TagFinder for the quantitative analysis of gas chromatography--mass spectrometry (GC-MS)-based metabolite profiling experiments

MOTIVATION: Typical GC-MS-based metabolite profiling experiments may comprise hundreds of chromatogram files, which each contain up to 1000 mass spectral tags (MSTs). MSTs are the characteristic patterns of approximately 25-250 fragment ions and respective isotopomers, which are generated after gas chromatography (GC) by electron impact ionization (EI) of the separated chemical molecules. These fragment ions are subsequently detected by time-of-flight (TOF) mass spectrometry (MS). MSTs of profiling experiments are typically reported as a list of ions, which are characterized by mass, chromatographic retention index (RI) or retention time (RT), and arbitrary abundance. The first two parameters allow the identification, the later the quantification of the represented chemical compounds. Many software tools have been reported for the pre-processing, the so-called curve resolution and deconvolution, of GC-(EI-TOF)-MS files. Pre-processing tools generate numerical data matrices, which contain all aligned MSTs and samples of an experiment. This process, however, is error prone mainly due to (i) the imprecise RI or RT alignment of MSTs and (ii) the high complexity of biological samples. This complexity causes co-elution of compounds and as a consequence non-selective, in other words impure MSTs. The selection and validation of optimal fragment ions for the specific and selective quantification of simultaneously eluting compounds is, therefore, mandatory. Currently validation is performed in most laboratories under human supervision. So far no software tool supports the non-targeted and user-independent quality assessment of the data matrices prior to statistical analysis. TagFinder may fill this gap. Strategy: TagFinder facilitates the analysis of all fragment ions, which are observed in GC-(EI-TOF)-MS profiling experiments. The non-targeted approach allows the discovery of novel and unexpected compounds. In addition, mass isotopomer resolution is maintained by TagFinder processing. This feature is essential for metabolic flux analyses and highly useful, but not required for metabolite profiling. Whenever possible, TagFinder gives precedence to chemical means of standardization, for example, the use of internal reference compounds for retention time calibration or quantitative standardization. In addition, external standardization is supported for both compound identification and calibration. The workflow of TagFinder comprises, (i) the import of fragment ion data, namely mass, time and arbitrary abundance (intensity), from a chromatography file interchange format or from peak lists provided by other chromatogram pre-processing software, (ii) the annotation of sample information and grouping of samples into classes, (iii) the RI calculation, (iv) the binning of observed fragment ions of equal mass from different chromatograms into RI windows, (v) the combination of these bins, so-called mass tags, into time groups of co-eluting fragment ions, (vi) the test of time groups for intensity correlated mass tags, (vii) the data matrix generation and (viii) the extraction of selective mass tags supported by compound identification. Thus, TagFinder supports both non-targeted fingerprinting analyses and metabolite targeted profiling. AVAILABILITY: Exemplary TagFinder workspaces and test data sets are made available upon request to the contact authors. TagFinder is made freely available for academic use from http://www-en.mpimp-golm.mpg.de/03-research/researchGroups/01-dept1/Root_Metabolism/smp/TagFinder/index.html.     

Evaluation of an innate immune reaction to parasites in earthworms

Encapsulation is an essential process of the invertebrate immune system and includes the prophenoloxidase (proPO) cascade. We present an assay for evaluating this immune response, now newly adapted to earthworms. Coelomic fluid is withdrawn and coelomocytes are stained with l-Dopa. We studied assay repeatability and the correlation between number of PO-active cells and infection level of the parasitic protozoan Monocystis sp. in the earthworm Lumbricus terrestris. Our study showed high assay repeatability although the expected negative relationship between PO-active coelomocytes and parasite load was not observed; yet a suggestion toward a positive relationship was detected. This finding is contrary to previous assumptions that presume coelomocyte concentrations to be the independent variable determining parasite load.     

蛇根木细胞悬浮培养进行紫杉醇的生物转化

通过理化及光谱学方法,从蛇根木(Rautwolfia serpentina(L.)Benth.et Kurz.)悬浮细胞内分离到3个紫杉醇同系物,高分辨1H-NMR和MS结构分析表明,它们分别为10-脱乙酰紫杉醇、baccatinⅢ和10-deacetylbaccatinⅢ.本实验未检测出紫杉醇的苷化或羟基化衍生物.     

Dermal application of nitric oxide releasing acidified nitrite-containing liniments significantly reduces blood pressure in humans

Vascular ischemic diseases, hypertension, and other systemic hemodynamic and vascular disorders may be the result of impaired bioavailability of nitric oxide (NO). NO but also its active derivates like nitrite or nitroso compounds are important effector and signal molecules with vasodilating properties. Our previous findings point to a therapeutical potential of cutaneous administration of NO in the treatment of systemic hemodynamic disorders. Unfortunately, no reliable data are available on the mechanisms, kinetics and biological responses of dermal application of nitric oxide in humans in vivo. The aim of the study was to close this gap and to explore the therapeutical potential of dermal nitric oxide application. We characterized with human skin in vitro and in vivo the capacity of NO, applied in a NO-releasing acidified form of nitrite-containing liniments, to penetrate the epidermis and to influence local as well as systemic hemodynamic parameters. We found that dermal application of NO led to a very rapid and significant transepidermal translocation of NO into the underlying tissue. Depending on the size of treated skin area, this translocation manifests itself through a significant systemic increase of the NO derivates nitrite and nitroso compounds, respectively. In parallel, this translocation was accompanied by an increased systemic vasodilatation and blood flow as well as reduced blood pressure. We here give evidence that in humans dermal application of NO has a therapeutic potential for systemic hemodynamic disorders that might arise from local or systemic insufficient availability of NO or its bio-active NO derivates, respectively.     

The Genetic Basis of Phenotypic Adaptation II: The Distribution of Adaptive Substitutions in the Moving Optimum Model

We consider a population that adapts to a gradually changing environment. Our aim is to describe how ecological and genetic factors combine to determine the genetic basis of adaptation. Specifically, we consider the evolution of a polygenic trait that is under stabilizing selection with a moving optimum. The ecological dynamics are defined by the strength of selection, , and the speed of the optimum, ; the key genetic parameters are the mutation rate Θ and the variance of the effects of new mutations, ω. We develop analytical approximations within an “adaptive-walk” framework and describe how selection acts as a sieve that transforms a given distribution of new mutations into the distribution of adaptive substitutions. Our analytical results are complemented by individual-based simulations. We find that (i) the ecological dynamics have a strong effect on the distribution of adaptive substitutions and their impact depends largely on a single composite measure , which combines the ecological and genetic parameters; (ii) depending on γ, we can distinguish two distinct adaptive regimes: for large γ the adaptive process is mutation limited and dominated by genetic constraints, whereas for small γ it is environmentally limited and dominated by the external ecological dynamics; (iii) deviations from the adaptive-walk approximation occur for large mutation rates, when different mutant alleles interact via linkage or epistasis; and (iv) in contrast to predictions from previous models assuming constant selection, the distribution of adaptive substitutions is generally not exponential.AN important aim for both empirical and theoretical evolutionary biologists is to better understand the genetics of adaptation (e.g., Orr 2005a). For example, among the multitude of mutations that arise in a population, which ones are eventually fixed and contribute to evolutionary change? That is, given a distribution of new mutations, what is the distribution of adaptive substitutions (or fixed mutations)? Here, distribution means the probability distribution of the effects of mutations on either the phenotype or the fitness of their carriers. In principle, both the distribution of new mutations and the distribution of adaptive substitutions can be measured empirically, the former from mutation accumulation experiments (Eyre-Walker and Keightley 2007) and the latter from QTL (e.g., Bradshaw et al. 1998) or experimental evolution (Elena and Lenski 2003) studies. However, as only a small subset of all mutations is beneficial, such measurements are difficult. Therefore, a large role in studying the genetics of adaptation has to be played by theoretical modeling.In recent years, several different approaches have emerged for modeling the process of adaptation. Considerable work exists, in particular, in the context of Fisher''s geometric model (e.g., Fisher 1930; Kimura 1983; Orr 1998; Welch and Waxman 2005; Martin and Lenormand 2006), Gillespie''s mutational landscape model (e.g., Gillespie 1983, 1984; Orr 2002), various models of so-called “adaptive walks” on rugged fitness landscapes (e.g., Kauffman and Levin 1987; Kauffman 1993), and models of clonal interference in asexual populations (e.g., Gerrish and Lenski 1998; Park and Krug 2007). Together, these models have yielded several robust predictions. For example, both Fisher''s geometric model and the mutational landscape model predict that the distribution of adaptive substitutions should be approximately exponential (with respect to either phenotype or fitness) (Orr 1998, 2002, 2005a,b). This means that most substitutions have little effect, but that a significant fraction of the overall evolutionary change is due to a small number of substitutions with large effects. These results are in qualitative agreement with empirical data (Orr 2005a; Elena and Lenski 2003) and have shed new light on the classical debate about micro- vs. macromutationalism (Fisher 1930; Provine 2001).One way to look at adaptation is to view selection as a sieve that transforms the distribution of new mutations into the distribution of adaptive substitutions (Turner 1981; Orr and Betancourt 2001). This perspective emphasizes the role of environmental factors and directly leads to the question of how different selective regimes (sieves) affect the adaptive process. Yet, almost all studies to date have focused on the simplest possible ecological scenario: a population that, after a sudden change in the environment, is now under constant stabilizing selection.In reality, however, environmental change is often gradual rather than sudden (e.g., Hairston et al. 2005; Thompson 2005; Parmesan 2006; Perron et al. 2008). To account for this possibility, several authors (Bello and Waxman 2006; Collins et al. 2007; Kopp and Hermisson 2007; Sato and Waxman 2008; Kopp and Hermisson 2009) have recently turned to the so-called moving optimum model, which was originally devised in the field of quantitative genetics (e.g., Lynch et al. 1991; Lynch and Lande 1993; Bürger and Lynch 1995; Bürger 1999; Waxman and Peck 1999; Bürger and Gimelfarb 2002; Nunney 2003; Jones et al. 2004). In this model, the selectively favored value of a quantitative trait changes over time, such that the trait is under a mixture of stabilizing and directional selection. An important aspect of the moving optimum model is that it introduces an additional timescale (the timescale of environmental change), which is absent in the previous models.In a recent article (Kopp and Hermisson 2009) and a previous note (Kopp and Hermisson 2007), we have used the moving optimum model to investigate the time to fixation of a single mutation and the order in which mutations of different phenotypic effect go to fixation. However, the fastest mutations in the short term are not necessarily those that dominate evolution in the long term. The present article focuses on this long-term evolution, which can be characterized by the distribution of adaptive substitutions.     

Deletion of complement factor H-related genes CFHR1 and CFHR3 is associated with atypical hemolytic uremic syndrome

Atypical hemolytic uremic syndrome (aHUS) is associated with defective complement regulation. Disease-associated mutations have been described in the genes encoding the complement regulators complement factor H, membrane cofactor protein, factor B, and factor I. In this study, we show in two independent cohorts of aHUS patients that deletion of two closely related genes, complement factor H-related 1 (CFHR1) and complement factor H-related 3 (CFHR3), increases the risk of aHUS. Amplification analysis and sequencing of genomic DNA of three affected individuals revealed a chromosomal deletion of approximately 84 kb in the RCA gene cluster, resulting in loss of the genes coding for CFHR1 and CFHR3, but leaving the genomic structure of factor H intact. The CFHR1 and CFHR3 genes are flanked by long homologous repeats with long interspersed nuclear elements (retrotransposons) and we suggest that nonallelic homologous recombination between these repeats results in the loss of the two genes. Impaired protection of erythrocytes from complement activation is observed in the serum of aHUS patients deficient in CFHR1 and CFHR3, thus suggesting a regulatory role for CFHR1 and CFHR3 in complement activation. The identification of CFHR1/CFHR3 deficiency in aHUS patients may lead to the design of new diagnostic approaches, such as enhanced testing for these genes.     

Determinants of the high-methionine trait in wild and exotic germplasm may have escaped selection during early cultivation of maize

The 18 kDa high-methionine δ-class zein gene from maize has been cloned, and its regulation, structure, and map position studied. These studies have shown that (i) zein genes may also contain tryptophan and lysine codons, (ii) the 18 kDa and the related 10 kDa zein gene are coordinately regulated, but their products accumulate to different levels in a genotype-dependent manner, (iii) the duplication of δ-zein genes probably involved unequal crossing over, (iv) no copy correction in either direction has occurred from teosinte to modern corn, and (v) the duplication of of the 18 kDa zein gene probably occurred before the tetraploidization of a progenitor chromosome. The work shows that important nutritional quality determinants like the high-methionine seed proteins are abundant in several exotic and wild corn varieties and low in most of the inbreds screened. The lack of a selectable phenotype for such quality traits during initial domestication and breeding of corn would have eliminated cis and trans regulatory determinants from the germplasm used in modern corn breeding. Examples of the high-methionine δ-class zeins shown here may be generally applicable in explaining the low nutritional quality of most present-day corn grown.