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Research paper thumbnail of Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop “Inclusivity in the Plant Sciences”

Plant Direct

A future in which scientific discoveries are valued and trusted by the general public cannot be a... more 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.

Research paper thumbnail of Natural Genetic And Epigenetic Variation At Retroposon Loci In Arabidopsis

In both plants and animals, transposable elements are epigenetically regulated to maintain genomi... more In both plants and animals, transposable elements are epigenetically regulated to maintain genomic integrity. DNA methylation (5-methylcytosine) is an important epigenetic modification that maintains transcriptional silencing at repetitive sequences and transposons. Here, I use the Sadhu family of non-LTR retroposons in Arabidopsis thaliana as models to understand the connection between genetic and epigenetic variation. There are only 16 full-length Sadhu elements in the Arabidopsis thaliana genome, and these elements are genetically diverged, sharing only 75% sequence identity. We analyzed both genetic and epigenetic variation in two different Sadhu elements, the heterochromatic Sadhu1-1 and the euchromatic Sadhu6-1. For both of these elements, we determined that Sadhu is not uniformly controlled but can exist in an epigenetically active or a repressed state. To test the source of variation in epigenetic state at these loci, we crossed two strains with differentially methylated Sadhu elements and observed no trans-activation of the silenced allele, nor repression of the transcribed element in the hybrids. Our results suggest that Sadhu elements are inherited as pure epialleles that differ between strains. Additionally, I investigated intrastrain stability of Sadhu transcription. I used a ddm1 mutation to genetically activate a silenced Sadhu1-1 epiallele. After restoring DDM1, we monitored transcription in these plants for eight meiotic generations and determined that transcription remains on, but is variable in these lines. My findings indicate that maintenance of DNA methylation is sufficient to silence Sadhu elements; however, a loss of methylation does not trigger de novo methylation and epigenetic silencing is not efficiently repaired. The variation within the Sadhu family provides new insights into the stability of DNA methylation at transposons and can serve as a model for natural epigenetic variation

Research paper thumbnail of Broadening the impact of plant science through innovative, integrative, and inclusive outreach

Plant Direct, 2021

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial ... more This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Research paper thumbnail of Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Plant Direct, 2020

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial ... more This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Research paper thumbnail of Reinventing postgraduate training in the plant sciences: T-training defined through modularity, customization, and distributed mentorship

Plant Direct, 2018

The Plant Science Research Network (PSRN) comprises scientific societies and organizations with a... more The Plant Science Research Network (PSRN) comprises scientific societies and organizations with a mission to build and communicate a consensus vision of the future of plant science research, education, and training. This report enumerates a set of farreaching recommendations for postgraduate training that emerged from workshops held in October 2016 and September 2017. These recommendations broaden and deepen the T-training concept presented in the Decadal Vision for Plant Science, which emphasizes experiential learning beyond the traditional disciplinary focus. Both workshops used the scenarios developed in Imagining Science in 2035 as a mechanism to encourage out-of-the-box thinking, an approach that led to the innovative recommendations and solutions described here. At the heart of our recommendations is the empowerment of trainees, who should be enabled to customize and take ownership of their training experiences. This fundamental concept is embodied in five principles: (a) Trainees should be provided guidance and resources needed to define and pursue career objectives within and beyond academia, conferring to them greater independence and responsibility in shaping their own future. (b) Learning should be flexible, adaptable, and distributed. Training should combine traditional and modular coursework to encompass both technical and professional skills. Guidance from diverse mentoring teams will support and tailor training toward diverse, personalized career paths. (c) Scientific research experiences should be broad and question-driven, whether motivated by basic discovery or seeking solutions to societal challenges. Trainees should continue to gain mastery of one or a few core scientific disciplines and their key tools and approaches. (d) Trainees should be skilled in science communication and incentivized to engage with and learn from the broader public community, helping to maintain an active dialogue among public, private, and academic sectors. (e) Training programs should foster and facilitate the inclusion of individuals with a diverse range of life experiences and should prioritize trainee well-being. The report recommendations call for a profound cultural shift, one that embraces and extends educational Consortium Name: Plant Science Research Network

Research paper thumbnail of Natural variation and persistent developmental instabilities in geographically diverse accessions of the allopolyploid Arabidopsis suecica

Physiologia Plantarum, 2011

Allopolyploids arise from the hybridization of two species concomitant to genome doubling. While ... more Allopolyploids arise from the hybridization of two species concomitant to genome doubling. While established allopolyploids are common in nature and vigorous in growth, early generation allopolyploids are often less fertile than their progenitors and display frequent phenotypic instabilities. It is commonly assumed that new allopolyploid species must pass through a bottleneck from which only those lines emerge that have reconciled genomic incompatibilities inherited from their progenitors in their combined genome, yet little is known about the processes following allopolyploidization over evolutionary time. To address the question if a single allopolyploidization event leads to a single new homogeneous species or may result in diverse offspring lines, we have investigated 13 natural accessions of Arabidopsis suecica, a relatively recent allopolyploid derived from a single hybridization event. The studied accessions display low genetic diversity between lines, yet show evidence of heritable phenotypic diversity of traits, some of which may be adaptive. Furthermore, our data show that contrary to the notion that unstable phenotypes in neoallopolyploids are eliminated rapidly in the new species, some instabilities are carried along throughout the species' evolution, persisting in the established allopolyploid. In summary, our results suggest that a single allopolyploidization event may lay the foundation for diverse populations of the new allopolyploid species.

Research paper thumbnail of Removing systemic barriers to equity, diversity, and inclusion: Report of the 2019 Plant Science Research Network workshop “Inclusivity in the Plant Sciences”

Plant Direct

A future in which scientific discoveries are valued and trusted by the general public cannot be a... more 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.

Research paper thumbnail of Natural Genetic And Epigenetic Variation At Retroposon Loci In Arabidopsis

In both plants and animals, transposable elements are epigenetically regulated to maintain genomi... more In both plants and animals, transposable elements are epigenetically regulated to maintain genomic integrity. DNA methylation (5-methylcytosine) is an important epigenetic modification that maintains transcriptional silencing at repetitive sequences and transposons. Here, I use the Sadhu family of non-LTR retroposons in Arabidopsis thaliana as models to understand the connection between genetic and epigenetic variation. There are only 16 full-length Sadhu elements in the Arabidopsis thaliana genome, and these elements are genetically diverged, sharing only 75% sequence identity. We analyzed both genetic and epigenetic variation in two different Sadhu elements, the heterochromatic Sadhu1-1 and the euchromatic Sadhu6-1. For both of these elements, we determined that Sadhu is not uniformly controlled but can exist in an epigenetically active or a repressed state. To test the source of variation in epigenetic state at these loci, we crossed two strains with differentially methylated Sadhu elements and observed no trans-activation of the silenced allele, nor repression of the transcribed element in the hybrids. Our results suggest that Sadhu elements are inherited as pure epialleles that differ between strains. Additionally, I investigated intrastrain stability of Sadhu transcription. I used a ddm1 mutation to genetically activate a silenced Sadhu1-1 epiallele. After restoring DDM1, we monitored transcription in these plants for eight meiotic generations and determined that transcription remains on, but is variable in these lines. My findings indicate that maintenance of DNA methylation is sufficient to silence Sadhu elements; however, a loss of methylation does not trigger de novo methylation and epigenetic silencing is not efficiently repaired. The variation within the Sadhu family provides new insights into the stability of DNA methylation at transposons and can serve as a model for natural epigenetic variation

Research paper thumbnail of Broadening the impact of plant science through innovative, integrative, and inclusive outreach

Plant Direct, 2021

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial ... more This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Research paper thumbnail of Plant science decadal vision 2020–2030: Reimagining the potential of plants for a healthy and sustainable future

Plant Direct, 2020

This is an open access article under the terms of the Creative Commons Attribution-NonCommercial ... more This is an open access article under the terms of the Creative Commons Attribution-NonCommercial License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited and is not used for commercial purposes.

Research paper thumbnail of Reinventing postgraduate training in the plant sciences: T-training defined through modularity, customization, and distributed mentorship

Plant Direct, 2018

The Plant Science Research Network (PSRN) comprises scientific societies and organizations with a... more The Plant Science Research Network (PSRN) comprises scientific societies and organizations with a mission to build and communicate a consensus vision of the future of plant science research, education, and training. This report enumerates a set of farreaching recommendations for postgraduate training that emerged from workshops held in October 2016 and September 2017. These recommendations broaden and deepen the T-training concept presented in the Decadal Vision for Plant Science, which emphasizes experiential learning beyond the traditional disciplinary focus. Both workshops used the scenarios developed in Imagining Science in 2035 as a mechanism to encourage out-of-the-box thinking, an approach that led to the innovative recommendations and solutions described here. At the heart of our recommendations is the empowerment of trainees, who should be enabled to customize and take ownership of their training experiences. This fundamental concept is embodied in five principles: (a) Trainees should be provided guidance and resources needed to define and pursue career objectives within and beyond academia, conferring to them greater independence and responsibility in shaping their own future. (b) Learning should be flexible, adaptable, and distributed. Training should combine traditional and modular coursework to encompass both technical and professional skills. Guidance from diverse mentoring teams will support and tailor training toward diverse, personalized career paths. (c) Scientific research experiences should be broad and question-driven, whether motivated by basic discovery or seeking solutions to societal challenges. Trainees should continue to gain mastery of one or a few core scientific disciplines and their key tools and approaches. (d) Trainees should be skilled in science communication and incentivized to engage with and learn from the broader public community, helping to maintain an active dialogue among public, private, and academic sectors. (e) Training programs should foster and facilitate the inclusion of individuals with a diverse range of life experiences and should prioritize trainee well-being. The report recommendations call for a profound cultural shift, one that embraces and extends educational Consortium Name: Plant Science Research Network

Research paper thumbnail of Natural variation and persistent developmental instabilities in geographically diverse accessions of the allopolyploid Arabidopsis suecica

Physiologia Plantarum, 2011

Allopolyploids arise from the hybridization of two species concomitant to genome doubling. While ... more Allopolyploids arise from the hybridization of two species concomitant to genome doubling. While established allopolyploids are common in nature and vigorous in growth, early generation allopolyploids are often less fertile than their progenitors and display frequent phenotypic instabilities. It is commonly assumed that new allopolyploid species must pass through a bottleneck from which only those lines emerge that have reconciled genomic incompatibilities inherited from their progenitors in their combined genome, yet little is known about the processes following allopolyploidization over evolutionary time. To address the question if a single allopolyploidization event leads to a single new homogeneous species or may result in diverse offspring lines, we have investigated 13 natural accessions of Arabidopsis suecica, a relatively recent allopolyploid derived from a single hybridization event. The studied accessions display low genetic diversity between lines, yet show evidence of heritable phenotypic diversity of traits, some of which may be adaptive. Furthermore, our data show that contrary to the notion that unstable phenotypes in neoallopolyploids are eliminated rapidly in the new species, some instabilities are carried along throughout the species' evolution, persisting in the established allopolyploid. In summary, our results suggest that a single allopolyploidization event may lay the foundation for diverse populations of the new allopolyploid species.