Metabolomics: back to basics

Metabolomics has developed into a major tool in functional genomics and plant systems biology. The various methods used for metabolomic analysis will be discussed from the analytical methods back to the preanalytical phase and the biological experiment. Particularly aspects of the preanalytical phase of the analysis is dealt with, including the risks of artefact formation with the various commonly used solvents. Metabolomics is like a snap shot, and conclusions from dynamic systems must be drawn with great care as demonstrated with a biosynthetic study of salicylate in Catharanthus roseus cell cultures.     

Getting back to basics

Advances in understanding basic developmental and physiological processes often have direct relevance to human disease. They provide insights into pathogenic mechanisms and reveal new pathways that can be exploited in diagnosis and the development of therapeutics.     

Functional diversity: back to basics and looking forward

Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.     

On the meanings of nestedness: back to the basics

The ecological concepts of nestedness and β‐diversity first appeared more than five decades ago, but there is still controversy over their precise meaning and application. Here, we focus on the concept of nestedness, the ordered loss of species along environmental or ecological gradients. Because there is no species replacement if the distribution of species among a number of sites is perfectly nested, some studies have defined nestedness as the inverse of species turnover. We argue that such a redefinition relies on a misinterpretation of the original concept of nestedness as the inverse of species replacement. Such a narrow interpretation might result in misleading conclusions about the mechanisms regulating species distribution patterns. We argue, in particular, that any quantification of nestedness must be as explicit as possible about the gradient to be analyzed.     

Climate change, connectivity and conservation decision making: back to basics

1.  The challenge of climate change forces us to re-examine the assumptions underlying conservation planning.
2.  Increasing 'connectivity' has emerged as the most favoured option for conservation in the face of climate change.
3.  We argue that the importance of connectivity is being overemphasized: quantifying the benefits of connectivity per se is plagued with uncertainty, and connectivity can be co-incidentally improved by targeting more concrete metrics: habitat area and habitat quality.
4.   Synthesis and applications . Before investing in connectivity projects, conservation practitioners should analyse the benefits expected to arise from increasing connectivity and compare them with alternative investments, to ensure as much biodiversity conservation and resilience to climate change as possible within their budget. Strategies that we expect to remain robust in the face of climate change include maintaining and increasing the area of high quality habitats, prioritizing areas that have high environmental heterogeneity and controlling other anthropogenic threatening processes.     

Herbage intake regulation and growth of rabbits raised on grasslands: back to basics and looking forward

Organic agriculture is developing worldwide, and organic rabbit production has developed within this context. It entails raising rabbits in moving cages or paddocks, which enables them to graze grasslands. As organic farmers currently lack basic technical information, the objective of this article is to characterize herbage intake, feed intake and the growth rate of rabbits raised on grasslands in different environmental and management contexts (weather conditions, grassland type and complete feed supplementation). Three experiments were performed with moving cages at an experimental station. From weaning, rabbits grazed a natural grassland, a tall fescue grassland and a sainfoin grassland in experiments 1, 2 and 3, respectively. Rabbit diets were supplemented with a complete pelleted feed limited to 69 g dry matter (DM)/rabbit per day in experiment 1 and 52 g DM/rabbit per day in experiments 2 and 3. Herbage allowance and fiber, DM and protein contents, as well as rabbit intake and live weight, were measured weekly. Mean herbage DM intake per rabbit per day differed significantly (P<0.001) between experiments. It was highest in experiment 1 (78.5 g DM/day) and was 43.9 and 51.2 g DM/day in experiments 2 and 3, respectively. Herbage allowance was the most significant determinant of herbage DM intake during grazing, followed by rabbit metabolic weight (live weight^0.75) and herbage protein and fiber contents. Across experiments, a 10 g DM increase in herbage allowance and a 100 g increase in rabbit metabolic weight corresponded to a mean increase of 6.8 and 9.6 g of herbage DM intake, respectively. When including complete feed, daily mean DM intakes differed significantly among experiments (P<0.001), ranging from 96.1 g DM/rabbit per day in experiment 2 to 163.6 g DM/rabbit per day in experiment 1. Metabolic weight of rabbits raised on grasslands increased linearly over time in all three experiments, yielding daily mean growth rates of 26.2, 19.2 and 28.5 g/day in experiments 1, 2 and 3, respectively. The highest growth rate was obtained on the sainfoin grassland despite lower concentrate supplementation. Thus, it seems possible to reduce complete feed supplementation without reducing animal performance. This possibility requires improving our knowledge about organic rabbit production systems and especially grazing and animal health management.     

Back to basics

A report on the annual Association of Biomolecular Resource Facilities (ABRF) meeting, Austin, Texas, 9-12 March 2002.     

Back to basics

Nucleic acids and the people and proteins that love them have been honored with awards this year. In so doing, the prize committees have reaffirmed the importance of basic research.     

Back to basics: using colour polymorphisms to study evolutionary processes

Here, I suggest that colour polymorphic study systems have been underutilized to answer general questions about evolutionary processes, such as morph frequency dynamics between generations and population divergence in morph frequencies. Colour polymorphisms can be used to study fundamental evolutionary processes like frequency‐dependent selection, gene flow, recombination and correlational selection for adaptive character combinations. However, many previous studies of colour polymorphism often suffer from weak connections to population genetic theory. I argue that too much focus has been directed towards noticeable visual traits (colour) at the expense of understanding the evolutionary processes shaping genetic variation and covariation associated with polymorphisms in general. There is thus no need for a specific evolutionary theory for colour polymorphisms beyond the general theory of the maintenance of polymorphisms in spatially or temporally variable environments or through positive or negative frequency‐dependent selection. I outline an integrative research programme incorporating these processes and suggest some fruitful avenues in future investigations of colour polymorphisms.     

Endocrine parameters of cystic fibrosis: Back to basics

Dramatic changes in the life expectancy of cystic fibrosis (CF) patients are occurring, creating a cohort of aging individuals experiencing long‐term complications of this chronic disease. The two most common of these complications include CF‐related diabetes and CF bone disease. The clinical implications of each have become better understood, as have potential therapies. However, data obtained from the basic science studies of both diseases have not been widely recognized. In this review, we focus on the known and hypothesized pathogenesis of these two disorders. Additionally, the molecular underpinnings of CF will be explained along with the potential interactions with endocrine disease phenotypes. J. Cell. Biochem. 108: 353–361, 2009. © 2009 Wiley‐Liss, Inc.     

Physician resource databank: numbers,distribution and activities of Canada's physicians

The physician resource databank, compiled and maintained by the Canadian Medical Association (CMA), contains functional information from 41 599 of Canada''s licensed physicians. The information was gathered from a 20-item questionnaire sent to 47 162 physicians. Of the total, 38 653 responses came from physicians who had completed their training and these were included in the analysis to produce a profile of the supply of physicians in Canada. The data from physicians younger than 35 years indicate some changes in the structure of the supply: 27% are women (compared with only about 9% of physicians older than 45 years).The implications of these statistics are not yet clear, but within the next decade the numbers in some specialties—surgery, anesthesia, obstetrics and gynecology, and radiology—may be too few to meet the demand as more than 20% of the current practitioners reach retirement age. Other findings are that [List: see text]