Strategic emphases for tropical diseases research: a TDR perspective

Setting priorities for health research is a difficult task, especially for the neglected diseases of the poor. A new approach to priority setting for tropical diseases research has been adopted by the UNDP/World Bank/WHO Special Programme for Research and Training in Tropical Diseases (known as the TDR). Priorities are defined on the basis of a comprehensive analysis of research needs and research opportunities for each of the ten major tropical diseases in the TDR portfolio. The resulting strategic emphases matrix reflects the priorities for tropical diseases research from the perspective of the TDR. Its purpose is not to impose global research priorities, but we believe the results could be useful to other organizations.     

Gene duplication as a mechanism of genomic adaptation to a changing environment

A subject of extensive study in evolutionary theory has been the issue of how neutral, redundant copies can be maintained in the genome for long periods of time. Concurrently, examples of adaptive gene duplications to various environmental conditions in different species have been described. At this point, it is too early to tell whether or not a substantial fraction of gene copies have initially achieved fixation by positive selection for increased dosage. Nevertheless, enough examples have accumulated in the literature that such a possibility should be considered. Here, I review the recent examples of adaptive gene duplications and make an attempt to draw generalizations on what types of genes may be particularly prone to be selected for under certain environmental conditions. The identification of copy-number variation in ecological field studies of species adapting to stressful or novel environmental conditions may improve our understanding of gene duplications as a mechanism of adaptation and its relevance to the long-term persistence of gene duplications.     

Aquatic hyphomycetes in a changing environment

In 1942, Ingold documented an ecologically defined group of fungi, aquatic hyphomycetes, on autumn-shed leaves decaying in streams. They were shown to be vital intermediaries between the nutritionally poor leaf substratum and leaf-eating invertebrates. Research has subsequently emphasized functional aspects such as leaf decomposition and nutritional conditioning by fungi. Structural aspects (community composition) have attracted less attention, partly because of the difficulties of identifying fungal mycelia in situ. Extraction, amplification (PCR, qPCR) and characterization of DNA and RNA, and, more recently, of proteins, allow much greater insights into the presence of fungal taxa, their metabolic status (dead, dormant or active), and their potential and actual participation in decomposition processes. This approach can yield huge amounts of data, and major challenges today are the development and application of suitable bioinformatics techniques. The complexity of data collection and evaluation favour interdisciplinary teams of researchers. Fungi are major players in most ecosystems and are increasingly affected by human impacts. Changing land use, eutrophication/pollution and climate change are among the major factors that affect diversity and ecological functions of aquatic hyphomycetes.     

Tropical forests in a changing environment

Understanding and mitigating the impact of an ever-increasing population and global economic activity on tropical forests is one of the great challenges currently facing biologists, conservationists and policy makers. Tropical forests currently face obvious regional changes, both negative and positive, and uncertain global changes. Although deforestation rates have increased to unprecedented levels, natural secondary succession has reclaimed approximately 15% of the area deforested during the 1990s. Governments have also protected 18% of the remaining tropical moist forest; however, unsustainable hunting continues to threaten many keystone mammal and bird species. The structure and dynamics of old-growth forests appear to be rapidly changing, suggesting that there is a pantropical response to global anthropogenic forcing, although the evidence comes almost exclusively from censuses of tree plots and is controversial. Here, I address ongoing anthropogenic change in tropical forests and suggest how these forests might respond to increasing anthropogenic pressure.     

Assessing rapid evolution in a changing environment

Climate change poses a serious threat to species persistence. Effective modelling of evolutionary responses to rapid climate change is therefore essential. In this review we examine recent advances in phylogenetic comparative methods, techniques normally used to study adaptation over long periods, which allow them to be applied to the study of adaptation over shorter time scales. This increased applicability is largely due to the emergence of more flexible models of character evolution and the parallel development of molecular technologies that can be used to assess adaptive variation at loci scattered across the genome. The merging of phylogenetic and population genetic approaches to the study of adaptation has significant potential to advance our understanding of rapid responses to environmental change.     

Perceptual classification in a rapidly changing environment

Humans and monkeys can learn to classify perceptual information in a statistically optimal fashion if the functional groupings remain stable over many hundreds of trials, but little is known about categorization when the environment changes rapidly. Here, we used a combination of computational modeling and functional neuroimaging to understand how humans classify visual stimuli drawn from categories whose mean and variance jumped unpredictably. Models based on optimal learning (Bayesian model) and a cognitive strategy (working memory model) both explained unique variance in choice, reaction time, and brain activity. However, the working memory model was the best predictor of performance in volatile environments, whereas statistically optimal performance emerged in periods of relative stability. Bayesian and working memory models predicted decision-related activity in distinct regions of the prefrontal cortex and midbrain. These findings suggest that perceptual category judgments, like value-guided choices, may be guided by multiple controllers.     

Human choice behaviour in a frequently changing environment

The present experiment provided a replication in humans of an experimental procedure that has been used frequently with nonhumans to investigate choice behaviour in a changing environment. Six volunteers played a computer game, which required tracking of a moving balloon on two simultaneously available response panels for monetary reinforcers. Each of the 15 sessions randomly arranged the following concurrent variable-interval reinforcement schedules, which were in effect until six reinforcers had been obtained: 27:1, 9:1, 3:1, 1:1, 1:3, 1:9, and 1:27. Although many aspects of human performance appeared to be qualitatively similar to that of nonhumans on this procedure, such as the rapid preference shifts towards the within-session reinforcer ratios and the presence of local effects of reinforcers, values of sensitivity to reinforcement were very variable in the present study, as commonly reported in human choice studies. Future variations and refinements of the experimental methods are needed to explore how this variability may be reduced.     

Lactic acid bacteria in a changing legislative environment

The benefits of using lactic acid bacteria in the food chain, both through direct consumption and production of ingredients, are increasingly recognised by the food industry and consumers alike. The regulatory environment surrounding these products is diverse, covering foods and food ingredients, processing aids, feed additives and dietary supplements. On a global basis, there are different approaches taken by the various regulatory authorities. While in Europe, the national legislation is gradually being harmonised, predominantly through the Novel Foods Regulation, there is still a wide disparity between the stringency of regulation of microbial products fed to animals and the comparatively relaxed approach to non-novel microbial products intended for human consumption. In the United States, the onus is on self-regulation of the manufacturer, with the Generally Recognised As Safe (GRAS) and Dietary Supplement Health Education Act (DSHEA) notification schemes encouraging industry to be more open about the ingredients they market. In Japan, the Foods for Special Health Use system continues to gain recognition as more products are approved, and is a potential model for other countries in regulating functional foods. Despite the different approaches to regulating these products, safety of microorganisms such as lactic acid bacteria in the food chain is paramount in all countries. This paper discusses the regulatory requirements of microbial products, predominantly lactic acid bacteria within the global markets, focusing mainly on the developments in Europe.     

Sex and adaptation in a changing environment.

In this study we consider a mathematical model of a sexual population that lives in a changing environment. We find that a low rate of environmental change can produce a very large increase in genetic variability. This may help to explain the high levels of heritability observed in many natural populations. We also study asexuality and find that a modest rate of environmental change can be very damaging to an asexual population, while leaving a sexual population virtually unscathed. Furthermore, in a changing environment, the advantages of sexuality over asexuality can be much greater than suggested by most previous studies. Our analysis applies in the case of very large populations, where stochastic forces may be neglected.     

Evolution of migration in a periodically changing environment

The ability to migrate can evolve in response to various forces. In particular, when selection is heterogeneous in space but constant in time, local adaptation induces a fitness cost on immigrants and selects against migration. The evolutionary outcome, however, is less clear when selection also varies temporally. Here, we present a two-locus model analyzing the effects of spatial and temporal variability in selection on the evolution of migration. The first locus is under temporally varying selection (various periodic functions are considered, but a general nonparametric framework is used), and the second locus is a modifier controlling migration ability. First, we study the dynamics of local adaptation and derive the migration rate that maximizes local adaptation as a function of the speed and geometry of the fluctuations in the environment. Second, we derive an analytical expression for the evolutionarily stable migration rate. When there is no cost of migration, we show that higher migration rates are favored when selection changes fast. When migration is costly, however, the evolutionarily stable migration rate is maximal for an intermediate speed of the variation of selection. This model may help in understanding the evolution of migration in a broad range of scenarios and, in particular, in host-parasite systems, where selection is thought to vary quickly in both space and time.     

Collaboration in scientific research: a critical need for freshwater ecology

1. Collaboration means actively working together to achieve things which could not be done alone. This article attempts to provide an overall, unified, guiding framework for collaboration in freshwater ecology by discussing aspects of collaboration at individual and organizational levels, and addressing international linkages.
2. The essential elements of collaboration are communication and trust, and effective project management. Barriers to effective collaboration include competition, organizational cultures and organizational instabilities.
3. The success of collaboration can be measured by tangible benefits such as increased numbers of peer-reviewed publications, the production of working models and a number of intangible benefits.
4. Interactions between individuals lie at the heart of an effective collaboration; organizational arrangements should facilitate this interaction. Some governments are encouraging collaboration to increase cost efficiency and allocate accountability. This trend should continue on an international level.
5. Collaboration is a key to future research in freshwater ecology.     

Growth of Chlorella outdoors in a changing light environment

Chlorella zofingiensis was grown in semi-continuous culture in an outdoor enclosed tubular photobioreactor. At the quasi-steady state, the response of the culture to changes in photosynthetically active radiance (PAR) was studied by following closely the dissolved O₂ concentration,biomass concentration and the carbohydrate and protein content of the biomass. Generally, O₂ production and the output of carbon and nitrogen of the biomass showed a linear correlation with incident PAR, suggesting that the cultures were light-limited. Photoinhibition was not observed in high light adapted cultures (on a sunny day), but was observed in shade adapted cultures(cloudy days) when there was a sudden four-fold increase in PAR. The output rate of biomass nitrogen observed on sunny days was, however, lower than that measured on cloudy days. On sunny days, a rapid increase in the C/N ratio of the biomass was seen. We attribute the increase in C/N ratio on sunny days to a slower response of protein synthesis to big increases in PAR, compared to carbohydrate synthesis. The possible influence of this C and N response pattern on the productivity of outdoor algal cultures is discussed. This revised version was published online in August 2006 with corrections to the Cover Date.