Involvement of polar auxin transport in the inhibition of Arabidopsis seedling growth induced by Stenotrophomonas maltophilia

A wide range of microorganisms found in the rhizhosphere are able to regulate plant growth and development, but little is known about the mechanism by which epiphytic microbes inhibit plant growth. Here, an epiphytic bacteria Stenotrophomonas maltophilia, named as LZMBW216, were isolated and identified from the potato (Solanum tuberosum L. cv. Da Xi Yang) leaf surface. They could decrease primary root elongation and lateral root numbers in Arabidopsis seedlings. The inhibitory effects of LZMBW216 on plant growth were not due to a reduced indole-3-acetic acid (IAA) content, as exogenously applied IAA did not recover the inhibition. Furthermore, LZMBW216 did not affect the expression of DR5::GUS and CycB1;1::GUS. However, we found that LZMBW216 exhibited little effect on the primary root elongation in the pin2 mutant and on the lateral root numbers in the aux1-7 mutant. Moreover, LZMBW216 decreased expressions of AUX1 and PIN2 proteins. Together, these results suggest that root system architecture alterations caused by LZMBW216 may involve polar auxin transport.     

Expression of a high sweetness and heat-resistant mutant of sweet-tasting protein,monellin, in <Emphasis Type="Italic">Pichia pastoris</Emphasis> with a constitutive GAPDH promoter and modified <Emphasis Type="Italic">N</Emphasis>-terminus

Objectives

To improve the stability and sweetness of the sweet-tasting protein, monellin, by using site-directed mutagenesis and a Pichia pastoris expression system with a GAPDH constitutive promoter.

Results

Both wild-type and E2 N mutant of single-chain monellin gene were cloned into the PGAPZαA vector and expressed in Pichia pastoris. The majority of the secreted recombinant protein, at 0.15 g/l supernatant, was monellin. This was purified by Sephadex G50 chromatography. The sweetness threshold of wild-type and E2 N were 30 μg/ml and 20 μg/ml, respectively. Compared with the proteins expressed in Escherichia coli, the thermostability of both proteins was improved. The N-terminal sequence is determinative for the sweetness of the proteins expressed in yeast strains.

Conclusions

Site-directed mutagenesis, modification of the N-terminus of monellin, and without the need of methanol induction in P. pastoris expression system, indicate the possibility for large-scale production of this sweet-tasting protein.

     

A comparative study of <Emphasis Type="Italic">k</Emphasis>-spectrum-based error correction methods for next-generation sequencing data analysis

Background

Innumerable opportunities for new genomic research have been stimulated by advancement in high-throughput next-generation sequencing (NGS). However, the pitfall of NGS data abundance is the complication of distinction between true biological variants and sequence error alterations during downstream analysis. Many error correction methods have been developed to correct erroneous NGS reads before further analysis, but independent evaluation of the impact of such dataset features as read length, genome size, and coverage depth on their performance is lacking. This comparative study aims to investigate the strength and weakness as well as limitations of some newest k-spectrum-based methods and to provide recommendations for users in selecting suitable methods with respect to specific NGS datasets.

Methods

Six k-spectrum-based methods, i.e., Reptile, Musket, Bless, Bloocoo, Lighter, and Trowel, were compared using six simulated sets of paired-end Illumina sequencing data. These NGS datasets varied in coverage depth (10× to 120×), read length (36 to 100 bp), and genome size (4.6 to 143 MB). Error Correction Evaluation Toolkit (ECET) was employed to derive a suite of metrics (i.e., true positives, false positive, false negative, recall, precision, gain, and F-score) for assessing the correction quality of each method.

Results

Results from computational experiments indicate that Musket had the best overall performance across the spectra of examined variants reflected in the six datasets. The lowest accuracy of Musket (F-score?=?0.81) occurred to a dataset with a medium read length (56 bp), a medium coverage (50×), and a small-sized genome (5.4 MB). The other five methods underperformed (F-score?<?0.80) and/or failed to process one or more datasets.

Conclusions

This study demonstrates that various factors such as coverage depth, read length, and genome size may influence performance of individual k-spectrum-based error correction methods. Thus, efforts have to be paid in choosing appropriate methods for error correction of specific NGS datasets. Based on our comparative study, we recommend Musket as the top choice because of its consistently superior performance across all six testing datasets. Further extensive studies are warranted to assess these methods using experimental datasets generated by NGS platforms (e.g., 454, SOLiD, and Ion Torrent) under more diversified parameter settings (k-mer values and edit distances) and to compare them against other non-k-spectrum-based classes of error correction methods.

     

青藏高原不同海拔高度下全缘叶绿绒蒿叶表皮特征研究

采用胶带粘取叶表皮法,利用光学显微镜观测不同海拔高度下全缘叶绿绒蒿叶片的表皮毛、气孔及表皮细胞结构特征,探讨全缘叶绿绒蒿叶表皮特征与海拔高度的关系。结果表明,随着海拔高度增加,全缘叶绿绒蒿叶片上、下表皮毛密度、气孔密度和表皮细胞密度逐渐增加;气孔器及表皮细胞的长度、宽度和面积逐渐减小;表皮细胞的形态随着海拔升高由无规则形向多边形变化,垂周壁由波状向弓形或平直变化。全缘叶绿绒蒿叶表皮结构在不同海拔高度下表现出的差异,可能是植物长期在高原生态环境下的综合反应,以结构上的变化来适应对高海拔地区的环境特点,为进一步研究高海拔地区植物的适应性提供一定依据。     

妊娠哺乳期乳腺癌患者的预后情况及其影响因素分析

目的:分析妊娠哺乳期乳腺癌患者的预后情况及其影响因素。方法:将2010年1月至2012年12月期间贵州省贵阳市妇幼保健院、贵州省医科大学和贵州省肿瘤医院收治的妊娠哺乳期乳腺癌患者60例作为研究组,选择同期收治的非妊娠哺乳期乳腺癌患者60例作为对照组,比较两组5年生存率和临床病理特征,并应用单因素和多因素Logistic回归分析患者预后的影响因素。结果:研究组5年生存率为61.67%(37/60),5年无病生存率为46.67%(28/60),均低于对照组的81.67%(49/60),73.33%(44/60)(P0.05)。研究组肿瘤最大直径、腋淋巴结转移率、TNM分期为III期的比例、雌激素受体阳性率、Ki67细胞阳性率≥20%的比例均高于对照组(P0.05),两组孕激素受体阳性率比较无统计学差异(P0.05)。单因素分析显示妊娠哺乳期乳腺癌患者总生存期与肿瘤最大直径、TNM分期、Ki67细胞阳性率≥20%的比例、腋淋巴结转移率有关(P0.05)。多因素Logistic回归分析显示,TNM分期为III期、Ki67细胞阳性率≥20%、腋淋巴结转移是影响妊娠哺乳期乳腺癌患者预后的独立危险因素(P0.05)。结论:妊娠哺乳期乳腺癌患者的预后较差,TNM分期为III期、Ki67细胞阳性率≥20%、腋淋巴结转移是影响患者预后的危险因素,对于临床防治具有重要的启示作用。     

成纤维细胞生长因子21对非酒精性脂肪性肝炎的作用及机制的研究

目的:探索成纤维细胞生长因子21(FGF-21)对非酒精性脂肪性肝炎(NASH)的作用及其机制。方法:用浓度为500μmol/L的油酸和棕榈酸混合物(摩尔比=2:1)诱导HepG2细胞建立NASH细胞模型,实验分为5组:正常对照组(Control)、模型组(Model)、低剂量FGF-21组(LFGF-21,0.5μmol/L)、中剂量FGF-21组(MFGF-21,1.0μmol/L)和高剂量FGF-21组(HFGF-21,2.0μmol/L),油红O染色法观察细胞内脂滴,全自动生化分析仪检测细胞内ALT、AST、TC、TG的水平,Real-time PCR和Western blot分别检测细胞内核因子E2相关因子-2(Nrf-2)、核苷酸结合寡聚化结构域样受体3(NLRP3)的m RNA和蛋白水平,ELISA检测IL-1β、TNF-α水平。结果:NASH细胞造模成功,油红O染色结果显示对照组细胞无明显脂滴蓄积,模型组细胞内可见大量橘红色脂滴,并出现融合现象。不同浓度FGF-21治疗组的细胞内红色脂滴明显减少,并呈剂量依赖性。模型组ALT、AST、TC、TG、IL-1β、TNF-α和NLRP3的水平均高于对照组(P0.05),FGF-21治疗组其水平低于模型组(P0.05)。模型组Nrf2的水平低于对照组(P0.05),FGF-21治疗组Nrf2的水平高于模型组(P0.05)。结论:FGF-21通过促进Nrf-2、抑制NLRP3减少非酒精性脂肪性肝炎细胞的脂质沉积,减轻炎症反应,对NASH有保护作用。     

外源性的电磁干预对神经病理性疼痛大鼠的镇痛效果研究

目的:探讨外源性的电磁干预方法对神经病理性疼痛大鼠的镇痛效果。方法:将30只成熟的雄性SD大鼠随机等分成3组:空白对照组(Control),坐骨神经慢性压迫损伤(CCI)组以及坐骨神经慢性压迫损伤协同电磁刺激组(CCI+EMF)。CCI组和CCI+EMF组的20只大鼠建立坐骨神经慢性压迫损伤模型,CCI+EMF组大鼠行外源性的全身性电磁刺激干预(脉冲波形,频率15 Hz,强度30 Gs),每天刺激6小时。在CCI模型构建的第0、3、6、9、12及15天对大鼠测试和比较足底机械痛阈值、足底热痛阈值、运动功能评分和神经传导速率。结果:CCI组大鼠的足底机械痛阈值、足底热痛阈值及感觉神经传导速率从CCI手术后的第3天即出现显著性降低,其6、9、12、15天足底机械痛阈值、足底热痛阈值及感觉神经传导速率均显著低于Control组(P0.01),而运动功能评分均显著高于Control组(P0.05)。CCI+EMF组大鼠的足底机械痛阈值、足底热痛阈值及感觉神经传导速率在第9、12、15天显著高于CCI组大鼠(P0.05),而运动功能评分均显著高于CCI l组。结论:外源性的电磁刺激对于神经病理性疼痛大鼠具有良好的镇痛效果,有望成为一种临床治疗神经病理性疼痛的新的物理治疗手段。