Quantitative metabolomics based on gas chromatography mass spectrometry: status and perspectives

Metabolomics involves the unbiased quantitative and qualitative analysis of the complete set of metabolites present in cells, body fluids and tissues (the metabolome). By analyzing differences between metabolomes using biostatistics (multivariate data analysis; pattern recognition), metabolites relevant to a specific phenotypic characteristic can be identified. However, the reliability of the analytical data is a prerequisite for correct biological interpretation in metabolomics analysis. In this review the challenges in quantitative metabolomics analysis with regards to analytical as well as data preprocessing steps are discussed. Recommendations are given on how to optimize and validate comprehensive silylation-based methods from sample extraction and derivatization up to data preprocessing and how to perform quality control during metabolomics studies. The current state of method validation and data preprocessing methods used in published literature are discussed and a perspective on the future research necessary to obtain accurate quantitative data from comprehensive GC-MS data is provided

Environmental Factors Affecting Large-Bodied Coral Reef Fish Assemblages in the Mariana Archipelago

Large-bodied reef fishes represent an economically and ecologically important segment of the coral reef fish assemblage. Many of these individuals supply the bulk of the reproductive output for their population and have a disproportionate effect on their environment (e.g. as apex predators or bioeroding herbivores). Large-bodied reef fishes also tend to be at greatest risk of overfishing, and their loss can result in a myriad of either cascading (direct) or indirect trophic and other effects. While many studies have investigated habitat characteristics affecting populations of small-bodied reef fishes, few have explored the relationship between large-bodied species and their environment. Here, we describe the distribution of the large-bodied reef fishes in the Mariana Archipelago with an emphasis on the environmental factors associated with their distribution. Of the factors considered in this study, a negative association with human population density showed the highest relative influence on the distribution of large-bodied reef fishes; however, depth, water temperature, and distance to deep water also were important. These findings provide new information on the ecology of large-bodied reef fishes can inform discussions concerning essential fish habitat and ecosystem-based management for these species and highlight important knowledge gaps worthy of additional research

Can volatile organic metabolites be used to simultaneously assess microbial and mite contamination level in cereal grains and coffee beans?

A novel approach based on headspace solid-phase microextraction (HS-SPME) combined with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (GC×GC-ToFMS) was developed for the simultaneous screening of microbial and mite contamination level in cereals and coffee beans. The proposed approach emerges as a powerful tool for the rapid assessment of the microbial contamination level (ca. 70 min versus ca. 72 to 120 h for bacteria and fungi, respectively, using conventional plate counts), and mite contamination (ca. 70 min versus ca. 24 h). A full-factorial design was performed for optimization of the SPME experimental parameters. The methodology was applied to three types of rice (rough, brown, and white rice), oat, wheat, and green and roasted coffee beans. Simultaneously, microbiological analysis of the samples (total aerobic microorganisms, moulds, and yeasts) was performed by conventional plate counts. A set of 54 volatile markers was selected among all the compounds detected by GC×GC-ToFMS. Principal Component Analysis (PCA) was applied in order to establish a relationship between potential volatile markers and the level of microbial contamination. Methylbenzene, 3-octanone, 2-nonanone, 2-methyl-3-pentanol, 1-octen-3-ol, and 2-hexanone were associated to samples with higher microbial contamination level, especially in rough rice. Moreover, oat exhibited a high GC peak area of 2-hydroxy-6-methylbenzaldehyde, a sexual and alarm pheromone for adult mites, which in the other matrices appeared as a trace component. The number of mites detected in oat grains was correlated to the GC peak area of the pheromone. The HS-SPME/GC×GC-ToFMS methodology can be regarded as the basis for the development of a rapid and versatile method that can be applied in industry to the simultaneous assessment the level of microbiological contamination and for detection of mites in cereals grains and coffee beans

Behavioral Assumptions in Models of Fish Movement and Their Influence on Population Dynamics

This study investigates the movement and growth of cohorts in a coastal fish stock by simulating animal responses to spatial heterogeneity of biotic and abiotic conditions in a dynamic marine landscape. A coastal bay is modeled using spatial and temporal data on prey distribution, benthic habitat, depth, and salinity. Prey abundance and salinity vary daily through an annual cycle to create a spatiotemporally dynamic environment with seasonal fluctuations in the quality and distribution of habitats favoring growth. Three movement behaviors—random walk, kinesis, and gradient response via restricted‐area search—simulate fish cohort movements in relation to environmental characteristics. A bioenergetic growth model is used to describe somatic growth by comparing spatiotemporally variable prey consumption rates and metabolic requirements. This facilitates evaluation of the way in which movement behavior influences the ability of cohorts to locate and occupy favorable habitats in a heterogeneous environment. Random movement behavior proved inefficient for locating preferable habitats and resulted in the lowest cohort growth trajectory and stock biomass per recruit. Kinesis and restricted‐area search behaviors resulted in similar spatial distributions and characteristics of stock biomass when cohorts were initially distributed at random. However, the results from the restricted‐area search simulations were highly sensitive to the initial positions of cohorts. The restricted‐area search simulations also resulted in high variation in growth rates among cohorts, reflecting complex interactions between behavioral mechanisms and the structure of local heterogeneity. The results show that movement models reflecting similar density patterns can differ in their influence on cohort growth and mortality. In particular, the presence of local optima can bias the results of movement models employing directional responses to a gradient structure. These results underscore the importance of sound theoretical assumptions in movement model construction and suggest that minimalism be adopted in the absence of empirical support for behavioral assumptions concerning animal responses to environmental cues

Schooling and migration of large pelagic fishes relative to environmental cues

A kinesis model driven by high‐resolution sea surface temperature maps is used to simulate Atlantic bluefin tuna movements in the Gulf of Maine during summer months. Simulations showed that individuals concentrated in areas of thermal preference. Results are compared to empirical distribution maps of bluefin tuna schools determined from aerial overflights of the stock during the same time periods. Simulations and empirical observations showed similar bluefin tuna distributions along fronts, although interannual variations in temperature ranges occupied suggest that additional foraging factors are involved. Performance of the model is further tested by simulating the relatively large‐scale annual north–south migrations of bluefin tuna that followed a preferred thermal regime. Despite the model’s relatively simple structure, results suggest that kinesis is an effective mechanism for describing movements of large pelagic fish in the expansive ocean environment

A mail survey to estimate the fishery dynamics of southern Florida's bonefish charter fleet

Bonefish, Albula vulpes (L.), support an economically important recreational fishery in southern Florida, USA that has received little scientific study and has never been adequately assessed. A mail survey of 322 captains that comprise the southern Florida bonefish charter fleet was conducted to acquire a baseline understanding of the primary fishery statistics. The response rate was 59% and a follow‐up telephone survey of non‐respondents indicated no non‐response bias. Experience in the fishery ranged from 3 to 61 years. The annual fishing effort was 30 875 boat days. The majority of the fleet fishing effort occurred in the northern Florida Keys and is presumed to reflect bonefish abundance. The instantaneous mortality rate of released fish was 0.11 year−1. The majority of the respondents indicated that the bonefish stock had declined over the past decade