芯片数据标准化方法比较研究

在基因芯片实验中,基因表达水平之间的相关性在推断基因间相互关系时起到非常重要的作用.未经标准化处理的芯片数据基因之间往往都呈现出很强的相关性,这些高相关性一部分是由基因表达水平变化引起的,而另外一部分是由系统偏差引起的.对芯片数据进行标准化处理的目的之一是消除系统偏差引起的高相关性,同时保留由真正生物学原因引起的基因表达水平高相关性.虽然目前对标准化方法已经有了不少比较研究,但还较少有人研究标准化方法对基因之间相关系数的影响,以及哪种方法最有利于恢复基因之间的相关性结构.通过对基因表达水平数据的模拟,具体比较了几种常用标准化方法的效果,从而给出最有利于恢复基因之间相关性结构的那种标准化方法.     

啮齿类螺杆菌不同检测方法的比较

目的确定用于实验啮齿类动物常规螺杆菌检测方法。方法选用针对螺杆菌属16S rRNA属特异性的4对引物进行了引物选择、取材部位以及与分离培养法比较。结果引物P7/P8的敏感性优于其它3对,检出限可达0.01 pg,对阳性动物群检出率80%-100%;分离培养法检出率40%-50%;盲肠、结肠检出率无显著差异。结论以引物P7/P8的PCR方法作为啮齿类实验动物螺杆菌初筛方法,分离培养法作为验证方法,取材部位可在盲肠或结肠。     

Comparison of Different Agar Diffusion Methods for the Detection of Antimicrobial Residues in Slaughter Animals

The different agar diffusion methods were compared using antibiotic and sulphonamide-impregnated filter-paper discs and the kidneys of healthy and emergency-slaughtered pigs and cows after slaughter. No method used seemed to be sensitive to all antimicrobial drugs preimpregnated onto discs. Tetracycline yielded a greater zone of inhibition at pH 6 than at pH 8 and aminoglycosides, erythromycin, polymyxin B and lin cornycin at pH 8 than at pH 6. It therefore seems necessary to use different pHs (6 and 8). The addition of trimethoprim to the medium is necessary for the detection of sulphonamides. Bacillus subtilis BGA used as the test organism was more sensitive to sulphonamides on the “Test agar for the inhibitor test” containing trimethoprim than on the “Iso-Sensitest agar” also containing trimethoprim. The addition of trimethoprim to “Test agar for the inhibitor test” is recommended at pH 8 but not at pH 6 because false-positive cases (with inhibition zones > 2 mm) were observed at pH 6 with trimethoprim on the kidneys of healthy pigs.     

A longitudinal follow-up study of the quantification of dopamine transporters with 123I-Ioflupane (DaTscan)

IntroductionThe aim of this study was to test a quantification tool to measure the evolution of the functional reserve of dopaminergic transporters, from two consecutive ¹²³I-Ioflupane Datscan.MethodsImages of 58 patients who underwent two consecutive ¹²³I-Ioflupane examinations (DaTscan^®) in the Nuclear Medicine Department of Toulouse University Hospital from 2002 to 2016 were analysed in this retrospective study. Twenty-four patients had a normal dopaminergic neuronal operation (N group), 34 had a pathological impairment of the dopamine transporters (P group) which 15 did not receive any treatment (PO group) and 16 who received treatment (P1 group). The DaTscan^® image quantification was performed with the DaTsofr3D^® software, permitting to measure the right and left binding potential (PL) of the caudate nucleus (NC), putamen (PU) and striatum (ST).ResultsIn the N group, the annual mean change of the binding potential (NC, PU, ST) was respectively (−0.03%/year, −0.96%/year, −0.43%/year) and did not significantly differ from the normal physiological decline of −0.66%/year. The annual binding potential mean changes of the P group (−9.6%/year, −13%/year, −11%/year) significantly differed not only from the N group but also from the physiological decline. No significant difference was shown between P0 and P1 groups.ConclusionThe DaTsoft3D^® quantification software permits to split up two groups according to the evolution of the dopamine transporter density with a significant difference in the binding potential mean annual rate.     

Normalization of Ventilation Data from 4D-CT to Facilitate Comparison between Datasets Acquired at Different Times

Purpose

The 4D-CT data used for comparing a patient’s ventilation distributions before and after lung radiotherapy are acquired at different times. As a result, an additional variable – the tidal volume (TV) – can alter the results. Therefore, in this paper we propose to normalize the ventilation to the same TV to eliminate that uncertainty.

Methods

Absolute ventilation (AV) data were generated for 6 stereotactic body radiation therapy (SBRT) cases before and after treatment, using the direct geometric algorithm and diffeomorphic morphons deformable image registration (DIR). Each pair of AV distributions was converted to TV-normalized, percentile ventilation (PV) and low-dose well-ventilated-normalized ventilation (LDWV) distributions. The ventilation change was calculated in various dose regions based on the treatment plans using the DIR-registered before and after treatment data sets. The ventilation change based on TV-normalized ventilation was compared with the AV as well as the data normalized by PV and LDWV.

Results

AV change may be misleading when the TV differs before and after treatment, which was found to be up to 6.7%. All three normalization methods produced a similar trend in ventilation change: the higher the dose to a region of lung, the greater the degradation in ventilation. In low dose regions (<5 Gy), ventilation appears relatively improved after treatment due to the relative nature of the normalized ventilation. However, the LDWV may not be reliable when the ventilation in the low-dose regions varies. PV exhibited a similar ventilation change trend compared to the TV-normalized in all cases. However, by definition, the ventilation distribution in the PV is significantly different from the original distribution.

Conclusion

Normalizing ventilation distributions by the TV is a simple and reliable method for evaluation of ventilation changes.     

Comparison of Normalization Methods for Construction of Large,Multiplex Amplicon Pools for Next-Generation Sequencing

Constructing mixtures of tagged or bar-coded DNAs for sequencing is an important requirement for the efficient use of next-generation sequencers in applications where limited sequence data are required per sample. There are many applications in which next-generation sequencing can be used effectively to sequence large mixed samples; an example is the characterization of microbial communities where ≤1,000 sequences per samples are adequate to address research questions. Thus, it is possible to examine hundreds to thousands of samples per run on massively parallel next-generation sequencers. However, the cost savings for efficient utilization of sequence capacity is realized only if the production and management costs associated with construction of multiplex pools are also scalable. One critical step in multiplex pool construction is the normalization process, whereby equimolar amounts of each amplicon are mixed. Here we compare three approaches (spectroscopy, size-restricted spectroscopy, and quantitative binding) for normalization of large, multiplex amplicon pools for performance and efficiency. We found that the quantitative binding approach was superior and represents an efficient scalable process for construction of very large, multiplex pools with hundreds and perhaps thousands of individual amplicons included. We demonstrate the increased sequence diversity identified with higher throughput. Massively parallel sequencing can dramatically accelerate microbial ecology studies by allowing appropriate replication of sequence acquisition to account for temporal and spatial variations. Further, population studies to examine genetic variation, which require even lower levels of sequencing, should be possible where thousands of individual bar-coded amplicons are examined in parallel.Emergent technologies that generate DNA sequence data are designed primarily to perform resequencing projects at reasonable cost. The result is a substantial decrease in per base costs from traditional methods. However, these next-generation platforms do not readily accommodate projects that require obtaining moderate amounts of sequence from large numbers of samples. These platforms also have per run costs that are significant and generally preclude large numbers of single-sample, nonmultiplexed runs. One example of research that is not readily supported is rRNA-directed metagenomics study of some human clinical samples or environmental rRNA analysis of samples from communities with low community diversity that require only thousands of sequences. Thus, strategies to utilize next-generation DNA sequencers efficiently for applications that require lower throughput are critical to capitalize on the efficiency and cost benefits of next-generation sequencing platforms.Directed metagenomics based on amplification of rRNA genes is an important tool to characterize microbial communities in various environmental and clinical settings. In diverse environmental samples, large numbers of sequences are required to fully characterize the microbial communities (15). However, a lower number of sequences is generally adequate to answer specific research questions. In addition, the levels of diversity in human clinical samples are usually lower than what is observed in environmental samples (for example, see reference 7).The Roche 454 genome sequencer system FLX pyrosequencer (which we will refer to as 454 FLX hereafter) is the most useful platform for rRNA-directed metagenomics because it currently provides the longest read lengths of any next-generation sequencing platform (1, 14). Computational analysis has shown that the 250-nucleotide read length (available from the 454 FLX-LR chemistry) is adequate for identification of bacteria if the amplified region is properly positioned within variable regions of the small-subunit rRNA (SSU-rRNA) gene (9, 10).In this study, we used the 454 FLX-LR genome sequencing platform and chemistry, which provides >400,000 sequences of ∼250 bp per run. After we conducted this study, a new reagent set (454 FLX-XLR titanium chemistry) was released, which further increases reads to >1,000,000 and read lengths to >400 bp (Roche). The 454 FLX platform dramatically reduces per base costs of obtaining sequence, and physical separation into between 2 and 16 lanes is available; this physical separation on the plate reduces sequencing output overall, up to 40% comparing 2 lanes versus 16 lanes. For applications where modest sequencing depth (∼1,000 sequences per sample) is adequate to address research questions, physical separation does not allow adequate sample multiplexing because even a 1/16 454 FLX-LR plate run is expected to produce ∼15,000 reads. Further, the utility of the platform as a screening tool at 16-plex is limited by cost per run.A solution to make next-generation sequencing economical for projects such as rRNA-directed metagenomics is to use bar-coded primers to multiplex amplicon pools so they can be sequenced together and computationally separated afterward (6). To successfully accomplish this strategy, precise normalization of the DNA concentrations of the individual amplicons in the multiplex pools is essential for effective multiplex sequencing when large numbers of pooled samples are sequenced in parallel. There are several potential methods available for normalizing concentrations of amplicons included in multiplex pools, but the relative and absolute performance of each approach has not been compared.In this study, we present a direct quantitative comparison of three available methods for amplicon pool normalization for downstream next-generation sequencing. The central goal of the study was to identify the most effective method for normalizing multiplex pools containing >100 individual amplicons. We evaluated each pooling approach by 454 sequencing and compared the observed frequencies of sequences from different pooled bar-coded amplicons. From these data, we determined the efficacy of each method based on the following factors: (i) how well normalized the sequences within the pool were, (ii) the proportion of samples failing to meet a minimum threshold of sequences per sample, and (iii) the overall efficiency (speed and labor required) of the process to multiplex samples.     

转bar基因小麦和非转基因小麦抗除草剂鉴定方法比较

方便、快捷、准确地对转基因小麦中的bar基因进行检测,对于筛选纯合稳定转基因植株、获得无筛选标记转基因植株、鉴定常规小麦品种和商品小麦中的bar基因成分等具有一定价值。本试验对叶片涂抹、植株喷洒、培养基添加除草剂3种方法鉴定转bar基因小麦植株的效果进行了比较,表明3种方法都能很好鉴定转基因小麦中的bar基因,叶片涂抹200mg/LLiberty鉴别的准确性高于PCR检测,植株喷洒Basta的适宜浓度为100mg/L,喷洒Liberty的适宜浓度为150mg/L,培养基添加Bialaphos的适宜浓度为5～8mg/L。叶片涂抹和植株喷洒除草剂方法受环境条件影响较大,区别转基因植株和非转基因植株的标准不够明确。相比之下,成熟胚离体培养除草剂筛选不受外界环境条件的影响,具有鉴定效果直观明了、操作简单、试验周期短等优点,在检测小麦转入或飘入的bar基因方面具有潜在应用前景。     

新城疫病毒3种检测方法的研究比较

目的:利用3种方法对新城疫(Newcastle disease virus, NDV)病毒进行检测并对这3种检测方法的优缺点做出比较。方法:分别将NDV强毒F48E9和弱毒Lasota接种SPF鸡胚后,获取尿囊液。利用双抗夹心ELISA法、悬液芯片系统以及RT-PCR进行检测。通过对制备的针对新城疫病毒的抗体4D9和6C4蛋白浓度测定后,选择6C4进行生物素标记,将4D9作为固相捕获抗体,利用生物素-链霉亲和素放大系统构建双抗夹心检测体系。通过对Genebank上已发表的新城疫强弱毒F基因进行电脑分析后,设计一组针对NDV强弱毒的通用型引物,分别对强弱毒进行RT-PCR并检测其检出限。结果:ELISA法对NDV强弱毒尿囊液的检出灵敏度为1:160,但操作繁琐,耗时长;液相芯片对强弱毒尿囊液的检出限为1:160和1:320,然而和ELISA相比,操作较为方便,但仪器设备昂贵。RT-PCR对强弱毒RNA检出限分别为259pg和14pg,与前两种方法相比,PR-PCR在核酸水平上对病毒进行检测,理论上灵敏度较高,但是所需试剂、设备昂贵,且实验人员还需一定的技能培训。     

不同样本前处理方法对高通量测序检测HBV、HCV、TTV结果的影响

目的:探索不同样品前处理方法对于不同类型病毒检测的效果。方法:分别将携带乙肝病毒(双链环状DNA病毒)、丙肝病毒(单正链RNA病毒)、TTV(Torque teno virus)(单链环状DNA病毒)的血清等比例混合,模拟混合感染,然后分别采用多重置换扩增(MDA)和随机锚定PCR扩增并进行高通量测序,同时以原始样品(未扩增)直接高通量测序作为对照。结果:原始样品(未扩增)直接测序,产出的数据大部分为人类的序列;MDA方法中绝大部分数据为TTV、乙肝病毒;随机锚定PCR扩增方法中绝大部分数据为乙肝病毒。结论:MDA方法适合扩增环状病毒,随机锚定PCR扩增适合含量高的病毒,不做任何处理直接高通量测序检测病毒效果最差。本研究可为指导不同类型病原体如何选择扩增方案提供借鉴。     

噬菌体浓缩方法的比较

目的：对不同噬菌体浓缩方法进行比较。方法：采用PEG沉淀、PEG反透析、阴阳离子结合树脂、超滤等5种方法对T4、T7、N4等3类噬菌体进行浓缩对比试验;在此基础上,用浓缩效果较好的方法对土壤和河道污水样本中的噬菌体进行浓缩,观察浓缩效果。结果：上述5种方法对3类噬菌体均有浓缩效果;超滤的浓缩效果最好,其次是PEG反透析,PEG沉淀没有很好的浓缩效果;河水样本中噬菌体的回收率比土壤样本高。结论：可通过PEG反透析、超滤或两者相结合的方法,得到高浓度的有活性的噬菌体。     

野生鸡枞菌种长期保存方法比较

野生鸡枞菌种质资源的有效保存是对野生鸡枞加以保护和利用的前提。以自行分离的5个野生鸡枞菌株作为研究对象,采用蒸馏水保藏法和-80°C冻结保藏法对野生鸡枞菌种长期保存的方法进行了实验研究,蒸馏水法分别保存于室温和4°C,-80°C冻结保藏同时采用程控降温法和泡沫盒降温法,保存20个月后对4种不同方法保存的5个菌株的保存效果进行比较。实验结果表明:蒸馏水室温保存法菌种存活率为100%,萌发期较短,为4-10 d,是一种简便、实用、有效而成本低廉的长期保存方法;-80°C冻结保藏法的存活率为56%-76%,萌发期7-16 d,泡沫盒降温法可以很好地控制降温速度,是一种简便有效的控温方法。     

红曲霉不同转化方法比较

为了研究红曲霉聚酮体途径,考察和比较了4种不同的转化方法以建立有效的红曲霉遗传转化系统。以潮霉素作为抗性筛选标记,pBC-Hygro作为转化载体,用基于原生质体的传统转化和电击转化、基于萌发孢子的电击转化以及REMI技术转化红曲霉。发现基于萌发孢子的电击转化由于转化率极低而不适于红曲霉转化。基于原生质体的传统转化和电击转化尽管每微克DNA分别能获得135个转化子和125个转化子,但因转化子稳定性差也适合红曲霉转化的转化。应用REMI技术,转化率提高约20倍,每微克DNA 2500个转化子,70%～75%的转化子的稳定,非常适合于红曲霉的转化。      

苯丙酮尿症常用筛查方法的比较

苯丙酮尿症是一种由于体内缺乏苯丙氨酸羟化酶所引起的遗传性代谢异常疾病,如果能够做到早诊断、早发现、早预防和早治疗,就可以避免患儿以后出现智能发育障碍,因此开展新生儿的筛查工作十分重要。简要介绍了苯丙酮尿症的基本情况以及目前应用于临床的常用筛查方法,如细菌抑制法、荧光法等,并从筛查原理、主要优缺点等方面进行了简单的比较。     

Comparison of Different pH Measurement Methods in Meat

The accuracy of portable pH meters and the nitrazine yellow method was compared with the reference method by determining the pH of 74 beef and 96 pork muscles. The pH was measured directly from the muscle. The results showed statistically significant differences (p < 0.001) between the different electrometric combinations. Combinations of portable pH meters with puncture electrodes gave systematically higher pH values than the reference method. These differences were not very large but they may be of practical significance. The use of a piercing cover on the electrode to help the insertion of the electrode into the meat is not recommended, since it may cause a rise in pH values. Electrometric methods were found to be more precise than the nitrazine yellow method. On the basis of these findings there still is a need of further harmonization of the methods used for pH measurement of meat.     

Comparison of Fluorescent-Antibody Methods and Enrichment Serology for the Detection of Salmonella

Four rapid methods for detection of Salmonella, (i) the conventional fluorescent-antibody (FA) technique, (ii) a rapid direct FA technique, (iii) microcolony FA, and (iv) enrichment serology (ES), were compared with conventional cultural procedures. A total of 347 subsamples representing 16 different food prototypes, alleged to be naturally contaminated with Salmonella, were analyzed. From these samples, 52 were found to contain Salmonella by cultural methods. Conventional FA identified all 52 culturally positive samples, ES identified 51, microcolony FA identified 48, and the rapid FA method identified 34. The number of false-positive samples for each procedure was: ES-selenite, 7; tetrathionate, 8; rapid FA, 26; microcolony FA, 33; conventional FA-selenite, 27; tetrathionate, 26. Tetrathionate enrichment was found to be superior to selenite for Salmonella recovery from most foods, but the concurrent use of both media allowed maximum recovery.     

Development and Application of Different Methods for the Detection of Toxoplasma gondii in Water

Two methods, centrifugation and flocculation, were evaluated to determine their efficiencies of recovery of Toxoplasma gondii oocysts from contaminated water samples. Demineralized and tap water replicates were inoculated with high numbers of sporulated or unsporulated T. gondii oocysts (1 × 10⁵ and 1 × 10⁴ oocysts). The strain, age, and concentration of the seeded oocysts were recorded. Oocysts were recovered either by centrifugation of the contaminated samples at various g values or by flocculation with two coagulants, Fe₂(SO₄)₃ and Al₂(SO₄)₃. The recovery rates were determined with the final pellets by phase-contrast microscopy. Sporulated oocysts were recovered more effectively by flocculation with Al₂(SO₄)₃ (96.5% ± 21.7%) than by flocculation with Fe₂(SO₄)₃ (93.1% ± 8.1%) or by centrifugation at 2,073 × g (82.5% ± 6.8%). For the unsporulated oocysts, flocculation with Fe₂(SO₄)₃ was more successful (100.3% ± 26.9%) than flocculation with Al₂(SO₄)₃ (90.4% ± 19.1%) or centrifugation at 2,565 × g (97.2% ± 12.5%). The infectivity of the sporulated oocysts recovered by centrifugation was confirmed by seroconversion of all inoculated mice 77 days postinfection. These data suggest that sporulated Toxoplasma oocysts purified by methods commonly used for waterborne pathogens retain their infectivity after mechanical treatment and are able to induce infections in mammals. This is the first step in developing a systematic approach for the detection of Toxoplasma oocysts in water.     

小鼠精原干细胞不同转染方法效率的比较

本研究采用腺病毒感染、慢病毒感染、脂质体转染和电穿孔转化方法将含有绿色荧光蛋白（GFP）的质粒转入经过差异贴壁法初步分离纯化的小鼠精原干细胞(SSCs)中,转染48 h后通过流式细胞仪检测GFP阳性细胞比例比较4种方法在体外转染精原干细胞的效率.结果显示,脂质体转染效率最高仅为8.64%,不能满足对精原干细胞进一步实验的要求;电穿孔法效率最高达到25.27%,但转化后细胞大量死亡;腺病毒转染细胞的效率达到了32.4%;慢病毒转染效率最高,达到74.25%. 因此,慢病毒转染法是体外转染小鼠精原干细胞的有效方法.