A collaborative approach to bridging the gap between wildlife managers and researchers

Although most wildlife professionals agree that science should inform wildlife management decisions, disconnect still exists between researchers and managers. If researchers are not striving to incorporate their findings into management decisions, support for research programs by managers can wane. If managers are not using research findings to inform management decisions, those decisions may be less effective or more vulnerable to legal challenges. Both of these situations can have negative consequences for wildlife conservation. We outline a collaborative research-management approach to bridging the gap between wildlife managers and researchers. We describe differences in perspectives, perceptions, and priorities between managers and researchers; outline how and why the divide between researchers and managers has likely occurred and continues to grow; and present specific strategies and recommendations to foster stronger collaborations between managers and researchers. We advocate increased synergy between managers and researchers based on a shared vision of conservation and a collaborative structure that rewards researchers and managers. Most importantly, we suggest that relationships and communication between managers and researchers must be established early in research development and decision-making processes, fostering the trust needed for collaboration. Institutions and agencies can facilitate these relationships by creating opportunities and incentives for integrating collaborative research into management decisions. We suggest this approach will strengthen ties between researchers and managers, increase relevance of research to management decisions, promote effectiveness of management decisions, reduce legal challenges, and ultimately produce positive, tangible, and lasting effects on wildlife conservation. © 2019 The Wildlife Society.     

The Barcode of Life Data Portal: bridging the biodiversity informatics divide for DNA barcoding

With the volume of molecular sequence data that is systematically being generated globally, there is a need for centralized resources for data exploration and analytics. DNA Barcode initiatives are on track to generate a compendium of molecular sequence-based signatures for identifying animals and plants. To date, the range of available data exploration and analytic tools to explore these data have only been available in a boutique form--often representing a frustrating hurdle for many researchers that may not necessarily have resources to install or implement algorithms described by the analytic community. The Barcode of Life Data Portal (BDP) is a first step towards integrating the latest biodiversity informatics innovations with molecular sequence data from DNA barcoding. Through establishment of community driven standards, based on discussion with the Data Analysis Working Group (DAWG) of the Consortium for the Barcode of Life (CBOL), the BDP provides an infrastructure for incorporation of existing and next-generation DNA barcode analytic applications in an open forum.     

Stably bridging a great divide: localization of the SpoIIQ landmark protein in Bacillus subtilis

Many bacterial proteins involved in fundamental processes such as cell shape maintenance, cell cycle regulation, differentiation, division and motility localize dynamically to specific subcellular regions. However, the mechanisms underlying dynamic protein localization are incompletely understood. Using the SpoIIQ protein in Bacillus subtilis as a case study, two reports present important novel insights into how a protein finds its right place at the right time and remains stably bound. During sporulation, SpoIIQ localizes in clusters in the forespore membrane at the interface that separates the forespore and mother cell and functions as a landmark protein for SpoIIIAH in the mother cell membrane. The extracellular domains of SpoIIQ and SpoIIIAH interact directly effectively bridging the gap between the two membranes. Here, SpoIIQ localization is shown to depend on two pathways, one involves SpoIIIAH, the second involves two peptidoglycan‐degrading enzymes SpoIIP and SpoIID; and, SpoIIQ is only delocalized in the absence of all three proteins. Importantly, in the absence of SpoIIIAH, SpoIIQ apparently localizes normally. However, FRAP experiments demonstrated that SpoIIQ is not stably maintained in the clusters in this mutant. Thus, a second targeting pathway can mask significant changes in the localization of a protein.     

Peptidomics: bridging the gap between proteome and metabolome

Studies of naturally occurring peptides and protein profiling by 'classical' proteomics are linked by common analytical objectives and methodologies. The first international workshop "Peptidomics: methods and applications" held on 6-7th September 2005 at Royal Holloway University of London confirmed that the science of peptidomics is a rapidly developing activity of high interest to both academia and industry. This meeting featured talks by over 20 leading international scientists detailing methods and typical applications, including newly-developed capabilities for protein and peptide analyses. It provided a definition of the scope of the subject in terms of current and future technologies together with applications ranging from studies of defined biological extracts to complete ecosystems. The proceedings of this meeting, speakers' contact details and other relevant information can be accessed at: www.rhul.ac.uk/biosci/meetings.     

Biodiversity: bridging the gap between condition and conservation

The aim of this study is to create a two-tiered assessment combining restoration and conservation, both needed for biodiversity management. The first tier of this approach assesses the condition of a site using a standard bioassessment method, AUSRIVAS, to determine whether significant loss of biodiversity has occurred because of human activity. The second tier assesses the conservation value of sites that were determined to be unimpacted in the first step against a reference database. This ensures maximum complementarity without having to set a priori target areas. Using the reference database, we assign site-specific and comparable coefficients for both restoration (Observed/Expected taxa with >50% probability of occurrence) and conservation values (O/E taxa with <50%, rare taxa). In a trial on 75 sites on rivers around Sydney, NSW, Australia we were able to identify three regions: (1) an area that may need restoration; (2) an area that had a high conservation value and; (3) a region that was identified as having significant biodiversity loss but with high potential to respond to rehabilitation and become a biodiversity hotspot. These examples highlight the use of the new framework as a comprehensive system for biodiversity assessment.     

Biodiversity and the divide between culture and nature

The term biodiversity may help us to reach beyond the nature–culture dualism that has a debilitating effect on conservation thinking. This, however, depends on how the term is actually used. The opportunity is that the term connects dialectically together biological entities and their conditions of reproduction and may, consequently, facilitate a shift from atomistic to processual thinking in ecology and conservation. Analogously, the term offers resources for analyzing the dynamic dependence of human activities on natural processes. Health offers a fruitful metaphor for evaluating the resilience and conditions of reproduction of ecosocial systems. On the other hand, problems and contradictions in the application of the term arise from too schematic a perception of the relationship between scientific knowledge and human, social agency. Science influences human agency primarily on the long term, by helping to form new perspectives on what it means to lead a human life. Conservation concerns have a great influence on such perspectives. However, an emphasis on crisis may be counterproductive: scientific arguments perform poorly in a crisis situation in which, instead, short-term interests of powerful social actors such as corporations, state agencies or professional groups may gain the upper hand.     

Bridging the divide between cytokinesis and cell expansion

Two of the most fundamental processes in plant development are cytokinesis, by which new cells are formed, and cell expansion, by which existing cells grow and establish their functional morphology. In this review we summarize recent progress in understanding the pathways necessary for cytokinesis and cell expansion, including the role of the cytoskeleton, cell wall biogenesis, and membrane trafficking. Here, we focus on genes and lipids that are involved in both cytokinesis and cell expansion and bridge the divide between these two processes. In addition, we discuss our understanding of and controversies surrounding the role of endocytosis in both of these processes.     

GTPase signaling: bridging the GAP between ARF and Rho

Membrane traffic and actin cytoskeleton dynamics are intimately linked, and GTPases of the Rho and ARF families may work together to regulate both. Recent studies have identified a family of GTPase activating proteins (GAPs) that contain both ARF-GAP and Rho-GAP domains, providing the first direct link between these two signaling pathways.     

Livestock genomics: bridging the gap between mice and men

Dissecting the genetic control of variation in complex traits, such as disease resistance and agricultural-product quality, remains very challenging. Farm animals are now well placed to bridge the gap between human biology and traditional model species. Livestock species share with model species the benefits of controlled breeding, and their biology is often much closer to that of humans. Genetic research in model species focuses on differences between homogenous lines, whereas genetic research in humans focuses on genetic variation within populations. Livestock genetics has the strengths of both human and model-species genetics because researchers can exploit both the abundant genetic variation between divergent breeds and the variation that is segregating within breeds. Therefore, livestock genomics fills the void where the genetics of model species proves intractable or where model species are not a good proxy for human biology.     

Tissue microarrays: bridging the gap between research and the clinic

Tissue microarrays are a high-throughput method for the investigation of biomarkers in multiple tissue specimens at once. This technique allows for the analysis of up to 500 tissue samples in a single experiment using immunohistochemistry and in situ hybridization. Recently, cell lines and xenografts have been reduced to a tissue microarray format and are being applied to preclinical drug development. In clinical research, tissue microarrays are applied at multiple levels: comprehensive analysis of samples in the context of a clinical trial or across a population. Tissue microarrays play a central role in translational research, facilitating the discovery of molecules that have potential roles in the diagnosis, prognosis and prediction of response to therapy.     

Tissue microarrays: bridging the gap between research and the clinic

Tissue microarrays are a high-throughput method for the investigation of biomarkers in multiple tissue specimens at once. This technique allows for the analysis of up to 500 tissue samples in a single experiment using immunohistochemistry and in situ hybridization. Recently, cell lines and xenografts have been reduced to a tissue microarray format and are being applied to preclinical drug development. In clinical research, tissue microarrays are applied at multiple levels: comprehensive analysis of samples in the context of a clinical trial or across a population. Tissue microarrays play a central role in translational research, facilitating the discovery of molecules that have potential roles in the diagnosis, prognosis and prediction of response to therapy.     

Atul Butte discusses the divide between bioinformatics and the clinic

Atul Butte is an Assistant in Endocrinology and Informatics and Attending Physician at Children's Hospital, Boston, USA (http://www.chip.org), and is an Instructor in Paediatrics at Harvard Medical School (http://www.harvard.edu). He received his undergraduate degree in Computer Science from Brown University in 1991, and worked in several stints as a software engineer at Apple Computer and Microsoft Corporation. He graduated from the Brown University School of Medicine in 1995, during which he worked as a research fellow at National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK; http://www.niddk.nih.gov) through the Howard Hughes/NIH Research Scholars Program. He completed his residency in Paediatrics and Fellowship in Paediatric Endocrinology in 2001, both at Children's Hospital. During his research under Isaac Kohane (at Children's Hospital) he developed a novel methodology for analyzing large data sets of RNA expression, called Relevance Networks. His recent awards include the 2003 Emory University School of Medicine, Pathology Residents’ Choice Award, 2002 American Association for Clinical Chemistry Outstanding Speaker Award, 2002 Endocrine Society Travel Award based on presentation merit, 2001 American Association for Cancer Research Scholar-In-Training Award and the 2001 Lawson Wilkins Paediatric Endocrine Society Clinical Scholar Award.     

Relations as patterns: bridging the gap between OBO and OWL

Background  

Most biomedical ontologies are represented in the OBO Flatfile Format, which is an easy-to-use graph-based ontology language. The semantics of the OBO Flatfile Format 1.2 enforces a strict predetermined interpretation of relationship statements between classes. It does not allow flexible specifications that provide better approximations of the intuitive understanding of the considered relations. If relations cannot be accurately expressed then ontologies built upon them may contain false assertions and hence lead to false inferences. Ontologies in the OBO Foundry must formalize the semantics of relations according to the OBO Relationship Ontology (RO). Therefore, being able to accurately express the intended meaning of relations is of crucial importance. Since the Web Ontology Language (OWL) is an expressive language with a formal semantics, it is suitable to de ne the meaning of relations accurately.