Sources of Variability in Metabolite Measurements from Urinary Samples

Background

The application of metabolomics in epidemiological studies would potentially allow researchers to identify biomarkers associated with exposures and diseases. However, within-individual variability of metabolite levels caused by temporal variation of metabolites, together with technical variability introduced by laboratory procedures, may reduce the study power to detect such associations. We assessed the sources of variability of metabolites from urine samples and the implications for designing epidemiologic studies.

Methods

We measured 539 metabolites in urine samples from the Navy Colon Adenoma Study using liquid chromatography-mass spectrometry (LC-MS) and gas chromatography-mass spectroscopy (GC-MS). The study collected 2–3 samples per person from 17 male subjects (age 38–70) over 2–10 days. We estimated between-individual, within-individual, and technical variability and calculated expected study power with a specific focus on large case-control and nested case-control studies.

Results

Overall technical reliability was high (median intraclass correlation = 0.92), and for 72% of the metabolites, the majority of total variance can be attributed to between-individual variability. Age, gender and body mass index explained only a small proportion of the total metabolite variability. For a relative risk (comparing upper and lower quartiles of “usual” levels) of 1.5, we estimated that a study with 500, 1,000, and 5,000 individuals could detect 1.0%, 4.5% and 75% of the metabolite associations.

Conclusions

The use of metabolomics in urine samples from epidemiological studies would require large sample sizes to detect associations with moderate effect sizes.     

How to Turn a Genetic Circuit into a Synthetic Tunable Oscillator,or a Bistable Switch

Systems and Synthetic Biology use computational models of biological pathways in order to study in silico the behaviour of biological pathways. Mathematical models allow to verify biological hypotheses and to predict new possible dynamical behaviours. Here we use the tools of non-linear analysis to understand how to change the dynamics of the genes composing a novel synthetic network recently constructed in the yeast Saccharomyces cerevisiae for In-vivo Reverse-engineering and Modelling Assessment (IRMA). Guided by previous theoretical results that make the dynamics of a biological network depend on its topological properties, through the use of simulation and continuation techniques, we found that the network can be easily turned into a robust and tunable synthetic oscillator or a bistable switch. Our results provide guidelines to properly re-engineering in vivo the network in order to tune its dynamics.     

Sources of Variability in the Measurement of Fungal Spore Yields

Variability in the production of fungal spores and in the measurement of spore yields was investigated in four species of fungi: Colletotrichum gloeosporioides, Colletotrichum coccodes, Colletotrichum phomoides, and Acremonium strictum. When the fungi were grown on solid medium in microplates and spore yields were measured by counting the subsamples with a hemacytometer, the variability among hemacytometer squares was always the largest source of variation, accounting for 51 to 91% of the total variation. Variability among replicate cultures and results of repeat experiments were generally also significant. The effect of square-to-square variability on the precision of spore yield measurement was minimized by counting a moderate number (ca. 30) of squares per culture. Culture-to-culture variability limited the practical precision of spore production measurements to a 95% confidence interval of approximately the mean ± 25%. We provide guidelines for determining the number of replicate cultures required to attain this or other degrees of precision. Particle counter-derived spore counts and counts based on spore weights were much less variable than were hemacytometer counts, but they did not improve spore production estimates very much because of culture-to-culture variability. Results obtained by both of these methods differed from those obtained with a hemacytometer; particle counter measurements required a correction for spore pairs, while the relationship between spore weights and spore counts changed as the cultures aged.     

人工会成柞蚕杀菌肽D基因的克隆及在大肠杆菌中的表达

以质粒pWR450为载体,克隆了人工合成的柞蚕杀菌肽D基因(122bp),构建的重组子pWR450-Cec转化大肠杆菌JM103、用限制性内切酶酶切鉴定。产物经SDS-聚丙烯酰胺凝胶电泳,结果显示可表达杀菌肽-β-gal融合蛋白。     

Sources of Variation and Measures of Variability in Even-aged Stands of Plants

A critical assessment is presented of the literature on variabilityin even-aged stands of plants. The variance of weight per plantaccumulates during two physiologically distinct periods of growth,pre- and post-seedling emergence, and can be expressed as afunction of the variances and covariances of three physiologicalvariables - the rate of growth, the duration of growth, andthe size per plant at the start of the period. This providesa quantitative framework for analyzing the physiological sourcesof variability in plant stands. Variation, competition, self-thinning, growth     

Extensive tRNA Gene Changes in Synthetic Brassica napus

Allopolyploidization, where two species come together to form a new species, plays a major role in speciation and genome evolution. Transfer RNAs (abbreviated tRNA) are typically 73–94 nucleotides in length, and are indispensable in protein synthesis, transferring amino acids to the cell protein synthesis machinery (ribosome). To date, the regularity and function of tRNA gene sequence variation during the process of allopolyploidization have not been well understood. In this study, the inter-tRNA gene corresponding to tRNA amplification polymorphism method was used to detect changes in tRNA gene sequences in the progeny of interspecific hybrids between Brassica rapa and B. oleracea, mimicking the original B. napus (canola) species formation event. Cluster analysis showed that tRNA gene variation during allopolyploidization did not appear to have a genotypic basis. Significant variation occurred in the early generations of synthetic B. napus (F₁ and F₂ generations), but fewer alterations were observed in the later generation (F₃). The variation-prone tRNA genes tended to be located in AT-rich regions. BlastN analysis of novel tRNA gene variants against a Brassica genome sequence database showed that the variation of these tRNA-gene-associated sequences in allopolyploidization might result in variation of gene structure and function, e.g., metabolic process and transport.     

人工合成人溶菌酶基因在大肠杆菌中表达

利用DNA重组技术生产自然界不能或难以得到的多肽产品用于医药、农业、食品工业等领域,目前在生物领域已有了很大的进展。近年来,科学工作者经体外合成人溶菌酶基因,经克隆、转化,在真核、原核细胞中获得表达^[1-3]。溶菌酶能水解革兰氏阳性菌细胞壁上的β-1,4糖苷键,在内部渗透压的作用下,细胞胀裂开[4,5]。它对有些革兰氏阴性菌,如埃希氏大肠杆菌、伤寒沙门氏菌,也有同样作用。因此此酶在食品,特别是在医药上具有重要意义。在这篇文章中,我们报道人工合成人溶酶的克隆和在 温控启动子P_RP_L调控下在大肠杆菌中的表达。     

Genetic Variants Contribute to Gene Expression Variability in Humans

Expression quantitative trait loci (eQTL) studies have established convincing relationships between genetic variants and gene expression. Most of these studies focused on the mean of gene expression level, but not the variance of gene expression level (i.e., gene expression variability). In the present study, we systematically explore genome-wide association between genetic variants and gene expression variability in humans. We adapt the double generalized linear model (dglm) to simultaneously fit the means and the variances of gene expression among the three possible genotypes of a biallelic SNP. The genomic loci showing significant association between the variances of gene expression and the genotypes are termed expression variability QTL (evQTL). Using a data set of gene expression in lymphoblastoid cell lines (LCLs) derived from 210 HapMap individuals, we identify cis-acting evQTL involving 218 distinct genes, among which 8 genes, ADCY1, CTNNA2, DAAM2, FERMT2, IL6, PLOD2, SNX7, and TNFRSF11B, are cross-validated using an extra expression data set of the same LCLs. We also identify ∼300 trans-acting evQTL between >13,000 common SNPs and 500 randomly selected representative genes. We employ two distinct scenarios, emphasizing single-SNP and multiple-SNP effects on expression variability, to explain the formation of evQTL. We argue that detecting evQTL may represent a novel method for effectively screening for genetic interactions, especially when the multiple-SNP influence on expression variability is implied. The implication of our results for revealing genetic mechanisms of gene expression variability is discussed.     

Intra and Inter-Spore Variability in Rhizophagus irregularis AOX Gene

Arbuscular mycorrhizal fungi (AMF) are root-inhabiting fungi that form mutualistic symbioses with their host plants. AMF symbiosis improves nutrient uptake and buffers the plant against a diversity of stresses. Rhizophagus irregularis is one of the most widespread AMF species in the world, and its application in agricultural systems for yield improvement has increased over the last years. Still, from the inoculum production perspective, a lack of consistency of inoculum quality is referred to, which partially may be due to a high genetic variability of the fungus. The alternative oxidase (AOX) is an enzyme of the alternative respiratory chain already described in different taxa, including various fungi, which decreases the damage caused by oxidative stress. Nevertheless, virtually nothing is known on the involvement of AMF AOX on symbiosis establishment, as well on the existence of AOX variability that could affect AMF effectiveness and consequently plant performance. Here, we report the isolation and characterisation of the AOX gene of R. irregularis (RiAOX), and show that it is highly expressed during early phases of the symbiosis with plant roots. Phylogenetic analysis clustered RiAOX sequence with ancient fungi, and multiple sequence alignment revealed the lack of several regulatory motifs which are present in plant AOX. The analysis of RiAOX polymorphisms in single spores of three different isolates showed a reduced variability in one spore relatively to a group of spores. A high number of polymorphisms occurred in introns; nevertheless, some putative amino acid changes resulting from non-synonymous variants were found, offering a basis for selective pressure to occur within the populations. Given the AOX relatedness with stress responses, differences in gene variants amongst R. irregularis isolates are likely to be related with its origin and environmental constraints and might have a potential impact on inoculum production.     

Sources of Variability among Replicate Samples Separated by Two-Dimensional Gel Electrophoresis

Two-dimensional gel electrophoresis (2DE) offers high-resolution separation for intact proteins. However, variability in the appearance of spots can limit the ability to identify true differences between conditions. Variability can occur at a number of levels. Individual samples can differ because of biological variability. Technical variability can occur during protein extraction, processing, or storage. Another potential source of variability occurs during analysis of the gels and is not a result of any of the causes of variability named above. We performed a study designed to focus only on the variability caused by analysis. We separated three aliquots of rat left ventricle and analyzed differences in protein abundance on the replicate 2D gels. As the samples loaded on each gel were identical, differences in protein abundance are caused by variability in separation or interpretation of the gels. Protein spots were compared across gels by quantile values to determine differences. Fourteen percent of spots had a maximum difference in intensity of 0.4 quantile values or more between replicates. We then looked individually at the spots to determine the cause of differences between the measured intensities. Reasons for differences were: failure to identify a spot (59%), differences in spot boundaries (13%), difference in the peak height (6%), and a combination of these factors (21). This study demonstrates that spot identification and characterization make major contributions to variability seen with 2DE. Methods to highlight why measured protein spot abundance is different could reduce these errors.     

人工合成小麦抗白粉病未知基因的SSR标记

YAV-2/TEZ//A.SQ(895)是硬粒小麦与粗山羊草杂交获得的抗白粉病人工合成小麦。本研究利用人工合成小麦YAV-2/TEZ//A.SQ(895)与感白粉病的普通小麦品系品资50098杂交和自交获得的F2代群体及F3家系,在温室条件下鉴定群体的白粉病抗性。遗传分析结果表明,该抗白粉病基因为显性单基因遗传。利用647对小麦SSR引物进行了白粉病抗性基因的分子标记分析,结果表明该白粉病抗性基因与2A染色体的6个SSR标记连锁,与标记Xcfa2086的遗传距离最近,为11.8cM。     

Sources of Biomass Feedstock Variability and the Potential Impact on Biofuels Production

Terrestrial lignocellulosic biomass has the potential to be a carbon neutral and domestic source of fuels and chemicals. However, the innate variability of biomass resources, such as herbaceous and woody materials, and the inconsistency within a single resource due to disparate growth and harvesting conditions, presents challenges for downstream processes which often require materials that are physically and chemically consistent. Intrinsic biomass characteristics, including moisture content, carbohydrate and ash compositions, bulk density, and particle size/shape distributions are highly variable and can impact the economics of transforming biomass into value-added products. For instance, ash content increases by an order of magnitude between woody and herbaceous feedstocks (from ～0.5 to 5 %, respectively) while lignin content drops by a factor of two (from ～30 to 15 %, respectively). This increase in ash and reduction in lignin leads to biofuel conversion consequences, such as reduced pyrolysis oil yields for herbaceous products as compared to woody material. In this review, the sources of variability for key biomass characteristics are presented for multiple types of biomass. Additionally, this review investigates the major impacts of the variability in biomass composition on four conversion processes: fermentation, hydrothermal liquefaction, pyrolysis, and direct combustion. Finally, future research processes aimed at reducing the detrimental impacts of biomass variability on conversion to fuels and chemicals are proposed.© 2015 Battelle Energy Alliance, LLC, contract manager for Idaho National Laboratory.