Small flies to tackle big questions: assaying complex bacterial virulence mechanisms using Drosophila melanogaster

A successful raid on a fortress requires ingenious strategies in addition to a large number of soldiers. When a microorganism faces a potential host many factors are important, including not only the capacity to proliferate but also the ability to hide, escape or subvert the defence arsenal of the infected organism. This ability confers microbial pathogenicity and relies on complex virulence mechanisms, which are tightly regulated during the course of the infection. The amazing versatility of some microbes that can infect a wide broad of hosts undoubtedly relies on virulence factors intent on fighting evolutionarily conserved innate immune mechanisms. This makes the use of alternative invertebrate models, which are of outstanding interest because they demand less ethical consideration and lower experimental costs, extremely relevant. These simpler organisms are used to analyse genes and mechanisms involved in resistance or tolerance to microorganisms. They can also be used to study bacterial virulence factors that allow proliferation or persistence in the host. In particular, the Drosophila fruit fly has a complex immune response (similar to the mammalian innate immune response) and is particularly appropriate for deciphering many events underlying bacterial pathogenicity from acute virulence to biofilm formation. As highlighted in this review, Drosophila has been notably extensively used to study virulence traits of the opportunistic bacteria Pseudomonas aeruginosa, such as proliferation or persistence, translocation through an epithelial barrier, subversion of the phagocytic machinery, in vivo biofilm formation and enhanced virulence provided by commensal flora or a polymicrobial community. Moreover, these small flies now appear to be a useful system for assaying chemicals with therapeutic potential.     

Climate change and the outdoor regional living plant collections: an example from mainland Portugal

Climate change threatens not only plant species occurring naturally, but also impacts on regional living plant collections, which play an important role in ex situ conservation strategies. In the last few years, several global circulation models have been used to predict different global climate change scenarios. Due to their coarse resolutions, and while more detailed regional approaches are not available, downscaling techniques have been proposed, as a very simple first approach to increase detail. We analysed seven sites on mainland Portugal with potential for species conservation (four botanic gardens and three universities), in the light of downscaled climate change scenarios, using an environmental envelope approach and a predefined bioclimatic neighbourhood for each site. Thresholds for the bioclimatic neighbourhood were based on Rivas-Martínez’s Bioclimatic Classification of the Earth. For each site, the expected geographical shift of its original bioclimatic neighbourhood (1950–2000) was mapped for 2020, 2050 and 2080. Analysing those shifts enabled us to delineate knowledge-transfer paths between sites, according to the analysed scenarios. We concluded that, according to the Intergovernmental Panel on Climate Change A2 scenario, all considered sites will be outside the predefined bioclimatic neighbourhood by 2080, while according to the B2 scenario all of them will be inside that neighbourhood, although sometimes marginally so. Therefore, the implementation of global sustainability measures as considered in the B2 scenario family can be of great importance in order to delay significantly the impacts of climate change, giving extra time for the adaptation of the outdoor regional living plant collections.     

Genetic collections: problems of formation, conservation and use

Classification of plant genepool collections are presented, the principal tasks worked on by collections are examined. Databases on genepool collections of the Institute of Cytology and Genetics of Syberian Branch of Russian Academy of Sciences (Russia) and the National Centre for Plant Genetic Resources of Ukraine are described. Principles of formation of genepool collections, their existing problems, the methods of maintenance of their viability and genetical authenticity are discussed. Necessary amount of collection accessions, differences and specificity of their reproduction and multiplication aims and tasks are proved. Gradations of the permissible changes of accessions in connection with the type and the purpose of collections are proposed. The necessity of specialized periodical edition on genepool collecting is emphasized.     

Climate and change in oceanic ecosystems: The value of time-series data

The consequences of climatic change for the structure and function of oceanic ecosystems are of considerable current interest. A predictive, mechanistic model of these consequences based on our scanty knowledge of the dynamics of the systems' components seems unlikely: a complex set of simultaneous partial differential equations depicting population interactions and transfer rates of energy and materials would be necessary. A second approach is simply to measure the phenomenology of variations in both climate and ecosystem components, for the purpose of detecting shared patterns. Two studies of the latter type have been done. Both have been successful in revealing relationships between climatic variation and large-scale, large-amplitude, low-frequency biological variability. Both sets of results can provide models for the prediction of consequences, and both can serve as baselines for the definition of 'change'.     

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.     

Climate change and Australia: Trends,projections and impacts

Abstract This review summarizes recent research in Australia on: (i) climate and geophysical trends over the last few decades; (ii) projections for climate change in the 21st century; (iii) predicted impacts from modelling studies on particular ecosystems and native species; and (iv) ecological effects that have apparently occurred as a response to recent warming. Consistent with global trends, Australia has warmed ～0.8°C over the last century with minimum temperatures warming faster than maxima. There have been significant regional trends in rainfall with the northern, eastern and southern parts of the continent receiving greater rainfall and the western region receiving less. Higher rainfall has been associated with an increase in the number of rain days and heavy rainfall events. Sea surface temperatures on the Great Barrier Reef have increased and are associated with an increase in the frequency and severity of coral bleaching and mortality. Sea level rises in Australia have been regionally variable, and considerably less than the global average. Snow cover and duration have declined significantly at some sites in the Snowy Mountains. CSIRO projections for future climatic changes indicate increases in annual average temperatures of 0.4–2.0°C by 2030 (relative to 1990) and 1.0–6.0°C by 2070. Considerable uncertainty remains as to future changes in rainfall, El Niño Southern Oscillation events and tropical cyclone activity. Overall increases in potential evaporation over much of the continent are predicted as well as continued reductions in the extent and duration of snow cover. Future changes in temperature and rainfall are predicted to have significant impacts on most vegetation types that have been modelled to date, although the interactive effect of continuing increases in atmospheric CO₂ has not been incorporated into most modelling studies. Elevated CO₂ will most likely mitigate some of the impacts of climate change by reducing water stress. Future impacts on particular ecosystems include increased forest growth, alterations in competitive regimes between C3 and C4 grasses, increasing encroachment of woody shrubs into arid and semiarid rangelands, continued incursion of mangrove communities into freshwater wetlands, increasing frequency of coral bleaching, and establishment of woody species at increasingly higher elevations in the alpine zone. Modelling of potential impacts on specific Australian taxa using bioclimatic analysis programs such as bioclim consistently predicts contraction and/or fragmentation of species' current ranges. The bioclimates of some species of plants and vertebrates are predicted to disappear entirely with as little as 0.5–1.0°C of warming. Australia lacks the long‐term datasets and tradition of phenological monitoring that have allowed the detection of climate‐change‐related trends in the Northern Hemisphere. Long‐term changes in Australian vegetation can be mostly attributed to alterations in fire regimes, clearing and grazing, but some trends, such as encroachment of rainforest into eucalypt woodlands, and establishment of trees in subalpine meadows probably have a climatic component. Shifts in species distributions toward the south (bats, birds), upward in elevation (alpine mammals) or along changing rainfall contours (birds, semiarid reptiles), have recently been documented and offer circumstantial evidence that temperature and rainfall trends are already affecting geographic ranges. Future research directions suggested include giving more emphasis to the study of climatic impacts and understanding the factors that control species distributions, incorporating the effects of elevated CO₂ into climatic modelling for vegetation and selecting suitable species as indicators of climate‐induced change.     

SWEET-DB: an attempt to create annotated data collections for carbohydrates

Complex carbohydrates are known as mediators of complex cellular events. Concerning their structural diversity, their potential of information content is several orders of magnitude higher in a short sequence than any other biological macromolecule. SWEET-DB (http://www.dkfz.de/spec2/sweetdb/) is an attempt to use modern web techniques to annotate and/or cross-reference carbohydrate-related data collections which allow glycoscientists to find important data for compounds of interest in a compact and well-structured representation. Currently, reference data taken from three data sources can be retrieved for a given carbohydrate (sub)structure. The sources are CarbBank structures and literature references (linked to NCBI PubMed service), NMR data taken from SugaBase and 3D co-ordinates generated with SWEET-II. The main purpose of SWEET-DB is to enable an easy access to all data stored for one carbohydrate structure entering a complete sequence or parts thereof. Access to SWEET-DB contents is provided with the help of separate input spreadsheets for (sub)structures, bibliographic data, general structural data like molecular weight, NMR spectra and biological data. A detailed online tutorial is available at http://www.dkfz.de/spec2/sweetdb/nar/.     

Climate variability and vulnerability to climate change: a review

The focus of the great majority of climate change impact studies is on changes in mean climate. In terms of climate model output, these changes are more robust than changes in climate variability. By concentrating on changes in climate means, the full impacts of climate change on biological and human systems are probably being seriously underestimated. Here, we briefly review the possible impacts of changes in climate variability and the frequency of extreme events on biological and food systems, with a focus on the developing world. We present new analysis that tentatively links increases in climate variability with increasing food insecurity in the future. We consider the ways in which people deal with climate variability and extremes and how they may adapt in the future. Key knowledge and data gaps are highlighted. These include the timing and interactions of different climatic stresses on plant growth and development, particularly at higher temperatures, and the impacts on crops, livestock and farming systems of changes in climate variability and extreme events on pest‐weed‐disease complexes. We highlight the need to reframe research questions in such a way that they can provide decision makers throughout the food system with actionable answers, and the need for investment in climate and environmental monitoring. Improved understanding of the full range of impacts of climate change on biological and food systems is a critical step in being able to address effectively the effects of climate variability and extreme events on human vulnerability and food security, particularly in agriculturally based developing countries facing the challenge of having to feed rapidly growing populations in the coming decades.     

From predicting mosquito habitat to malaria seasons using remotely sensed data: practice, problems and perspectives

Remote sensing techniques are becoming increasingly important for identifying mosquito habitats, investigating malaria epidemiology and assisting malaria control. Here, Simon Hay, Bob Snow and David Rogers review the development of these techniques, from aerial photographic identification of mosquito larval habitats on the local scale through to the space-based survey of malaria risk over continental areas using increasingly sophisticated airborne and satellite-sensor technology. They indicate that previous constraints to uptake are becoming less relevant and suggest how future delays in the use of remotely sensed data in malaria control might be avoided.     

Climate change, species-area curves and the extinction crisis

An article published in the journal Nature in January 2004-in which an international team of biologists predicted that climate change would, by 2050, doom 15-37% of the earth's species to extinction-attracted unprecedented, worldwide media attention. The predictions conflict with the conventional wisdom that habitat change and modification are the most important causes of current and future extinctions. The new extinction projections come from applying a well-known ecological pattern, the species-area relationship (SAR), to data on the current distributions and climatic requirements of 1103 species. Here, I examine the scientific basis to the claims made in the Nature article. I first highlight the potential and pitfalls of using the SAR to predict extinctions in general. I then consider the additional complications that arise when applying SAR methods specifically to climate change. I assess the extent to which these issues call into question predictions of extinctions from climate change relative to other human impacts, and highlight a danger that conservation resources will be directed away from attempts to slow and mitigate the continuing effects of habitat destruction and degradation, particularly in the tropics. I suggest that the most useful contributions of ecologists over the coming decades will be in partitioning likely extinctions among interacting causes and identifying the practical means to slow the rate of species loss.     

From functional genomics to functional immunomics: new challenges, old problems, big rewards

The development of DNA microarray technology a decade ago led to the establishment of functional genomics as one of the most active and successful scientific disciplines today. With the ongoing development of immunomic microarray technology—a spatially addressable, large-scale technology for measurement of specific immunological response—the new challenge of functional immunomics is emerging, which bears similarities to but is also significantly different from functional genomics. Immunonic data has been successfully used to identify biological markers involved in autoimmune diseases, allergies, viral infections such as human immunodeficiency virus (HIV), influenza, diabetes, and responses to cancer vaccines. This review intends to provide a coherent vision of this nascent scientific field, and speculate on future research directions. We discuss at some length issues such as epitope prediction, immunomic microarray technology and its applications, and computation and statistical challenges related to functional immunomics. Based on the recent discovery of regulation mechanisms in T cell responses, we envision the use of immunomic microarrays as a tool for advances in systems biology of cellular immune responses, by means of immunomic regulatory network models.     

Research challenges to improve the management and conservation of subtropical reefs to tackle climate change threats

This paper reports on a workshop conducted in Australia in 2010, entitled ‘Management, Conservation, and Scientific Challenges on Subtropical Reefs under Climate Change’. The workshop brought together 26 experts actively involved in the science and management of subtropical reefs. Its primary aim was to identify the areas of research that need to be most urgently addressed to improve the decision‐making framework for managers of subtropical reefs. The main findings of the workshop were a sustainable subtropical reefs declaration that highlights seven research priorities for subtropical reefs. These are to (i) conduct research and management activities across local government, state and bioregion borders; (ii) understand natural variability of environmental conditions; (iii) quantify socio‐economic factors and ecosystem services; (iv) benchmark cross‐realm connectivity; (v) know marine population connectivity; (vi) habitat mapping and ecological research; and (v) determine refugia. These findings are hoped to form a basis for focussing research efforts, leveraging funds and assisting managers with allocation of resources.