Full-Length Transcriptome Sequencing Combined with RNA-Seq to Analyze Genes Related to Terpenoid Biosynthesis in Cinnamomum burmannii

Cinnamomum burmannii is a cinnamomum plant rich in natural D-borneol. Natural D-borneol is a bicycle monoterpenoid compound widely used in the food, pharmaceutical, and cosmetic industries. Therefore, analyzing the biosynthesis mechanism of natural D-borneol in C. burmannii at the molecular level is helpful for directional breeding in the future and further development and utilization of C. burmannii and its related gene resources. In our study, 76 genes related to terpene metabolism were analyzed through third-generation sequencing and second-generation sequencing. Of these genes, 57 were associated with the synthesis of the terpenoid skeleton, and 19 belonged to terpenoid synthase, including four monoterpenoid synthases, seven sesquiterpenoid synthases, and eight diterpenoid synthases. Two genes in diterpenoid synthase were differentially expressed in high D-borneol and low D-borneol plants. It was speculated that these two genes might be related to D-borneol synthesis. How these two genes participate in the synthesis of D-borneol needs further study.     

Electron microscopy holdings of the Protein Data Bank: the impact of the resolution revolution,new validation tools,and implications for the future

As a discipline, structural biology has been transformed by the three-dimensional electron microscopy (3DEM) “Resolution Revolution” made possible by convergence of robust cryo-preservation of vitrified biological materials, sample handling systems, and measurement stages operating a liquid nitrogen temperature, improvements in electron optics that preserve phase information at the atomic level, direct electron detectors (DEDs), high-speed computing with graphics processing units, and rapid advances in data acquisition and processing software. 3DEM structure information (atomic coordinates and related metadata) are archived in the open-access Protein Data Bank (PDB), which currently holds more than 11,000 3DEM structures of proteins and nucleic acids, and their complexes with one another and small-molecule ligands (~ 6% of the archive). Underlying experimental data (3DEM density maps and related metadata) are stored in the Electron Microscopy Data Bank (EMDB), which currently holds more than 21,000 3DEM density maps. After describing the history of the PDB and the Worldwide Protein Data Bank (wwPDB) partnership, which jointly manages both the PDB and EMDB archives, this review examines the origins of the resolution revolution and analyzes its impact on structural biology viewed through the lens of PDB holdings. Six areas of focus exemplifying the impact of 3DEM across the biosciences are discussed in detail (icosahedral viruses, ribosomes, integral membrane proteins, SARS-CoV-2 spike proteins, cryogenic electron tomography, and integrative structure determination combining 3DEM with complementary biophysical measurement techniques), followed by a review of 3DEM structure validation by the wwPDB that underscores the importance of community engagement.     

Studying bona fide SARS-CoV-2 biology in a BSL-2 biosafety environment using a split-virus-genome system

<正>Dear Editor,Severe acute respiratory syndrome coronavirus 2(SARSCoV-2) was identified as the pathogen causing the coronavirus disease(COVID-19), which sometimes resulted in fatal pneumonia(Hu et al., 2021). SARS-CoV-2 is a biosafety level 3(BSL-3) pathogen, and the requirement for high containment conditions is a bottleneck for basic research on viral biology.     

基于FMT-AHP的海南农垦花岗岩类多雨区橡胶园地力评价

海南农垦是中国最大的天然橡胶生产基地,自第二次全国土壤普查以来橡胶园养分状况已发生了很大变化,但具体情况如何尚不清楚。运用耕地地力评价方法对海南农垦主要橡胶园的地力进行了系统评价,以期为橡胶园地力提升和天然橡胶的可持续发展提供理论支持。以土壤母质类型和降雨量为依据,首次将海南农垦橡胶园划分为8个类型区,并选取占海南农垦橡胶园总面积56.97%的花岗岩类多雨区作为评价区域,采集7204个0—20 cm层的土壤样品,运用特尔菲法、模糊数学理论和层次分析法确定11个评价指标及其权重,将评价区橡胶园地力划分为5等。研究结果发现:评价区以中间地力水平的二等、三等、四等橡胶园为主,占评价区橡胶园总面积的85.85%,它们广泛分布于琼中、屯昌、澄迈、儋州、万宁、保亭、乐东、三亚、陵水、定安、琼海、五指山、昌江、文昌和东方15个县市;一等地面积很小且分散,五等地相对集中面积也很小。相关分析表明土壤pH、有机质、有效磷和速效钾含量是影响评价区橡胶园地力水平的重要因素。评价区橡胶园土壤pH适宜橡胶树正常生长,但该区域土壤有机质和有效磷含量不能满足橡胶树正常生长的需要,而该区域一、二等地土壤速效钾含量能满足橡胶树正常生长,其三、四等地土壤速效钾含量仅达到橡胶树正常生长所需水平,随着地力下降到五等其土壤速效钾含量已不适宜橡胶树正常生长。根据上述研究结果,笔者建议橡胶园应大力间作绿肥,在增施有机质的基础上补氮、补钾、施用钙镁磷肥,同时加强养分管理,提高肥料利用率。     

贵州百花湖夏季浮游植物昼夜垂直分布特征

为了探讨浮游植物在水体中的昼夜垂直分布格局,于2012年7月31日至8月1日对百花湖(水库)浮游植物进行昼夜24 h定点分层研究。研究结果表明:蓝藻、绿藻、硅藻种类数在水体中具有明显的分层现象,蓝藻种类数在0.5—2 m居多,绿藻种类数在0.5—6 m明显多于7—14 m,硅藻种类数主要分布在6 m及以深的水层中。湖泊假鱼腥藻(Pseudanabaena limnetica)为绝对优势种,相对丰度为82.69%。8:00时湖泊假鱼腥藻在2—3 m处聚集程度最高,10:00时聚集程度最高的水层上升至0.5 m,10:00—12:00湖泊假鱼腥藻的细胞丰度由0.5 m向2 m扩增,12:00时在2 m处达到全天峰值,此时0.5 m处的细胞丰度是除6:00外的最小值,12:00—14:00湖泊假鱼腥藻的细胞丰度由2 m向0.5 m扩增,16:00时又大量聚集于1 m处,说明湖泊假鱼腥藻在白天具有明显的垂直迁移现象;湖泊假鱼腥藻丰度的MI指数白天在1.45—2.07之间,夜间在1.40—1.46之间,变化趋势与时间深度等值图结果相符,说明湖泊假鱼腥藻在水体中昼夜均呈聚集分布,且白天的聚集程度及变化幅度大于夜间;百花湖浮游植物总丰度的昼夜垂直分布格局与湖泊假鱼腥藻一致;水体中浮游植物总丰度和湖泊假鱼腥藻丰度夜间低于白天。光照的昼夜交替和水柱温差的昼夜变化是影响浮游植物总丰度和湖泊假鱼腥藻垂直分布格局昼夜变化的重要环境因素。     

High-level cryIVD and cytA gene expression in Bacillus thuringiensis does not require the 20-kilodalton protein, and the coexpressed gene products are synergistic in their toxicity to mosquitoes.

Interactions among the 20-kDa protein gene and the cytA and cryIVD genes located in a 9.4-kb HindIII fragment were studied. A series of plasmids containing a combination of these different genes was constructed by using the Escherichia coli/Bacillus thuringiensis shuttle vector pHT3101. The plasmids were then used to transform an acrystalliferous strain, cryB, derived from B. thuringiensis subsp. kurstaki. The results from sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analyses suggest that although the 20-kDa protein is required for the efficient CytA protein production in E. coli, it is not required in B. thuringiensis. With or without the truncated 20-kDa protein gene, the CtyA and/or CryIVD proteins are produced and form parasporal inclusions in B. thuringiensis cells. However, more-efficient expression is obtained when a second protein, probably acting as a chaperonin, is present. In addition, the time course studies show that the CytA and CryIVD proteins are coordinately produced. Both the crude B. thuringiensis culture and purified inclusions from each recombinant B. thuringiensis strain are toxic to Culex quinquefasciatus larvae. The parasporal inclusions formed in B. thuringiensis cells are mosquitocidal, with CytA synergizing CryIVD toxicity.     

利用假型反转录病毒对大部分胰腺切除后再生细胞的世系追踪

胰腺是一个重要的内外分泌混合腺, 胰腺发生损伤后能够再生。为了探讨胰腺活体细胞世系追踪的方法和胰腺损伤后再生细胞的来源,分别通过胰腺伤口涂抹并胰内注射、尾静脉注射及腹腔注射三种方法, 利用假型反转录病毒对成体小鼠大部分切除后胰腺的细胞进行世系追踪。结果发现在活体条件下, 与尾静脉注射及腹腔注射法相比, 胰腺伤口涂抹并胰腺内注射反转录病毒的方法能够更有效的标记胰腺细胞; 而且, 通过对标记细胞的世系追踪研究证明, 在胰腺损伤后, 胰腺腺泡细胞能够接受损伤信号刺激发生再生。为今后进一步利用反转录假病毒对活体胰腺进行细胞命运追踪研究奠定基础, 为利用反转录病毒载体进行胰腺疾病的基因治疗提供线索。