应用生物信息学技术对植物表达序列标签(EST)的大规模分析

目前 ,一些基因组较小的植物 (如拟南芥 ,水稻等 )的全基因组已经基本完成测序 ,较大基因组的测序工作则主要集中在基因组中表达基因的测序上 ,表达序列标签 (EST)计划由此产生。研究表明 ,对EST进行大规模研究已成为功能基因组学研究的最佳途经之一。本文着重介绍和讨论应用生物信息学技术对植物EST数据的大规模分析。     

鸭瘟病毒gB蛋白N端主要抗原域的表达及间接ELISA检测

在分析鸭瘟病毒gB蛋白抗原性的基础上,设计一对引物克隆gB蛋白N端抗原性较好的抗原域编码基因.将克隆的基因定向插入pET-32a的EcoR Ⅰ和HindⅢ之间,构建了gB蛋白主要抗原域原核表达载体pET-gB1.将pET-gB1质粒转化BL(21)宿主菌后,对培养和表达条件进行了优化,实现了DPV gB蛋白主要抗原域的高效表达.免疫印迹试验表明获得的表达产物具有良好的反应原性.应用His·Bind亲和层析柱纯化重组DPV gB蛋白,以纯化的重组gB1蛋白作为检测抗原,初步建立了检测鸭瘟病毒抗体的igB1-ELISA.结果表明,抗原的最佳包被浓度为6.5μg/mL,血清的最佳稀释度为1∶80,阳性标准初步定为:待检血清OD490＞0.4,且待检血清OD490/阴性血清OD490＞2.应用igB1-ELISA对鸭血清样品进行检测,结果表明igB1-ELISA与全病毒包被的iDPV-ELISA符合率达到95.6%.     

Bioactivities of simplified adociaquinone B and naphthoquinone derivatives against Cdc25B,MKP-1, and MKP-3 phosphatases

Some simplified adociaquinone B analogs and a series of 1,4-naphthoquinone derivatives were synthesized and tested against the three enzymes Cdc25B, MKP-1, and MKP-3. Cdc25B and MKP-1 in particular are enzymes overexpressed in human cancer cells, and they represent potential molecular targets for novel cancer chemotherapeutic treatments. A number of analogs exhibited significant inhibitory activity against these enzymes, and the bioassay data in addition to structure–activity relationships of these compounds will be discussed.     

Activation characteristics of transient receptor potential ankyrin 1 and its role in nociception

Transient receptor potential (TRP) ankyrin 1 (TRPA1) is a Ca(2+)-permeant, nonselective cationic channel. It is predominantly expressed in the C afferent sensory nerve fibers of trigeminal and dorsal root ganglion neurons and is highly coexpressed with the nociceptive ion channel transient receptor potential vanilloid 1 (TRPV1). Several physical and chemical stimuli have been shown to activate the channel. In this study, we have used electrophysiological techniques and behavioral models to characterize the properties of TRPA1. Whole cell TRPA1 currents induced by brief application of lower concentrations of N-methyl maleimide (NMM) or allyl isothiocyanate (AITC) can be reversed readily by washout, whereas continuous application of higher concentrations of NMM or AITC completely desensitized the currents. The deactivation and desensitization kinetics differed between NMM and AITC. TRPA1 current amplitude increased with repeated application of lower concentrations of AITC, whereas saturating concentrations of AITC induced tachyphylaxis, which was more pronounced in the presence of extracellular Ca(2+). The outward rectification exhibited by native TRPA1-mediated whole cell and single-channel currents was minimal as compared with other TRP channels. TRPA1 currents were negatively modulated by protons and polyamines, both of which activate the heat-sensitive channel, TRPV1. Interestingly, neither protein kinase C nor protein kinase A activation sensitized AITC-induced currents, but each profoundly sensitized capsaicin-induced currents. Current-clamp experiments revealed that AITC produced a slow and sustained depolarization as compared with capsaicin. TRPA1 is also expressed at the central terminals of nociceptors at the caudal spinal trigeminal nucleus. Activation of TRPA1 in this area increases the frequency and amplitude of miniature excitatory or inhibitory postsynaptic currents. In behavioral studies, intraplantar and intrathecal administration of AITC induced more pronounced and prolonged changes in nociceptive behavior than those induced by capsaicin. In conclusion, the characteristics of TRPA1 we have delineated suggest that it might play a unique role in nociception.     

High‐fat diet‐induced dysbiosis mediates MCP‐1/CCR2 axis‐dependent M2 macrophage polarization and promotes intestinal adenoma‐adenocarcinoma sequence

High‐fat diet (HFD) is a well‐known risk factor for gut microbiota dysbiosis and colorectal cancer (CRC). However, evidence relating HFD, gut microbiota and carcinogenesis is limited. Our study aimed to demonstrate that HFD‐induced gut dysbiosis promoted intestinal adenoma‐adenocarcinoma sequence. In clinical study, we found that HFD increased the incidence of advanced colorectal neoplasia (AN). The expression of monocyte chemoattractant protein 1 (MCP‐1), CC chemokine receptor 2 (CCR2) and CD163 in CRC patients with HFD was significantly higher than that in CRC patients with normal diet. When it comes to the Apc^min/+ mice, HFD consumption could induce gut dysbiosis and promote intestinal carcinogenesis, accompanying with activation of MCP‐1/CCR2 axis that recruited and polarized M2 tumour‐associated macrophages. Interestingly, transfer of faecal microbiota from HFD‐fed mice to another batch of Apc^min/+ mice in the absence of HFD could also enhance carcinogenesis without significant body weight gain and induced MCP‐1/CCR2 axis activation. HFD‐induced dysbiosis could also be transmitted. Meanwhile, antibiotics cocktail treatment was sufficient to inhibit HFD‐induced carcinogenesis, indicating the vital role of dysbiosis in cancer development. Conclusively, these data indicated that HFD‐induced dysbiosis accelerated intestinal adenoma‐adenocarcinoma sequence through activation of MCP‐1/CCR2 axis, which would provide new insight into better understanding of the mechanisms and prevention for HFD‐related CRC.     

哌替啶对心室肌收缩的抑制作用及其机制

为明确哌替啶对心脏收缩的直接效应 ,并探讨其相关机制。采用Langendorff灌流心脏模型 ,观察了哌替啶对大鼠心室收缩功能的影响 ,并用荧光测钙技术和膜片钳技术探讨了哌替啶作用的钙离子机制。结果显示 ,哌替啶剂量依赖性地降低离体灌流心脏的LVDP×HR、 +dP/dt和 -dP/dt,而升高LVEDP。在酶解分离的心室肌细胞上 ,哌替啶剂量依赖性地降低细胞收缩时的钙瞬变幅度 ,并升高舒张末期的钙水平。哌替啶不影响高浓度咖啡因诱导的内钙释放。哌替啶使L 型钙电流强度降低到给药前的 67 4± 10 1% ,而不改变钙通道的激活和失活电位。哌替啶减弱钙电流的作用并不能被阿片受体阻断剂纳洛酮所阻断。以上结果表明 ,哌替啶能通过非阿片受体介导的途径阻断细胞外钙离子的内流 ,对心室收缩产生直接的抑制作用     

西双版纳热带雨林中两种生态型蕨类植物的光合特性比较研究

通过比较分布于西双版纳热带雨林林下生境中的附生鸟巢蕨（Neottopteris nidus）和地生网脉铁角蕨（Asplenium finlaysonianum）的光合特征和光合诱导特性,来研究不同生态型蕨类植物的光斑利用策略。研究结果表明,2种蕨类植物的最大净光合速率、暗呼吸速率、表观量子效率、光饱和点和光补偿点没有显著差异,但网脉铁角蕨的最大气孔导度远远高于鸟巢蕨,表明后者具有更强的光合水分利用效率。在暗处理3／J＇,时接着光照（光强为20I~mol-m-2,s。‘）30分钟后,网脉铁角蕨的初始气孔导度显著高于鸟巢蕨。连续照射饱和强光后,网脉铁角蕨达到最大净光合速率50％（T50％）和90％的时间（T90%）比鸟巢蕨短：网脉铁角蕨和鸟巢蕨的T50%分别为0．57和5．31分钟,T90％分别为5．85和26．33分钟。诱导过程中,气孔导度对强光的响应明显滞后于净光合速率。鸟巢蕨达到最大气孔导度的时间明显比网脉铁角蕨慢,但在光合诱导消失过程中2种蕨类植物的光合诱导维持能力却没有显著差异。上述结果表明,与大多数地生林下植物（如网脉铁角蕨）相比,附生鸟巢蕨的水分保护比碳获得更重要,但却限制了附生蕨对光斑的利用。     

两种热带木质藤本幼苗形态、生长和光合能力对光强和养分的响应

比较了两种不同攀援习性,卷须缠绕种薄叶羊蹄甲（Bauhinia tenuiflora）和茎缠绕种刺果藤（Byttneria aspera）,木质藤本植物的形态、生长及光合特性对不同光强（4％、35％和全光照）和土壤养分（高和低）的响应。两种藤本植物大部分表型特征主要受光照的影响,而受土壤养分的影响较小。弱光促进地上部分生长,弱光下两种植物均具有较大的比叶面积（specific leaf area,SLA）、茎生物量比（stem mass ratio,SMR）和平均叶面积比（mean leaf area ratio,LARm）。高光强下,两种植物的总生物量和投入到地下部分的比重增加,具有更大的根生物量比（root mass ratio,RMR）、更多的分枝数、更高的光合能力（maximum photosynthetic rate,Pmax）和净同化速率（net assimilation rate,NAR）,综合表现为相对生长速率（relative growth rate,RGR）增加。两种藤本植物的Pmax与叶片含氮量的相关性均未达显著水平,但刺果藤的Pmax与SU志间呈显著的正相关,而薄叶羊蹄甲的Pmax与SLA之间相关性不显著。在相同光照强度和土壤养分条件下,卷须缠绕种薄叶羊蹄甲的RGR显著高于茎缠绕种刺果藤。薄叶羊蹄甲的RGR与NAR呈显著正相关,其RGR与SLA、平均叶面积比（EARm）及Pmax之间相关性不显著。刺果藤的RGR与NAR呈显著的正相关,而与SLA存在显著的负相关。上述结果表明,与土壤养分相比,光照强度可能是决定木质藤本分布更为重要的生态因子。卷须缠绕种薄叶羊蹄甲由于具有特化的攀援器官,在形态上和生理上具有更大的可塑性,这使得卷须缠绕种木质藤本在与其它植物的竞争中更具优势。     

Changes of soil organic and inorganic carbon in relation to grassland degradation in Northern Tibet

The effect of livestock grazing on grassland degradation and the resulting impact on soil carbon concentration is an important factor in carbon estimation. We addressed this issue using field observations and laboratory analysis of samples from Tibetan grassland. Based on the field measurements, we investigated the soil organic carbon (SOC) and soil inorganic carbon (SIC) under two contrasting degradation states: lightly or non-degraded grasslands (LDG) and heavily degraded grasslands (HDG). We assessed their relationships with environmental factors using data collected from 99 sites across Northern Tibet during 2011–2012. Data were analyzed using a linear mixed-effects model and one-way ANOVA. The results showed that: (1) SOC concentration decreased and SIC concentration increased following grassland degradation, especially at soil depths in the range of 0–10 cm (P < 0.05); (2) the major environmental factors affecting SOC and SIC were soil pH and plant biomass; (3) spatially, the SOC density increased with the mean annual temperature and mean annual precipitation, whereas SIC exhibited the opposite trend; (4) the SOC density increased at first and then decreased with increasing grazing intensity, with an opposite trend in SIC; and (5) soil carbon storage in this region was 0.14 Pg smaller in the HDG than in the LDG. This study suggests that grassland degradation can significantly affect the vertical distribution and storage of SOC and SIC. The carbon sequestration capacity of the top 100 cm of soil in Northern Tibet was estimated as 0.14 Pg.     

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

Background

Pathogens identification is critical for the proper diagnosis and precise treatment of infective endocarditis (IE). Although blood and valve cultures are the gold standard for IE pathogens detection, many cases are culture-negative, especially in patients who had received long-term antibiotic treatment, and precise diagnosis has therefore become a major challenge in the clinic. Metagenomic sequencing can provide both information on the pathogenic strain and the antibiotic susceptibility profile of patient samples without culturing, offering a powerful method to deal with culture-negative cases.

Methods

To assess the feasibility of a metagenomic approach to detect the causative pathogens in resected valves from IE patients, we employed both next-generation sequencing and Oxford Nanopore Technologies MinION nanopore sequencing for pathogens and antimicrobial resistance detection in seven culture-negative IE patients. Using our in-house developed bioinformatics pipeline, we analyzed the sequencing results generated from both platforms for the direct identification of pathogens from the resected valves of seven clinically culture-negative IE patients according to the modified Duke criteria.

Results

Our results showed both metagenomics methods can be applied for the causative pathogen detection in all IE samples. Moreover, we were able to simultaneously characterize respective antimicrobial resistance features.

Conclusion

Metagenomic methods for IE detection can provide clinicians with valuable information to diagnose and treat IE patients after valve replacement surgery. However, more efforts should be made to optimize protocols for sample processing, sequencing and bioinformatics analysis.