Variance Component Estimation for Mixed Model Analysis of cDNA Microarray Data

Microarrays provide a valuable tool for the quantification of gene expression. Usually, however, there is a limited number of replicates leading to unsatisfying variance estimates in a gene‐wise mixed model analysis. As thousands of genes are available, it is desirable to combine information across genes. When more than two tissue types or treatments are to be compared it might be advisable to consider the array effect as random. Then information between arrays may be recovered, which can increase accuracy in estimation. We propose a method of variance component estimation across genes for a linear mixed model with two random effects. The method may be extended to models with more than two random effects. We assume that the variance components follow a log‐normal distribution. Assuming that the sums of squares from the gene‐wise analysis, given the true variance components, follow a scaled χ²‐distribution, we adopt an empirical Bayes approach. The variance components are estimated by the expectation of their posterior distribution. The new method is evaluated in a simulation study. Differentially expressed genes are more likely to be detected by tests based on these variance estimates than by tests based on gene‐wise variance estimates. This effect is most visible in studies with small array numbers. Analyzing a real data set on maize endosperm the method is shown to work well. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Mixed-model of ANOVA for measurement reproducibility in proteomics

This work is a statistical analysis of reproducibility of a MALDI-TOF mass spectrometry experiment. Its aim is to evaluate measurement variability and compare peak intensities from two types of MALDI-TOF platforms. We compared and commented on the abilities of Principal Component Analysis and mixed-model analysis of variance to evaluate the biological variability and the technical variability of peak intensities in different patients. The properties and hypotheses of both methods are summarized and applied to spectra from plasma of patients with Hodgkin lymphoma. Principal Component Analysis checks rapidly the balance between the two variabilities; however, a mixed-model analysis of variance is necessary to quantify the biological and technical components of the experimental variance as well as their interactions and to split the total variance into between-subjects and within-subject components. The latter method helped to assess the reproducibility of measurements from two MALDI-TOF platforms and to decompose the technical variability according to the experimental design.     

Cytokine-induced activation of mixed lineage kinase 3 requires TRAF2 and TRAF6

Mixed lineage kinase 3 (MLK3) is a mitogen-activated protein kinase kinase kinase (MAP3K) that activates multiple mitogen-activated protein kinase (MAPK) pathways in response to growth factors, stresses and the pro-inflammatory cytokine, tumor necrosis factor (TNF). MLK3 is required for optimal activation of stress activated protein kinase/c-Jun N-terminal kinase (SAPK/JNK) signaling by TNF, however, the mechanism by which MLK3 is recruited and activated by the TNF receptor remains poorly understood. Here we report that both TNF and interleukin-1β (IL-1β) stimulation rapidly activate MLK3 kinase activity. We observed that TNF stimulates an interaction between MLK3 and TNF receptor associated factor (TRAF) 2 and IL-1β stimulates an interaction between MLK3 and TRAF6. RNA interference (RNAi) of traf2 or traf6 dramatically impairs MLK3 activation by TNF indicating that TRAF2 and TRAF6 are critically required for MLK3 activation. We show that TNF also stimulates ubiquitination of MLK3 and MLK3 can be conjugated with lysine 48 (K48)- and lysine 63 (K63)-linked polyubiquitin chains. Our results suggest that K48-linked ubiquitination directs MLK3 for proteosomal degradation while K63-linked ubiquitination is important for MLK3 kinase activity. These results reveal a novel mechanism for MLK3 activation by the pro-inflammatory cytokines TNF and IL-1β.     

一株可同时降解多种高环PAHs的丝状真菌——宛氏拟青霉(Paecilomyces variotii)

采用液体培养的方法,分离纯化了丝状真菌宛氏拟青霉(Paecilomyces variotii)并研究了其对苯并[a]蒽、苯并[a]芘、苯并[b]荧蒽、苯并[k]荧蒽、茚并[1,2,3-cd]芘的降解效果.结果表明:接种处理30 d,该菌株对混合体系中5种PAHs的降解率为16.1%～24.6%,而对单一体系中的降解率为10.4%～33.3%;同时,对单一与混合体系中PAHs的降解作用存在一定差异,苯并[k]荧蒽和苯并[b]荧蒽在单一体系中降解率增大,而其他种类的则减小.本研究结果为高环多环芳烃共代谢机理研究和多环芳烃复合污染水土环境的生物修复提供了一种新的种质资源.     

Statistical analysis and optimization of nitrogen,phosphorus, and inoculum concentrations for the biodegradation of petroleum hydrocarbons by response surface methodology

In order to optimize and evaluate the influence of nitrogen, phosphorus, and inoculum concentrations on the biodegradation of hydrocarbon contaminated effluents, experiments based on central composite design (CCD) method were carried out for 3 days, employing C1 mixed culture and intermittent aeration. The independent variables were nitrogen concentration (X ₁), phosphorus concentration (X ₂), and inoculum concentration (X ₃) and the removal of total petroleum hydrocarbons (TPH) was the dependent variable. The optimized nutrients ratio (C:N:P = 100:20:2.7) and inoculum concentration (1.32 g/l) provided TPH removal of 71.8% after processing for three days. Analysis using gas chromatography identified five hydrocarbons classes: paraffins, isoparaffins, olefins, naphthenics, and aromatics. The naphthenic compounds did not degrade as readily as the other hydrocarbons that were identified. The following degradation percentages were obtained: 87.1% for the paraffins, 77.7% for the isoparaffins, 78.6% for the olefins, 38.4% for the naphthenics, and 71.7% for the aromatics.     

Selective inhibition of methanogenesis to enhance ethanol and n-butyrate production through acetate reduction in mixed culture fermentation

Acetate reduction is an alternative digestion process to convert organic waste into ethanol. Using acetate for fuel ethanol production offers the opportunity to use organic waste materials instead of sugar-containing feedstock. Methanogenesis, however, competes with acetate reduction for acetate and hydrogen and lowers the final efficiency. The aim of this research is to selectively inhibit methanogenesis and to enhance acetate reduction. Acetate reduction was stimulated in batch tests at pH between 4.5 and 8; and at pH 6 with and without thermal pre-treatment. It was found that methanogenesis was selectively inhibited while acetate reduction was enhanced after thermal pre-treatment incubated at pH 6. Initially the acetate reduction yielded 7.7 ± 3.2 mM ethanol with an efficiency of 60.2 ± 8.7%, but later on it was consumed to form 7.02 ± 0.85 mM n-butyrate with an efficiency of 76.2 ± 14.0%. It was the first time demonstrated that n-butyrate can be produced by mixed cultures from only acetate and hydrogen.     

Phase behaviour of oleanolic acid/stearyl stearate binary mixtures in bulk and at the air-water interface

The solid-liquid phase behaviour of oleanolic acid (OLA)/stearyl stearate (SS) was investigated by differential scanning calorimetry and polarizing optical microscopy. A eutectic type diagram, with the eutectic composition close to pure SS was obtained. Complementary studies by NMR, X-ray diffraction (XRD) and diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy were performed. A mutual influence was detected in mixtures: the low melting form of SS is favoured at low OLA molar fractions (X_OLA) and spherulitic structures appear at high X_OLA and high temperature. Additionally, H-bonding between OLA carbonyl groups increases in the presence of SS. The study of OLA/SS by the Langmuir method and Brewster angle microscopy revealed the organization at the air-water interface: OLA interacts with water in the first layer, while SS is completely segregated to the upper layer for X_OLA > 0.3, and it distributes in the first and upper layers for X_OLA < 0.3.     

Mixed fermentation for natural product drug discovery

Natural products continue to play a major role in drug discovery and development. However, chemical redundancy is an ongoing problem. Genomic studies indicate that certain groups of bacteria and fungi have dozens of secondary metabolite pathways that are not expressed under standard laboratory growth conditions. One approach to more fully access the metabolic potential of cultivatable microbes is mixed fermentation, where the presence of neighboring microbes may induce secondary metabolite synthesis. Research to date indicates that mixed fermentation can result in increased antibiotic activity in crude extracts, increased yields of previously described metabolites, increased yields of previously undetected metabolites, analogues of known metabolites resulting from combined pathways and, importantly, induction of previously unexpressed pathways for bioactive constituents.     

Improved ethanol tolerance of Saccharomyces cerevisiae in mixed cultures with Kluyveromyces lactis on high-sugar fermentation

The influence of non-Saccharomyces yeast, Kluyveromyces lactis, on metabolite formation and the ethanol tolerance of Saccharomyces cerevisiae in mixed cultures was examined on synthetic minimal medium containing 20% glucose. In the late stage of fermentation after the complete death of K. lactis, S. cerevisiae in mixed cultures was more ethanol-tolerant than that in pure culture. The chronological life span of S. cerevisiae was shorter in pure culture than mixed cultures. The yeast cells of the late stationary phase both in pure and mixed cultures had a low buoyant density with no significant difference in the non-quiescence state between both cultures. In mixed cultures, the glycerol contents increased and the alanine contents decreased when compared with the pure culture of S. cerevisiae. The distinctive intracellular amino acid pool concerning its amino acid concentrations and its amino acid composition was observed in yeast cells with different ethanol tolerance in the death phase. Co-cultivation of K. lactis seems to prompt S. cerevisiae to be ethanol tolerant by forming opportune metabolites such as glycerol and alanine and/or changing the intracellular amino acid pool.     

厌氧菌和需氧菌性阴道混合感染发病调查

目的对妇女厌氧菌和需氧菌性阴道混合感染发病进行调查分析。方法分别采用Donders高倍镜湿片镜检法和细菌预成酶快速检测法对257例患者进行联合检测。结果257例患者中共检出单纯的需氧菌性阴道感染患者52例,占总人数的20．2％,检出单纯的厌氧菌阴道感染患者125例,占总人数的48．6％,检出厌氧菌和需氧菌性阴道混合感染患者67例,占总人数的26．1％,检出其他感染患者13例,占总人数的5％,经统计学分析,患者的厌氧菌和需氧菌性阴道混合感染的检出率差异无统计学意义（P〉0．05）。结论厌氧菌和需氧菌性阴道混合感染,可以给临床医生应采取合理有效的措施进行及时治疗,防止阴道上行感染的发生。