中国生物多样性研究的30个核心问题

在联合国《生物多样性公约》生效30年和《生物多样性》创刊30周年之际, 我们通过问卷调查从281名中国研究人员收集到763个生物多样性相关的研究问题, 通过归纳与整理, 并参考英国生态学会提出的100个生态学基本问题, 从中筛选出30个核心问题。这些问题涉及7个方面: 演化与生态(6个问题)、种群(4个问题)、群落与多样性(7个问题)、生态系统与功能(3个问题)、人类影响与全球变化(4个问题)、方法与监测(4个问题)、生物多样性保护(2个问题)。前5个方面主要聚焦在物种形成、生物多样性维持等的关键过程与机制、生物多样性与生态功能关系、全球变化对生物多样性的影响机制等, 第6方面主要涉及生物监测与预测、数据共享等, 第7方面涉及多样性保护、自然与人类健康关系这两个与公众息息相关的重要话题。这30个问题的筛选难免存在偏颇, 希望能以此为契机, 促进我国生物多样性研究人员对本领域核心问题的深入思考与探讨。     

Comparison of alternative analytical techniques for the characterisation of the human serum proteome in HUPO Plasma Proteome Project

Based on the same HUPO reference specimen (C1-serum) with the six proteins of highest abundance depleted by immunoaffinity chromatography, we have compared five proteomics approaches, which were (1) intact protein fractionation by anion-exchange chromatography followed by 2-DE-MALDI-TOF-MS/MS for protein identification (2-DE strategy); (2) intact protein fractionation by 2-D HPLC followed by tryptic digestion of each fraction and microcapillary RP-HPLC/microESI-MS/MS identification (protein 2-D HPLC fractionation strategy); (3) protein digestion followed by automated online microcapillary 2-D HPLC (strong cation-exchange chromatography (SCX)-RPC) with IT microESI-MS/MS; (online shotgun strategy); (4) same as (3) with the SCX step performed offline (offline shotgun strategy) and (5) same as (4) with the SCX fractions reanalysed by optimised nanoRP-HPLC-nanoESI-MS/MS (offline shotgun-nanospray strategy). All five approaches yielded complementary sets of protein identifications. The total number of unique proteins identified by each of these five approaches was (1) 78, (2) 179, (3) 131, (4) 224 and (5) 330 respectively. In all, 560 unique proteins were identified. One hundred and sixty-five proteins were identified through two or more peptides, which could be considered a high-confidence identification. Only 37 proteins were identified by all five approaches. The 2-DE approach yielded more information on the pI-altered isoforms of some serum proteins and the relative abundance of identified proteins. The protein prefractionation strategy slightly improved the capacity to detect proteins of lower abundance. Optimising the separation at the peptide level and improving the detection sensitivity of ESI-MS/MS were more effective than fractionation of intact proteins in increasing the total number of proteins identified. Overall, electrophoresis and chromatography, coupled respectively with MALDI-TOF/TOF-MS and ESI-MS/MS, identified complementary sets of serum proteins.     

Genome Sequence of Pseudomonas aeruginosa DQ8, an Efficient Degrader of n-Alkanes and Polycyclic Aromatic Hydrocarbons

Pseudomonas aeruginosa DQ8, which was isolated from the crude oil polluted soil in the Daqing oilfield of China, can efficiently degrade diesel, crude oil, n-alkanes, and polycyclic aromatic hydrocarbons (PAHs). Here, we present a 6.8-Mb assembly of its genome sequence. We have annotated 23 coding sequences (CDSs) responsible for catabolism of n-alkanes and PAHs.     

Preparation and Affinity-Purification of Supervillin Isoform 4 (SV4) Specific Polyclonal Antibodies

Human Supervillin isoform 4 (SV4), a bigger splicing isoform of Supervillin, contains extra coding exons 3, 4 and 5 (E345), compared to Supervillin isoform 1. Although previous studies have shown that SV4 associated with membrane and cytoskeleton, regulated cell migration and cell survival, its functions are still largely unknown. To broaden our understanding, SV4 specific antibody is important for further study in signaling pathway. The His-SV4 (E345) and GST-SV4 (E345) fusion proteins, which contained SV4 specific domain E345, were purified from bacteria. The His-SV4 (E345) proteins were injected in rabbits as immunogen to produce anti-SV4 serum, and SV4 antibodies were purified by GST-SV4 (E345) proteins cross-linked to affinity resins. SV4 antibodies exclusively recognized SV4 protein both in vitro and in vivo through multi-step testing by ELISA, western blot, immunoprecipitation, and immunofluorescence. Taken together, our data demonstrate a novel SV4-specific polyclonal antibody which will provide a useful tool for further characterization of SV4 function.     

Genome Sequences of Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R,Two Efficient Carbazole-Degrading Strains

Pseudomonas luteola XLDN4-9 and Pseudomonas stutzeri XLDN-R are two efficient carbazole-degrading pseudomonad strains. Here we present 4.63- and 4.70-Mb assemblies of their genomes. Their annotated key genes for carbazole catabolism are similar, which may provide further insights into the molecular mechanism of carbazole degradation in Pseudomonas.     

Base editing-mediated targeted evolution of ACCase for herbicide-resistant rice mutants

Improved cytosine and adenine base editors and an efficient dual editor were applied in targeted evolution of ACETYL COA CARBOXYLASE in rice, resulting in the generation of dozens of herbicide-resistant mutations, at least three of which, W2125L, W2125Q and C2186H, have not been reported previously.     

Comparison of Chemical Constituents and Pharmacological Effects of Different Varieties of Chrysanthemum Flos in China

Chrysanthemum Flos is the prestigious traditional Chinese medicinal material and the popular health drink. This article comprehensively evaluated the chemical constituents, antioxidant activity, and hepatoprotective effects of 25 common chrysanthemum varieties in China. Firstly, we analyzed the chemical compositions of water extracts of chrysanthemum using UPLC/Q-TOF-MS, and identified 29 chemical components. The results displayed that chrysanthemum was rich in chemical constituents, but there were significant differences in the contents of four phenolic acids and five flavonoids among different varieties, and the coefficient of variation (CVs) ranged from 35.96 % to 114.62 %. Then, the antioxidant activities of different chrysanthemums were investigated, respectively via 1,1-diphenyl-2-picrylhydrazyl (DPPH), 2,2’-azinobis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS), and Ferric Reducing Antioxidant Power (FRAP) assays. The spectrum-effect relationships between nine main components and antioxidant activities were investigated to identify the antioxidant constitutes in chrysanthemums. Meanwhile, H₂O₂-induced hepatocyte injury testing showed wide variation in cultivar antioxidant capacity, with Tongchengju (TCJ) producing the best effect (90.32 %), followed by Chuju (CJ; 85.78 %). In addition, the hepatoprotective effects of 8 mainstream varieties were determined by the model of acute alcoholic liver injury. They protected liver from injury by affecting relevant liver function and antioxidant indexes. Huangshangongju (HSG) could decrease aspartate aminotransferase (AST) activity by 39.27 % in liver tissue; Hangju-Fubaiju (HJ-FBJ), Jinsihuangju (JSH), and Chuju (CJ) significantly decreased the malondialdehyde (MDA) content of liver tissue, which reduced by more than 40 %; Jinsihuangju (JSH) of used for tea could double the content of glutathione (GSH) and had the similar effect on superoxide dismutase (SOD) as the positive group, showing significant antioxidant capacity. Therefore, this study confirmed that chrysanthemums are potential resources as antioxidants, functional foods, and medicinal materials. Importantly, it may provide a scientific support for further development and utilization of chrysanthemum, and screen excellent varieties for different demands.     

拟南芥和琴叶拟南芥中MADS-box基因的比较进化分析

MADS-box基因编码一类转录因子。在被子植物中,MADS-box基因对于营养生长和生殖发育都有重要的调控作用,是植物体(特别是花序、花和果实)的正常发育所不可或缺的。为了理解近缘物种在遗传基础上的异同,我们对拟南芥(Arabidopsis thaliana)和琴叶拟南芥(A.lyrata)基因组中MADS-box基因的拷贝数目和进化式样进行了比较分析。通过搜索公共数据库,我们在拟南芥和琴叶拟南芥中分别鉴定出了106和115个基因。系统发育分析的结果表明,这些基因属于I型和II型MADS-box基因。在两个物种分化之后,II型基因的拷贝数目变化不大,I型基因则经历了多次独立的基因丢失和获得事件。通过比较这些基因在染色体上的排列,我们不但鉴定出了存在微共线性的基因组区段,而且发现新基因产生的主要机制是串联重复和散在重复。分子进化的研究进一步表明,I型和II型基因在进化式样上存在着显著差异:II型基因在进化中一般都受到了较强的选择压力,而I型基因大多受到的选择压力较弱。本研究将为深入理解近缘物种在基因和基因组层面上的异同、探讨物种分化和生物多样性形成的机制等问题提供新思路。