Mfuzz: a software package for soft clustering of microarray data

For the analysis of microarray data, clustering techniques are frequently used. Most of such methods are based on hard clustering of data wherein one gene (or sample) is assigned to exactly one cluster. Hard clustering, however, suffers from several drawbacks such as sensitivity to noise and information loss. In contrast, soft clustering methods can assign a gene to several clusters. They can overcome shortcomings of conventional hard clustering techniques and offer further advantages. Thus, we constructed an R package termed Mfuzz implementing soft clustering tools for microarray data analysis. The additional package Mfuzzgui provides a convenient TclTk based graphical user interface. AVAILABILITY: The R package Mfuzz and Mfuzzgui are available at http://itb1.biologie.hu-berlin.de/~futschik/software/R/Mfuzz/index.html. Their distribution is subject to GPL version 2 license.     

Bayesian tests for random mating in polyploids

Hardy–Weinberg proportions (HWP) are often explored to evaluate the assumption of random mating. However, in autopolyploids, organisms with more than two sets of homologous chromosomes, HWP and random mating are different hypotheses that require different statistical testing approaches. Currently, the only available methods to test for random mating in autopolyploids (i) heavily rely on asymptotic approximations and (ii) assume genotypes are known, ignoring genotype uncertainty. Furthermore, these approaches are all frequentist, and so do not carry the benefits of Bayesian analysis, including ease of interpretability, incorporation of prior information, and consistency under the null. Here, we present Bayesian approaches to test for random mating, bringing the benefits of Bayesian analysis to this problem. Our Bayesian methods also (i) do not rely on asymptotic approximations, being appropriate for small sample sizes, and (ii) optionally account for genotype uncertainty via genotype likelihoods. We validate our methods in simulations and demonstrate on two real datasets how testing for random mating is more useful for detecting genotyping errors than testing for HWP (in a natural population) and testing for Mendelian segregation (in an experimental S1 population). Our methods are implemented in Version 2.0.2 of the hwep R package on the Comprehensive R Archive Network https://cran.r-project.org/package=hwep .     

Tau蛋白核心片段306~378的异源表达、纯化及聚集特性验证*

Tau是一种微管相关蛋白,其生理功能是与微管蛋白结合促进其聚合形成微管并维持微管的稳定。由于Tau蛋白异常聚集沉淀而导致的疾病被称为Tau蛋白病,其中阿尔茨海默病是最常见的一种类型。全序列Tau含有441个氨基酸残基,其中306~378肽段(Tau_306-378)为驱动其聚集的核心区域。Tau_306-378包含R3和R4微管结合序列以及从R4序列C端向后延伸的10个氨基酸残基。首先利用pET22b载体在大肠杆菌中表达获得了Tau_306-378,然后用镍亲和层析进行纯化,终产量约为10.35mg/L。利用SDS-PAGE、Western blot和基质辅助激光解析电离飞行时间质谱依次对Tau_306-378进行了鉴定。其中SDS-PAGE和基质辅助激光解析电离飞行时间质谱的研究结果表明,表达的Tau_306-378主要以单体形式存在,但同时含有部分二聚体。最后,硫黄素T荧光染色实验显示该重组蛋白具有良好的聚集特性,可用于体外Tau蛋白的聚集特性、毒性及相关抑制剂开发的研究。     

STATISTICAL ANALYSES FOR R-INDEX

R‐index is an important statistic for testing and measuring product effects. The validation and merits of R‐index are to a great extent due to the fact that it is closely related to the famous Mann–Whitney U statistic. Based on this fortunate relationship, statistical analyses for R‐index are explored. The statistical analyses include estimations of R‐index and its null and nonconditional variances with and without assuming continuity of data; difference and similarity tests using R‐index; powers and sample sizes for the tests; linking R‐index with Thurstonian δ (or d′). The new techniques developed in the paper extend greatly the original R‐index analysis for categorical ratings data. It is expected that the recognition of the profound theoretical origin of R‐index and the available statistical analyses for R‐index will provide the impetus for the resurgence of interest in using R‐index in sensory and consumer researches.     

Dual-signal analysis eliminates requirement for milk sample pretreatment

Detection of analytes in complex biological samples, such as milk and blood, normally requires sample pretreatment. These pretreatment regimes reduce assay throughput and increase testing costs. Technologies that make it possible to eliminate sample pretreatment are of great industrial interest. Here we report the development of a dual-signal flow injected analysis device which eliminates the need for sample pretreatment. The device employs thermal traducers to measure the signal from an enzyme and a reference column. This makes it possible to independently monitor and correct for non-specifically generated heat, thereby eliminating the need for sample pretreatment. The ability of the dual-signal device to determine urea and lactate in milk samples without any prior treatment was evaluated. The spiked milk samples, the urea assay had a linear range from 0.1 to 50mM (R=0.996), and the lactate assay had a linear range from 0.025 to 5.0mM (R=0.9998). The linear regression values for urea and lactate for 0.5%, 1.5% and 3.0% fat milk were at least 0.990. The dual-signal design improves assay reproducibility, accuracy and sensitivity. Addition benefits are shorter assay times and lowers costs, as well as reducing equipment and training requirements. The potential application of the technology for multi-analyte analysis in point of care and decentralized diagnostic testing in healthcare, agriculture and environmental areas is discussed.     

Methods for the spiral Salmonella mutagenicity assay including specialized applications

An automated approach to bacterial mutagenicity testing - the spiral Salmonella assay - was developed to simplify testing and to reduce the labor and materials required to generate dose-responsive mutagenicity information. This document provides the reader with an overview of the spiral assay and a discussion of its application for examining the mutagenic potential of pure compounds, complex environmental mixtures, and interactive effects. Guidelines for performing a routine spiral assay are presented, and alternative test methods intended to overcome a variety of technical difficulties (such as restricted sample availability, sample viscosity or volatility, etc.) are recommended. Methods for the computerized analysis of data and the interpretation of results are discussed.     

A biphasic and brain-region selective down-regulation of cyclic adenosine monophosphate concentrations supports object recognition in the rat

Background

We aimed to further understand the relationship between cAMP concentration and mnesic performance.

Methods and Findings

Rats were injected with milrinone (PDE3 inhibitor, 0.3 mg/kg, i.p.), rolipram (PDE4 inhibitor, 0.3 mg/kg, i.p.) and/or the selective 5-HT4R agonist RS 67333 (1 mg/kg, i.p.) before testing in the object recognition paradigm. Cyclic AMP concentrations were measured in brain structures linked to episodic-like memory (i.e. hippocampus, prefrontal and perirhinal cortices) before or after either the sample or the testing phase. Except in the hippocampus of rolipram treated-rats, all treatment increased cAMP levels in each brain sub-region studied before the sample phase. After the sample phase, cAMP levels were significantly increased in hippocampus (1.8 fold), prefrontal (1.3 fold) and perirhinal (1.3 fold) cortices from controls rat while decreased in prefrontal cortex (∼0.83 to 0.62 fold) from drug-treated rats (except for milrinone+RS 67333 treatment). After the testing phase, cAMP concentrations were still increased in both the hippocampus (2.76 fold) and the perirhinal cortex (2.1 fold) from controls animals. Minor increase were reported in hippocampus and perirhinal cortex from both rolipram (respectively, 1.44 fold and 1.70 fold) and milrinone (respectively 1.46 fold and 1.56 fold)-treated rat. Following the paradigm, cAMP levels were significantly lower in the hippocampus, prefrontal and perirhinal cortices from drug-treated rat when compared to controls animals, however, only drug-treated rats spent longer time exploring the novel object during the testing phase (inter-phase interval of 4 h).

Conclusions

Our results strongly suggest that a “pre-sample” early increase in cAMP levels followed by a specific lowering of cAMP concentrations in each brain sub-region linked to the object recognition paradigm support learning efficacy after a middle-term delay.     

汉逊酵母重组表达的人胃蛋白酶原Ⅱ校准品研制

目的：探索一种高效制备人胃蛋白酶原Ⅱ（pepsiongenⅡ,PGⅡ）体外诊断试剂用校准品的方法。方法：以汉逊酵母ATCC26012作为宿主菌,以携带Zeocin及G418双重筛选标记的pRMHP2.1质粒为载体,以遗传密码子优化设计后的PGⅡ序列为目的基因,通过电转化及后续多轮次的传代与稳定,筛选获得高水平分泌表达PGII蛋白的重组菌株26012/PGⅡ。采用Ni柱亲和层析的方法从200L发酵罐大量制备的培养液中纯化出高纯度的重组PGⅡ蛋白,将该蛋白质进行校准定值后配制成6种不同浓度的成套PGⅡ校准品,并对该系列校准品的实时稳定性、加速破坏性及开瓶稳定性展开评价。结果：筛选获得的重组汉逊酵母菌株26012/PGⅡ外源基因整合拷贝数高于40个且整合于染色体的rDNA位置,该菌株以分泌形式表达重组PGⅡ蛋白,表达量超过50mg/L,发酵培养液经Ni柱亲和层析纯化后,重组PGⅡ蛋白纯度达93.8%。通过免疫比浊试剂盒定量检测,该PGⅡ蛋白的活性定值与实际蛋白质量之间的比值达0.85,配制后的PGⅡ校准品在4℃实时保存1年、37℃加速破坏2周及4℃开盖保存2周后,校准品定值的平均下降幅度都不超过10%,其稳定性能不逊色于商品化的校准品。结论：汉逊酵母重组表达的PGⅡ蛋白可用作体外诊断试剂的校准品。     

蝉花虫草活性成分的抗惊厥作用

本研究采用活性追踪的方法,逐步从人工培养蝉花虫草分离获得A（50%乙醇回流提取）、B（膜分离）、C（大孔树脂洗脱）和D（Sephadex LH20柱纯化）等4种样品,单一化合物D纯度为98.62%,鉴定为N6‐(2‐羟乙基)腺苷[N6‐(2‐hydroxyethyl)‐adenosine,HEA]。研究各样品对戊四唑（pentylenetetrazol,PTZ）诱导的小鼠惊厥模型的影响,以及选择性腺苷A1受体（AA1R）拮抗剂DPCPX或选择性腺苷A2A受体（AA2AR）拮抗剂ZM241385对HEA作用的影响,并采用苏木精-伊红（hematoxylin-eosin,HE）染色、免疫组化（immunohistochemical,IHC）染色和蛋白质免疫印迹（Western blot,WB）等技术进一步探究HEA抗惊厥作用的机制。结果表明,各样品（i.p.）均有抗惊厥活性,HEA（40–60mg/kg,i.p.）能显著延长惊厥小鼠的存活时间和降低死亡率,DPCPX（2mg/kg,i.p.）能够拮抗HEA的抗惊厥作用,而ZM241385无此作用;HE、IHC和WB的结果进一步揭示DPCPX显著降低HEA的作用。综上所述,蝉花虫草的HEA具有抗惊厥作用,并且可能通过激活腺苷A1受体而起作用。     

重组EpoAB-NGF模拟肽的神经营养功能

目的:研究重组融合蛋白红细胞生成素AB肽-神经生长因子模拟肽(EpoAB-NGF9和EpoAB-NGF/12)的神经营养作用。方法:构建pET-42a-EpoAB-NGF9/12原核表达质粒,转化大肠杆菌BL21(DE3),以IPTG诱导表达,亲和层析纯化重组蛋白,显微镜观察PC12细胞诱导分化,流式细胞仪检测凋亡细胞。结果:大肠杆菌表达的重组融合蛋白GST-EpoAB-NGF9/12分子量约为30kDa,抗GST抗体免疫印迹反应呈阳性。融合蛋白可以诱导PC12细胞分化,促进轴突生长。R2L1细胞去血清培养,凋亡细胞占(31.7±0.60)%,去血清后加入融合蛋白GST-EpoAB-NGF9/12,细胞凋亡率分别为(25.2±3.52)%、(25.7±1.46)%,呈现一定程度的抑制细胞凋亡的活性。结论:重组EpoAB-NGF模拟肽融合蛋白具有与NGF类似的神经营养作用。     

FDR control by the BH procedure for two-sided correlated tests with implications to gene expression data analysis

The multiple testing problem attributed to gene expression analysis is challenging not only by its size, but also by possible dependence between the expression levels of different genes resulting from coregulations of the genes. Furthermore, the measurement errors of these expression levels may be dependent as well since they are subjected to several technical factors. Multiple testing of such data faces the challenge of correlated test statistics. In such a case, the control of the False Discovery Rate (FDR) is not straightforward, and thus demands new approaches and solutions that will address multiplicity while accounting for this dependency. This paper investigates the effects of dependency between bormal test statistics on FDR control in two-sided testing, using the linear step-up procedure (BH) of Benjamini and Hochberg (1995). The case of two multiple hypotheses is examined first. A simulation study offers primary insight into the behavior of the FDR subjected to different levels of correlation and distance between null and alternative means. A theoretical analysis follows in order to obtain explicit upper bounds to the FDR. These results are then extended to more than two multiple tests, thereby offering a better perspective on the effect of the proportion of false null hypotheses, as well as the structure of the test statistics correlation matrix. An example from gene expression data analysis is presented.     

Evaluation of PCR assays for quantifying seed-borne infection by Fusarium and Microdochium seedling blight pathogens

Aims:  To evaluate competitive PCR assays for quantifying seed-borne Microdochium and Fusarium seedling blight pathogen DNA and to determine test and year repeatability and sources of variability.
Methods and Results:  Relationships between DNA and plate counts were significant for Fusarium and Microdochium seedling blight pathogens in 152 seed batches from 3 years. Coefficient of determinations, however, differed greatly ( Fusarium ; R ² = 0·25, P  =   0·029, Microdochium ; R ² = 0·73, P  <   0·001). Significant differences between years were observed in the regression slopes for Microdochium . Pathogen DNA quantified in 16 extractions after sampling was highly correlated to results following storage for 1–2 years ( R ² > 0·90). Residual maximum likelihood analysis showed that the least and greatest variance components of the testing procedure were DNA extraction subsampling and PCR assay respectively.
Conclusions:  Amount of pathogen DNA is a useful estimator of seed batch contamination for Microdochium but not Fusarium seedling blight pathogens. Although reproducible over time, improvements to the testing procedure should focus on repeated PCR amplifications to reduce assay variability.
Significance and Impact of the Study:  Replacing plate counts with competitive PCR for determining the severity of seed batch contamination is feasible in areas where Microdochium seedling blight pathogens predominate.     

可溶性白细胞介素6受体基因在链霉菌的克隆表达研究

以分离提取的ＨｅＬａ细胞总ＲＮＡ为模板,通过ＲＴ－ＰＣＲ反应扩增得到了１０１７ｂｐ的人可溶性白细胞介素６受体（ｓＩＬ－６Ｒ）ｃＤＮＡ片段,将扩增片段克隆到ｐＵＣ１９质粒中进行序列测定。结果证明该片的序列与文献报道的ｓＩＬ－６ＲｃＤＮＡ的序列完全一致,将ｓＩＬ－６ＲｃＤＮＡ与链霉素信号肽ｍｅｌＣｌ的编码序列融合后得到的融合基因ｍｅｌ／ｓＩＬ－６Ｒ克隆到链霉菌质粒ｐＬＪ４５９中,构建成重组表达质粒ｐＬ     

Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway’s involvement in juvenile myelomonocytic leukemia

Background: Clinical studies and genetic analyses have revealed that juvenile myelomonocytic leukemia (JMML) is caused by somatic and/or germline mutations of genes involved in the RAS/MAPK signalling pathway. Given the vastly different clinical prognosis among individual patients that have had this disease, mutations in genes of other pathways may be involved. Methods: In this study, we conducted whole-exome and cancer-panel sequencing analyses on a bone marrow sample from a 2-year old juvenile myelomonocytic leukemia patient. We also measured the microRNA profile of the same patient’s bone marrow sample and the results were compared with the normal mature monocytic cells from the pooled peripheral blood. Results: We identified additional novel mutations in the PI3K/AKT pathway and verified with a cancer panel targeted sequencing. We have confirmed the previously tested PTPN11 gene mutation (exon 3 181G>T) in the same sample and identified new nonsynonymous mutations in NTRK1, HMGA2, MLH3, MYH9 and AKT1 genes. Many of the microRNAs found to be differentially expressed are known to act as oncogenic MicroRNAs (onco-MicroRNAs or oncomiRs), whose target genes are enriched in the PI3K/AKT signalling pathway. Conclusions: Our study suggests an alternative mechanism for JMML pathogenesis in addition to RAS/MAPK pathway. This discovery may provide new genetic markers for diagnosis and new therapeutic targets for JMML patients in the future.     

Quantification of the geocarposphere and rhizosphere effect of peanut (Arachis hypogaea L.)

Roots and pods of field-grown peanut (groundnut) (Arachis hypogaea L.) were sampled at the R3, R5, and R7 developmental stages and examined in comparison to root- and pod-free soil for microbial population densities to assess the geocarposphere and rhizosphere effects. G/ S (no. geocarposphere microorganisms/no. soil microorganisms) and R/S (no. rhizosphere microorganisms/no. soil microorganisms) ratios were calculated for total fungi,Asperigillus flavus, spore-forming bacilli, coryneform bacteria, fluorescent pseudomonads, and total bacteria isolated on low- and high-nutrient media. A clear geocarposphere effect was evidenced by increased population densities of bacteria and fungi associated with developing pods compared to soil. G/S and R/S ratios were generally greater than 1.0 for all groups of microorganisms except bacilli. G/S ratios were greater for total bacteria than for total fungi at two of the three sample times, suggesting that bacteria were stimulated more than fungi in the zone around developing pods. In contrast, R/S ratios, were higher for total fungi than for total bacteria at two of three sample times. The preferential association of fungi and bacteria with early developmental stages of the pod indicates that some microorganisms are particularly well adapted for colonization of the peanut geocarposphere. These microorganisms are logical candidates for evaluation as biological control candiates forA. flavus.     

菘蓝APX基因克隆及序列分析

为进一步研究菘蓝APX基因的功能,构建了菘蓝APX基因真核表达载体。从菘蓝植株中提取总RNA,逆转录为cDNA,根据APX基因在该类植物中的同源性设计简并引物,利用PCR方法钓取目的基因,将目的基因与T载体连接,PCR检测阳性克隆,同时菌液送往测序公司进行测序。结果表明:测序片段的生物信息学分析证实了该序列与GenBank登录的APX基因一致。说明成功构建了菘蓝APX重组质粒和克隆鉴定了菘蓝APX基因,可进一步用于基因表达和表达产物的功能研究。     

人白介素2受体γ链胞外区在巴斯德毕赤酵母中的表达

目的:在毕赤酵母GS115中表达重组人白细胞介素2受体γ链(rhsIL-2Rγ)胞外区。方法:用RT-PCR法从正常人淋巴细胞中获得IL-2Rγ胞外区基因;构建重组质粒pPIC9K-hsIL-2Rγ,用聚乙二醇法转入感受态GS115菌株,MD平板筛选His+转化子,用BMMY培养基诱导表达rhsIL-2Rγ;对重组蛋白进行免疫酶染色、SDS-PAGE及Western印迹鉴定。结果:克隆到目的片段,构建了重组质粒pPIC9K-hsIL-2Rγ;免疫酶染色、Western印迹等结果显示,重组质粒已成功转化GS115,并获得诱导表达的rhsIL-2Rγ。结论:在毕赤酵母GS115中表达了rhsIL-2Rγ,其蛋白条带有上移现象,分子较大,可能其糖基化过度或存在二聚体。     

The loss of statistical power to distinguish populations when certain samples are ambiguous

Case-control studies are used to map loci associated with a genetic disease. The usual case-control study tests for significant differences in frequencies of alleles at marker loci. In this paper, we consider the problem of comparing two or more marker loci simultaneously and testing for significant differences in haplotype rather than allele frequencies. We consider two situations. In the first, genotypes at marker loci are resolved into haplotypes by making use of biochemical methods or by genotyping family members. In the second, genotypes at marker loci are not resolved into haplotypes, but, by assuming random mating, haplotypes can be inferred using a likelihood method such as the expectation-maximization (EM) algorithm. We assume that a causative locus has two alleles with a multiplicative effect on the penetrance of a disease, with one allele increasing the penetrance by a factor pi. We find, for small values of pi-1 and large sample sizes, asymptotic results that predict the statistical power of a test for significant differences in haplotype frequencies between cases and a random sample of the population, both when haplotypes can be resolved and when haplotypes have to be inferred. The increase in power when haplotypes can be resolved can be expressed as a ratio R, which is the increase in sample size needed to achieve the same power when haplotypes are resolved over when they are not resolved. In general, R depends on the pattern of linkage disequilibrium between the causative allele and the marker haplotypes but is independent of the frequency of the causative allele and, to a first approximation, is independent of pi. For the special situation of two di-allelic marker loci, we obtain a simple expression for R and its upper bound.