Towards a unified data infrastructure to support European and global microbiome research: a call to action

High-quality microbiome research relies on the integrity, management and quality of supporting data. Currently biobanks and culture collections have different formats and approaches to data management. This necessitates a standard data format to underpin research, particularly in line with the FAIR data standards of findability, accessibility, interoperability and reusability. We address the importance of a unified, coordinated approach that ensures compatibility of data between that needed by biobanks and culture collections, but also to ensure linkage between bioinformatic databases and the wider research community.     

Commentary: Biological standardisation in haemostasis and haematology

This collection of reviews on biological standardisation has been prepared by leading standardisation scientists with a wealth of expertise in the practical problems associated with standardising measurements in the field of haemostasis and haematology. The breadth of areas covered is significant, including coagulation, fibrinolysis, genetic reference materials and anaemia. The topics covered are also extensive and the reviews cover the basic principles and history of standardisation, the science underpinning different approaches to diverse problems and also practical information on how reference materials are developed and eventually established and made available for use in laboratories around the world.     

Biological collections and ecological/environmental research: a review,some observations and a look to the future

Housed worldwide, mostly in museums and herbaria, is a vast collection of biological specimens developed over centuries. These biological collections, and associated taxonomic and systematic research, have received considerable long‐term public support. The work remaining in systematics has been expanding as the estimated total number of species of organisms on Earth has risen over recent decades, as have estimated numbers of undescribed species. Despite this increasing task, support for taxonomic and systematic research, and biological collections upon which such research is based, has declined over the last 30‐40 years, while other areas of biological research have grown considerably, especially those that focus on environmental issues. Reflecting increases in research that deals with ecological questions (e.g. what determines species distribution and abundance) or environmental issues (e.g. toxic pollution), the level of research attempting to use biological collections in museums or herbaria in an ecological/environmental context has risen dramatically during about the last 20 years. The perceived relevance of biological collections, and hence the support they receive, should be enhanced if this trend continues and they are used prominently regarding such environmental issues as anthropogenic loss of biodiversity and associated ecosystem function, global climate change, and decay of the epidemiological environment. It is unclear, however, how best to use biological collections in the context of such ecological/environmental issues or how best to manage collections to facilitate such use. We demonstrate considerable and increasingly realized potential for research based on biological collections to contribute to ecological/environmental understanding. However, because biological collections were not originally intended for use regarding such issues and have inherent biases and limitations, they are proving more useful in some contexts than in others. Biological collections have, for example, been particularly useful as sources of information regarding variation in attributes of individuals (e.g. morphology, chemical composition) in relation to environmental variables, and provided important information in relation to species' distributions, but less useful in the contexts of habitat associations and population sizes. Changes to policies, strategies and procedures associated with biological collections could mitigate these biases and limitations, and hence make such collections more useful in the context of ecological/environmental issues. Haphazard and opportunistic collecting could be replaced with strategies for adding to existing collections that prioritize projects that use biological collections and include, besides taxonomy and systematics, a focus on significant environmental/ecological issues. Other potential changes include increased recording of the nature and extent of collecting effort and information associated with each specimen such as nearby habitat and other individuals observed but not collected. Such changes have begun to occur within some institutions. Institutions that house biological collections should, we think, pursue a mission of ‘understanding the life of the planet to inform its stewardship’ ( Krishtalka & Humphrey, 2000 ), as such a mission would facilitate increased use of biological collections in an ecological/environmental context and hence lead to increased appreciation, encouragement and support from the public for these collections, their associated research, and the institutions that house them.     

Marine biological collections in the 21st century

From the time of Linnaeus forward, it has been appreciated that collections, not least marine biological collections, are fundamental to the understanding of the biodiversity of life on earth, especially when they contain type specimens which define individual species. Historical collections are particularly rich in types and also represent a model of the biodiversity of marine life at the time of the collection, often centuries ago. The taxonomic and systematic importance of collections is well appreciated, as is the significance of time series of data in this period of anthropogenic environmental change. The application of new techniques increases the value of collected material even further, for example, molecular biology techniques allowing the recognition of new (often cryptic) taxa and their distributions, and stable isotope analyses releasing information on past and present ontogenies, geographical distributions and diets. Moreover the new era of information technology with associated digitization enables the release of the information stored in the collections to the scientists of the world.     

A Hybrid Approach of Gene Sets and Single Genes for the Prediction of Survival Risks with Gene Expression Data

Accumulated biological knowledge is often encoded as gene sets, collections of genes associated with similar biological functions or pathways. The use of gene sets in the analyses of high-throughput gene expression data has been intensively studied and applied in clinical research. However, the main interest remains in finding modules of biological knowledge, or corresponding gene sets, significantly associated with disease conditions. Risk prediction from censored survival times using gene sets hasn’t been well studied. In this work, we propose a hybrid method that uses both single gene and gene set information together to predict patient survival risks from gene expression profiles. In the proposed method, gene sets provide context-level information that is poorly reflected by single genes. Complementarily, single genes help to supplement incomplete information of gene sets due to our imperfect biomedical knowledge. Through the tests over multiple data sets of cancer and trauma injury, the proposed method showed robust and improved performance compared with the conventional approaches with only single genes or gene sets solely. Additionally, we examined the prediction result in the trauma injury data, and showed that the modules of biological knowledge used in the prediction by the proposed method were highly interpretable in biology. A wide range of survival prediction problems in clinical genomics is expected to benefit from the use of biological knowledge.     

Large-scale mutagenesis: yeast genetics in the genome era

The completion of the DNA sequence of the budding yeast Saccharomyces cerevisiae resulted in the identification of a large number of genes. However, the function of most of these genes is not known. One of the best ways to determine gene function is to carry out mutational and phenotypic analysis. In recent years, several approaches have been developed for the mutational analysis of yeast genes on a large scale. These include transposon-based insertional mutagenesis, and systematic deletions using PCR-based approaches. These projects have produced collections of yeast strains and plasmid alleles that can be screened using novel approaches. Analysis of these collections by the scientific community promises to reveal a great deal of biological information about this organism.     

Richard Meinertzhagen—a case of fraud examined

Museum collections are rich repositories of information. The specimens and the data they bear continue to provide new insights into ornithology and biological processes decades or even centuries after they were collected. The benefits to be gained from museum collections depend implicitly upon the accuracy of the information associated with the specimens and the correct interpretation of those data (Parkes 1989, Knox & Walters 1992). Collectors and dealers have often been suspected of fabricating data for a variety of reasons, but proven cases have been documented only rarely (e.g. Nicholson & Ferguson-Lees 1962). This paper examines one such case.     

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/.     

A DNA ‘Barcode Blitz’: Rapid Digitization and Sequencing of a Natural History Collection

DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity – insects.     

Integrated analysis of gene expression by association rules discovery

Background  

Microarray technology is generating huge amounts of data about the expression level of thousands of genes, or even whole genomes, across different experimental conditions. To extract biological knowledge, and to fully understand such datasets, it is essential to include external biological information about genes and gene products to the analysis of expression data. However, most of the current approaches to analyze microarray datasets are mainly focused on the analysis of experimental data, and external biological information is incorporated as a posterior process.     

To Imagine an Australian Museum

ABSTRACT

Museums are our memory banks. They tell us where we have come from. They also allow us to imagine where we are heading. Which is why it should trouble us that there has never been a truly Australian museum. Each of our state and federal museums has been built on Aboriginal collections, and each has been built on distinctly Western or European concepts, values, categories and practices. Some of these are unavoidable, but are they all? Are we too far down the path to restump the foundations of our institutions and the narratives they perpetuate in public life? The South Australian Museum holds one of the most important collections of Aboriginal material culture in the world. It is, therefore, given the story it can tell about ancient and enduring cultures, one of the most important collections of human heritage on our planet. What we do with such collections, and what we don’t, defines us. This is the great challenge of contemporary custodianship. These collections are calling us out. In this lecture I examine the South Australian Museum’s response to this challenge. Over the past two years our Museum has undertaken a comprehensive rethink of our policies and practices and the politics of both. We are also transforming the way we work with Aboriginal communities and custodians. This is not simply a question of how collections are displayed or exhibitions are developed. We are rethinking the terms of our custodianship, and the kind of truly Australian Museum that could evolve around those new foundations.     

Cryopreservation of the unicellular marine alga, Nannochloropsis oculata

In microalgal culture collections, as in many biological resource centres, cryoconservation is the most attractive method for the long-term, secure storage of living material. Nannochloropsis oculata, a marine unicellular alga, is of interest in the field of biotechnology due to its high lipid content. Of various cryoprotectants tested for their toxicity and for their ability to prevent cryoinjury, glycerol (final concentration 1.1 M) was the most efficient. When glycerol-treated cultures were submitted to a strictly regulated cooling rate (-3 degrees C min(-1)), they attained the control culture density within 13 d after thawing.     

Reliability analysis of fish traits reveals discrepancies among databases

1. Trait-based approaches are commonly used in ecology to understand the relationship between biodiversity and ecosystem functioning, environmental filtering or biotic responses to anthropogenic perturbations. However, little is known about the reliability of assigned traits and the consistency of trait information among different databases currently in use.
2. Using 99 native and alien Iberian inland fish species, we investigated a total of 27 biological and ecological traits for their consistency among 19 different databases and identified less reliable traits, that is, traits with high disagreement among databases. Specifically, we used generalised linear models and inter-rater reliability statistics (Krippendorff's α) to test for differences in trait values among databases. We also identified well-studied versus data-deficient traits and species.
3. Our results show notable discrepancies and low reliability for several biological and ecological traits such as microhabitat preference, omnivory, invertivory, rheophily, and limnophily. Least reliable traits were mainly categorical (rather than continuous) and established by expert judgment and without a clear definition or a common methodology. Interestingly, categorical traits such as rheophily or limnophily, which showed significantly lower reliability, concurrently showed higher data availability and use than continuously scaled traits.
4. Such uncertainties in trait assignments could affect bioassessment and other ecological analyses. Species with smaller distributional ranges and those that have been described more recently, presented lower coverage and data availability in trait databases.
5. We encourage further standardisation of fish trait measurement protocols to help improve the robust application of bioassessment indices and trait-based approaches.

     

Genes,culture, and the human niche: An overview

The sharp distinction between biological traits and culturally based traits, which had long been standard in evolutionary approaches to behavior, was blurred in the early 1980s by mathematical models that allowed a co‐dependent evolution of genetic transmission and cultural information. Niche‐construction theory has since added another contrast to standard evolutionary theory, in that it views niche construction as a cause of evolutionary change rather than simply a product of selection. While offering a new understanding of the coevolution of genes, culture, and human behavior, niche‐construction models also invoke multivariate causality, which require multiple time series to resolve. The empirical challenge lies in obtaining time‐series data on causal pathways involved in the coevolution of genes, culture, and behavior. This is a significant issue in archeology, where time series are often sparse and causal behaviors are represented only by proxies in the material record.     

New strategy for the representation and the integration of biomolecular knowledge at a cellular scale

The combination of sequencing and post-sequencing experimental approaches produces huge collections of data that are highly heterogeneous both in structure and in semantics. We propose a new strategy for the integration of such data. This strategy uses structured sets of sequences as a unified representation of biological information and defines a probabilistic measure of similarity between the sets. Sets can be composed of sequences that are known to have a biological relationship (e.g. proteins involved in a complex or a pathway) or that share similar values for a particular attribute (e.g. expression profile). We have developed a software, BlastSets, which implements this strategy. It exploits a database where the sets derived from diverse biological information can be deposited using a standard XML format. For a given query set, BlastSets returns target sets found in the database whose similarity to the query is statistically significant. The tool allowed us to automatically identify verified relationships between correlated expression profiles and biological pathways using publicly available data for Saccharomyces cerevisiae. It was also used to retrieve the members of a complex (ribosome) based on the mining of expression profiles. These first results validate the relevance of the strategy and demonstrate the promising potential of BlastSets.     

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods,challenges, applications,and future directions

Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.     

<Emphasis Type="Italic">In vitro</Emphasis> conservation of European bryophytes

The use of in vitro techniques for conservation has been rising steadily since their inclusion in The Convention on Biological Diversity and The Global Strategy for Plant Conservation. Unfortunately, bryophytes are often overlooked in conservation initiatives, but they are important in a number of large-scale ecosystem processes, i.e. nutrient, water and carbon cycling. There is a long history of the use of tissue culture in cultivating bryophytes, and many species respond well to in vitro techniques. For 6 yr (2000–2006), The Royal Botanic Gardens, Kew and the UK statutory conservation agencies supported a project for the ex situ conservation of bryophytes. Living and cryopreserved collections of UK threatened species were successfully established and the cryopreserved collection continues to be maintained. Other in vitro conservation collections are maintained over Europe, at botanic gardens, museums and by individual university researchers, but there is no coherent European collection of bryophytes for conservation, or standardisation of techniques. A major issue for many in vitro collections is the maintenance of within species genetic diversity. Such diversity is considered to be important, as it is the basis by which populations of species can adapt to new conditions and evolve. We are proposing to establish a European network for in vitro conservation of bryophytes. We envisage that this will include living collections, cryopreserved collections and spore collections. Conservation of genetic diversity would be a priority and the collections would provide a valuable resource for conservation initiatives and support research into rare and threatened species.     

Natural product-like synthetic libraries

There is a paucity of chemical matter suitably poised for effective drug development. Improving the quality and efficiency of research early on in the drug discovery process has been a long standing objective for the drug industry and improvements to the accessibility and quality of compound screening decks might have a significant and positive impact. In the absence of specific molecular information that can be modeled and used predicatively we are far from identifying which small molecules are most relevant to emerging biological targets such as protein-protein interactions. Natural products have been historically successful as an entry point for drug discovery and recently screening libraries are being synthesized to emulate natural product like features.     

WHO/Health Canada meeting on regulatory considerations for evaluation and licensing of new meningococcal Group B vaccines,Ottawa, Canada, 3–4 October 2011

Serogroup B Neisseria meningitides (MenB) is a significant cause of endemic and epidemic outbreaks of the disease worldwide. Although polysaccharide and conjugate vaccines are available against other meningococcal serogroups, the poor immunogenicity of MenB polysaccharide has led to the development of protein-based vaccines. However, the diversity and antigenic variability of MenB strains has been a major challenge. Recently a new generation of MenB vaccines that contain conserved antigens has been developed to provide broader coverage and they are in an advanced stage of development and regulatory consideration. In October 2011, the World Health Organization and Health Canada jointly organized a consultation on regulatory considerations for the evaluation and licensing of new MenB vaccines. The aim was to seek consensus on key regulatory issues relevant to the evaluation of candidate MenB vaccines and on approaches to the standardisation of in vitro assays used in the evaluation process. Participants agreed that functional antibodies as measured in the Serum Bactericidal Activity (SBA) assay could be used to evaluate MenB vaccine efficacy and ways of improving assay standardization proposed. Approaches to bridging SBA data to large collections of strains in order to give an indication of the prospective breadth of vaccine coverage were discussed.     

Fast Fenton footprinting: a laboratory-based method for the time-resolved analysis of DNA, RNA and proteins

‘Footprinting’ describes assays in which ligand binding or structure formation protects polymers such as nucleic acids and proteins from either cleavage or modification; footprinting allows the accessibility of individual residues to be mapped in solution. Equilibrium and time-dependent footprinting links site-specific structural information with thermodynamic and kinetic transitions. The hydroxyl radical (·OH) is a particularly valuable footprinting probe by virtue of it being among the most reactive of chemical oxidants; it reports the solvent accessibility of reactive sites on macromolecules with as fine as a single residue resolution. A novel method of millisecond time-resolved ·OH footprinting has been developed based on the Fenton reaction, Fe(II) + H₂O₂ → Fe(III) + ·OH + OH⁻. This method can be implemented in laboratories using widely available three-syringe quench flow mixers and inexpensive reagents to study local changes in the solvent accessibility of DNA, RNA and proteins associated with their biological function.