Genomic insights into speciation history and local adaptation of an alpine aspen in the Qinghai–Tibet Plateau and adjacent highlands

Natural selection serves as an important agent to drive and maintain interspecific divergence. Populus rotundifolia Griff. is an alpine aspen species that mainly occurs in the Qinghai–Tibet Plateau (QTP) and adjacent highlands, whereas its sister species, P. davidiana Dode, is distributed across southwest and central to northeast China in much lower altitude regions. In this study, we collected genome resequencing data of 53 P. rotundifolia and 42 P. davidiana individuals across their natural distribution regions. Our population genomic data suggest that the two species are well delimitated in the allopatric regions, but with hybrid zones in their adjacent region in the eastern QTP. Coalescent simulations suggest that P. rotundifolia diverged from P. davidiana in the middle Pleistocene with following continuous gene flow since divergence. In addition, we found numerous highly diverged genes with outlier signatures that are likely associated with high-altitude adaptation of these alpine aspens. Our finding indicate that Quaternary climatic changes and natural selection have greatly contributed to the origin and distinction maintenance of P. rotundifolia in the QTP.     

Thermococcus sp.B1001环糊精酶的重组表达及在麦芽七糖制备中的应用

成功构建pET-24a-tscd质粒,实现Thermococcus sp.Strain B1001来源的环糊精酶(TsCDase)在Es-cherichia coli BL21(DE3)中表达.通过热处理和镍柱分离对重组TsCDase进行纯化.酶学性质研究表明,重组TsCDase的比活为1 208.04 U/mg,最适温度为90℃、最适pH值为5.5.重组酶TsCDase在85℃、90℃、95℃条件下的半衰期分别为180、120、30min.酶转化研究表明,以80 g/L β-环糊精为底物,当酶转化温度为90℃、反应pH值为5.5～6.0,加酶量为25 U/g,反应时间为4 h时,麦芽七糖产率为81.19％和85.95％,七糖占产物麦芽寡糖的比例为95.24％和92.92％.本研究结果为工业化制备麦芽七糖奠定良好基础.     

Long noncoding RNA AANCR modulates innate antiviral responses by blocking miR-210-dependent MITA downregulation in teleost fish,Miichthys miiuy

Viral infection induces the initiation of antiviral effectors and cytokines which are critical mediators of innate antiviral responses.The critical molecular determinants are responsible for triggering an appropriate immune response. Long noncoding RNAs(lncRNAs) have emerged as new gene modulators involved in various biological processes, while how lncRNAs operate in lower vertebrates are still unknown. Here, we discover a long noncoding RNA, termed antiviral-associated long noncoding RNA(AANCR), as a novel regulator for innate antiviral responses in teleost fish. The results indicate that fish MITA plays an essential role in host antiviral responses and inhibition of Siniperca chuatsi rhabdovirus(SCRV) production. miR-210 reduces MITA expression and suppress MITA-mediated antiviral responses, which may help viruses evade host antiviral responses. Further,AANCR functions as a competing endogenous RNA(ceRNA) for miR-210 to control protein abundance of MITA, thereby inhibiting SCRV replication and promoting antiviral responses. Our data not only shed new light on understanding the function role of lncRNA in biological processes in teleost fish, but confirmed the hypothesis that ceRNA networks exist widely in vertebrates.     

Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath

The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.     

肺结节病合并Alternaria alternata所致皮肤链格孢病1例

患者,女,61岁,确诊肺结节病、口服糖皮质激素7月,双手背及腕部红色斑块3个月。组织病理示表皮轻度棘层增厚,真皮浅、中层中性粒细胞、淋巴、组织细胞、浆细胞、多核巨细胞混合性浸润,可见散在双轮廓厚壁酵母样结构。六铵银染色见不规则肿胀菌丝及酵母样厚壁孢子。真菌培养见棕/灰褐色菌落,镜下见棕色分隔孢子。ITS区序列分析鉴定为Alternaria alternate。口服伊曲康唑胶囊200 mg/d,联合外用硝酸舍他康唑乳膏2次/d,连续用药4个月后皮损完全消退,随访半年,未见复发。     

6种复配杀虫剂对七星瓢虫的毒力测定及风险评估

采用药膜法分别测定了10％甲维盐·茚虫威悬浮剂、12％甲维盐·虫螨腈悬浮剂、12％虫螨腈·虱螨脲悬浮剂、14％呋虫胺·螺虫乙酯悬浮剂、22％吡虫啉·螺虫乙酯悬浮剂和6％吡虫啉·高效氯氟氰菊酯悬浮剂6种复配杀虫剂对七星瓢虫Coccinella septempunctata Linnaeus幼虫急性毒性,并进行了初级风险评估.结果 显示,6种药剂对七星瓢虫48 h的LR5o(半致死用量,Median lethal rate)分别为0.812、2.255、4.082、22.735、6.755和0.00467 g a.i/hm2.在农田内暴露场景下,6种复配杀虫剂对七星瓢虫风险均不可接受;在农田外暴露场景下,仅有14％呋虫胺·螺虫乙酯悬浮剂和22％吡虫啉·螺虫乙酯悬浮剂对七星瓢虫风险可接受,其它均不可接受.结果 表明在田间最大推荐用量下,6种药剂对七星瓢虫的初级风险评价均存在高风险.     

A whole-genome association approach for large-scale interspecies traits

Science China Life Sciences -     

A practical guide to amplicon and metagenomic analysis of microbiome data

Advances in high-throughput sequencing(HTS)have fostered rapid developments in the field of microbiome research,and massive microbiome datasets are now being generated.However,the diversity of software tools and the complexity of analysis pipelines make it difficult to access this field.Here,we systematically summarize the advantages and limitations of micro-biome methods.Then,we recommend specific pipelines for amplicon and metagenomic analyses,and describe commonly-used software and databases,to help researchers select the appropriate tools.Furthermore,we introduce statistical and visualization methods suit-able for microbiome analysis,including alpha-and beta-diversity,taxonomic composition,difference compar-isons,correlation,networks,machine learning,evolu-tion,source tracing,and common visualization styles to help researchers make informed choices.Finally,a step-by-step reproducible analysis guide is introduced.We hope this review will allow researchers to carry out data analysis more effectively and to quickly select the appropriate tools in order to efficiently mine the bio-logical significance behind the data.     

First record of organic-walled microfossils from the Tonian Shiwangzhuang Formation of the Tumen Group in western Shandong,North China

Organic-walled microfossils offer important information on the biospheric evolution in pre-Cryogenian and provide biostratigraphic implications for many Proterozoic fossiliferous sequences that are poorly age constrained for the lack of reliable radiometric date. Recently, macroscopic carbonaceous compression fossils have been reported for the first time from the Tonian Shiwangzhuang Formation of the Tumen Group in western Shandong, North China. However, organic-walled microfossils have never been discovered from this formation up till now. To improve our knowledge about Proterozoic biodiversity in North China, we conducted a micropaleontological survey on the argillaceous limestone samples of the Shiwangzhuang Formation, which also contain macroscopic carbonaceous compression fossils, from the Baishicun section in Anqiu, western Shandong, North China. Our investigation shows that the Shiwangzhuang microfossil assemblage is dominated by smooth-walled sphaeromorphic acritarchs and cyanobacterium-like filaments and relatively low abundance of other acritarchs, including 16 taxa, such as Polysphaeroides filliformis, Ostiana microcystis, Simia annulare, ?Jacutianema sp., Arctacellularia tetragonala, Pellicularia tenera, Polythrichoides lineatus, and Navifusa actinomorpha. The Shiwangzhuang organic-walled microfossil assemblage, although consisting of long-ranging and not age diagnostic taxa, is consistent with a Tonian age suggested by macroscopic carbonaceous compression fossils, including the Chuaria-Tawuia and Sinosabellidites-Protoarenicola-Pararenicola assemblages, revealed from the same fossiliferous horizon of the Shiwangzhuang Formation and by organic-walled microfossil assemblage, including the late Mesoproterozoic to Tonian index fossil Trachyhystrichosphaera aimika, from the underlying Tongjiazhuang Formation. However, it is also worth noting that a Cryogenian or Ediacaran age cannot be completely excluded based just on the Shiwangzhuang microfossils because of their limited biostratigraphic utility.