黄唇鱼(Bahaba flavolabiata)的全基因组测序和基因组特征研究

黄唇鱼(Bahaba flavolabiata)为国家二级重点保护野生动物、IUCN(世界自然保护联盟)红色名录的极度濒危物种(CR)。基于其样本数量极其有限,全基因组研究可以提供大量与重要性状相关的功能基因和分子标记,从而揭示其重要生命现象的遗传机制。采用二代测序技术于2018年5月完成了黄唇鱼基因组精细图的测序,分析结果表明,测序得到约202 Gb的高质量数据,总测序深度约为317×;组装得到的基因组大小为637.43 Mb,Contig N50约为88 Kb,Scaffold N50约为4.65 Mb;重复序列约142.72 Mb,占比22.39%,预测得到23743个基因、920个t RNA、85个rRNA、176个假基因;98.46%的基因可以注释到NR、GO等数据库中;有67个基因家族是黄唇鱼所特有的。本研究从单碱基错误率、核心基因完整性及二代Reads比对分析3个方面对黄唇鱼基因组精细图的组装结果进行了评估,结果显示所组装的基因区的完整性较好。黄唇鱼基因组序列图谱的绘制完成,对于黄唇鱼自然资源的保护和种质资源挖掘具有极其重要的科学意义。     

Chromosome‐level genome assembly of the greenhouse whitefly (Trialeurodes vaporariorum Westwood)

The greenhouse whitefly, Trialeurodes vaporariorum Westwood, is an agricultural pest of global importance. Here we report a 787‐Mb high‐quality draft genome sequence of T. vaporariorum assembled from PacBio long reads and Hi‐C chromatin interaction maps, which has scaffold and contig N50 lengths of 70 Mb and 500 kb, respectively, and contains 18,275 protein‐coding genes. About 98.8% of the assembled contigs were placed onto the 11 T. vaporariorum chromosomes. Comparative genomic analysis reveals significantly expanded gene families such as aspartyl proteases in T. vaporariorum compared to Bemisia tabaci Mediterranean (MED) and Middle East‐Asia Minor 1 (MEAM1). Furthermore, the cytochrome CYP6 subfamily shows significant expansion in T. vaporariorum and several genes in this subfamily display developmental stage‐specific expression patterns. The high‐quality T. vaporariorum genome provides a valuable resource for research in a broad range of areas such as fundamental molecular ecology, insect–plant/insect–microorganism or virus interactions and pest resistance management.     

青藏高原东缘半湿润沙地典型生态恢复模式的效果比较研究

草地退化与沙化直接影响草地生态系统的功能与服务,植被恢复是沙地恢复治理的重要方式之一,但是探究沙化草地典型生态恢复模式的恢复效果及模式优化研究不足。以野外调查与室内分析相结合的方法,以重度沙化草地为对照（CK）,比较研究了青藏高原东缘沙地三种典型生态恢复模式（围栏封育（Fencing enclosure,FE）、布设高山柳沙障（Salix cupularis sandy barrier,SCSB）、布设高山柳沙障+种草（Salix cupularis sandy barrier plus planting grasses,SCSBPPG））对草本植物群落和土壤理化性质的影响。结果显示：（1）与CK相比,FE的地上草本盖度、生物量、Margalef丰富度指数和Shannon-Weiner多样性指数分别显著提高了13.54倍、13倍、3.09倍和1.80倍,且SCSBPPG的这些指标分别显著提高了11.24倍、10.50倍、1.05倍和0.83倍（P < 0.05）,而SCSB对以上指标影响均不显著。（2）三种典型生态恢复模式对沙地的土壤容重无显著影响,而三种典型生态恢复模式0-10 cm、10-20 cm和20-30 cm土层土壤含水量变化规律一致（SCSBPPG > FE > SCSB）,且SCSBPPG和FE的0-10 cm土层土壤含水量的增加最明显,分别为244.90%、176.92%（P < 0.05）,而SCSB土壤含水量相较于CK无显著差异。（3）该研究区的pH在5.74-6.21之间,FE和SCSBPPG较CK显著降低了0-30 cm各土层土壤pH（P < 0.05）。此外,三种生态恢复模式0-30 cm各土层土壤有机质、全N、全P、全K含量递减变化规律为FE > SCSBPPG > SCSB,FE和SCSBPPG各土层土壤有机质、全N、全P均高于CK,且都在土层10-20 cm增幅最大,FE的最大增幅分别为243.62%、93.94%、68.97%,SCSBPPG的最大增幅分别为118.46%、45.45%、41.38%,而SCSB显著降低了各土层土壤有机质、全N和全P量（P < 0.05）。因此,在青藏高原高寒轻度沙化草地围栏封育有利于其恢复,而重度沙化草地的生态恢复需采用植灌和种草结合的模式。研究结果可为沙地的恢复治理和可持续管理提供依据。     

北京市湿地生态补偿标准研究

确定合理的湿地生态补偿标准是构建有效湿地生态补偿机制的关键。以北京市境内的湿地为研究对象,利用DPSIR模型明晰北京市湿地生态补偿的机理;基于问卷调查数据,分别利用二元Logistic模型和Tobit模型对影响受调查者受偿态度和受偿意愿的相关因素进行分析;运用条件价值法以及考虑时间价值和经济社会发展阶段的修正湿地生态系统服务价值确定最终的生态补偿标准,并对北京市制定湿地生态补偿机制提出了政策建议。研究结果表明：（1）北京市合理的湿地生态补偿标准为2.728×10⁴-4.84×10⁴元hm^-2a^-1;（2）地区差异、受调查者对湿地保护政策的了解程度以及湿地与社区之间的关系显著影响其受偿态度;（3）地区差异、年龄、受教育程度、家庭收入情况、对生态补偿的了解程度显著影响其受偿意愿;（4）为减少将来推进湿地生态补偿过程中可能遭遇的潜在阻碍,北京市应该加强湿地保护相关政策的宣传普及工作,注重对基层政策落实情况的监督,协调湿地政策与社区的关系;（5）有必要结合地区特征制定差异化的湿地生态补偿标准。研究结果可为今后北京市探索建立湿地生态补偿机制、提升湿地保护效率提供科学数据和理论参考。     

The Alteration of MiR-222 and Its Target Genes in Nickel-Induced Tumor

Nickel is an important kind of metal and a necessary trace element in people’s production and livelihood; it is also a well-confirmed human carcinogen. In the past few years, researchers did a large number of studies about the molecular mechanisms of nickel carcinogenesis, and they focused on activation of proto-oncogenes and inactivation of anti-oncogenes caused by gene point mutation, gene deletion, gene amplification, DNA methylation, chromosome condensation, and so on that were induced by nickel. However, the researches on tumorigenic molecular mechanisms regulated by microRNAs (miRNAs) are rare. In this study, we established nickel-induced tumor by injecting Ni₃S₂ compounds to Wistar Rattus. By establishing a cDNA library of miRNA from rat muscle tumor tissue induced by Ni₃S₂, we found that the expression of miR-222 was significantly upregulated in tumor tissue compared with the normal tissue. As we expected, the expression levels of target genes of miR-222, CDKN1B and CDKN1C, were downregulated in the nickel-induced tumor. The same alteration of miR-222 and its target genes was also found in malignant 16HBE cells induced with Ni₃S₂ compounds. We conclude that miR-222 may promote cell proliferation infinitely during nickel-induced tumorigenesis in part by regulating the expression of its target genes CDKN1B and CDKN1C. Our study elucidated a novel molecular mechanism of nickel-induced tumorigenesis.     

Regulation of a Dynamic Interaction between Two Microtubule-binding Proteins,EB1 and TIP150, by the Mitotic p300/CBP-associated Factor (PCAF) Orchestrates Kinetochore Microtubule Plasticity and Chromosome Stability during Mitosis

The microtubule cytoskeleton network orchestrates cellular dynamics and chromosome stability in mitosis. Although tubulin acetylation is essential for cellular plasticity, it has remained elusive how kinetochore microtubule plus-end dynamics are regulated by p300/CBP-associated factor (PCAF) acetylation in mitosis. Here, we demonstrate that the plus-end tracking protein, TIP150, regulates dynamic kinetochore-microtubule attachments by promoting the stability of spindle microtubule plus-ends. Suppression of TIP150 by siRNA results in metaphase alignment delays and perturbations in chromosome biorientation. TIP150 is a tetramer that binds an end-binding protein (EB1) dimer through the C-terminal domains, and overexpression of the C-terminal TIP150 or disruption of the TIP150-EB1 interface by a membrane-permeable peptide perturbs chromosome segregation. Acetylation of EB1-PCAF regulates the TIP150 interaction, and persistent acetylation perturbs EB1-TIP150 interaction and accurate metaphase alignment, resulting in spindle checkpoint activation. Suppression of the mitotic checkpoint serine/threonine protein kinase, BubR1, overrides mitotic arrest induced by impaired EB1-TIP150 interaction, but cells exhibit whole chromosome aneuploidy. Thus, the results identify a mechanism by which the TIP150-EB1 interaction governs kinetochore microtubule plus-end plasticity and establish that the temporal control of the TIP150-EB1 interaction by PCAF acetylation ensures chromosome stability in mitosis.     

Synthesis and acrosin inhibitory activities of 5-phenyl-1H-pyrazole-3-carboxylic acid amide derivatives

A series of novel 5-phenyl-1H-pyrazole-3-carboxylic acid amide derivatives were designed, synthesized, and their acrosin inhibitory activities in vitro were evaluated. The results of the acrosin inhibitory activity showed that all target compounds were more potent than control TLCK. Compounds AQ-A1, AQ-D3, AQ-D4, AQ-E4 and AQ-E5 exhibited stronger acrosin inhibitory activities than control ISO-1. Especially, compound AQ-E5 displayed the most potent acrosin inhibitory activity in all the compounds, with an IC₅₀ of 0.01 μmol/mL. This study provided a new structural class for the development of novel acrosin inhibitory agents.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

Arginine carrier peptide bearing Ni(II) chelator to promote cellular uptake of histidine-tagged proteins

Arginine-rich peptide-mediated protein delivery into living cells is a novel technology for controlling cell functions with therapeutic potential. In this report, a novel approach for the intracellular delivery of histidine-tagged proteins was introduced where a Ni(II) chelate of octaarginine peptide bearing nitrilotriacetic acid [R8-NTA-Ni(II)] was used as a membrane-permeable carrier molecule. Significant internalization of histidine-tagged enhanced green fluorescent protein (EGFP) into HeLa cells was observed by confocal microscopic observation in the presence of R8-NTA-Ni(II). Nuclear condensation characteristic in apoptotic cell death was also induced in the cells treated with a histidine-tagged apoptosis-inducing peptide [pro-apoptotic domain peptide (PAD)], indicating that the cargo molecules really went through the membrane to reach the cytosol. The apoptosis-inducing activity of the peptide thus delivered was compared with that of the PAD peptide covalently connected with the octaarginine peptide.