Defining freshwater as a natural resource: a framework linking water use to the area of protection natural resources

The International Journal of Life Cycle Assessment - While many examples have shown unsustainable use of freshwater resources, existing LCIA methods for water use do not comprehensively address...     

Internet: a major resource for toxicologists

Use of the Internet in developing countries is now growing faster. Internet has created a new conduit not only for communication but also in the access, sharing and exchange of information among scientists. The Internet is now viewed as the world's biggest library where retrieval of scientific literature and other information resources are possible within seconds. Large volumes of toxicological information resources are available on the Internet. This review outlines some sites that may be of great importance and useful to the toxicologist.     

PIR: a new resource for bioinformatics

SUMMARY: The Protein Information Resource (PIR) has greatly expanded its Web site and developed a set of interactive search and analysis tools to facilitate the analysis, annotation, and functional identification of proteins. New search engines have been implemented to combine sequence similarity search results with database annotation information. The new PIR search systems have proved very useful in providing enriched functional annotation of protein sequences, determining protein superfamily-domain relationships, and detecting annotation errors in genomic database archives. AVAILABILITY: http://pir.georgetown.edu/. CONTACT: mcgarvey@nbrf.georgetown.edu     

Having your water and drinking it too: resource limitation modifies density regulation

Determining the interaction between extrinsic and intrinsic drivers of variation in population abundance through time continues to challenge ecologists. Chamaillé-Jammes and colleagues (this issue) examined African elephant time series to explore how water availability alters the density feedback mechanisms restricting population growth. The relationship between population growth rate and density shifted from an upward convex to a more linear form after controlling for rainfall. Spatial variation in water availability also attenuated density dependence as elephants adjusted their distribution relative to current environmental conditions. This work has important climate change implications for the conservation management of African herbivores.     

Experimental separation of resource quantity from temporal variability: seedling responses to water pulses

We tested the hypothesis that higher temporal variability in water supply will promote higher species richness of germinating and surviving seedlings using assemblages of 70 species of herbaceous plants from limestone pavement habitats. In a two-factor greenhouse experiment, doubling the total volume of water added led to greater germination (measured as number of germinated seeds and species) and establishment (survival and biomass) but the effects of temporal variability depended on the response variable considered. Low pulse frequencies of water addition with total volume added held constant resulted in greater temporal variability in soil moisture concentration that in turn promoted higher density and richness of germinated seedlings. Low pulse frequencies caused an eight-fold greater mortality in the low total volume treatment and biomass production to decline by one-third in the high total volume treatment. The effects of increasing temporal variability in water supply during recruitment stages can thus be opposite on different components of plant fitness and may also depend on total resource quantity. While greater species richness in more temporally variable soil moisture conditions was attributable to sampling effects rather than species-specific responses to the water treatments, species relative abundances did vary significantly with temporal variability. Changes in the amplitude or frequency of resource fluctuations may alter recruitment patterns, and could have severe and relatively rapid effects on community structure in unproductive ecosystems.Electronic Supplementary Material The French version of this article is available in the form of electronic supplementary material at.     

SimFection: a digital resource for vaccination education

Vaccination coverage in the United Kingdom is below the level recommended by the World Health Organisation, and when vaccination coverage is not sufficient, outbreaks of infectious diseases can occur. In 2015, coverage of the first dose of the Measles-Mumps-Rubella vaccine declined in the United Kingdom for the first time since 2008, indicating a need to raise public awareness and understanding of the importance of vaccination to public health. Identifying 16 – 18-year olds as a target audience, being future parents who would make decisions regarding vaccination of their children, a digital educational resource (‘SimFection’) was developed to deliver key messages about the spread and control of vaccine-preventable infectious diseases (identified via school curricula). The process of development utilised an iterative approach, involving a cyclic process of prototyping, testing, analysis and refinement with a range of audiences including students, schoolchildren, and trainee teachers. The completed resource is now available online for free download.     

UniCarb-DB: a database resource for glycomic discovery

Glycosylation is one of the most important post-translational modifications of proteins, known to be involved in pathogen recognition, innate immune response and protection of epithelial membranes. However, when compared to the tools and databases available for the processing of high-throughput proteomic data, the glycomic domain is severely lacking. While tools to assist the analysis of mass spectrometry (MS) and HPLC are continuously improving, there are few resources available to support liquid chromatography (LC)-MS/MS techniques for glycan structure profiling. Here, we present a platform for presenting oligosaccharide structures and fragment data characterized by LC-MS/MS strategies. The database is annotated with high-quality datasets and is designed to extend and reinforce those standards and ontologies developed by existing glycomics databases. AVAILABILITY: http://www.unicarb-db.org     

Gramene: a resource for comparative grass genomics

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on Oracle. Gramene provides curated and integrative information about maps, sequence, genes, genetic markers, mutants, QTLs, controlled vocabularies and publications. Its aims are to use the rice genetic, physical and sequence maps as fundamental organizing units, to provide a common denominator for moving from one crop grass to another and is to serve as a portal for interconnecting with other web-based crop grass resources. This paper describes the initial steps we have taken towards realizing these goals.     

Avianbase: a community resource for bird genomics

Giving access to sequence and annotation data for genome assemblies is important because, while facilitating research, it places both assembly and annotation quality under scrutiny, resulting in improvements to both. Therefore we announce Avianbase, a resource for bird genomics, which provides access to data released by the Avian Phylogenomics Consortium.Access to complete genome sequences provides the first step towards the understanding of the biology of organisms. It is the template that underpins the phenotypic characteristics of individuals and ultimately separates species due to the accumulation and fixation of mutations over evolutionary timescales. In terms of the available genomic datasets for species, birds, as our more distant relatives, have been historically underrepresented. The high cost of sequencing and annotation in the past led to a bias towards accumulating data for species that are either established model organisms or economically significant (that is, chicken, turkey and duck, representing two sister orders within the Galloanseriformes clade from the large and diverse phylogeny of birds). The recent release of genome assemblies and initial predictions of protein-coding genes [1-4] for 44 bird species, including representatives from all major branches of the bird phylogeny, is, therefore, highly significant.One of the major challenges with the release of this number of newly sequenced genomes and the many more to come [5] is how to make these available to the various research communities in a way that supports basic research. Providing access to the sequences and initial annotations in the format of text files will limit the potential usage of the data as they require significant resources, including bioinformatics personnel and computer infrastructure in place to access and mine - for example, searching for genes belonging to certain protein families or searching for orthologous genes. These overheads pose a serious bottleneck that can hinder research and requires concerted action by the relevant research communities.Once genomes are submitted to public databases, genome-wide annotations are frequently generated and released either via the Ensembl project [6] or by the National Center for Biotechnology Information [7] and sequence and annotation are then made visually available online in integrated views via the Ensembl or the University of California Santa Cruz (UCSC) genome browsers [8]. These systems provide search facilities, sequence alignment tools like BLAT/BLAST and various analysis tools to facilitate subsetting and computational retrieval of the data, including UCSC’s Table Browser or Ensembl’s Perl and REST APIs and BioMart system.While these systems have become almost indispensable for research, not all sequenced genomes are annotated and displayed in genome browsers. Full genome annotation remains time consuming and resource intensive: a full evidence-based Ensembl genebuild takes approximately 4 months. Thus, the list of species represented is currently limited and depends on various factors, including the completeness of the assembled genome sequence and the overall demand in the scientific community for the resources, including whether the species is a model organism (for example, human or mouse), economically important (for example, farmed animals) or of specific phylogenetic interest. Many of the recently sequenced bird genomes do not obviously fall within these categories.     

The FSG's land: managing a fieldwork resource

The Field Studies Council occupies land for at least three purposes. At all ten Field Centres the immediate surroundings contribute significantly to the ambience in which the visitor/staff community lives and works. Secondly, it is a great advantage for a Centre to have working land free from the encumbrances of regular negotiations with its owner; land which can be managed to suit the requirements of the teaching programme. At six of the Field Centres, the 'estate' is large enough to contribute to this purpose.
The third reason for occupying land is, perhaps, the most important. We ought to want to demonstrate that we can apply our ecological knowledge for its own practical end. We should be able to show how to manipulate succession, how to crop the stand, how to maintain the view, and how to recycle the energy and the materials. I would like to think that the holding of land (and water) and the demonstration of its sound management was part of the working ethic of the Field Studies Council. We need to manage a range of habitats, stands and communities, to maintain their qualities and to demonstrate that we care about and can care for each of them. All this presupposes that we develop or invest in the skills and background necessary for the process.
The land we manage tells its own story. If we manage it well it will increase our corporate and individual satisfactions. It could mean that we have within our ranks the new yeomen; with them we could lead the original yeoman into a new attitude and enterprise which will maintain, and may even enhance, the face of Britain when the odds might otherwise be against it.     

Olfactory receptor database: a sensory chemoreceptor resource

The Olfactory Receptor Database (ORDB) is a WWW-accessible database that has been expanded from an olfactory receptor resource to a chemoreceptor resource. It stores data on six classes of G-protein-coupled sensory chemoreceptors: (i) olfactory receptor-like proteins, (ii) vomeronasal receptors, (iii) insect olfactory receptors, (iv) worm chemo-receptors, (v) taste papilla receptors and (vi) fungal pheromone receptors. A complementary database of the ligands of these receptors (OdorDB) has been constructed and is publicly available in a pilot mode. The database schema of ORDB has been changed from traditional relational to EAV/CR (Entity-Attribute-Value with Classes and Relationships), which allows the interoperability of ORDB with other related databases as well as the creation of intra-database associations among objects. This inter-operability facilitates users to follow information from odor molecule binding to its putative receptor, to the properties of the neuron expressing the receptor, to a computational model of activity of olfactory bulb neurons. In addition, tools and resources have been added allowing users to access interactive phylogenetic trees and alignments of sensory chemoreceptors. ORDB is available via the WWW at http://ycmi.med. yale.edu/senselab/ordb/     

pTransgenesis: a cross-species, modular transgenesis resource

As studies aim increasingly to understand key, evolutionarily conserved properties of biological systems, the ability to move transgenesis experiments efficiently between organisms becomes essential. DNA constructions used in transgenesis usually contain four elements, including sequences that facilitate transgene genome integration, a selectable marker and promoter elements driving a coding gene. Linking these four elements in a DNA construction, however, can be a rate-limiting step in the design and creation of transgenic organisms. In order to expedite the construction process and to facilitate cross-species collaborations, we have incorporated the four common elements of transgenesis into a modular, recombination-based cloning system called pTransgenesis. Within this framework, we created a library of useful coding sequences, such as various fluorescent protein, Gal4, Cre-recombinase and dominant-negative receptor constructs, which are designed to be coupled to modular, species-compatible selectable markers, promoters and transgenesis facilitation sequences. Using pTransgenesis in Xenopus, we demonstrate Gal4-UAS binary expression, Cre-loxP-mediated fate-mapping and the establishment of novel, tissue-specific transgenic lines. Importantly, we show that the pTransgenesis resource is also compatible with transgenesis in Drosophila, zebrafish and mammalian cell models. Thus, the pTransgenesis resource fosters a cross-model standardization of commonly used transgenesis elements, streamlines DNA construct creation and facilitates collaboration between researchers working on different model organisms.     

Optimal cell size for resource uptake in fluids: a new facet of resource competition

Planktonic microorganisms are affected by various size-dependent processes both from the bottom up and from the top down. We developed a simple resource-consumer model to explore how size-dependent resource uptake and resource loss influence the growth of, and competition between, planktonic microorganisms. We considered three steps of resource uptake: diffusive transport of resource molecules, uptake by membrane transporters, and cellular enzymatic catalysis, and we investigated optimal cell size when one, two, or three of those steps limit resource uptake. Optimal cell size depends negatively on the size of resource molecules when resource uptake is limited by diffusive transport and membrane uptake. When competing for two resources of different molecular sizes, two different-sized consumers can coexist if the inputs of resources and sizes of consumers are correctly chosen. The model suggests that mixtures of various-sized resources can promote coexistence and size diversity of microorganisms even if the availability of one element, such as carbon, nitrogen, or phosphorus, limits the whole community. Model predictions include that bacteria grown on maltose or polysaccharides should be smaller compared with those grown on glucose under carbon limitation. Our results suggest that size of resource molecules can be an important factor in microbial resource competition in aquatic environments.