Genetic Analysis of Human Adenovirus Type 7 Strains Circulating in Different Parts of China

To investigate the molecular epidemiology and genetic variation of human adenovirus type 7(HAdV-7) in children with acute respiratory infections(ARI) in China. HAdV-7-positive respiratory samples collected from children with ARI in Beijing, Shijiazhuang, Wenzhou and Guangzhou from 2014–2018 were selected for gene amplification and sequence analysis. Fifty-seven HAdV-7 clinical strains with hexon, penton base and fiber gene sequences were obtained. Meanwhile17 strains were selected randomly from different cities for whole genome sequencing. Phylogenetic and variation analyses were performed based on the obtained sequences, HAdV-7 prototype strain Gomen(AY594255), vaccine strains(AY495969 and AY594256) and representative sequences of strains. The phylogenetic trees constructed based on whole genome sequences, major capsid protein genes(hexon, penton base and fiber) and the early genes(E1, E2, E3 and E4) were not completely consistent. The HAdV-7 strains obtained in this study always clustered with most of the circulating strains worldwide from the 1980 s to the present. Compared with the HAdV-7 prototype strain Gomen(AY594255), some amino acid mutations in loop1 and loop2 of hexon and the RGD loop region of the penton base gene were observed. Recombination analysis showed that partial regions of 55 k Da protein and 100 kDa hexon-assembly associated protein genes among all HAdV-7 strains in this study were from HAdV-16 and HAdV-3, respectively. Our study demonstrated the molecular evolution characteristics of HAdV-7 strains circulating in China and provided basic reference data for the prevention, control and vaccine development of HAdV-7.     

Evolution and diversity of axon guidance Robo receptor family genes

The diversity of axon guidance (AG) receptors reflects gains in complexity of the animal nervous system during evolution. Members of the Roundabout (Robo) family of receptors interact with Slit proteins and play important roles in many developmental processes, including AG and neural crest cell migration. There are four members of the Robo gene family. However, the evolutionary history of Robo family genes remain obscure. We analyzed the distribution of Robo family members in metazoan species ranging in complexity from hydras to humans. We undertook a phylogenetic analysis in metazoans, synteny analysis, and ancestral chromosome mapping in vertebrates, and detected selection pressure and functional divergence among four mammalian Robo paralogs. Based on our analysis, we proposed that the ancestral Robo gene could have undergone a tandem duplication in the vertebrate ancestor; then one round of whole genome duplication events occurred before the divergence of ancestral lamprey and gnathostome, generating four paralogs in early vertebrates. Robo4 paralog underwent segmental loss in the following evolutionary process. Our results showed that Robo3 paralog is under more powerful purifying selection pressure compared with other three paralogs, which could correlate with its unique expression pattern and function. Furthermore, we found four sites under positive selection pressure on the Ig1‐2 domains of Robo4 that might interfere with its binding to Slits ligand. Diverge analysis at the amino acid level showed that Robo4 paralog have relatively greater functional diversifications than other Robo paralogs. This coincides with the fact that Robo4 predominantly functions in vascular endothelial cells but not the nervous system.     

The spatial variation of soil bacterial community assembly processes affects the accuracy of source tracking in ten major Chinese cities

Urban soils harbor billions of bacterial cells and millions of species. However, the distribution patterns and assembly processes of bacterial communities remain largely uncharacterized in urban soils. It is also unknown if we can use the bacteria to track soil sources to certain cities and districts. Here, Illumina MiSeq sequencing was used to survey soil bacterial communities from 529 random plots spanning 61 districts and 10 major cities in China. Over a 3,000 km range, community similarity declined with increasing geographic distance(Mantel r=0.62), and community composition was clustered by city(R~2=0.50). Within cities(100 km), the aforementioned biogeographic patterns were weakened. Process analysis showed that homogenizing dispersal and dispersal limitation dominated soil bacterial assembly at small and large spatial scales, respectively. Accordingly, the probabilities of accurately tracking random soil sources to certain cities and districts were 90.0% and 66.7%, respectively. When the tested samples originated from cities that were more than 1,265 km apart, the soil sources could be identified with nearly 100% accuracy. Overall, this study demonstrates the strong distance-decay relationship and the clear geographic zoning of urban soil bacterial communities among cities. The varied importance of different community assembly processes at multiple spatial scales strongly affects the accuracy of microbial source tracking.     

高速逆流色谱法制备灵芝萜烯酮醇

本研究建立一种从灵芝子实体提取物中快速制备灵芝萜烯酮醇的方法。以沪农灵芝1号子实体为原料,经乙醇提取、D101大孔树脂富集后,再经一次正相色谱柱层析,获得富含灵芝萜烯酮醇的流分。采用高速逆流色谱法对该流分进行分离,优化分离条件,获得的最佳条件为：溶剂体系为正己烷-乙酸乙酯-甲醇-水（V/V/V/V,12:24:18:9）,流速2.0mL/min,转速900r/min,上样量500mg,一次上样可得到纯度为90.9%的灵芝萜烯酮醇52.1mg,得率达到10.4%。该方法具有操作简单、污染小、成本低、得率和纯度高的特点,是规模化制备灵芝萜烯酮醇的一种新方法。     

混合接种球孢白僵菌与摩西球囊霉对烟草促生抗逆影响

利用球孢白僵菌Beauveria bassiana与摩西球囊霉菌Glomus mosseae以单独和混合接种的方式在烟草Nicotiana tabacum苗期进行接种处理,检测烟草苗期和成熟期的农艺性状和生理特性。结果表明：在育苗期,混合接种处理烟苗具有最大的叶长和最大叶宽,与对照相比提高了30.27%和42.98%,球孢白僵菌处理组生物量最大,AM真菌处理组烟草株高最高;在成熟期,混合接种处理组烟草的株高、最大叶长、最大叶宽、茎围、生物量等指标均优于单接种处理,且过氧化氢酶（CAT）、超氧化物歧化酶（SOD）、过氧化物酶（POD）等抗氧化酶活性最高,丙二醛（MDA）含量最低。球孢白僵菌和AM真菌可协同提高烟草生长和抗逆能力。     

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.     

The ScCas9++ variant expands the CRISPR toolbox for genome editing in plants

The development of clustered regularly interspaced palindromic repeats (CRISPR)-associated protein (Cas) variants with a broader recognition scope is critical for further improvement of CRISPR/Cas systems. The original Cas9 protein from Streptococcus canis (ScCas9) can recognize simple NNG-protospacer adjacent motif (PAM) targets, and therefore possesses a broader range relative to current CRISPR/Cas systems, but its editing efficiency is low in plants. Evolved ScCas9⁺ and ScCas9⁺⁺ variants have been shown to possess higher editing efficiencies in human cells, but their activities in plants are currently unknown. Here, we utilized codon-optimized ScCas9, ScCas9⁺ and ScCas9⁺⁺ and a nickase variant ScCas9n⁺⁺ to systematically investigate genome cleavage activity and cytidine base editing efficiency in rice (Oryza sativa L.). This analysis revealed that ScCas9⁺⁺ has higher editing efficiency than ScCas9 and ScCas9⁺ in rice. Furthermore, we fused the evolved cytidine deaminase PmCDA1 with ScCas9n⁺⁺ to generate a new evoBE4max-type cytidine base editor, termed PevoCDA1-ScCas9n⁺⁺. This base editor achieved stable and efficient multiplex-site base editing at NNG-PAM sites with wider editing windows (C₋₁–C₁₇) and without target sequence context preference. Multiplex-site base editing of the rice genes OsWx (three targets) and OsEui1 (two targets) achieved simultaneous editing and produced new rice germplasm. Taken together, these results demonstrate that ScCas9⁺⁺ represents a crucial new tool for improving plant editing.