Illumina-Solexa测序数据质量评估系统的构建

目的：针对下一代测序数据量大、序列长度短的特点,研究数据分析和质量评估方法。方法：选择已发布的Illumina-Solexa平台测序数据为研究对象,通过MAQ软件将测序数据与人类全基因组序列进行比对,并以外显子区域为例,在位点水平对测序数据质量进行评估。结果：结合已有软件系统和本文自创线性算法,建立了一套包括比对、拼接在内的测序数据质量评估系统。比对分析后,发现原始测序序列共覆盖了127,113,378个位点,涉及24条染色体上的64868个外显子。其中,每个位点都被测到的外显子为0.50%,位点平均测序深度大于等于1的外显子为3.98%。结论：成功构建了基于Illumina-Solexa测序平台的数据分析和质量评估方法,其可适用于其它第二代测序平台。研究者可在质量评估的基础上完善测序试验设计,并进行SNP和突变筛选及后续功能性研究。     

Non-destructive assessment of flesh firmness and dietary antioxidants of greenhouse-grown tomato (Solanum lycopersicum L.) at different fruit maturity stages

Non-destructive methods have been widely recognized for evaluating fruit quality traits of many horticultural crops and food processing industry. Destructive (analytical) test, and non-destructive evaluation of the quality traits were investigated and compared for ‘Red Rose’ tomato (Solanum lycopersicum L.) fruit grown under protected environment. Fresh tomato fruit at five distinctive maturity stages namely; breaker (BK), turning (TG), pink (PK), light-red (LR), and red (RD) were labeled and scanned using the handheld near infra-red (NIR) enhanced spectrometer at a wavelength range of 285–1200 nm. The labeled tomato samples were then measured analytically for flesh firmness, lycopene, β-carotene, total phenolic content (TPC) and total flavonoids content (TFC). The results revealed that quality traits could be estimated using NIR spectroscopy with a relatively high coefficient of determination (R²): 0.834 for total phenolic content, 0.864 for lycopene, 0.790 for total flavonoid content, 0.708 for β-carotene; and 0.679 for flesh firmness. The accumulation of Lyco and β-Car rapidly increased in tomatoes harvested between the TG and the LR maturity stages. Harvesting tomatoes at BK maturity stage resulted in significantly higher flesh firmness than harvesting at the later maturity stages. Tomato fruits had the lowest TPC and TFC contents at the earliest maturity stage (BK), while they had intermediate TPC and TFC levels at LR and RD maturity stages. NIR spectroscopic measurements of fruit firmness and lipophilic antioxidants in tomato fruit at various maturity stages were partially in accordance with those estimated by destructive (analytical) methods. Based on these findings, we recommend using non-destructive NIR spectroscopy as an effective tool for predicting tomato fruit quality during harvest stage and postharvest processing.     

低温等离子髓核消融术治疗高原地区椎间盘源性下腰痛的疗效及对患者生活质量的影响

目的:研究低温等离子髓核消融术(LTPNPA)治疗高原地区椎间盘源性下腰痛(DLBP)的疗效及对患者生活质量的影响。方法:选择从2015年9月到2017年1月在我院接受治疗的高原地区DLBP患者,随机分为对照组(n=59)和观察组(n=59),对照组患者给予常规腰椎牵引治疗,观察组患者则予以LTPNPA术式治疗,对所有患者进行为期6个月的随访,并对比两组疗效、临床指标(疼痛缓解时间和住院时间)、治疗前后的椎间隙高度R值和Oswestry功能障碍指数(ODI)评分以及不同时期的日常生活能力量表(ADL)评分。结果:观察组的优良率是98.31%,高于对照组的88.14%(P0.05)。观察组的疼痛缓解时间及住院时间均少于对照组(P0.05)。治疗后两组的ODI评分均低于治疗前,且观察组较对照组偏低(P0.05)。治疗后两组的椎间隙高度R值相比差异无统计学意义(P0.05)。治疗后1个月、3个月、6个月两组的ADL评分均高于治疗前,治疗后3个月和6个月高于治疗后1个月,治疗后6个月高于治疗后3个月,且观察组均较对照组偏高(P0.05)。结论:对高原地区DLBP患者应用LTPNPA术式治疗,具有明显疗效,还可提升其生活质量,临床上可考虑在高原地区推广LTPNPA术式,从而使患者获得最佳疗效。     

Rapid evaluation and quality control of next generation sequencing data with FaQCs

Background

Next generation sequencing (NGS) technologies that parallelize the sequencing process and produce thousands to millions, or even hundreds of millions of sequences in a single sequencing run, have revolutionized genomic and genetic research. Because of the vagaries of any platform’s sequencing chemistry, the experimental processing, machine failure, and so on, the quality of sequencing reads is never perfect, and often declines as the read is extended. These errors invariably affect downstream analysis/application and should therefore be identified early on to mitigate any unforeseen effects.

Results

Here we present a novel FastQ Quality Control Software (FaQCs) that can rapidly process large volumes of data, and which improves upon previous solutions to monitor the quality and remove poor quality data from sequencing runs. Both the speed of processing and the memory footprint of storing all required information have been optimized via algorithmic and parallel processing solutions. The trimmed output compared side-by-side with the original data is part of the automated PDF output. We show how this tool can help data analysis by providing a few examples, including an increased percentage of reads recruited to references, improved single nucleotide polymorphism identification as well as de novo sequence assembly metrics.

Conclusion

FaQCs combines several features of currently available applications into a single, user-friendly process, and includes additional unique capabilities such as filtering the PhiX control sequences, conversion of FASTQ formats, and multi-threading. The original data and trimmed summaries are reported within a variety of graphics and reports, providing a simple way to do data quality control and assurance.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-014-0366-2) contains supplementary material, which is available to authorized users.     

Hypoxia triggers endothelial endoplasmic reticulum stress and apoptosis via induction of VLDL receptor

Endothelial cells express very low density lipoprotein receptor (VLDLr). Beyond the function as peripheral lipoprotein receptor, other roles of VLDLr in endothelial cells have not been completely unraveled. In the present study, human umbilical vein endothelial cells were subjected to hypoxia, and VLDLr expression, endoplasmic reticulum (ER) stress, and apoptosis were assessed. Hypoxia triggered endothelial ER stress and apoptosis, and induced VLDLr expression. Silencing or stabilization of HIF-1α reduced and enhanced VLDLr expression, respectively. HIF-1α affected vldlr promoter activity by interacting with a hypoxia-responsive element (HRE). Knockdown or overexpression of VLDLr alleviated and exacerbated hypoxia-induced ER stress and apoptosis, respectively. Thus, hypoxia induces VLDLr expression through the interaction of HIF-1α with HRE at the vldlr promoter. VLDLr then mediates ER stress and apoptosis.     

不同基肥对退化坡地及牧草产量和质量的影响

探讨了不同基肥组合处理对退化坡地的改造利用和对牧草生产的影响．在相同的肥水管理条件下,以“鸡粪＋牛粪＋石灰”的基肥组合（Ａ）处理退化坡地土壤,可使皇草、杂交狼尾草、矮象草和墨西哥玉米的年产量比“猪粪＋牛粪＋石灰”的组合（Ｂ）处理分别高出９．７％、１２．８％、４３．０％和９．９％,前者（Ａ）生产出的牧草的粗蛋白含量略高于后者（Ｂ）,粗纤维含量略低于后者,而粗灰分含量显著高于后者．     

Hsp70 promotes epithelial sodium channel functional expression by increasing its association with coat complex II and its exit from endoplasmic reticulum

The epithelial sodium channel (ENaC) plays an important role in the homeostasis of blood pressure and of the airway surface liquid, and inappropriate regulation of ENaC results in refractory hypertension (in Liddle syndrome) and impaired mucociliary clearance (in cystic fibrosis). The regulation of ENaC by molecular chaperones, such as the 70-kDa heat shock protein Hsp70, is not completely understood. Building on the previous suggestion by our group that Hsp70 promotes ENaC functional and surface expression in Xenopus oocytes, we investigated the mechanism by which Hsp70 acts upon ENaC in epithelial cells. In Madin-Darby canine kidney cells stably expressing epitope-tagged αβγ-ENaC and with tetracycline-inducible overexpression of Hsp70, treatment with 1 or 2 μg/ml doxycycline increased total Hsp70 expression ~2-fold and ENaC functional expression ~1.4-fold. This increase in ENaC functional expression corresponded to an increase in ENaC expression at the apical surface of the cells and was not present when an ATPase-deficient Hsp70 was similarly overexpressed. The increase in functional expression was not due to a change in the rate at which ENaC was retrieved from the apical membrane. Instead, Hsp70 overexpression increased the association of ENaC with the Sec24D cargo recognition component of coat complex II, which carries protein cargo from the endoplasmic reticulum to the Golgi. These data support the hypothesis that Hsp70 promotes ENaC biogenesis and trafficking to the apical surface of epithelial cells.     

光电阅读机在大人群现场调查中数据处理及质量控制 的应用

目的:探讨光电阅读机在大样本现场调查项目质量控制和数据录入中的作用.方法:使用光电阅读机读入《子宫颈癌危险因素调查表》信息并进行表格质量评估,核查调查表中调查对象编码缺失、重复及进行读入信息一致性比对.结果:在录入的70160份数据中,调查对象编码缺失率为0.87％,调查对象编码重复率为0.79％,信息一致率为99.47％.3个项目点连续三个月质量控制,表格不合格率略有下降.结论:在大人群现场调查项目中通过光电阅读机进行质量控制及数据录入,能快速准确的将纸质信息转化为电子信息,并对电子信息进行核查,能迅速将调查表评估结果和建议反馈给调查表填写人员,及时指导调查员改进调查项目的编写方法和调查表内容的填写方法,从而提高了调查表信息采集质量,促进项目科研数据真实可信.     

Auxiliary KChIP4a Suppresses A-type K+ Current through Endoplasmic Reticulum (ER) Retention and Promoting Closed-state Inactivation of Kv4 Channels

In the brain and heart, auxiliary Kv channel-interacting proteins (KChIPs) co-assemble with pore-forming Kv4 α-subunits to form a native K⁺ channel complex and regulate the expression and gating properties of Kv4 currents. Among the KChIP1–4 members, KChIP4a exhibits a unique N terminus that is known to suppress Kv4 function, but the underlying mechanism of Kv4 inhibition remains unknown. Using a combination of confocal imaging, surface biotinylation, and electrophysiological recordings, we identified a novel endoplasmic reticulum (ER) retention motif, consisting of six hydrophobic and aliphatic residues, 12–17 (LIVIVL), within the KChIP4a N-terminal KID, that functions to reduce surface expression of Kv4-KChIP complexes. This ER retention capacity is transferable and depends on its flanking location. In addition, adjacent to the ER retention motif, the residues 19–21 (VKL motif) directly promote closed-state inactivation of Kv4.3, thus leading to an inhibition of channel current. Taken together, our findings demonstrate that KChIP4a suppresses A-type Kv4 current via ER retention and enhancement of Kv4 closed-state inactivation.     

遗传标记和免疫学方法在实验动物质量控制中的应用

生命科学发展迅速,实验动物级别逐渐提高,在保证生物制品实验结果可靠性前提下,完善动物由低级别向高级别过渡显得十分必要,最终目的达到实验动物标准化和动物实验规范化。对实验动物质量控制中的遗传标记和免疫学方法进行了综述。