Biological Collections Ensuring Critical Research and Education for the 21st Century (2020) / Chapter Skim
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2 Advancing Discovery, Inspiring Innovation, and Informing Societal Challenges
2 Advancing Discovery, Inspiring Innovation, and Informing Societal Challenges
Pages 45-70
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From page 45... ...
This chapter outlines the fundamental ways in which biological collections support scientific research by preserving biological and ecological knowledge over time and space, enabling new biological discoveries, deepening and widening the scientific understanding of complex societal challenges, and driving scientific innovations. The chapter also touches on best practices for evaluating and consistently measuring the impact of biological collections and how their contributions to science and society continually expand.
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From page 46... ...
. This is analogous to 1 The Integrated Digitized Biocollections is the most comprehensive listing of natural history collections in the United States and lists 1,600 natural history collections in the United States associated with 729 different institutions.
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Sometimes a single natural history or living specimen is all that is known about a species, but these specimens contain the genetic benchmarks and baseline data against which all modern observations and experimentations can be compared. More generally, biological collections serve as the primary source of research material for studying species as well as the main source of information about species, including information about their genetic material, geographic ranges, and morphological characteristics -- all of which is used to define the basic units of life on Earth along with their evolutionary histories, their distributions, and the processes that gave rise to them.
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As local ecosystems are modified and sometimes destroyed, biological collections become the only remaining representations of endangered species that may be driven to extinction, making the specimen information these collections contain essential for biodiversity conservation efforts. For example, a recent National Academies report on the taxonomic status of the endangered red wolf and Mexican wolf reviewed many studies using morphological traits as well as genetic analyses of specimens, many of which are housed in natural history collections (NASEM, 2019a)
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For this to happen, specimens need to be collected with a more diverse set of research objectives in mind, from stable isotopes and transcriptome and epigenetic studies to host–parasite interactions, microbiome diversity, and the dynamics of biological communities. To future-proof this critical infrastructure, the biological collections community needs to engage with diverse research communities to gain an understanding of the best strategies and priorities for sampling contemporary biodiversity to build collections with maximum utility in the future.
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More recently, next-generation sequencing, especially shortread technology and sequence capture of targeted genes, has expanded the scope of DNA-based phylogenetic and functional studies and is enabling the inclusion of thousands of species in a single analysis, with samples obtained from natural history collections (Kates et al., 2018, 2019)
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Beyond the traditional fields of research described above, biological collections have been a major source of inspiration for scientists from other disciplines, such as physics, chemistry, and engineering. 6 All states party to the Treaty are obliged to recognize microorganisms deposited as a part of the patent procedure, irrespective of where the depository authority is located.
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coli Genetic Stock Center at Yale University, have played key roles in major discoveries that have been awarded Nobel Prizes: • 1958: Lederberg: genetic recombination and the organization of the ge netic material of bacteria • 1959: Ochoa and Kornberg: DNA replication, how life copies its genetic code • 1965: Jacob, Lwoff, and Monod: gene regulation, how genes are turned on or off • 1968: Holley, Khorana, and Nirenberg: genetic code, the language in which our DNA is written • 1969: Delbrück, Hershey, and Luria: virus replication, how viruses repro duce inside cells • 1978: Arber, Nathans, and Smith: restriction enzymes, cellular "scissors" that allow scientists to cut DNA • 1980: Berg, Gilbert, and Sanger: recombinant DNA, the creation of the first genetically engineered DNA For example, unconventional uses of collections in the field of synthetic biology and biomimetics -- which are explored in this section -- emphasize the potential transdisciplinary opportunities that biological collections can help fulfill. Supporting Synthetic Biology Living collections have been instrumental in the development of tools -- and still provide the founding material -- for synthetic biology, an interdisciplinary field that spans biology and engineering.
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coli, many specimens from numerous biological collections have been tapped to develop BioBricks (Kahl and Endy, 2013; Radeck et al., 2013) and other innovations in synthetic biology.
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. Both natural history collections, including fossils, and living collections are potential sources of innovation, with applications in such areas as textiles, advanced materials, aerospace, electronics, and even wound care through the use of biofilms from living stocks.
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. For example, hormones can be extracted from decades-old natural history collections, making it possible to infer the physiological state of the individuals at the time of capture (Schmitt et al., 2018)
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. Natural history collections, whose specimens range from fungi to dinosaurs and from bacteria to sequoias, are like libraries that chronicle the history of life on Earth.
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Varying levels of mercury contamination can be evaluated by comparing archived specimens in natural history collections with contemporary specimens, and this can, in turn, be used to inform policymakers (EPA, 2002; Stoner, 2002)
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Natural history observations, gained in part through biological collections, have been key to the development of successful integrated pest management and biological control (Tewksbury et al., 2014) , which in turn have resulted in increased crop yields (Pretty et al., 2006)
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. Culture collections provide a critical and robust platform with which to preserve newly emergent strains and also distribute materials in response to public emergencies, including providing the tools needed to diagnose and control diseases.
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Unanticipated Use of Biological Collections Technological innovation will continue to increase our ability to extract information from samples and expand our knowledge by addressing questions that were not even envisioned when specimens were originally collected (i.e., serendipity) , just as specimens collected centuries ago are today used in new ways, such as genomics, unimaginable at the time of collection.
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. For such unanticipated discoveries from both natural history and living collections to continue, specimens need to be collected with a more diverse set of research objectives in mind, from stable isotopes and transcriptome and epigenetic studies to host–parasite interactions, microbiome diversity, and dynamics of biological communities.
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Some biological collections track and document the use of specimens and their associated biological materials and data through published citations. Specimens in natural history collections and strains in living collections have unique numbers that can be tracked in the literature.
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Today, living collections and natural history collections have begun to use data aggregators such as Google Scholar to compile research publications that result from collections-based work (Winker and Withrow, 2013)
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Some of the most powerful metrics for evaluating biological collections could be qualitative. For example, sentiments about the ease of use of specimen data portals would be important information related to improving access to data for different types of uses.
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TABLE 2-1 Key Evaluation Terminology and Example Questionsa Term Definition Examples Evaluation Questions Inputs The resources needed for • Strategic plans • What is the quality of the inputs? program planning and • Budget • Are the inputs sufficient?
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TABLE 2-1 Continued 66 Term Definition Examples Evaluation Questions Outcomes The intended effects on people, • Meta-analyses (analyses that combine • To what extent are the target communities, or institutions as a data from multiple studies) audiences aware of the outputs?
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A Community-Wide Vision Although individual biological collections may vary in their specific goals and desired outcomes, they share the goal of providing effective and impactful access to physical and digital objects for use in research, innovation, and education. Given this shared goal, along with nascent connections among many collections stemming from NSF's Advancing Digitization of Biodiversity Collections program, the collections community has the opportunity to develop a community-wide vision for evaluating its collective impact and how to measure it.
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Unless the biological collections community participates meaningfully in these larger evaluation schemes, it risks isolating itself by only developing community-specific measures of impact. To the extent that different biological collections develop a set of shared metrics, they will benefit from selecting best practices or exemplars that show biological collections metrics activities that are consonant with the general discussions occurring about the impact of science.
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Analytical capabilities (both tools and training) to enable transformative research using biological collections and associated data will be needed to ensure that biological collections are rigorously archived to fuel the greatest diversity of new technologies and approaches.
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