1
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Stern DB. Revolutionizing academic hiring: a faculty cluster hire emphasizing teamwork. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00185-7. [PMID: 39122564 DOI: 10.1016/j.tplants.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/19/2024] [Indexed: 08/12/2024]
Abstract
The Boyce Thompson Institute (BTI) executed a faculty cluster hiring initiative to find scientists driven by the possibilities of collaboration. Given that academic hiring rarely evaluates and rewards teamwork, BTI invented a process that would. In doing so, the Institute was able to reduce gender bias commonly found in a typical academic search.
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Affiliation(s)
- David B Stern
- Boyce Thompson Institute, 533 Tower Rd., Ithaca, NY 14853, USA.
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2
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Narayanan KK, Weigle AT, Xu L, Mi X, Zhang C, Chen LQ, Procko E, Shukla D. Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601307. [PMID: 39005363 PMCID: PMC11244857 DOI: 10.1101/2024.06.28.601307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein science is entering a transformative phase enabled by deep mutational scans that provide an unbiased view of the residue level interactions that mediate function. However, it has yet to be extensively used to characterize the mutational and evolutionary landscapes of plant proteins. Here, we apply the method to explore sequence-function relationships within the sugar transporter AtSWEET13. DMS results describe how mutational interrogation throughout different regions of the protein affects AtSWEET13 abundance and transport function. Our results identify novel transport-enhancing mutations that are validated using the FRET sensor assays. Extending DMS results to phylogenetic analyses reveal the role of transmembrane helix 4 (TM4) which makes the SWEET family transporters distinct from prokaryotic SemiSWEETs. We show that transmembrane helix 4 is intolerant to motif swapping with other clade-specific SWEET TM4 compositions, despite accommodating single point-mutations towards aromatic and charged polar amino acids. We further show that the transfer learning approaches based on physics and ML based In silico variant prediction tools have limited utility for engineering plant proteins as they were unable to reproduce our experimental results. We conclude that DMS can produce datasets which, when combined with the right predictive computational frameworks, can direct plant engineering efforts through derivative phenotype selection and evolutionary insights.
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Affiliation(s)
- Krishna K. Narayanan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Austin T. Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyun Xu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chen Zhang
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li-Qing Chen
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Erik Procko
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cyrus Biotechnology, Inc., Seattle, Washington 98121, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering; Department of Plant Biology; Department of Bioengineering; Department of Chemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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3
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Tuggle CK, Clarke JL, Murdoch BM, Lyons E, Scott NM, Beneš B, Campbell JD, Chung H, Daigle CL, Das Choudhury S, Dekkers JCM, Dórea JRR, Ertl DS, Feldman M, Fragomeni BO, Fulton JE, Guadagno CR, Hagen DE, Hess AS, Kramer LM, Lawrence-Dill CJ, Lipka AE, Lübberstedt T, McCarthy FM, McKay SD, Murray SC, Riggs PK, Rowan TN, Sheehan MJ, Steibel JP, Thompson AM, Thornton KJ, Van Tassell CP, Schnable PS. Current challenges and future of agricultural genomes to phenomes in the USA. Genome Biol 2024; 25:8. [PMID: 38172911 PMCID: PMC10763150 DOI: 10.1186/s13059-023-03155-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (phenomics). Identifying the most critical opportunities and challenges in genome to phenome (G2P) research is the focus of this paper. Previously (Genome Biol, 23(1):1-11, 2022), we laid out how Agricultural Genome to Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand public-private partnerships, and engage with external stakeholders to achieve a shared vision of future the AG2PI. Acting on this latter step, AG2PI organized the "Thinking Big: Visualizing the Future of AG2PI" two-day workshop held September 9-10, 2022, in Ames, Iowa, co-hosted with the United State Department of Agriculture's National Institute of Food and Agriculture (USDA NIFA). During the meeting, attendees were asked to use their experience and curiosity to review the current status of agricultural genome to phenome (AG2P) work and envision the future of the AG2P field. The topic summaries composing this paper are distilled from two 1.5-h small group discussions. Challenges and solutions identified across multiple topics at the workshop were explored. We end our discussion with a vision for the future of agricultural progress, identifying two areas of innovation needed: (1) innovate in genetic improvement methods development and evaluation and (2) innovate in agricultural research processes to solve societal problems. To address these needs, we then provide six specific goals that we recommend be implemented immediately in support of advancing AG2P research.
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4
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Bibik JD, Hamberger B. Plant Engineering to Enable Platforms for Sustainable Bioproduction of Terpenoids. Methods Mol Biol 2024; 2760:3-20. [PMID: 38468079 DOI: 10.1007/978-1-0716-3658-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Terpenoids represent the most diverse class of natural products, with a broad spectrum of industrial relevance including applications in green solvents, flavors and fragrances, nutraceuticals, colorants, and therapeutics. They are typically challenging to extract from their natural sources, where they occur in small amounts and mixtures of related but unwanted byproducts. Formal chemical synthesis, where established, is reliant on petrochemistry. Hence, there is great interest in developing sustainable solutions to assemble biosynthetic pathways in engineered host organisms. Metabolic engineering for chemical production has largely focused on microbial hosts, yet plants offer a sustainable production platform. In addition to containing the precursor pathways that generate the terpenoid building blocks as well as the cell structures and compartments required, or tractable localization for the enzymes involved, plants may provide a low input system to produce these chemicals using carbon dioxide and sunlight only. There have been significant recent advancements in the discovery of pathways to terpenoids of interest as well as strategies to boost yields in host plants. While part of the phytochemical field is focusing on the discovery of biosynthetic pathways, this review will focus on advancements using the pathway toolbox and toward engineering plants for the production of terpenoids. We will highlight strategies currently used to produce target products, optimization of known pathways to improve yields, compartmentalization of pathways within cells, and genetic tools developed to facilitate complex engineering of biosynthetic pathways. These advancements in Synthetic Biology are bringing engineered plant systems closer to commercially relevant hosts for the bioproduction of terpenoids.
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Affiliation(s)
- Jacob D Bibik
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA
- MelaTech, LLC, Baltimore, MD, USA
| | - Björn Hamberger
- Department of Biochemistry, Michigan State University, East Lansing, MI, USA.
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5
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Yang Q, Van Haute M, Korth N, Sattler SE, Toy J, Rose DJ, Schnable JC, Benson AK. Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome. Nat Commun 2022; 13:5641. [PMID: 36163368 PMCID: PMC9513080 DOI: 10.1038/s41467-022-33419-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 09/16/2022] [Indexed: 12/20/2022] Open
Abstract
Prebiotic fibers, polyphenols and other molecular components of food crops significantly affect the composition and function of the human gut microbiome and human health. The abundance of these, frequently uncharacterized, microbiome-active components vary within individual crop species. Here, we employ high throughput in vitro fermentations of pre-digested grain using a human microbiome to identify segregating genetic loci in a food crop, sorghum, that alter the composition and function of human gut microbes. Evaluating grain produced by 294 sorghum recombinant inbreds identifies 10 loci in the sorghum genome associated with variation in the abundance of microbial taxa and/or microbial metabolites. Two loci co-localize with sorghum genes regulating the biosynthesis of condensed tannins. We validate that condensed tannins stimulate the growth of microbes associated with these two loci. Our work illustrates the potential for genetic analysis to systematically discover and characterize molecular components of food crops that influence the human gut microbiome. Diet affects the human gut microbiome, but studies linking crop genetics to seed traits that influence the human gut microbiome are lacking. Here, the authors develop an in vitro microbiome screening method and reveal the association between sorghum genes regulating condensed tannin biosynthesis and human gut microbiome.
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Affiliation(s)
- Qinnan Yang
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.,Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA
| | - Mallory Van Haute
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.,Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA
| | - Nate Korth
- Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.,Complex Biosystems Graduate Program, University of Nebraska, Lincoln, NE, USA
| | - Scott E Sattler
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, NE, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | - John Toy
- Wheat, Sorghum and Forage Research Unit, USDA-ARS, Lincoln, NE, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | - Devin J Rose
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA.,Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA
| | - James C Schnable
- Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.,Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska, Lincoln, NE, USA
| | - Andrew K Benson
- Department of Food Science and Technology, University of Nebraska, Lincoln, NE, USA. .,Nebraska Food for Health Center, University of Nebraska, Lincoln, NE, USA.
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6
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Henkhaus NA, Busch W, Chen A, Colón‐Carmona A, Cothran M, Diaz N, Dundore‐Arias JP, Gonzales M, Hadziabdic D, Hayes RA, MacIntosh GC, Na A, Nyamasoka‐Magonziwa B, Pater D, Peritore‐Galve FC, Phelps‐Durr T, Rouhier K, Sickler DB, Starnes JH, Tyler QR, Valdez‐Ward E, Vega‐Sánchez ME, Walcott RR, Ward JK, Wyatt SE, Zapata F, Zemenick AT, Stern DB. Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop "Inclusivity in the Plant Sciences". PLANT DIRECT 2022; 6:e432. [PMID: 36035898 PMCID: PMC9399870 DOI: 10.1002/pld3.432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/06/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
A future in which scientific discoveries are valued and trusted by the general public cannot be achieved without greater inclusion and participation of diverse communities. To envision a path towards this future, in January 2019 a diverse group of researchers, educators, students, and administrators gathered to hear and share personal perspectives on equity, diversity, and inclusion (EDI) in the plant sciences. From these broad perspectives, the group developed strategies and identified tactics to facilitate and support EDI within and beyond the plant science community. The workshop leveraged scenario planning and the richness of its participants to develop recommendations aimed at promoting systemic change at the institutional level through the actions of scientific societies, universities, and individuals and through new funding models to support research and training. While these initiatives were formulated specifically for the plant science community, they can also serve as a model to advance EDI in other disciplines. The proposed actions are thematically broad, integrating into discovery, applied and translational science, requiring and embracing multidisciplinarity, and giving voice to previously unheard perspectives. We offer a vision of barrier-free access to participation in science, and a plant science community that reflects the diversity of our rapidly changing nation, and supports and invests in the training and well-being of all its members. The relevance and robustness of our recommendations has been tested by dramatic and global events since the workshop. The time to act upon them is now.
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Affiliation(s)
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology LaboratorySalk Institute for Biological StudiesLa JollaCAUSA
| | | | | | | | | | | | | | | | | | - Gustavo C. MacIntosh
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular BiologyIowa State UniversityAmesIAUSA
| | - Ali Na
- Film and MediaQueen's UniversityKingstonONCanada
| | | | | | | | | | | | | | - John H. Starnes
- Mathematics and SciencesSouthcentral Kentucky Community and Technical CollegeBowling GreenKYUSA
| | - Quentin R. Tyler
- College of Agriculture and Natural ResourcesMichigan State UniversityEast LansingMIUSA
| | | | | | - Ron R. Walcott
- College of Agricultural and Environmental Sciences/Plant PathologyUniversity of GeorgiaAthensGAUSA
| | - Joy K. Ward
- Dean of Arts and SciencesCase Western Reserve UniversityClevelandOHUSA
| | | | - Felipe Zapata
- Department of Ecology and Evolutionary BiologyUniversity of California, Los AngelesLos AngelesCAUSA
| | - Ash T. Zemenick
- Sagehen Creek Field StationUniversity of California, BerkeleyTruckeeCAUSA
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7
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dos Santos C, Franco OL. Advances in the use of plants as potential biofactories in the production of antimicrobial peptides. Pept Sci (Hoboken) 2022. [DOI: 10.1002/pep2.24290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Cristiane dos Santos
- S‐Inova Biotech, Pós‐Graduação em Biotecnologia Universidade Católica Dom Bosco Campo Grande Brazil
| | - Octávio Luiz Franco
- S‐Inova Biotech, Pós‐Graduação em Biotecnologia Universidade Católica Dom Bosco Campo Grande Brazil
- Centro de Análises Proteômicas e Bioquímica, Pós‐Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília Brasília Brazil
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8
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Genetic Manipulation and Bioreactor Culture of Plants as a Tool for Industry and Its Applications. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030795. [PMID: 35164060 PMCID: PMC8840042 DOI: 10.3390/molecules27030795] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 12/31/2022]
Abstract
In recent years, there has been a considerable increase in interest in the use of transgenic plants as sources of valuable secondary metabolites or recombinant proteins. This has been facilitated by the advent of genetic engineering technology with the possibility for direct modification of the expression of genes related to the biosynthesis of biologically active compounds. A wide range of research projects have yielded a number of efficient plant systems that produce specific secondary metabolites or recombinant proteins. Furthermore, the use of bioreactors allows production to be increased to industrial scales, which can quickly and cheaply deliver large amounts of material in a short time. The resulting plant production systems can function as small factories, and many of them that are targeted at a specific operation have been patented. This review paper summarizes the key research in the last ten years regarding the use of transgenic plants as small, green biofactories for the bioreactor-based production of secondary metabolites and recombinant proteins; it simultaneously examines the production of metabolites and recombinant proteins on an industrial scale and presents the current state of available patents in the field.
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9
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Abstract
Auxin biology as a field has been at the forefront of advances in delineating the structures, dynamics, and control of plant growth networks. Advances have been enabled by combining the complementary fields of top-down, holistic systems biology and bottom-up, build-to-understand synthetic biology. Continued collaboration between these approaches will facilitate our understanding of and ability to engineer auxin's control of plant growth, development, and physiology. There is a need for the application of similar complementary approaches to improving equity and justice through analysis and redesign of the human systems in which this research is undertaken.
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Affiliation(s)
- R Clay Wright
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, Virginia 24061, USA
| | - Britney L Moss
- Department of Biology, Whitman College, Walla Walla, Washington 99362, USA
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10
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Moore VM, Schlautman B, Fei SZ, Roberts LM, Wolfe M, Ryan MR, Wells S, Lorenz AJ. Plant Breeding for Intercropping in Temperate Field Crop Systems: A Review. FRONTIERS IN PLANT SCIENCE 2022; 13:843065. [PMID: 35432391 PMCID: PMC9009171 DOI: 10.3389/fpls.2022.843065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/07/2022] [Indexed: 05/14/2023]
Abstract
Monoculture cropping systems currently dominate temperate agroecosystems. However, intercropping can provide valuable benefits, including greater yield stability, increased total productivity, and resilience in the face of pest and disease outbreaks. Plant breeding efforts in temperate field crops are largely focused on monoculture production, but as intercropping becomes more widespread, there is a need for cultivars adapted to these cropping systems. Cultivar development for intercropping systems requires a systems approach, from the decision to breed for intercropping systems through the final stages of variety testing and release. Design of a breeding scheme should include information about species variation for performance in intercropping, presence of genotype × management interaction, observation of key traits conferring success in intercropping systems, and the specificity of intercropping performance. Together this information can help to identify an optimal selection scheme. Agronomic and ecological knowledge are critical in the design of selection schemes in cropping systems with greater complexity, and interaction with other researchers and key stakeholders inform breeding decisions throughout the process. This review explores the above considerations through three case studies: (1) forage mixtures, (2) perennial groundcover systems (PGC), and (3) soybean-pennycress intercropping. We provide an overview of each cropping system, identify relevant considerations for plant breeding efforts, describe previous breeding focused on the cropping system, examine the extent to which proposed theoretical approaches have been implemented in breeding programs, and identify areas for future development.
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Affiliation(s)
- Virginia M. Moore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- *Correspondence: Virginia M. Moore,
| | | | - Shui-zhang Fei
- Department of Horticulture, Iowa State University, Ames, IA, United States
| | - Lucas M. Roberts
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Marnin Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- Department of Crop, Soil and Environmental Sciences, College of Agriculture, Auburn University, Auburn, AL, United States
| | - Matthew R. Ryan
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Samantha Wells
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
| | - Aaron J. Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, United States
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11
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Monfils AK, Krimmel ER, Linton DL, Marsico TD, Morris AB, Ruhfel BR. Collections Education: The Extended Specimen and Data Acumen. Bioscience 2021; 72:177-188. [PMID: 35145351 PMCID: PMC8824687 DOI: 10.1093/biosci/biab109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Biodiversity scientists must be fluent across disciplines; they must possess the quantitative, computational, and data skills necessary for working with large, complex data sets, and they must have foundational skills and content knowledge from ecology, evolution, taxonomy, and systematics. To effectively train the emerging workforce, we must teach science as we conduct science and embrace emerging concepts of data acumen alongside the knowledge, tools, and techniques foundational to organismal biology. We present an open education resource that updates the traditional plant collection exercise to incorporate best practices in twenty-first century collecting and to contextualize the activities that build data acumen. Students exposed to this resource gained skills and content knowledge in plant taxonomy and systematics, as well as a nuanced understanding of collections-based data resources. We discuss the importance of the extended specimen in fostering scientific discovery and reinforcing foundational concepts in biodiversity science, taxonomy, and systematics.
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Affiliation(s)
- Anna K Monfils
- Central Michigan University, Mount Pleasant, Michigan, United States
| | - Erica R Krimmel
- Florida State University, Tallahassee, Florida, United States
| | - Debra L Linton
- Central Michigan University, Mount Pleasant, Michigan, United States
| | | | - Ashley B Morris
- Furman University, Greenville, South Carolina, United States
| | - Brad R Ruhfel
- University of Michigan, Ann Arbor, Michigan, United States
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12
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Jha SG, Borowsky AT, Cole BJ, Fahlgren N, Farmer A, Huang SSC, Karia P, Libault M, Provart NJ, Rice SL, Saura-Sanchez M, Agarwal P, Ahkami AH, Anderton CR, Briggs SP, Brophy JAN, Denolf P, Di Costanzo LF, Exposito-Alonso M, Giacomello S, Gomez-Cano F, Kaufmann K, Ko DK, Kumar S, Malkovskiy AV, Nakayama N, Obata T, Otegui MS, Palfalvi G, Quezada-Rodríguez EH, Singh R, Uhrig RG, Waese J, Van Wijk K, Wright RC, Ehrhardt DW, Birnbaum KD, Rhee SY. Vision, challenges and opportunities for a Plant Cell Atlas. eLife 2021; 10:e66877. [PMID: 34491200 PMCID: PMC8423441 DOI: 10.7554/elife.66877] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/26/2021] [Indexed: 02/06/2023] Open
Abstract
With growing populations and pressing environmental problems, future economies will be increasingly plant-based. Now is the time to reimagine plant science as a critical component of fundamental science, agriculture, environmental stewardship, energy, technology and healthcare. This effort requires a conceptual and technological framework to identify and map all cell types, and to comprehensively annotate the localization and organization of molecules at cellular and tissue levels. This framework, called the Plant Cell Atlas (PCA), will be critical for understanding and engineering plant development, physiology and environmental responses. A workshop was convened to discuss the purpose and utility of such an initiative, resulting in a roadmap that acknowledges the current knowledge gaps and technical challenges, and underscores how the PCA initiative can help to overcome them.
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Affiliation(s)
- Suryatapa Ghosh Jha
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Alexander T Borowsky
- Department of Botany and Plant Sciences, University of California, RiversideRiversideUnited States
| | - Benjamin J Cole
- Joint Genome Institute, Lawrence Berkeley National LaboratoryWalnut CreekUnited States
| | - Noah Fahlgren
- Donald Danforth Plant Science CenterSt. LouisUnited States
| | - Andrew Farmer
- National Center for Genome ResourcesSanta FeUnited States
| | | | - Purva Karia
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Cell and Systems Biology, University of TorontoTorontoCanada
| | - Marc Libault
- Department of Agronomy and Horticulture, University of Nebraska-LincolnLincolnUnited States
| | - Nicholas J Provart
- Department of Cell and Systems Biology and the Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Selena L Rice
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Maite Saura-Sanchez
- Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos AiresBuenos AiresArgentina
| | - Pinky Agarwal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Amir H Ahkami
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Christopher R Anderton
- Environmental Molecular Sciences Division, Pacific Northwest National LaboratoryRichlandUnited States
| | - Steven P Briggs
- Department of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | | | | | - Luigi F Di Costanzo
- Department of Agricultural Sciences, University of Naples Federico IINapoliItaly
| | - Moises Exposito-Alonso
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
- Department of Plant Biology, Carnegie Institution for ScienceTübingenGermany
| | | | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast LansingUnited States
| | - Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universitaet zu BerlinBerlinGermany
| | - Dae Kwan Ko
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast LansingUnited States
| | - Sagar Kumar
- Department of Plant Breeding & Genetics, Mata Gujri College, Fatehgarh Sahib, Punjabi UniversityPatialaIndia
| | - Andrey V Malkovskiy
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Naomi Nakayama
- Department of Bioengineering, Imperial College LondonLondonUnited Kingdom
| | - Toshihiro Obata
- Department of Biochemistry, University of Nebraska-LincolnMadisonUnited States
| | - Marisa S Otegui
- Department of Botany, University of Wisconsin-MadisonMadisonUnited States
| | - Gergo Palfalvi
- Division of Evolutionary Biology, National Institute for Basic BiologyOkazakiJapan
| | - Elsa H Quezada-Rodríguez
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de MéxicoLeónMexico
| | - Rajveer Singh
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhianaIndia
| | - R Glen Uhrig
- Department of Science, University of AlbertaEdmontonCanada
| | - Jamie Waese
- Department of Cell and Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of TorontoTorontoCanada
| | - Klaas Van Wijk
- School of Integrated Plant Science, Plant Biology Section, Cornell UniversityIthacaUnited States
| | - R Clay Wright
- Department of Biological Systems Engineering, Virginia TechBlacksburgUnited States
| | - David W Ehrhardt
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
| | - Kenneth D Birnbaum
- Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Seung Y Rhee
- Department of Plant Biology, Carnegie Institution for ScienceStanfordUnited States
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13
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Grumet R, McCreight JD, McGregor C, Weng Y, Mazourek M, Reitsma K, Labate J, Davis A, Fei Z. Genetic Resources and Vulnerabilities of Major Cucurbit Crops. Genes (Basel) 2021; 12:1222. [PMID: 34440396 PMCID: PMC8392200 DOI: 10.3390/genes12081222] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Revised: 07/27/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
The Cucurbitaceae family provides numerous important crops including watermelons (Citrullus lanatus), melons (Cucumis melo), cucumbers (Cucumis sativus), and pumpkins and squashes (Cucurbita spp.). Centers of domestication in Africa, Asia, and the Americas were followed by distribution throughout the world and the evolution of secondary centers of diversity. Each of these crops is challenged by multiple fungal, oomycete, bacterial, and viral diseases and insects that vector disease and cause feeding damage. Cultivated varieties are constrained by market demands, the necessity for climatic adaptations, domestication bottlenecks, and in most cases, limited capacity for interspecific hybridization, creating narrow genetic bases for crop improvement. This analysis of crop vulnerabilities examines the four major cucurbit crops, their uses, challenges, and genetic resources. ex situ germplasm banks, the primary strategy to preserve genetic diversity, have been extensively utilized by cucurbit breeders, especially for resistances to biotic and abiotic stresses. Recent genomic efforts have documented genetic diversity, population structure, and genetic relationships among accessions within collections. Collection size and accessibility are impacted by historical collections, current ability to collect, and ability to store and maintain collections. The biology of cucurbits, with insect-pollinated, outcrossing plants, and large, spreading vines, pose additional challenges for regeneration and maintenance. Our ability to address ongoing and future cucurbit crop vulnerabilities will require a combination of investment, agricultural, and conservation policies, and technological advances to facilitate collection, preservation, and access to critical Cucurbitaceae diversity.
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Affiliation(s)
- Rebecca Grumet
- Department of Horticulture, Michigan State University, East Lansing, MI 48824, USA
| | - James D. McCreight
- USDA, ARS, Crop Improvement and Protection Research Unit, Salinas, CA 93905, USA;
| | - Cecilia McGregor
- Department of Horticulture and Institute of Plant Breeding, Genetics & Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Yiqun Weng
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706, USA;
| | - Michael Mazourek
- School of Integrative Plant Science, Plant Breeding & Genetics Section, Cornell University, Ithaca, NY 14853, USA;
| | - Kathleen Reitsma
- North Central Regional Plant Introduction Station, Iowa State University, Ames, IA 50014, USA;
| | - Joanne Labate
- Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, Geneva, NY 14456, USA;
| | - Angela Davis
- Sakata Seed America, Inc., Woodland, CA 95776, USA;
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA;
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14
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Wolfe MD, Jannink JL, Kantar MB, Santantonio N. Multi-Species Genomics-Enabled Selection for Improving Agroecosystems Across Space and Time. FRONTIERS IN PLANT SCIENCE 2021; 12:665349. [PMID: 34249037 PMCID: PMC8261054 DOI: 10.3389/fpls.2021.665349] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/12/2021] [Indexed: 05/27/2023]
Abstract
Plant breeding has been central to global increases in crop yields. Breeding deserves praise for helping to establish better food security, but also shares the responsibility of unintended consequences. Much work has been done describing alternative agricultural systems that seek to alleviate these externalities, however, breeding methods and breeding programs have largely not focused on these systems. Here we explore breeding and selection strategies that better align with these more diverse spatial and temporal agricultural systems.
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Affiliation(s)
- Marnin D. Wolfe
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
| | - Jean-Luc Jannink
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, United States
- United States Department of Agriculture – Agriculture Research Service, Ithaca, NY, United States
| | - Michael B. Kantar
- Department of Tropical Plant and Soil Science, University of Hawai‘i at Mānoa, Honolulu, HI, United States
| | - Nicholas Santantonio
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
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15
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Hiatt AC, Hove AA, Ward JR, Ventura L, Neufeld HS, Boyd A, Clarke HD, Horton JL, Murrell ZE. AUTHENTIC RESEARCH IN THE CLASSROOM INCREASES APPRECIATION FOR PLANTS IN UNDERGRADUATE BIOLOGY STUDENTS. Integr Comp Biol 2021; 61:969-980. [PMID: 34050739 DOI: 10.1093/icb/icab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Engaging students in authentic research increases student knowledge, develops STEM skills, such as data analysis and scientific communication, and builds community. Creating authentic research opportunities in plant biology might be particularly crucial in addressing plant awareness disparity (formerly known as plant blindness), producing graduates with botanical literacy, and preparing students for plant-focused careers. Our consortium created four CUREs (course-based undergraduate research experiences) focused on dual themes of plant biology and global change, designed to be utilized by early and late-career undergraduates across a variety of educational settings. We implemented these CURES for four semesters, in a total of 15 courses, at four institutions. Pre- and post-course assessments used the Affective Elements of Science Learning Questionnaire and parts of a "plant blindness" instrument to quantify changes in scientific self-efficacy, science values, scientific identity, and plant awareness or knowledge. Qualitative assessment also queried self-efficacy, science values, and scientific identity. Data revealed significant and positive shifts in awareness of and interest in plants across institutions. Quantitative gains in self-efficacy and scientific identity, however, were only found at two of four institutions tested. This project demonstrates that implementing plant CUREs can produce affective and cognitive gains across institutional types and course levels. Focusing on real-world research questions that capture students' imaginations and connect to their sense of place could create plant awareness while anchoring students in scientific identities. While simple interventions can alleviate plant awareness disparity, implementing multiple CUREs per course, or focusing more on final CURE products, could promote larger and more consistent affective gains across institutions.
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Affiliation(s)
- Anna C Hiatt
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, NE
| | - Alisa A Hove
- Biology Department, Warren Wilson College, Asheville, NC P.O. Box 9000
| | - Jennifer Rhode Ward
- Biology Department, University of North Carolina, Asheville, 1 University Heights, Asheville, NC
| | - Liane Ventura
- Department of Health Services Management & Policy, East Tennessee State University, College of Public Health, Johnson City, TN PO Box 70264
| | - Howard S Neufeld
- Department of Biology, Appalachian State University, 572 Rivers St, Boone, NC
| | - Amy Boyd
- Biology Department, Warren Wilson College, Asheville, NC P.O. Box 9000
| | - H David Clarke
- Biology Department, University of North Carolina, Asheville, 1 University Heights, Asheville, NC
| | - Jonathan L Horton
- Biology Department, University of North Carolina, Asheville, 1 University Heights, Asheville, NC
| | - Zack E Murrell
- Department of Biology, Appalachian State University, 572 Rivers St, Boone, NC
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16
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Colléony A, Geisler G, Shwartz A. Exploring biodiversity and users of campsites in desert nature reserves to balance between social values and ecological impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 770:145255. [PMID: 33736367 DOI: 10.1016/j.scitotenv.2021.145255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
Protected areas (PAs) are key conservation areas designed to limit the impacts of human activities on biodiversity. PAs also provide great opportunities for individuals to experience nature complexity, through recreational activities, and can contribute to restore the non-material and intangible services nature provides to people (i.e., cultural ecosystem services). However, recreational activities may negatively affect biodiversity. Identifying the right balance between promoting nature interactions and safeguarding biodiversity in PAs is challenging. Current knowledge gaps on the social value and ecological impacts of recreational activities, such as camping in PAs, hinder our ability to address this challenge. This is particularly true for PAs located in desert ecosystems. In this interdisciplinary study, we surveyed biodiversity and people to assess ecological impacts and social values of campsites in desert PAs in Israel. Ecological surveys included birds, plants, rodents and scorpions in campsites and control plots. We conducted two social surveys: (1) in situ survey of campsite users (N = 280) on satisfaction, motivations and perceptions of campsites and (2) online nation-wide survey (N = 322) on perceptions of campsites and investigation of the attributes individuals prioritize in campsites. Our results demonstrate that when desert campsites are located outside nature-rich areas (i.e. the wadis), they have relatively moderate negative impact on biodiversity for three out of the four taxa studied (birds, scorpions and rodents). Bird communities were dominated by synanthropic species in high intensity campsites. Surprisingly, even when campsites were located in nature-poor areas, users' satisfaction was relatively high. Among the broader population, ecological quality (i.e. vegetation complexity) did not have strong influence on people's preferences of/for campsites, and comfort-related aspects were prioritized over vegetation in campsites. Overall, our results demonstrate that placing desert campsites outside ecologically rich areas can serve as optimal solution to balance impacts on biodiversity and social value of recreation activities in PAs.
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Affiliation(s)
- Agathe Colléony
- Human and Biodiversity Research Lab, Faculty of Architecture and Town Planning, Technion - Israel Institute of Technology, Haifa, 32000 Israel.
| | - Gal Geisler
- Human and Biodiversity Research Lab, Faculty of Architecture and Town Planning, Technion - Israel Institute of Technology, Haifa, 32000 Israel
| | - Assaf Shwartz
- Human and Biodiversity Research Lab, Faculty of Architecture and Town Planning, Technion - Israel Institute of Technology, Haifa, 32000 Israel
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17
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Jensen-Ryan D, Murren CJ, Bisner A, Rutter MT, Strand A. Engaging Undergraduates in Research Experiences at a Distance: Insights and Recommendations for Remote URE. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:22.1.37. [PMID: 33884060 PMCID: PMC8011901 DOI: 10.1128/jmbe.v22i1.2375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Undergraduates phenotyping Arabidopsis knockouts (unPAK) is a biology research network that has provided undergraduate research experiences (URE) since 2010. In 2019, unPAK expanded to include a summer URE that engaged undergraduate researchers from across the network in an intensive collaborative program. In response to the COVID-19 pandemic in 2020, unPAK rapidly shifted to provide the summer URE program remotely. This article describes (i) the instructional and communication processes of unPAK in the remote URE; and (ii) a summative assessment of the outcomes associated with the remote summer program as compared with the 2019 in-person program. We conclude by offering timely recommendations for educators in biology that emerged from the 2020 remote summer research experience, which may be applicable to other remote UREs and course-based research experiences (CUREs).
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Affiliation(s)
| | | | - April Bisner
- Department of Biology, College of Charleston, Charleston, SC 29424
| | - Matt T. Rutter
- Department of Biology, College of Charleston, Charleston, SC 29424
| | - Allan Strand
- Department of Biology, College of Charleston, Charleston, SC 29424
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18
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Williamson HF, Brettschneider J, Caccamo M, Davey RP, Goble C, Kersey PJ, May S, Morris RJ, Ostler R, Pridmore T, Rawlings C, Studholme D, Tsaftaris SA, Leonelli S. Data management challenges for artificial intelligence in plant and agricultural research. F1000Res 2021; 10:324. [PMID: 36873457 PMCID: PMC9975417 DOI: 10.12688/f1000research.52204.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Artificial Intelligence (AI) is increasingly used within plant science, yet it is far from being routinely and effectively implemented in this domain. Particularly relevant to the development of novel food and agricultural technologies is the development of validated, meaningful and usable ways to integrate, compare and visualise large, multi-dimensional datasets from different sources and scientific approaches. After a brief summary of the reasons for the interest in data science and AI within plant science, the paper identifies and discusses eight key challenges in data management that must be addressed to further unlock the potential of AI in crop and agronomic research, and particularly the application of Machine Learning (AI) which holds much promise for this domain.
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Affiliation(s)
- Hugh F Williamson
- Exeter Centre for the Study of the Life Sciences & Institute for Data Science and Artificial Intelligence, University of Exeter, Exeter, UK
| | | | - Mario Caccamo
- NIAB, National Research Institute of Brewing, East Malling, UK
| | | | - Carole Goble
- Department of Computer Science, University of Manchester, Manchester, UK
| | | | - Sean May
- School of Biosciences, University of Nottingham, Loughborough, UK
| | | | - Richard Ostler
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpendem, UK
| | - Tony Pridmore
- School of Computer Science, University of Nottingham, Nottingham, UK
| | - Chris Rawlings
- Department of Computational and Analytical Sciences, Rothamsted Research, Harpendem, UK
| | | | - Sotirios A Tsaftaris
- Institute of Digital Communications, University of Edinburgh, Edinburgh, UK.,Alan Turing Institute, London, UK
| | - Sabina Leonelli
- Exeter Centre for the Study of the Life Sciences & Institute for Data Science and Artificial Intelligence, University of Exeter, Exeter, UK.,Alan Turing Institute, London, UK
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