinting. However, little attention has been paid to how information generated by these means can be utilised for detailed protein characterisation. Here we present an approach for the systematic characterisation of proteins using mass spectrometry and a software tool FindMod. This tool, available on the internet at http://www.expasy.ch/sprot/findmod.html , examines peptide mass fingerprinting data for mass differences between empirical and theoretical peptides. Where mass differences correspond to a post-translational modification, intelligent rules are applied to predict the amino acids in the peptide, if any, that might carry the modification. FindMod rules were constructed by examining 5153 incidences of post-translational modifications documented in the SWISS-PROT database, and for the 22 post-translational modifications currently considered (acetylation, amidation, biotinylation, C-mannosylation, deamidation, flavinylation, farnesylation, formylation, geranyl-geranylation, gamma-carboxyglutamic acids, hydroxylation, lipoylation, methylation, myristoylation, N -acyl diglyceride (tripalmitate), O-GlcNAc, palmitoylation, phosphorylation, pyridoxal phosphate, phospho-pantetheine, pyrrolidone carboxylic acid, sulphation) a total of 29 different rules were made. These consider which amino acids can carry a modification, whether the modification occurs on N-terminal, C-terminal or internal amino acids, and the type of organisms on which the modification can be found. We illustrate the utility of the approach with proteins from 2-D gels of Escherichia coli and sheep wool, where post-translational modifications predicted by FindMod were confirmed by MALDI post-source decay peptide fragmentation. As the approach is amenable to automation, it presents a potentially large-scale means of protein characterisation in proteome projects.     

Large structural variations in the haplotype-resolved African cassava genome

Cassava (Manihot esculenta Crantz, 2n = 36) is a global food security crop. It has a highly heterozygous genome, high genetic load, and genotype-dependent asynchronous flowering. It is typically propagated by stem cuttings and any genetic variation between haplotypes, including large structural variations, is preserved by such clonal propagation. Traditional genome assembly approaches generate a collapsed haplotype representation of the genome. In highly heterozygous plants, this results in artifacts and an oversimplification of heterozygous regions. We used a combination of Pacific Biosciences (PacBio), Illumina, and Hi-C to resolve each haplotype of the genome of a farmer-preferred cassava line, TME7 (Oko-iyawo). PacBio reads were assembled using the FALCON suite. Phase switch errors were corrected using FALCON-Phase and Hi-C read data. The ultralong-range information from Hi-C sequencing was also used for scaffolding. Comparison of the two phases revealed >5000 large haplotype-specific structural variants affecting over 8 Mb, including insertions and deletions spanning thousands of base pairs. The potential of these variants to affect allele-specific expression was further explored. RNA-sequencing data from 11 different tissue types were mapped against the scaffolded haploid assembly and gene expression data are incorporated into our existing easy-to-use web-based interface to facilitate use by the broader plant science community. These two assemblies provide an excellent means to study the effects of heterozygosity, haplotype-specific structural variation, gene hemizygosity, and allele-specific gene expression contributing to important agricultural traits and further our understanding of the genetics and domestication of cassava.