The challenges faced by living stock collections in the USA

McCluskey, Kevin; Boundy‐Mills, Kyria; Dye, Greg; Ehmke, Erin; Gunnell, Gregg F.; Kiaris, Hippokratis; Richmond, Maxi Polihronakis; Yoder, Anne D.; Zeigler, Daniel R.; Zehr, Sarah; Grotewold, Erich

doi:10.7554/elife.24611

Cited by 9 publications

(16 citation statements)

References 31 publications

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“…Ideally, BEBs should be fully and permanently funded, as human biobanks and biomedical model animal collections often are (McCluskey 2017, McCluskey et al 2017a. Available financial resources are often too scarce to support the whole spectrum of BEB activities, organising expeditions, hiring sufficient staff, developing protocols, maintaining databases, and buying equipment (Ashmore 1997, Franco et al 2006, Rice et al 2006, Gostel et al 2016, McCluskey 2017, Leroy et al 2019, Collins et al 2021, Perez Ortega 2022.…”

Section: Biobank Management and Facilitiesmentioning

confidence: 99%

“…Biobanks vary widely in scope and are housed in different settings such as botanical gardens, zoos, natural history museums (Zika et al 2011) and other agencies. BEBs focus on living collections (McCluskey et al 2017a), DNA, RNA, and/or fixed tissues, all of which represent valuable genetic resources, usually for a wide range of species. Culture collections of microorganisms (protists, fungi, bacteria), livestock biobanks, and agricultural seed banks have been well-established for decades and procedures are consistent, as they must guarantee viability and availability of resources for use (Engels & Fassil 2009).…”

Section: Introductionmentioning

confidence: 99%

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Biodiversity biobanks: a landscape analysis

Corrales¹,

Luciano²,

Astrin³

2023

Preprint

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Biobanks are curated collections of biological samples that are preserved at the molecular level, usually frozen, along with associated data, and managed to high scientific standards. We conducted a 'landscape analysis'—based both on a community survey and a literature review—to determine commonalities, information gaps, and challenges in the various workflows of biodiversity and environmental biobanks. The survey was completed by 55 institutions from more than 20 countries. Its results were compared to other collection-based surveys and complemented by literature research in the areas of general biobank management, staffing, sample handling, storage, (cryo-/)preservation, policies, databases, and networking. We illustrate the strengths and weaknesses of biodiversity and environmental biobanks and provide some basic recommendations for improving biobank procedures. In general, we found that increased efforts are needed to standardise biobank workflows or individual workflow components. While general, organism-independent biobanking guidelines already exist, more detailed guidance documents to date mostly address only human biobanking, or a narrow range of biodiversity. We hope to start closing that gap by providing an overview of current protocols and practices in biodiversity and environmental biobanking in form of a handbook, to which the present work is directly related. The handbook is available open-access under https://doi.org/10.3897/ab.e101876.

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Section: Biobank Management and Facilitiesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Biodiversity biobanks: a landscape analysis

Corrales¹,

Luciano²,

Astrin³

2023

Preprint

View full text Add to dashboard Cite

show abstract

“…Here, it is worth noting the perhaps unappreciated value of zoos and other living‐stock collections for enabling these leaps into new organismal systems. These collections offer precious opportunities for incorporating multigeneration pedigrees, as well as comprehensive databases of individual life history records including age, sex, number of offspring over lifespan, longitudinal health records, cause of death and other fundamental aspects of a given organism's biology (McCluskey et al, 2017). Thus, with a combination of technical, computational, and existing biological resources, we can be confident that classic hypotheses of molecular evolution will be increasingly refined with biological and functional sophistication.…”

Section: The Path Forwardmentioning

confidence: 99%

The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals

Yoder

Tiley

2021

Molecular Ecology

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Spontaneous de novo mutations (DNMs) in the germline fuel the engine of evolution. Without them, natural selection has no material on which to act. The distribution and frequency of DNMs across the genome contribute to virtually every aspect of an organism's function and fitness. Consequently, the mechanisms by which they are generated and transmitted from one generation to the next is of fundamental interest to the field of molecular ecology. Accurate mutation rate estimates within species and populations can inform essential evolutionary parameters such as the timing of speciation events and key

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“…An invaluable role has been and continues to be played by public repositories, such as the Fungal Genetics Stock Center in the USA. However, lack of funding for such organizations both threatens these and undermines decades of research and limits the potential to perform experiments into the future [ 234 ]. In addition to the physical resources, online databases of genomes, T-DNA insertions and phenotypes (Fig.…”

Section: The Future and Further Maximizing The Impact Of Atmentioning

confidence: 99%

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

Idnurm

Bailey

Cairns

et al. 2017

Fungal Biol Biotechnol

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The implementation of Agrobacterium tumefaciens as a transformation tool revolutionized approaches to discover and understand gene functions in a large number of fungal species. A. tumefaciens mediated transformation (AtMT) is one of the most transformative technologies for research on fungi developed in the last 20 years, a development arguably only surpassed by the impact of genomics. AtMT has been widely applied in forward genetics, whereby generation of strain libraries using random T-DNA insertional mutagenesis, combined with phenotypic screening, has enabled the genetic basis of many processes to be elucidated. Alternatively, AtMT has been fundamental for reverse genetics, where mutant isolates are generated with targeted gene deletions or disruptions, enabling gene functional roles to be determined. When combined with concomitant advances in genomics, both forward and reverse approaches using AtMT have enabled complex fungal phenotypes to be dissected at the molecular and genetic level. Additionally, in several cases AtMT has paved the way for the development of new species to act as models for specific areas of fungal biology, particularly in plant pathogenic ascomycetes and in a number of basidiomycete species. Despite its impact, the implementation of AtMT has been uneven in the fungi. This review provides insight into the dynamics of expansion of new research tools into a large research community and across multiple organisms. As such, AtMT in the fungi, beyond the demonstrated and continuing power for gene discovery and as a facile transformation tool, provides a model to understand how other technologies that are just being pioneered, e.g. CRISPR/Cas, may play roles in fungi and other eukaryotic species.

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The challenges faced by living stock collections in the USA

Cited by 9 publications

References 31 publications

Biodiversity biobanks: a landscape analysis

Biodiversity biobanks: a landscape analysis

The challenge and promise of estimating the de novo mutation rate from whole‐genome comparisons among closely related individuals

A silver bullet in a golden age of functional genomics: the impact of Agrobacterium-mediated transformation of fungi

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