Impact of irrigation on malaria in Africa: paddies paradox

The high population growth rate of the African continent has led to an increased demand for food and is in danger of outstripping agricultural production. In order to meet this need, many governments have sought ways of improving food production by initiating large-scale irrigation projects, involving reclamation of arid and semi-arid areas for the cultivation of crops. Although crop irrigation promises one solution to alleviating hunger and encourages economic growth, irrigation has often been blamed for aggravating disease in local communities. Malaria is one of the major tropical diseases associated with irrigation schemes, and changes in the transmission pattern of this disease following irrigation development have been a perennial subject of debate. It has often been assumed that high numbers of malaria vector Anopheles mosquitoes (Diptera: Culicidae) resulting from irrigation schemes lead inevitably to increased malaria in local communities. However, recent studies in Africa have revealed a more complex picture. Increased numbers of vectors following irrigation can lead to increased malaria in areas of unstable transmission, where people have little or no immunity to malaria parasites, such as the African highlands and desert fringes. But for most of sub-Saharan Africa, where malaria is stable, the introduction of crop irrigation has little impact on malaria transmission. Indeed, there is growing evidence that for many sites there is less malaria in irrigated communities than surrounding areas. The explanation for this finding is still unresolved but, in some cases at least, can be attributed to displacement of the most endophilic and anthropophilic malaria vector Anopheles funestus Giles by An. arabiensis Patton with lower vectorial capacity, as the latter thrives more than the former in ricefields. Similarly, among members of the An. gambiae complex, some cytotypes of An. gambiae sensu stricto are more vectorial than others. For example, the Mopti form has high vectorial capacity and breeds perennially in irrigated sites, whereas the savanna form is often sympatric but more seasonal. Also we suggest that many communities near irrigation schemes benefit from the greater wealth created by these schemes. Consequently irrigation communities often have greater use of bednets, better access to improved healthcare and receive fewer infective bites compared with those outside such development schemes. Thus, in most cases, irrigation schemes in Africa do not appear to increase malaria risk, except in areas of unstable transmission. However, developers should take the opportunity to improve health-care facilities for local communities when planning irrigation schemes wherever they occur.     

Do small-scale exclosure/enclosure experiments predict the effects of large-scale extirpation of freshwater migratory fauna?

A variety of theoretical and empirical studies indicate that the abilities of small-scale experiments to predict responses to large-scale perturbations vary. Small-scale experiments often do not predict the directions of large-scale responses, and relatively few empirical studies have examined whether small-scale experiments predict the magnitudes of large-scale responses. Here we present an empirical example of small-scale manipulations predicting not only the directions but also the magnitudes of the effects of whole-catchment, decades-long decimation of migratory freshwater shrimp populations. In streams of Puerto Rico (USA), we used arena sizes of < 2 m² in 1- to 4-week exclosure/enclosure experiments. Effects of small-scale experiments largely matched those of large-scale shrimp loss above dams for a variety of response variables (abiotic and biotic factors including epilithic fine sediments, algae and organic matter, and invertebrate grazers, detritivores, and predators). The results of our extrapolation contrast with studies of small- versus large-scale perturbations in the temperate zone. Our findings are likely explained by: a set of response variables that are more dominated by within-patch processes than exchange processes, an experimental manipulation that encompassed the characteristic scales of response variables, our use of open arenas lacking cage artifacts, and/or our combination of two distinct experimental approaches (exclosures and enclosures). Based on our study design, we suggest that extrapolation across experimental scales can be greatly enhanced by embedding open arenas within large-scale conditions that represent all treatment levels. Electronic Supplementary Material Supplementary material is available to authorised users in the online version of this article at .     

A Life-Cycle Model of Human Social Groups Produces a U-Shaped Distribution in Group Size

One of the central puzzles in the study of sociocultural evolution is how and why transitions from small-scale human groups to large-scale, hierarchically more complex ones occurred. Here we develop a spatially explicit agent-based model as a first step towards understanding the ecological dynamics of small and large-scale human groups. By analogy with the interactions between single-celled and multicellular organisms, we build a theory of group lifecycles as an emergent property of single cell demographic and expansion behaviours. We find that once the transition from small-scale to large-scale groups occurs, a few large-scale groups continue expanding while small-scale groups gradually become scarcer, and large-scale groups become larger in size and fewer in number over time. Demographic and expansion behaviours of groups are largely influenced by the distribution and availability of resources. Our results conform to a pattern of human political change in which religions and nation states come to be represented by a few large units and many smaller ones. Future enhancements of the model should include decision-making rules and probabilities of fragmentation for large-scale societies. We suggest that the synthesis of population ecology and social evolution will generate increasingly plausible models of human group dynamics.     

The challenges of community-based conservation in developing countries—A case study from Lake Alaotra,Madagascar

Nature conservation in tropical developing countries is particularly challenging as the human population is highly dependent on natural resources. Several approaches, such as small-scale, community-based conservation projects aiming to generate benefits for the community, have been applied to alleviate poverty and at the same time promote conservation. In Madagascar such projects are considered a promising alternative as large-scale conservation often fails. However, few evaluations to date have analyzed both ecological and socioeconomic aspects. Our study focuses on the ecological and socioeconomic aspects of a small-scale, community-based conservation project, called “Park Bandro”, at Lake Alaotra, Madagascar. At first glance, the area seems to conserve its natural flora and fauna. However, closer examination shows that the park suffers from isolation, disconnectivity and illegal activities, while its management suffers from an unequal distribution of benefits and a lack of recognition at community level. We use our results to discuss where challenges arise and to draw recommendations which will be relevant beyond Lake Alaotra. We show that institutional settings can foster the detachment of local management associations from the community and facilitate elite capture. Existing conflicts of interests and a lack of transparency in administration hinders long-term success. The managerial framework needs to be revised and adapted to foster capacity building, providing a basis for negotiation with the community and the integration of different social groups.     

Fertiliser drawn forward osmosis desalination: the concept, performance and limitations for fertigation

With the world??s population growing rapidly, pressure is increasing on the limited fresh water resources. Membrane technology could play a vital role in solving the water scarcity issues through alternative sources such as saline water sources and wastewater reclamation. The current generation of membrane technologies, particularly reverse osmosis (RO), has significantly improved in performance. However, RO desalination is still energy intensive and any effort to improve energy efficiency increases total cost of the product water. Since energy, environment and climate change issues are all inter-related, desalination for large-scale irrigation requires new novel technologies that address the energy issues. Forward osmosis (FO) is an emerging membrane technology. However, FO desalination for potable water is still a challenge because, recovery and regeneration of draw solutes require additional processes and energy. This article focuses on the application of FO desalination for non-potable irrigation where maximum water is required. In this concept of fertiliser drawn FO (FDFO) desalination, fertilisers are used as draw solutions (DS). The diluted draw solution after desalination can be directly applied for fertigation without the need for recovery and regeneration of DS. FDFO desalination can make irrigation water available at comparatively lower energy than the current desalination technologies. As a low energy technology, FDFO can be easily powered by renewable energy sources and therefore suitable for inland and remote applications. This article outlines the concept of FDFO desalination and critically evaluates the scope and limitations of this technology for fertigation, including suggestions on options to overcome some of these limitations.     

Dating and functional characterization of duplicated genes in the apple (<Emphasis Type="Italic">Malus domestica</Emphasis> Borkh.) by analyzing EST data

Background  

Gene duplication is central to genome evolution. In plants, genes can be duplicated through small-scale events and large-scale duplications often involving polyploidy. The apple belongs to the subtribe Pyrinae (Rosaceae), a diverse lineage that originated via allopolyploidization. Both small-scale duplications and polyploidy may have been important mechanisms shaping the genome of this species.     

Molecular Detection, Quantification, and Diversity Evaluation of Microalgae

This study reviews the available molecular methods and new high-throughput technologies for their practical use in the molecular detection, quantification, and diversity assessment of microalgae. Molecular methods applied to other groups of organisms can be adopted for microalgal studies because they generally detect universal biomolecules, such as nucleic acids or proteins. These methods are primarily related to species detection and discrimination among various microalgae. Among current molecular methods, some molecular tools are highly valuable for small-scale detection [e.g., single-cell polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and biosensors], whereas others are more useful for large-scale, high-throughput detection [e.g., terminal restriction length polymorphism, isothermal nucleic acid sequence-based amplification, loop-mediated isothermal amplification, microarray, and next generation sequencing (NGS) techniques]. Each molecular technique has its own strengths in detecting microalgae, but they may sometimes have limitations in terms of detection of other organisms. Among current technologies, qPCR may be considered the best method for molecular quantification of microalgae. Metagenomic microalgal diversity can easily be achieved by 454 pyrosequencing rather than by the clone library method. Current NGS, third and fourth generation technologies pave the way for the high-throughput detection and quantification of microalgal diversity, and have significant potential for future use in field monitoring.     

Do different irrigation techniques affect the small-scale patterns of plant diversity and soil characteristics in mountain hay meadows?

Traditional management practices are suggested to maintain species-rich grasslands. In the Valais, an arid region of Switzerland, hay meadows are traditionally irrigated using open water channels. However, in the past decades this irrigation technique has been increasingly replaced by sprinkler irrigation, which is assumed to result in a more homogeneous water distribution than open water channels. This study examined whether the change in irrigation technique affected the small-scale distribution of plants and soil characteristics in hay meadows in the Valais. Three plots consisting of 13 subplots of increasing size (0.1 × 0.1 to 6.4 × 6.4 m) were installed in six traditionally and six sprinkler-irrigated meadows. In all subplots, plant species richness and soil characteristics [moisture, pH, total organic nitrogen, organic matter content (SOM), total and plant available phosphorus] were recorded. The type of irrigation technique did not affect the shape of the plant species–area relationship. In none of the meadows did the species area–curves reach the asymptote within the range of plot sizes examined. Mantel r statistics showed that spatial autocorrelation in the soil characteristics examined was low and their small-scale distributions were not influenced by the irrigation technique except for soil pH and SOM. Our results indicate a pronounced small-scale heterogeneity in the distribution of plant species and soil characteristics for both types of irrigation technique. This can partly be explained by the fact that sprinklers distribute the water less homogeneously than commonly assumed. As applied in the Valais, sprinkler irrigation does not reduce the spatial heterogeneity and hence biodiversity of hay meadows.     

GERMINATE. a generic database for integrating genotypic and phenotypic information for plant genetic resource collections

The extensive germplasm resource collections that are now available for major crop plants and their wild relatives will increasingly provide valuable biological and bioinformatics resources for plant physiologists and geneticists to dissect the molecular basis of key traits and to develop highly adapted plant material to sustain future breeding programs. A key to the efficient deployment of these resources is the development of information systems that will enable the collection and storage of biological information for these plant lines to be integrated with the molecular information that is now becoming available through the use of high-throughput genomics and post-genomics technologies. The GERMINATE database has been designed to hold a diverse variety of data types, ranging from molecular to phenotypic, and to allow querying between such data for any plant species. Data are stored in GERMINATE in a technology-independent manner, such that new technologies can be accommodated in the database as they emerge, without modification of the underlying schema. Users can access data in GERMINATE databases either via a lightweight Perl-CGI Web interface or by the more complex Genomic Diversity and Phenotype Connection software. GERMINATE is released under the GNU General Public License and is available at http://germinate.scri.sari.ac.uk/germinate/.     

Targeted sequence capture as a powerful tool for evolutionary analysis1

Next-generation sequencing technologies (NGS) have revolutionized biological research by significantly increasing data generation while simultaneously decreasing the time to data output. For many ecologists and evolutionary biologists, the research opportunities afforded by NGS are substantial; even for taxa lacking genomic resources, large-scale genome-level questions can now be addressed, opening up many new avenues of research. While rapid and massive sequencing afforded by NGS increases the scope and scale of many research objectives, whole genome sequencing is often unwarranted and unnecessarily complex for specific research questions. Recently developed targeted sequence enrichment, coupled with NGS, represents a beneficial strategy for enhancing data generation to answer questions in ecology and evolutionary biology. This marriage of technologies offers researchers a simple method to isolate and analyze a few to hundreds, or even thousands, of genes or genomic regions from few to many samples in a relatively efficient and effective manner. These strategies can be applied to questions at both the infra- and interspecific levels, including those involving parentage, gene flow, divergence, phylogenetics, reticulate evolution, and many more. Here we provide a brief overview of targeted sequence enrichment, and emphasize the power of this technology to increase our ability to address a wide range of questions of interest to ecologists and evolutionary biologists, particularly for those working with taxa for which few genomic resources are available.     

Ovum pick up and in vitro production in the bovine after use in several generations: a 2005 status

The first In Vitro Produced (IVP) calf was born in 1981 and the non-surgical Ovum Pick Up (OPU) technique for the bovine was adapted from the human in 1987. Since then, considerable research has been aimed at improving both technologies in the bovine. Both OPU and IVP can now be seen as mature technologies. It can be estimated that more than 200,000 IVP calves have been born world wide to date, and when the two technologies are combined they are capable of producing over 50 calves per donor cow per year, albeit with a large variation between donors. Not many new breakthroughs are expected for OPU. For IVP however, automation and miniaturization as well as a greater understanding of the embryo through the application of gene based technologies such as micro-arrays, may provide an in vitro environment that is more in vivo-like than traditional micro drop/well systems. This improved environment should result in higher embryo developmental rates as well as improved quality and welfare of subsequent offspring. The application of OPU/IVP has progressed from treating infertile high genetic multiple ovulation and embryo transfer (MOET) cows in commercial situations to enhancing breeding scheme designs. With the bovine genome being rapidly sequenced and bovine genes for traits of economic interest becoming available in the coming years, OPU/IVP will prove invaluable in rapidly multiplying rare genes or Quantitative Trait Loci (QTL) of high value. In due course, it is anticipated that Marker Assisted Selection or Gene Assisted Selection (MAS/GAS) schemes will be more widely implemented. In addition, OPU, and particularly IVP, provide the basis for more advanced technologies such as cloning and transgenics. This paper is dedicated to celebrate and recognize the significant contributions made by Theo Kruip (1939-2003) to the wide area of bovine OPU and IVP.     

High-throughput bioinformatics with the Cyrille2 pipeline system

Background  

Modern omics research involves the application of high-throughput technologies that generate vast volumes of data. These data need to be pre-processed, analyzed and integrated with existing knowledge through the use of diverse sets of software tools, models and databases. The analyses are often interdependent and chained together to form complex workflows or pipelines. Given the volume of the data used and the multitude of computational resources available, specialized pipeline software is required to make high-throughput analysis of large-scale omics datasets feasible.     

Healing small-scale fisheries by facilitating complex socio-ecological systems

The current global fisheries crises have immense implications for the health and viability of animal populations, as well as the ecosystems and habitats that support this biodiversity. These crises have provoked a wide variety of management solutions and alternatives that are closely aligned with other small-scale resource extraction conservation approaches, but have been analyzed separately from the common-pool resource management literature. We summarize findings from an analysis of progressive small-scale fisheries worldwide and find that solutions arise from a historical trial and error management process as problems become dire. We find high success in the social organization and regulation of resources among these progressive fisheries but poor evidence for improved ecosystems. Based on evidence provided by the most progressive fisheries, we suggest a change in policy towards the management of small-scale fisheries. This change includes four major avenues of problem solving that focus on facilitating socio-ecological processes rather than primarily promoting a high level of quantitative science and implementing findings, technological concepts, or tools. Adoption is often culturally and context specific and, therefore, the above often have poor success when not socially integrated. We encourage facilitating and catalyzing local-level adoption of rules that create limits to appropriation and technology, since it is increasingly recognized that such limits are key solutions to the threats. This will be achieved if policy and actions (1) encourage professionalism (formation of “societies”, setting standards, certification, self-policing, appropriate technology, etc.), (2) create forums where all opinions about solutions, the status of targeted species, and environmental requirements are represented, (3) promote social rules that consider the realities and limits of the households and local social economy, and (4) craft solutions tailored to the specific and agreed upon diagnoses. We predict that as this socio-ecological process matures, it will also increase the inclusiveness of resource management goals to include non-use factors, such as biodiversity and other ecosystem services, which are still poorly evaluated and managed in even the most progressive small-scale fisheries.     

Genomic resources for flatfish research and their applications

Flatfishes are a group of teleosts of high commercial and environmental interest, whose biology is still poorly understood. The recent rapid development of different 'omic' technologies is, however, enhancing the knowledge of the complex genetic control underlying different physiological processes of flatfishes. This review describes the different functional genomic approaches and resources currently available for flatfish research and summarizes different areas where microarray-based gene expression analysis has been applied. The increase in genome sequencing data has also allowed the construction of genetic linkage maps in different flatfish species; these maps are invaluable for investigating genome organization and identifying genetic traits of commercial interest. Despite the significant progress in this field, the genomic resources currently available for flatfish are still scarce. Further intensive research should be carried out to develop larger genomic sequence databases, high-density microarrays and, more detailed, complete linkage maps, using second-generation sequencing platforms. These tools will be crucial for further expanding the knowledge of flatfish physiology, and it is predicted that they will have important implications for wild fish population management, improved fish welfare and increased productivity in aquaculture.     

RATT: Rapid Annotation Transfer Tool

Second-generation sequencing technologies have made large-scale sequencing projects commonplace. However, making use of these datasets often requires gene function to be ascribed genome wide. Although tool development has kept pace with the changes in sequence production, for tasks such as mapping, de novo assembly or visualization, genome annotation remains a challenge. We have developed a method to rapidly provide accurate annotation for new genomes using previously annotated genomes as a reference. The method, implemented in a tool called RATT (Rapid Annotation Transfer Tool), transfers annotations from a high-quality reference to a new genome on the basis of conserved synteny. We demonstrate that a Mycobacterium tuberculosis genome or a single 2.5 Mb chromosome from a malaria parasite can be annotated in less than five minutes with only modest computational resources. RATT is available at http://ratt.sourceforge.net.     

Visual Data Mining of Biological Networks: One Size Does Not Fit All

High-throughput technologies produce massive amounts of data. However, individual methods yield data specific to the technique used and biological setup. The integration of such diverse data is necessary for the qualitative analysis of information relevant to hypotheses or discoveries. It is often useful to integrate these datasets using pathways and protein interaction networks to get a broader view of the experiment. The resulting network needs to be able to focus on either the large-scale picture or on the more detailed small-scale subsets, depending on the research question and goals. In this tutorial, we illustrate a workflow useful to integrate, analyze, and visualize data from different sources, and highlight important features of tools to support such analyses.     

The spread of inequality

The causes of socioeconomic inequality have been debated since the time of Plato. Many reasons for the development of stratification have been proposed, from the need for hierarchical control over large-scale irrigation systems to the accumulation of small differences in wealth over time via inheritance processes. However, none of these explains how unequal societies came to completely displace egalitarian cultural norms over time. Our study models demographic consequences associated with the unequal distribution of resources in stratified societies. Agent-based simulation results show that in constant environments, unequal access to resources can be demographically destabilizing, resulting in the outward migration and spread of such societies even when population size is relatively small. In variable environments, stratified societies spread more and are also better able to survive resource shortages by sequestering mortality in the lower classes. The predictions of our simulation are provided modest support by a range of existing empirical studies. In short, the fact that stratified societies today vastly outnumber egalitarian societies may not be due to the transformation of egalitarian norms and structures, but may instead reflect the more rapid migration of stratified societies and consequent conquest or displacement of egalitarian societies over time.