Characterizing mobile element insertions in 5675 genomes

Mobile element insertions (MEIs) are a major class of structural variants (SVs) and have been linked to many human genetic disorders, including hemophilia, neurofibromatosis, and various cancers. However, human MEI resources from large-scale genome sequencing are still lacking compared to those for SNPs and SVs. Here, we report a comprehensive map of 36 699 non-reference MEIs constructed from 5675 genomes, comprising 2998 Chinese samples (∼26.2×, NyuWa) and 2677 samples from the 1000 Genomes Project (∼7.4×, 1KGP). We discovered that LINE-1 insertions were highly enriched in centromere regions, implying the role of chromosome context in retroelement insertion. After functional annotation, we estimated that MEIs are responsible for about 9.3% of all protein-truncating events per genome. Finally, we built a companion database named HMEID for public use. This resource represents the latest and largest genomewide study on MEIs and will have broad utility for exploration of human MEI findings.     

CircKIF2A contributes to cell proliferation,migration, invasion and glycolysis in human neuroblastoma by regulating miR-129-5p/PLK4 axis

Molecular and Cellular Biochemistry - Multiple circular RNAs (circRNAs) have been identified to act as essential mediators in diverse human cancers. However, the roles of circRNAs in neuroblastoma...     

DNA barcoding of the <Emphasis Type="Italic">Lemnaceae</Emphasis>, a family of aquatic monocots

Background  

Members of the aquatic monocot family Lemnaceae (commonly called duckweeds) represent the smallest and fastest growing flowering plants. Their highly reduced morphology and infrequent flowering result in a dearth of characters for distinguishing between the nearly 38 species that exhibit these tiny, closely-related and often morphologically similar features within the same family of plants.     

The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway

正Plants, as primary producers, have been playing an indispensable role in other organisms’ survival and the balance of whole ecosystem on Earth. Especially, they provide the main source of energy, food, and medicine for human beings, some of which are derived from the primary or secondary metabolites     

A New Tool for Exploring Climate Change Induced Range Shifts of Conifer Species in China

It is inevitable that tree species will undergo considerable range shifts in response to anthropogenic induced climate change, even in the near future. Species Distribution Models (SDMs) are valuable tools in exploring general temporal trends and spatial patterns of potential range shifts. Understanding projections to future climate for tree species will facilitate policy making in forestry. Comparative studies for a large number of tree species require the availability of suitable and standardized indices. A crucial limitation when deriving such indices is the threshold problem in defining ranges, which has made interspecies comparison problematic until now. Here we propose a set of threshold-free indices, which measure range explosion (I), overlapping (O), and range center movement in three dimensions (Dx, Dy, Dz), based on fuzzy set theory (Fuzzy Set based Potential Range Shift Index, F-PRS Index). A graphical tool (PRS_Chart) was developed to visualize these indices. This technique was then applied to 46 Pinaceae species that are widely distributed and partly common in China. The spatial patterns of the modeling results were then statistically tested for significance. Results showed that range overlap was generally low; no trends in range size changes and longitudinal movements could be found, but northward and poleward movement trends were highly significant. Although range shifts seemed to exhibit huge interspecies variation, they were very consistent for certain climate change scenarios. Comparing the IPCC scenarios, we found that scenario A1B would lead to a larger extent of range shifts (less overlapping and more latitudinal movement) than the A2 and the B1 scenarios. It is expected that the newly developed standardized indices and the respective graphical tool will facilitate studies on PRS''s for other tree species groups that are important in forestry as well, and thus support climate adaptive forest management.     

顺磁探针16－NS和荧光探针DPH在DPPG交插脂双层中的行为研究

研究了１６—ＮＳ和ＤＰＨ在被山莨菪碱诱导形成交插脂结构的ＤＰＰＧ脂质体中的行为。在交插脂双层结构中,标记在脂酰链末端的１６—ＮＳ的序参数明显增大,即同标记在靠脂酰链头部的５—ＮＳ的序参数的差距缩小。这些颇磁探针在交插脂双层结构中的运动比在非交插脂双层结构中受到更大的限制。ＤＰＨ荧光强度在ＤＰＰＧ由非交插脂双层转变为交插脂双层结构时急剧下降。引起这种下降的原因可能是膜脂在从非交插脂双层结构向交插脂双层结构的转变过程中使得ＤＰＨ处于一个更为亲水的环境中。     

哺乳动物抑制型转录因子及启动子对的全新设计与构建

转录因子及启动子是基因回路的基础。相较于原核启动子,真核启动子作用机制复杂,增加了全新设计与改造的难度。目前有限数量的真核转录因子及启动子成为在哺乳动物细胞中设计并实现复杂基因回路以满足各类临床或工业应用需求的瓶颈。文中介绍了基于能够结合特定DNA序列的DNA结合结构域,通过柔性连接肽连接到转录抑制模块KRAB,构建抑制型转录因子以及通过在SV40启动子下游插入结合序列构建对应启动子的方法。而后,在哺乳动物细胞系中通过流式细胞术对其抑制转录的强度、不同转录因子及启动子对之间的正交性进行了测定。文中提供了一套标准化的、可调节的转录因子及启动子的全新设计与构建方案。基于该方案所构建的5对抑制型转录因子及启动子对能够在哺乳动物细胞中起到不同程度的抑制效果且相互正交。文中构建的哺乳动物转录因子及启动子对扩充了哺乳动物生物元件库,为构建复杂真核基因回路打下了基础;运用该设计方法能够根据需求构建更多正交的人工转录因子及启动子对。     

华北低丘山地不同土地利用方式下土壤团聚体及其有机碳分布特征

土地利用变化影响土壤团聚性及有机碳分布,进而改变土壤碳循环过程。对太行山南部50年刺槐人工林（R50）、17年刺槐人工林（R17）、自然恢复林（NR）和农田（CL）等不同土地利用方式下的表层土壤（0-20 cm）进行了系统研究,利用湿筛法对土壤团聚体进行分级,并计算土壤结构稳定性参数（平均重量直径MWD,团聚体比例AR）及不同粒径团聚体有机碳贡献率,进而分析弃耕后土壤团聚体分布及团聚体有机碳含量变化。结果表明,土地利用方式对土壤团聚体粒径分布及团聚体有机碳含量有显著影响,自然恢复林与刺槐林的大团聚体（>0.25 mm）含量都高于农田,且自然恢复林的大团聚体增加更显著。MWD的计算结果表明：自然恢复林 > 刺槐人工林 > 农田,说明该区域的自然恢复方式更容易促进大团聚体的形成,并显著改良土壤结构及增强土壤团聚体稳定性。弃耕后,不同土地利用方式0-10 cm土层各粒径团聚体有机碳含量均高于农田,且团聚体有机碳含量与团聚体稳定性呈正相关。这些结果说明,研究区域的自然植被恢复和人工造林都可以显著提高土壤的固碳能力,且储存的有机碳主要存于大团聚体中,而农田的有机碳大都存于粘粒+粉粒团聚体中。自然植被恢复和人工造林均提高了土壤结构稳定性,是改善团粒结构、提高土壤质量的有效方式。