Frequently asked questions about in vivo chlorophyll fluorescence: practical issues

The aim of this educational review is to provide practical information on the hardware, methodology, and the hands on application of chlorophyll (Chl) a fluorescence technology. We present the paper in a question and answer format like frequently asked questions. Although nearly all information on the application of Chl a fluorescence can be found in the literature, it is not always easily accessible. This paper is primarily aimed at scientists who have some experience with the application of Chl a fluorescence but are still in the process of discovering what it all means and how it can be used. Topics discussed are (among other things) the kind of information that can be obtained using different fluorescence techniques, the interpretation of Chl a fluorescence signals, specific applications of these techniques, and practical advice on different subjects, such as on the length of dark adaptation before measurement of the Chl a fluorescence transient. The paper also provides the physiological background for some of the applied procedures. It also serves as a source of reference for experienced scientists.     

Aquatic ecosystem as a bioreactor: water purification and some other functions.

A fundamental concept is proposed of aquatic ecosystem as a bioreactor that carries out the function of water purification in natural water bodies and streams. The ecosystem as a bioreactor has the following characteristic attributes: (1) it is a large-scale (large-volume) bioreactor; (2) it is a diversified (in terms of the number of taxa and the scope of functional activities) bioreactor; (3) it possesses a broad range of biocatalytic (chemical-transforming and degrading) capabilities. New experimental data on xenobiotics-induced inhibition of the functioning of the molluscs Unio tu- midus, U. pictorum, M. galloprovincialis and Limnaea stagnalis emphasize the potential ecological hazard from sublethal concentrations of pollutants (including those exemplified by synthetic surfactants and detergents).     

Taking physiology to the field: using physiological approaches to answer questions about animals in their environments

Both technological and conceptual advances continue to enhance our ability to evaluate physiological mechanisms in free-living animals. Although complex and uncontrolled natural environments may challenge our ability to define causal mechanistic relationships, they provide opportunities not available in more conventional laboratory settings. Among these opportunities are the ability to observe the interplay between physiology and behavior, the potential inspiration to physiological studies from novel observations in the field, and the ability to evaluate the extent to which particular physiological systems are challenged under natural conditions. As we accumulate information about physiological function in the field, we are often forced to reconsider established paradigms: hibernating bears may contract their muscles to maintain strength and tone, testosterone levels in male stonechats maintaining territories in winter are exceptionally low, wintering emperor penguins may risk overheating, and large desert mammals may eschew brain-cooling mechanisms. Measuring and quantifying the organismal response to a changing environment provides a link between mechanistic physiology and behavior, ecology, and evolution and gives us new tools to understand population, community, and ecosystem-level processes.     

Perceptions,paradigms and ethics: A perspective on the social context of environmental issues

The rapid evolution in public perceptions and understandings of environmental issues in Canada has evolved to the point where today such issues are beginning to be seen as cultural issues. The array of environmental and other societal problems is bringing into question the taken-for-granted assumptions or the worldview of cultural paradigm common to all industrialized countries. Many social analysts are suggesting that these problems are inherent in the industrial worldview and can therefore only be resolved by moving onward to another way of making sense of the world around us, and that elements of a new paradigm appear to be emerging. The major characteristics of the industrial worldview are described, and those of an emerging alternate worldview are sketched. Part of this societal questioning is evidenced in a resurgence of interest in environmental ethics but, except for deep ecology, this debate has yet to be linked to the broader discussion of shifting cultural paradigms. The changing social context suggests that there are opportunities to use different policy instruments than regulation that would prevent the occurence of environmental damage in the first place. It also suggests that the active involvement of thoughtful and responsible citizens is essential if the current period of questioning is to lead to a society that is sound and dynamic in ecological and human terms.     

Pre-classification improves relationships between water clarity, light attenuation, and suspended particulates in turbid inland waters

Relationships between water clarity, light attenuation, and concentration of suspended particulates are important in water optics and remote sensing, but are not well described yet, especially for optically complex turbid inland waters. In this study, based on 3-year data from Chinese lakes (Lake Taihu, Lake Chaohu, and Three Gorges reservoir), we propose a new approach to describe the inter-relationships of these bio-optical variables. This approach includes a pre-classification step of the waters into three types based on a semi-analytical parameter C _s before establishing the relationships. Our results showed that the pre-classification of waters increased model accuracies both for Z _SD (Secchi depth) versus K _d (diffuse attenuation coefficient) and K _d versus TSM (total suspended matter concentration). The quasi-theoretical model described better the relationship between Z _SD and K _d than the empirical model. For the K _d versus TSM relationship, linear models proved suitable for the Type 2 and Type 3 waters, whereas the power function model gave a better fit for the Type 1 water. Testing of the proposed relations with an independent dataset showed mean absolute percentage errors (MAPE) mostly below 30%. The findings of this study clarify the relationships between Z _SD, K _d, and TSM, and improve our bio-optical understanding of complex turbid inland waters.     

Pain detection and amelioration in animals on the farm: issues and options

Pain in nonhuman animals is a difficult concept to identify and measure. This article briefly describes the consequences of pain in animals on the farm and explains the reasons for the minimal use of analgesics in farmed animals. Pain can have implications for both animal welfare and economics. The reasons for a low use of analgesics in farmed animals include the lack of recognition of animal pain owing to the apparent lack of anthropomorphically identifiable behavioral changes, concern over human food safety, and lack of research efforts to develop safe analgesics for farm use. Treatment cost relative to the benefits expected is another hindering factor. Interventions to minimize pain must begin with developing objective and practical measures for pain identification and measurement at the farm level. A suggested use of a combination of different behavioral and physiological indicators would help to identify pain in animals. To facilitate continued usage of the methodologies on the farm it also is necessary to evaluate the economic implication of the pain alleviation intervention.     

The thermal, oxygen and light regimes in isolated columns of water in a turbid impoundment

SUMMARY. Temperature, oxygen and secchi disc transparency were measured in 5-m diameter isolation columns positioned in water approximately 4 m deep. In general the difference in thermal conditions between the adjacent open water and columns was slight. Oxygen levels in bottom waters in the enriched columns were often slightly lower than in the open water but never dropped below 50% saturation. It seems unlikely that sufficient depletion occurred to markedly increase release of phosphorus from the sediment. Light penetration in the columns was more varied than in the open water but was seldom sufficient to permit the development of large stands of benthic algae.     

Quantitative analysis of eumelanin and pheomelanin in humans,mice, and other animals: a comparative review

The color of hair, skin, and eyes in animals mainly depends on the quantity, quality, and distribution of the pigment melanin, which occurs in two types: black to brown eumelanin and yellow to reddish pheomelanin. Microanalytical methods to quantify the amounts of eumelanin and pheomelanin in biological materials were developed in 1985. The methods are based on the chemical degradation of eumelanin to pyrrole-2,3,5-tricarboxylic acid and of pheomelanin to aminohydroxyphenylalanine isomers, which can be analyzed and quantitated by high performance liquid chromatography. This review summarizes and compares eumelanin and pheomelanin contents in various pigmented tissues obtained from humans, mice, and other animals. These methods have become valuable tools to study the functions of melanin, the control of melanogenesis, and the actions and interactions of pigmentation genes. The methods have also found applications in many clinical studies. High levels of pheomelanin are found only in yellow to red hairs of mammals and in red feathers of birds. It remains an intriguing question why lower vertebrates such as fishes do not synthesize pheomelanin. Detectable levels of pheomelanin are detected in human skin regardless of race, color, and skin type. However, eumelanin is always the major constituent of epidermal melanin, and the skin color appears to be determined by the quantity of melanin produced but not by the quality.     

NIH initiative to balance sex of animals in preclinical studies: generative questions to guide policy,implementation, and metrics

In May of 2014, the NIH Director together with the Director of the Office of Research on Women’s Health announced plans to take a multi-dimensional approach to address the over reliance on male cells and animals in preclinical research. The NIH is engaging the scientific community in the development of policies to improve the sex balance in research. The present, past, and future presidents of the Organization for the Study of Sex Differences, in order to encourage thoughtful discussion among scientists, pose a series of questions to generate ideas in three areas: 1. research strategies, 2. educational strategies, and 3. strategies to monitor effectiveness of policies to improve the sex balance in research. By promoting discussion within the scientific community, a consensus will evolve that will move science forward in a productive and effective manner.     

Aquatic macrophytes, macroinvertebrate associations and water levels in a lowland Tasmanian river

Aquatic macrophytes are a common habitat for macroinvertebrates and may occupy depth zones in the littoral region of lowland rivers. Studies have indicated that different species of macrophyte typically support different assemblages, abundances and numbers of species of macroinvertebrates. This has often been attributed to differences in the dissectedness of stems and leaves of the macrophytes, resulting in differences in the surface area and/or the number of microhabitats available to invertebrates. I set out to measure the abundance and taxonomic richness and to describe the macroinvertebrate assemblages associated with three species of aquatic macrophyte in a pool in the Macquarie River, Tasmania and to examine responses of these variables to changes in water levels over summer. The macrophyte species sampled wereMyriophyllum simulans/variifolium, Triglochin procera} and Eleocharis sphacelata, each one differing in the dissectedness of its stems and leaves and its location in the littoral zone. Whereas the greatest abundance of macroinvertebrates was found associated in all months (i.e. at all water levels) with the structurally complex and shallowest macrophyte species, Myriophyllum, the number of taxa associated with this species was in several cases lower than for the structurally simpler and deeper water Triglochin and Eleocharis. While water depth and total plant biomass of samples were often correlated with invertebrate abundance and richness, these relationships were different for each macrophyte species. Of the nine most common invertebrate taxa collected from all samples, the abundances of more than half showed consistent differences among macrophyte species across months, two showed differences among macrophytes, but with an interaction with month and two showed no differences among macrophytes. There were major differences in the invertebrate assemblages associated with each macrophyte species in any one month, however, there was also a large turnover of taxa associated with the species of macrophytes from one month to the next. Changes in water level and concomitant changes in environmental variables are suggested as factors influencing the invertebrate fauna in the littoral zone of the pool of the Macquarie River. It is thus important for river managers to be aware that species of macroinvertebrates are not evenly distributed across species of macrophyte and that water levels and their influence on macrophytes as invertebrate habitat may play an integral part in determining the abundance, richness and assemblage of invertebrates in rivers.     

Regulatory issues surrounding the use of companion animals in clinical investigations,trials, and studies

Laboratory animal veterinarians sometimes encounter animals with rare conditions and may subsequently become involved in the performance of related animal research outside the laboratory, in homes, in veterinary clinics, or in universities to which owners have donated their animals for study. Similarly, veterinarians may monitor animal companion vaccination studies, performed to optimize preventive health care or minimize physiological variability and research confounders associated with a preventive medicine program for dogs and cats utilized for research procedures. These nontraditional uses of dogs, cats, and other companion animals in research have spurred the establishment of regulations to ensure that the animals benefit from clinical veterinary products and techniques. Included and described are the 2002 Public Health Service Policy, the Animal Welfare Act (AWA), the Federal Food, Drug, and Cosmetic Act, and the regulations of the US Department of Agriculture in response to the AWA. The complexities of clinical research with companion animals outside standard biomedical research facilities are discussed.