古生物多样性统计中的偏差及其校正

地质历史时期生物多样性统计中的偏差是普遍存在的。文中以奥陶纪海洋生物和二叠纪腕足动物分异度为例介绍和讨论古生物多样性统计中的偏差问题。认为在研究某些时段分异度时不能依靠单一的种、属或科的数量来建立分异度模式,而需要用生物分异度、灭绝率和新生率等多种计算方法来综合分析。同时古生物分异度的研究受到化石记录的完整性、研究、保存和采集程度、时间段的不均一性等多种因素影响,因此,大多需要应用稀疏标准化法等对不同时段或化石群在同等量化标准的基础上进行比较和校正后,才能得到比较符合实际的分异度模式。     

Milk metabolites can characterise individual differences in animal resilience to a nutritional challenge in lactating dairy goats

The aim of this study is built in two phases: to quantify the ability of novel milk metabolites to measure between-animal variability in response and recovery profiles to a short-term nutritional challenge, then to derive a resilience index from the relationship between these individual variations. At two different stages of lactation, sixteen lactating dairy goats were exposed to a 2-d underfeeding challenge. The first challenge was in late lactation, and the second was carried out on the same goats early in the following lactation. During the entire experiment period, samples were taken at each milking for milk metabolite measures. For each metabolite, the response profile of each goat was characterised using a piecewise model for describing the dynamic pattern of response and recovery profiles after the challenge relative to the start of the nutritional challenge. Cluster Analysis identified three types of response/recovery profiles per metabolite. Using cluster membership, multiple correspondence analyses (MCAs) were performed to further characterise response profile types across animals and metabolites. This MCA analysis identified three groups of animals. Further, discriminant path analysis was able to separate these groups of multivariate response/recovery profile type based on threshold levels of three milk metabolites: β-hydroxybutyrate, free glucose and uric acid. Further analyses were done to explore the possibility of developing an index of resilience from milk metabolite measures. Different types of performance response to short-term nutritional challenge can be distinguished using multivariate analyses of a panel of milk metabolites.     

Metabolic changes in Atlantic salmon exposed to Aeromonas salmonicida detected by 1H-nuclear magnetic resonance spectroscopy of plasma

1H-NMR (nuclear magnetic resonance)-based chemometric methods have been applied for the first time to investigate changes in the plasma metabolite profiles of Atlantic salmon Salmo salar as a result of exposure to Aeromonas salmonicida subsp. salmonicida, a Gram-negative bacterium that is the etiological agent of furunculosis. Plasma samples were obtained from salmon that survived 21 d post exposure to A. salmonicida, and from a control group maintained under similar conditions. 1D 1H-NMR spectra were acquired and principal components analysis (PCA) was used to assess differences between the spectral profiles of plasma from salmon that survived an A. salmonicida challenge, and non-infected controls. PCA enables simultaneous comparison of spectra, presenting a simplified overview of the relationship between spectral data, where spectra cluster based on metabolite profile similarities and differences; information regarding the metabolite variations can therefore be readily deciphered. The major metabolite changes responsible for the spectral differences were related to modification in the lipoprotein profile and choline-based residues, with minor changes in carbohydrates, glycerol, trimethylamine-N-oxide and betaine. These changes indicated that exposure to A. salmonicida induced a characteristic biochemical response which could be used to determine the health status of salmon. This study suggests that with further development this metabolite profiling technique may be a useful tool for diagnosis of disease states in salmon and could provide a better understanding of the host-pathogen relationship which at present is poorly understood for A. salmonicida and Atlantic salmon.     

The phytopathogenic fungi Leptosphaeria maculans and Leptosphaeria biglobosa: chemotaxonomical characterization of isolates and metabolite production in different culture media

Previous molecular chemotaxonomic analyses of isolates of the plant pathogenic fungus Leptosphaeria maculans (Desm.) Ces. et de Not. (asexual stage Phoma lingam (Tode ex Fr.) Desm.) in a chemically defined medium suggested that this species complex was composed of at least three distinct groups. Subsequently, a group within L. maculans was classified as Leptosphaeria biglobosa, on the basis of morphologic characteristics and the lack of sexual crossing. To obtain clarification regarding the metabolite profiles of the various groups or species of blackleg fungi, the objectives of this work were (i) to determine the chemical structures of metabolites produced by Canadian V isolates and Polish-type isolates in potato dextrose broth (PDB) and (ii) to determine the chemotaxonomic relationship among French isolates of L. biglobosa and among Canadian W isolates and Thlaspi isolates of L. maculans. Here, we report for the first time that Canadian V isolates grown in PDB produced 2,4-dihydroxy-3,6-dimethylbenzaldehyde, a metabolite never reported from L. maculans, but none of the usual phytotoxins (sirodesmins). In addition, we report a new metabolite, 2-[2-(5-hydroxybenzofuranyl)]-3-(4-hydroxyphenyl)propanenitrile, from Polish-type isolates of L. maculans grown in PDB and the metabolite profiles of 16 Thlaspi isolates. The metabolite profiles of Thlaspi isolates indicate that these are part of two distinct groups, the Polish W group and the Canadian W group, i.e., L. biglobosa. Finally, we demonstrate that the metabolite profiles of the French isolates classified as L. biglobosa are similar to those of Canadian W isolates.     

Use of the ITS primers, ITS1F and ITS4, to characterize fungal abundance and diversity in mixed-template samples by qPCR and length heterogeneity analysis

Molecular-based approaches to assess microbial biomass and diversity from soil and other ecosystems are rapidly becoming the standard methodology for analysis. While these techniques are advantageous, because they do not rely on the need to culture organisms, each technique may have its own biases and/or limitations when used to assess fungal diversity from mixed-template samples. In this study, we analyzed PCR specificity and efficiency of the ITS primers (ITS1F and ITS4) in a series of single- and mixed-template samples using a combined quantitative PCR-length heterogeneity analysis (LH-qPCR) approach. As expected, these primers successfully amplified all higher fungal species tested (10 ascomycetes, 6 basidiomycetes, and 4 zygomycetes) and no members of the oomycetes. Based on our results, and a search of the GenBank database, amplicons of the ITS1F and ITS4 primer set exhibit considerable variability (420 to 825 bp), but due to similarities in amplicon sizes of some fungal species, actual species diversity in environmental samples may be underestimated approximately two-fold. The addition of an initial qPCR step allowed for the accurate quantitation of total fungal DNA in mixed-template samples over five orders of magnitude (10(-)(1) to 10(3) pg microl(-)(1)). PCR biases between individuals in mixed-templates rendered it impossible to determine the absolute quantity of any individual within a population from its individual peak height. However, relative changes in individuals within a mixed-template sample could be determined due to a constant proportionality between peak heights and starting template concentration. Variability associated with the individual steps of the LH-qPCR analysis was also determined from environmental samples.     

Statistical model of variable allometric growth: otolith growth in Micropogonias furnieri(Actinopterygii, Sciaenidae)

The main objective of this study was to develop a statistical model for accurate estimates of relative growth. The method was based on identifying patterns of the residuals obtained from the Huxley's allometric equation. Three different approaches were applied: (1) growth with variable proportionality and constant allometry coefficient, (2) growth with constant proportionality and variable allometry coefficient and (3) distinct growth phases in which proportionality and allometry coefficients remained constant. The proposed statistical models were applied to the relationship of the otolith size and fish size of whitemouth croaker Micropogonias furnieri . The best fit was obtained when using approach (3). A change in the growth parameters was associated with the attainment of sexual maturity.     

怀槐细胞悬浮培养的结构化动力学模型

为探明怀槐细胞生长、异黄酮染料木素合成与底物消耗间的关系,建立了怀槐细胞悬浮培养的结构化动力学模型。模型预测分析了胞内外的蔗糖代谢、胞内结构组分变化、胞内中间组分的变化、细胞呼吸损失以及胞内外异黄酮染料木素的合成情况。模型各参数灵敏度的分析表明kb1、kb2和kp是最为灵敏的参数,其调节10%时,目标函数变化的最大比例分别达12.8%、4.61%和2.54%,其它参数对目标函数变化的影响均小于0.5%。该模型预测值与实验值具有较好的吻合性。     

Reliable profile detection in comparative metabolomics

A strategy for processing of metabolomic GC/MS data is presented. By considering the relationship between quantity and quality of detected profiles, representative data suitable for multiple sample comparisons and metabolite identification was generated. Design of experiments (DOE) and multivariate analysis was used to relate the changes in settings of the hierarchical multivariate curve resolution (H-MCR) method to quantitative and qualitative characteristics of the output data. These characteristics included number of resolved profiles, chromatographic quality in terms of reproducibility between analytical replicates, and spectral quality defined by purity and number of spectra containing structural information. The strategy was exemplified in two datasets: one containing 119 common metabolites, 18 of which were varied according to a DOE protocol; and one consisting of rat urine samples from control rats and rats exposed to a liver toxin. It was shown that the performance of the data processing could be optimized to produce metabolite data of high quality that allowed reliable sample comparisons and metabolite identification. This is a general approach applicable to any type of data processing where the important processing parameters are known and relevant output data characteristics can be defined. The results imply that this type of data quality optimization should be carried out as an integral step of data processing to ensure high quality data for further modeling and biological evaluation. Within metabolomics, this degree of optimization will be of high importance to generate models and extract biomarkers or biomarker patterns of biological or clinical relevance.     

Tissue preservation biases in stable isotopes of fishes and molluscs from Patagonian lakes

Field work commonly involves preserving samples for later use; however, most preservation methods distort stable‐isotope (SI) signatures that are of interest to ecologists. Although preservation of muscle samples with table salt and rubbing alcohol affected the SI (δ¹³C and δ¹⁵N) of important consumers in Patagonian lakes (molluscs and fishes), variation among individuals and lakes generally exceeded that among preservation treatments. Mathematical corrections for these preservation biases are provided, and a potentially bias‐free preservation by air‐drying is suggested.     

Myonemal contraction of Spirostomum. III. The thermal dependence of contraction, relaxation and excitation-contraction coupling.

A microphotometric technique that displays rapid length changes of Spirostomum has been used to follow the variation with temperature of these kinetic parameters of myonemal contraction: contraction rate, relaxation rate and stimulus duration at threshold. In each case the exponential form of the relationship indicated that the gross rate constant might be equated with the limiting rate constant, k, of a driving chemical reaction, and from standard expressions of chemical kinetics the change in activation free energy appropriate to this reaction has been computed.     

Tobacco use vs. helminths in Congo basin hunter-gatherers: self-medication in humans?

We tested a novel hypothesis that recreational use of neurotoxic plants helps defend against parasites. Specifically, we investigated the relationship between smoking and helminthiasis among the Aka, a remote population of Central African foragers who are avid tobacco smokers, suffer high rates of helminthiasis, and have little-to-no access to commercial anthelmintics. Two hundred and six healthy Aka men provided saliva and stool samples. Saliva samples were assayed for cotinine, a nicotine metabolite; a subsample was genotyped for the CYP2A6 enzyme, which metabolizes nicotine. Stool samples were assayed for intestinal helminth eggs as an index of worm burden. After 1 year, a subsample of participants was located and provided additional saliva and stool samples. We found (1) an exceptionally high prevalence of tobacco use, (2) a significant negative correlation between cotinine (a nicotine metabolite) and worm burden, (3) that treating helminths with albendazole, a commercial anthelmintic, reduced cotinine concentration two weeks later, compared to placebo controls, (4) among treated participants, higher cotinine concentrations in year 1 predicted less reinfection by year 2, and (5) younger and older participants with slow nicotine-metabolizing CYP2A6 alleles had lower worm burdens compared to those with extensive metabolizing alleles. These results provide the first evidence of a link between helminthiasis and smoking. They also suggest that, in populations where intestinal helminths are endemic, tobacco use might protect against helminth infection and reduce worm burden among infected individuals, and that individuals modulate nicotine exposure in response to infection. The results thus support the hypothesis that substance use helps defend against parasites.     

Mathematical model of L5178Y mouse lymphoma forward mutation assay

A mathematical model of the biological protocol for the Mouse Lymphoma L5178Y Forward Mutation Bioassay is presented. The model relates the mutant progenitor frequency (MPF), the number of cells per million surviving cells with DNA damage after exposure to the chemical, to the mutant frequency (MF), the number of TFT-resistant cells per million survivors. For a given expression time, the deterministic relationship is linear and the proportionality constant depends on the relative suspension growth factor (rg) and relative cloning efficiencies (rc) of mutants to those of wild type cells: MF = (rg X rc) X MPF. Experimental noise leads to variations in the values of rg and rc and lack of reproducibility in the system. If mutant progenitors and their progeny grow as well as wild-type cells and if all of the parental mutant progenitors express the mutant phenotype, then rg = 1/2 and rc = 1. Biological mechanisms, such as differential growth characteristics of mutant and wild-type cells or DNA repair, can make the mutant frequency an inaccurate estimate of the MPF. For the assay to be useful as a screen for the mutagenic activity of chemicals, rg X rc has to be reasonably constant from chemical to chemical.     

Predictive metabolite profiling applying hierarchical multivariate curve resolution to GC-MS data--a potential tool for multi-parametric diagnosis

A method for predictive metabolite profiling based on resolution of GC-MS data followed by multivariate data analysis is presented and applied to three different biofluid data sets (rat urine, aspen leaf extracts, and human blood plasma). Hierarchical multivariate curve resolution (H-MCR) was used to simultaneously resolve the GC-MS data into pure profiles, describing the relative metabolite concentrations between samples, for multivariate analysis. Here, we present an extension of the H-MCR method allowing treatment of independent samples according to processing parameters estimated from a set of training samples. Predictions or inclusion of the new samples, based on their metabolite profiles, into an existing model could then be carried out, which is a requirement for a working application within, e.g., clinical diagnosis. Apart from allowing treatment and prediction of independent samples the proposed method also reduces the time for the curve resolution process since only a subset of representative samples have to be processed while the remaining samples can be treated according to the obtained processing parameters. The time required for resolving the 30 training samples in the rat urine example was approximately 13 h, while the treatment of the 30 test samples according to the training parameters required only approximately 30 s per sample (approximately 15 min in total). In addition, the presented results show that the suggested approach works for describing metabolic changes in different biofluids, indicating that this is a general approach for high-throughput predictive metabolite profiling, which could have important applications in areas such as plant functional genomics, drug toxicity, treatment efficacy and early disease diagnosis.     

Species variation in the fecal metabolome gives insight into differential gastrointestinal function

The metabolic composition of fecal extracts provides a window for elucidating the complex metabolic interplay between mammals and their intestinal ecosystems, and these metabolite profiles can yield information on a range of gut diseases. Here, the metabolites present in aqueous fecal extracts of humans, mice and rats were characterized using high-resolution (1)H NMR spectroscopy coupled with multivariate pattern recognition techniques. Additionally, the effects of sample storage and preparation methods were evaluated in order to assess the stability of fecal metabolite profiles, and to optimize information recovery from fecal samples. Finally, variations in metabolite profiles were investigated in healthy mice as a function of time. Interspecies variation was found to be greater than the variation due to either time or sample preparation. Although many fecal metabolites were common to the three species, such as short chain fatty acids and branched chain amino acids, each species generated a unique profile. Relatively higher levels of uracil, hypoxanthine, phenylacetic acid, glucose, glycine, and tyrosine amino acids were present in the rat, with beta-alanine being unique to the rat, and glycerol and malonate being unique to the human. Human fecal extracts showed a greater interindividual variation than the two rodent species, reflecting the natural genetic and environmental diversity in human populations. Fecal composition in healthy mice was found to change over time, which might be explained by altered gut microbial presence or activity. The systematic characterization of fecal composition across humans, mice, and rats, together with the evaluation of inherent variation, provides a benchmark for future studies seeking to determine fecal biomarkers of disease and/or response to dietary or therapeutic interventions.     

Hyperlog-a flexible log-like transform for negative, zero, and positive valued data.

BACKGROUND: The remarkable success of cytometry over the past 30 years is largely due to its uncanny ability to display populations that vastly differ in numbers and fluorescence intensities on one scale. The log transform implemented in hardware as a log amplifier or in software normalizes signals or channels so that these populations appear as clearly discernible peaks. With the advent of multiple fluorescence cytometry, spectral crossover compensation of these signals has been necessary to properly interpret the data. Unfortunately, because compensation is a subtractive process, it can produce negative and zero valued data. The log transform is undefined for these values and, as a result, forces computer algorithms to truncate these values, creating a few problems for cytometrists. Data truncation biases displays making properly compensated data appear undercompensated; thus, enticing many operators to overcompensate their data. Also, events truncated into the first histogram channel are not normally visible with typical two-dimensional graphic displays, thus hiding a large number of events and obscuring the true proportionality of negative distributions. In addition, the log transform creates unequal binning that can dramatically distort negative population distributions. METHODS AND RESULTS: The HyperLog transform is a log-like transform that admits negative, zero, and positive values. The transform is a hybrid type of transform specifically designed for compensated data. One of its parameters allows it to smoothly transition from a logarithmic to linear type of transform that is ideal for compensated data. CONCLUSIONS: The HyperLog transform is easily implemented in computer systems and results in display systems that present compensated data in an unbiased manner.     

Classical and epigenetic approaches to metabolite diversification in filamentous fungi

Studies on fungal metabolites have produced an overwhelming expectation concerning the production of novel bioactive compounds for pharmaceutical applications. The adding of various biosynthetic precursors and the changing of nutritional components in the fermentation medium can change biosynthesis pathways, also leading to the production of novel metabolites. In addition, several growing conditions can be classically manipulated to modify fungal metabolite profiles. Recently, modern genome sequence tools have shown that not all gene clusters are regularly expressed in conventional growing conditions, thus expanding the possibilities of modulating the chemical metabolite profiles produced by filamentous fungi. This review discusses and exemplifies classical and epigenetic tools successfully applied to diversify metabolite production and to produce fungal metabolites from silent metabolic pathways.     

Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing

Deep sequencing of small RNAs (sRNA-seq) is now the gold standard for small RNA profiling and discovery. Biases in sRNA-seq have been reported, but their etiology remains unidentified. Through a comprehensive series of sRNA-seq experiments, we establish that the predominant cause of the bias is the RNA ligases. We further demonstrate that RNA ligases have strong sequence-specific biases which distort the small RNA profiles considerably. We have devised a pooled adapter strategy to overcome this bias, and validated the method through data derived from microarray and qPCR. In light of our findings, published small RNA profiles, as well as barcoding strategies using adapter-end modifications, may need to be revisited. Importantly, by providing a wide spectrum of substrate for the ligase, the pooled-adapter strategy developed here provides a means to overcome issues of bias, and generate more accurate small RNA profiles.     

Complete genome sequence of human adenovirus prototype 17

As one of the first five human adenoviruses (HAdVs) to be sequenced, type 17 was important as a reference tool for comparative genomics of recently isolated HAdV pathogens in species D. HAdV-D17 was the first species D adenovirus to be sequenced and was deposited in GenBank in 1999. These genome data were not of high quality, and a redetermination of the same stock virus provides corrected data; among the differences are a length of 35,139 bp versus 35,100 bp in the original, and 160 mismatches to the original genome were found. Annotation of the coding sequences reveals 39 as opposed to 8, a finding which is important for phylogenomic studies.     

Preparation and some properties of a derivative of wheat germ agglutinin with altered biological activity

An inactive derivative of wheat germ agglutinin, which is a strong activator of blood platelets, was prepared by selective chemical modification of the lectin with cyanogen bromide at acid pH. The derivative was then used as a probe to learn about the initial events in platelet stimulation by physiological agents. Amino acid analysis of the modified lectin confirmed specific cleavage of a methionine residue. Gel filtration studies indicated a molecular weight for the lectin derivative similar to the unmodified lectin. In gel electrophoresis in the presence of sodium dodecyl sulfate, reduced samples of the derivative showed two bands and the main component migrated slightly faster than the native lectin. The derivative retained the capacity to precipitate an antibody to the lectin although at least one of the antigenic sites was lost due to chemical modification. The derivative did not compete with the unmodified lectin for binding to platelets. Unlike the parent lectin, the derivative did not aggregate platelets even at a ten fold higher concentration. Under similar conditions, there were about 1.0 X 10(5) binding sites/platelet for the lectin derivative with an apparent dissociation constant of 1.7 microM compared to 5 X 10(5) sites/cell and a dissociation constant of 0.4 microM for the native lectin. Overnight incubation of platelets or red cells with the derivative in microtiter plates showed about 2-5% agglutinating activity for the derivative compared to the unmodified lectin. Incubation of platelets with the lectin derivative inhibited platelet aggregation by thrombin while aggregation induced by a number of other agents was not significantly affected. This inhibitory effect of the lectin derivative on thrombin-induced platelet aggregation could be readily reversed with GlcNAc. The lectin derivative may be a useful tool to explore the structure-function relationship of cell surface components.     

Phenolic constituents and genetic profile of Hypericum perforatum L. from India

The content of hypericins (hypericin and pseudohypericin), hyperforin, and flavonoids (rutin, hyperoside, quercitrin, and quercetin) and genetic profiles of eight accessions of Hypericum perforatum L., collected from different locations in India, have been determined. The secondary metabolite content was determined using a highly selective LC/MS/MS method. Pearson and Spearman's correlation coefficient were used to investigate the relationships between the secondary metabolites and a significant positive correlation was found between hypericin and pseudohypericin contents. Genetic profiling was undertaken using the random amplification of polymorphic DNA (RAPD) and single sequence repeat (SSR) methods. Among the 49 random primers used for the initial screening, only nine yielded polymorphic RAPD profiles. The SSR analysis shows that seven out of the 11 primers were polymorphic. There exists only a partial correlation between the chemical content and genetic profiling data among the accessions under study.