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Specimen collection is essential for modern science.

ABSTRACT: Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

SUBMITTER: Nachman MW

PROVIDER: S-EPMC10664955 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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Specimen collection is essential for modern science.

Nachman Michael W MW Beckman Elizabeth J EJ Bowie Rauri Ck RC Cicero Carla C Conroy Chris J CJ Dudley Robert R Hayes Tyrone B TB Koo Michelle S MS Lacey Eileen A EA Martin Christopher H CH McGuire Jimmy A JA Patton James L JL Spencer Carol L CL Tarvin Rebecca D RD Wake Marvalee H MH Wang Ian J IJ Achmadi Anang A Álvarez-Castañeda Sergio Ticul ST Andersen Michael J MJ Arroyave Jairo J Austin Christopher C CC Barker F Keith FK Barrow Lisa N LN Barrowclough George F GF Bates John J Bauer Aaron M AM Bell Kayce C KC Bell Rayna C RC Bronson Allison W AW Brown Rafe M RM Burbrink Frank T FT Burns Kevin J KJ Cadena Carlos Daniel CD Cannatella David C DC Castoe Todd A TA Chakrabarty Prosanta P Colella Jocelyn P JP Cook Joseph A JA Cracraft Joel L JL Davis Drew R DR Davis Rabosky Alison R AR D'Elía Guillermo G Dumbacher John P JP Dunnum Jonathan L JL Edwards Scott V SV Esselstyn Jacob A JA Faivovich Julián J Fjeldså Jon J Flores-Villela Oscar A OA Ford Kassandra K Fuchs Jérôme J Fujita Matthew K MK Good Jeffrey M JM Greenbaum Eli E Greene Harry W HW Hackett Shannon S Hamidy Amir A Hanken James J Haryoko Tri T Hawkins Melissa Tr MT Heaney Lawrence R LR Hillis David M DM Hollingsworth Bradford D BD Hornsby Angela D AD Hosner Peter A PA Irham Mohammad M Jansa Sharon S Jiménez Rosa Alicia RA Joseph Leo L Kirchman Jeremy J JJ LaDuc Travis J TJ Leaché Adam D AD Lessa Enrique P EP López-Fernández Hernán H Mason Nicholas A NA McCormack John E JE McMahan Caleb D CD Moyle Robert G RG Ojeda Ricardo A RA Olson Link E LE Kin Onn Chan C Parenti Lynne R LR Parra-Olea Gabriela G Patterson Bruce D BD Pauly Gregory B GB Pavan Silvia E SE Peterson A Townsend AT Poe Steven S Rabosky Daniel L DL Raxworthy Christopher J CJ Reddy Sushma S Rico-Guevara Alejandro A Riyanto Awal A Rocha Luiz A LA Ron Santiago R SR Rovito Sean M SM Rowe Kevin C KC Rowley Jodi J Ruane Sara S Salazar-Valenzuela David D Shultz Allison J AJ Sidlauskas Brian B Sikes Derek S DS Simmons Nancy B NB Stiassny Melanie L J MLJ Streicher Jeffrey W JW Stuart Bryan L BL Summers Adam P AP Tavera Jose J Teta Pablo P Thompson Cody W CW Timm Robert M RM Torres-Carvajal Omar O Voelker Gary G Voss Robert S RS Winker Kevin K Witt Christopher C Wommack Elizabeth A EA Zink Robert M RM

PLoS biology 20231122 11

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection. ...[more]

PMID: 37992027

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Project description:With a realistic threat against biodiversity in rain forests and in the sea, a sustainable use of natural products is becoming more and more important. Basic research directed against different organisms in Nature could reveal unexpected insights into fundamental biological mechanisms but also new pharmaceutical or biotechnological possibilities of more immediate use. Many different strategies have been used prospecting the biodiversity of Earth in the search for novel structure-activity relationships, which has resulted in important discoveries in drug development. However, we believe that the development of multidisciplinary incentives will be necessary for a future successful exploration of Nature. With this aim, one way would be a modernization and renewal of a venerable proven interdisciplinary science, Pharmacognosy, which represents an integrated way of studying biological systems. This has been demonstrated based on an explanatory model where the different parts of the model are explained by our ongoing research. Anti-inflammatory natural products have been discovered based on ethnopharmacological observations, marine sponges in cold water have resulted in substances with ecological impact, combinatory strategy of ecology and chemistry has revealed new insights into the biodiversity of fungi, in depth studies of cyclic peptides (cyclotides) has created new possibilities for engineering of bioactive peptides, development of new strategies using phylogeny and chemography has resulted in new possibilities for navigating chemical and biological space, and using bioinformatic tools for understanding of lateral gene transfer could provide potential drug targets. A multidisciplinary subject like Pharmacognosy, one of several scientific disciplines bridging biology and chemistry with medicine, has a strategic position for studies of complex scientific questions based on observations in Nature. Furthermore, natural product research based on intriguing scientific questions in Nature can be of value to increase the attraction for young students in modern life science.

Project description:Background and Aims: The Genomics Working Group (of the Cancer Research Network (CRN) Pharmacovigilance Project) explored single-site experiences with genomic studies to understand challenges and opportunities for collecting and using biological specimens. Its specific aims were to:Methods: We distributed a survey on existing biospecimen availability to principal investigators at all CRN Pharmacovigilance sites. Information collected included the number of specimens, storage methods, and type of specimens available. Investigators were also asked to identify past and current studies at their institutions in order to collect information on successful specimen collection strategies. A literature review was conducted both to identify potential barriers to participation and to understand the feasibility of various recruitment procedures. Benefits and limitations of ?opt-out? and ?opt-in? specimen collection methods were examined. Lastly, we developed study documents, including recruitment letters and informed consent forms, for future saliva and blood specimen collection efforts.Results: Two of the CRN HMOs currently have large-scale banked blood or saliva specimens (>20,000) within existing repositories. One site has two large-scale studies (>20,000 participants each) with banked specimens able to provide DNA for future research. Whole blood or blood components are the most commonly collected specimen types, and multiple CRN sites have access to banked tumor blocks. There were 33 past or current studies that included biospecimen collection. There was a trade-off between intensive data collection requirements and recruitment yield, cost, and participation burden.Conclusions: There is great potential for collection, storage, and use of biospecimen samples for research within the CRN. For future collection efforts, ?opt-out? models allow fast sample accrual, but impact data de-identification requirements. ?Opt-in? models allow for broad data collection, but are resource and time intensive. Pathology time and support may be a barrier to future use of stored samples.

Project description:Under current climate warming predictions, the future of coral reefs is dire. With projected coral reef decline, it is likely that coral specimens for bleaching research will increasingly become a more limited resource in the future. By adopting a holistic approach through increased collaborations, coral bleaching scientists can maximize a specimen's investigative yield, thus reducing the need to remove more coral material from the reef. Yet to expand a specimen's utility for additional analytic methods, information on how corals are collected is essential as many methods are variably sensitive to upstream handling and processing. In an effort to identify common practices for coral collection, sacrifice, preservation, and processing in coral bleaching research, we surveyed the literature from the last 6.5 years and created and analyzed the resulting dataset of 171 publications. Since January 2014, at least 21,890 coral specimens were collected for bleaching surveys or bleaching experiments. These specimens spanned 122 species of scleractinian corals where the most frequently sampled were Acropora millepora, Pocillopora damicornis, and Stylophora pistillata. Almost 90% of studies removed fragments from the reef, 6% collected skeletal cores, and 3% collected mucus specimens. The most common methods for sacrificing specimens were snap freezing with liquid nitrogen, chemical preservation (e.g., with ethanol or nucleic acid stabilizing buffer), or airbrushing live fragments. We also characterized 37 distinct methodological pathways from collection to processing of specimens in preparation for a variety of physiological, -omic, microscopy, and imaging analyses. Interestingly, almost half of all studies used only one of six different pathways. These similarities in collection, preservation, and processing methods illustrate that archived coral specimens could be readily shared among researchers for additional analyses. In addition, our review provides a reference for future researchers who are considering which methodological pathway to select to maximize the utility of coral bleaching specimens that they collect.

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Specimen collection is essential for modern science.

Publications

Specimen collection is essential for modern science.

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