|Equity, Diversity, and Inclusion||Beyond Law - Providing Accessibility & Inclusion Just Because||Most approaches to accessibility & inclusion for disabled people in academia and in workplaces focus on legal compliance rather than eagerness to work with and include another human being. This workshop will include tips on making scientific workplaces, processes, and communications accessible, but will challenge participants to go beyond. Rethinking what our goals really are as communicators, teachers, PIs, managers, and scientists can help us redesign for a better, more humane and productive environment for all of us. And that helps make plant science accessible, pleasurable, and sustainable to as many people as possible!|
|Equity, Diversity, and Inclusion||Breakfast Panel: Building Sustained Commitments to Equity and Inclusion||The Black Lives Matter movement, and its heightened urgency in the wake of summer 2020 murders, has prompted many conversations in academia and industry on our collective role supporting BIPOC careers in science. The Women in Plant Biology Committee (WiPB) and Equity, Diversity, and Inclusion Committee (EDIC) hope to help convert these conversations into action. To this end, the joint committees propose an ASPB 2021 panel to highlight previous and ongoing success stories, i.e. initiatives at various career stages that have provided tangible support for BIPOC careers in plant biology. Potential initiatives to highlight include undergraduate peer mentorship, graduate recruitment, graduate and postdoc level networking, faculty cluster hiring/retention, and burden-sharing at all levels. We propose to bring leaders and decision makers together to provide a first-hand account of challenges, goals, strategies, and “on the ground” activities that led to success. We hope to focus especially on activities that have expanded the pipeline of outstanding candidates at all career stages. Panelists will be encouraged to discuss how these initiatives can scale or port into other settings -- for example, other teams, departments, and universities. We propose to host approximately 5 panelists for a 90-minute panel and Q&A. The panel can be held either at breakfast or lunch depending on scheduling needs. We will recruit panelists at the undergraduate, graduate, postdoctoral, faculty, industry, and government (NSF/USDA/DOE/EPA) levels to describe their activities. The organizers will work through existing networks to recruit panelists; these networks include the Arabidopsis/NAASC PEER cohort organizers, SACNAS, HHMI, and cross-university Slack pages such as “Planty Good Trouble” and consider already invited speakers and/or attendees. We hope participants will take back to their workplaces constructive action items with clear steps toward implementation. A short report co-authored by panelists and organizers will be published on the Plantae website and ASPB newsletter to ensure dissemination to a larger audience.|
|Equity, Diversity, and Inclusion||Surviving Academia and Industry||Navigating the scientific workforce can be challenging for anyone at all career stages but is particularly stressful for Black, Indigenous, and People of Color (BIPOC) scientists. Many BIPOC scientists face some level of discrimination/microaggressions associated with conscious and unconscious biases in the workplace that non-BIPOC scientists do not normally experience. In this interactive, hands-on workshop, we aim to give plant scientists tools needed to recognize the effects (physical, mental, emotional, societal, and monetary) of systematic and institutional oppression and how everyday choices and activities contribute to systematic and institutional oppression in - academic and industry institutions. The activity will involve placing participants in a simulated environment. Participants will be placed on an island where they will choose a character class: Survivor or Zombie. Participants will then follow a booklet with scenarios (similar to a “choose your own adventure” novel) that related to situations that BIPOC experience everyday but will be extrapolated to fit the “zombie island” narrative. Participants will be asked to make choices based on these scenarios. These choices will correspond with a tool that participants will select (either physically or virtually) to add to their survival toolkit. Each tool represents an action or coping mechanism that participants can use to deal with everyday discrimination/microaggression incidents. Before the activity begins, facilitators will introduce the activity, explaining all definitions, the flow of the activity, how to seek help, etc. During the activity, facilitators will help participants progress through their story as needed and will pass out appropriate tools. After the story progression time is over (1 hour) participants and facilitators will reconvene together to discuss selected scenarios, what each tool represents, and other takeaway messages from the activity including activity feedback (45 minutes to 1 hour). Depending on the success of the activity, we will consider offering this activity again. Gameplay will occur in real time online and in person at the PB2021 conference. Physical facilitators will direct those in the physical conference space and throughout the booklet. Online facilitators will help direct answer questions and direct individuals online through chat as needed. This number will be determined at a later date. Online space:|
|Professional Development||Systems Thinking framework for Plant Science Undergraduate Education||Our workshop focuses on how we teach plant science concepts and processes in undergraduate classrooms. Plants are integral to atmospheric cycles, energy and biomass flow through systems, and belowground processes. As a central hub for multiple interacting systems, including human systems, it is important to frame plants as part of a complex system. This workshop seeks to train educators at all levels on how to leverage a Systems Thinking framework for teaching and learning.
Incorporating Systems Thinking into instruction can help students relate new information to their previous knowledge and experiences and deepen their understanding of scientific concepts and processes. By guiding students through the complex systems where plants are fundamental to their function, students can gain a deeper understanding of how plants impact biology, the environment, and human lives.
As part of the workshop, participants will learn about Systems Thinking (ST) as an approach to instruction, how to incorporate ST into their courses, and practice framing course concepts as part of a system with many interacting parts. Participants will also be invited to join a collaborative online learning community of instructors interested in Plant Science & Systems Thinking (PSST). By the end of the workshop, instructors should feel confident in their ability to transform their courses to improve student learning outcomes, provide equitable instruction for all students, and discuss pedagogical techniques with fellow instructors from around the world.
|Professional Development||Best practices for teaching plant biology online||One side effect of the coronavirus pandemic was the sudden need to move traditionally face-to-face courses to an online format. Although the initial pivot to online instruction was unforeseen and implemented in a rapid manner, it is clear that online instruction will continue to be important moving forward. Where there was grace and understanding at the beginning of this switch, educators are now expected to be effective and efficient in guiding remote instruction. The purpose of this workshop is to discuss best practices in teaching plant biology online. The workshop will cover aspects of education related to traditional lecture, laboratory activities, student research, and community outreach and will highlight techniques to promote inclusion and active learning. Moderators will organize small-group discussions where participants will share their experiences, best practices, and helpful strategies (in addition to those that weren't as successful). When the full group reconvenes, the workshop will culminate with the sharing and discussion of ideas generated in the small-group sessions.|
|Professional Development||Bioeconomy Careers Beyond Academia||In concert with the PB21 theme of the bioeconomy, the panel will 5-6 people working in industry, government, or non-profit organizations whose jobs center on advancing plant biology research for applications to new products. This will include researchers, as well as folks who may have a background in research but now work as managers, intellectual property, investment and venture capital, and more. The goal of this panel is to give early career researchers into (1) the types of careers possible with undergraduate and graduate degrees in plant science, and (2) how to obtain a job and succeed in these careers. Panelists may be sourced from large ag companies such as Bayer or Syngenta, as well as smaller companies such as Ginkgo Bioworks. The panel will answer prepared questions moderated by Katie Murphy, as well as those from the audience after 30 minutes of lunch/breakfast and open networking time at the tables. Panelists will be chosen when we know conference attendees to reduce costs and select those already attending.|
|Professional Development||Reproducibility for Everyone||Rigor and reproducibility are at the core of modern science and set apart scientific inquiry from pseudoscience. Many new initiatives and tools have been established to address barriers to reproducibility. While very welcome, these projects have led to a proliferation of online tools and resources which can be hard to sift through.
Reproducibility for Everyone (R4E) is a global, community-led reproducibility education initiative. R4E runs practical and accessible workshops to introduce the concept of reproducibility to researchers. We demonstrate reproducible tools and methods that can improve research by making it more efficient, transparent, and rigorous. Since 2018, R4E volunteer instructors have reached over 2000 researchers around the world through over 30 workshops.
This workshop will introduce reproducible workflows and a range of tools for plant biologists along the themes of organization, documentation, analysis, and dissemination. After a brief introduction to the topic of reproducibility, the workshop will provide specific tips and tools useful in improving daily research workflows. The content will include modules such as data management, electronic lab notebooks, reproducible bioinformatics tools and methods, protocol and reagent sharing, data visualization, and version control. The methods and tools introduced help researchers share work with their future self, their immediate colleagues, and the wider scientific community.
Following this workshop, participants will be able to:
1. Apply a conceptual framework for reproducibility, replicability, and robustness of research.
2. Explore practical, accessible tools and methods for advancing the reproducibility of research.
3. Reuse and adapt the Reproducibility for Everyone modular curriculum to their own training and research needs.
|Professional Development||Developing a Course based Undergraduate Research Experience (CURE) from your plant biology research||Developing a Course based Undergraduate Research Experience (CURE) from your plant biology research
While some faculty and researchers in biology and discipline based education research have embraced, developed and taught Course based Undergraduate Research Experiences (CUREs), majority still lag behind due to a lack of awareness. This workshop seeks to improve awareness of CUREs in the plant biology community and to equip plant biologists with skills that will enable them to integrate their research into teaching laboratories of undergraduate students to improve student engagement and interest in plant biology. CUREs are research experiences that have been inserted into college curricula teaching laboratories and designed to successfully engage large numbers of undergraduate students at all levels in scientific research. CUREs, unlike inquiry-based laboratories, are characterized by five attributes: iteration, collaboration, scientific process, broad relevance and discovery of new knowledge (Auchincloss et al. 2014). CUREs have numerous outcomes for undergraduate students including; stimulated interest in STEM fields and careers, increased knowledge and learning of STEM content, increased graduation rates and STEM degree completion (Siritunga et al. 2011; Shaffer et al. 2014; Kerr et al. 2016; Wolkow et al. 2014; 2019; Rodenbusch et al. 2016). Additionally, through CUREs, undergraduate students are provided opportunities to contribute new scientific knowledge, gain skills in scientific competence and science communication (Shelby, 2019; Ward et al. 2014; Sweat et al. 2018), and to improve science practice and experimental design skills (Shelby, 2019; Ward et al. 2014; Peteroy-Kelley et al. 2017). Furthermore, participation in CUREs has been found to increase student self-efficacy and interest in STEM careers as well as retention (Shelby, 2019; Ward et al. 2014; Harrison et al. 2011). Moreover CUREs also provide faculty with tools to connect teaching with research, avenues to recruit students into their research laboratories and student contributions to their data collection and scientific publications (Shortlidge et al. 2017). CUREs can be derived from faculty research projects (Bakshi et al. 2016; Laungani et al. 2018) or from national programs like the Howard Hughes Medical Institute (HHMI) funded Science Education Alliance – Phage Hunters (SEA-PHAGES) and the Genomic Education Partnership (www.seaphages.org; Shaffer et al. 2014).
|Professional Development||Delivering your message: tools for better presentations||Communication is gaining more and more importance in a researcher’s agenda. When discussing with other members of our team, our close colleagues in the lab, or with other researchers in a conference, sharing our science in an understandable way is critical! But it is also a challenge we were rarely trained to accomplish.
Combining knowledge from written communication, graphic design, and theatre, this workshop provides tools to deliver effective scientific posters and presentations, two of the main forms of communication in academia.
The workshop will be divided into three main areas: Choosing the right message for each audience, preparing the supporting material, and delivering the message. This includes topics like word choices and message clarity, preferred layouts for each kind of presentation, colour and text use for inclusive communication, strategies for better visualization of figures and tables, tips for voice control and to nervous management, among others. All the tools provided by this training are universal and can be used in any kind of graphic design or presentation software. Moreover, most of the topics can be applied in our day-to-day communication, not just on posters and oral presentations.
As scientists ourselves, we understand the struggle and the time constrictions researchers are imposed when preparing to communicate their work. That is why all the tips and tools provided by this workshop are aimed at simplifying the enterprise of delivering academic posters and presentations, while also making them more inclusive and assertive to the different types of audiences.
|Professional Development||Grow mentoring skills and inspire future plant scientists with PlantingScience.org|
|Professional Development||Grad School Q&A Panel||For the benefit of the undergraduate attendees of Plant Biology ‘21, the Early Career Plant Scientists (ECPS) Section wishes to organize a Q&A panel focused on applying to and navigating graduate school. ECPS plans to emulate a similar event we organized for PB20 that drew nearly 90 attendees and was met with overwhelmingly positive feedback. Last year’s panel was assembled with a diverse group of graduate students from varied backgrounds and institutions. Panelists took questions from the audience ranging from how to make the decision to go to grad school to strategies for finding a mentor and managing mental health. Feedback from last year’s meeting suggests this workshop added a tremendous amount of value to undergraduate meeting attendance, and we would like to provide that same opportunity to the undergraduate attendees for PB21. If the meeting is in-person, panelists will be assembled from conference attendees to mitigate cost. No special accommodations will be required for this event (standard AV, one screen, and standard seating will all be adequate).|
|Professional Development||You can publish this too! Developing, publishing, and highlighting innovative classroom activities in CourseSource||CourseSource is an online open-access and peer-reviewed journal of evidence-based teaching activities that are aligned with learning frameworks developed by professional societies, including ASPB. CourseSource includes teaching materials that are organized and formatted for ease of replicability. This format means adopters of active-learning have a place to go to obtain expert-vetted teaching materials.
In this workshop, prospective CourseSource authors learn about the journal and submission guidelines, and discuss manuscript ideas. Authors can highlight their publications in job applications, teaching philosophy statements, and tenure and promotion documents. We will share how journal metrics can be highlighted and collaborations with co-authors can provide evidence for institutional change. Finally, we will discuss how authors can publish articles in education research journals and corresponding instructional materials in CourseSource.
|Professional Development||PUI Faculty Development Workshop||This workshop is for faculty currently working at primarily undergraduate institutions (PUIs) or early career scientists who would like to get a job at a PUI. PUIs are defined as institutions that offer few or no PhDs in the sciences. While teaching is a large part of being a PUI faculty member, maintaining a successful research program is also critical for career advancement and for providing undergraduates with high-caliber research experiences. This workshop will include presentations and discussions of inclusivity in research and mentoring. There will be a panel discussion and small-group conversations dedicated to broadening access to undergraduate research that is designed to specifically address the needs of PUI faculty. Small group discussions will focus on developing summer research programs, improving CUREs, recruiting and retaining URM students, and implementing inclusive mentoring practices.|
|Professional Development||Why be a professor at a Primarily Undergraduate Institution (PUI)||This workshop is for people interested in working at a Primarily Undergraduate Institution (PUI). This is a networking opportunity to develop connections with people at PUIs and to help people pursue a job at a PUI. This workshop is also for faculty at research institutions (R1) who want to pass on information to their students and postdocs. The workshop will include career presentations from a panel and discussion groups about jobs at PUIs. The panelists will represent private and public PUIs who will discuss a diversity of career trajectories, and career stages. Panelists will participate in whole group Q&A as well as break-out conversations. PUIs are defined by the NSF as “accredited colleges and universities (including two-year community colleges) that award Associate's degrees, Bachelor's degrees, and/or Master's degrees in NSF-supported fields, but have awarded 20 or fewer Ph.D./D.Sci. degrees in all NSF-supported fields during the combined previoZPUIus two academic years. There will be 2 breakout groups that are 20 minutes each.|
|Professional Development||Building an international career||The International Committee will host a workshop tailored for early career researchers (graduate students, postdoctoral fellows) to discuss experience with and provide advice for building an international career. We will hear from experienced science globetrotters what to consider when planning for graduate studies or postdoctoral work abroad, and how to access scholarships for international mobility.
The workshop will consist of three elements:
• Panel discussion with senior and junior researchers with international careers
• Short presentation by a representative of funding agencies awarding mobility grants
• Virtual Mixer: Participants will be invited to socialize with the panelists and other scientific globetrotters.
|Professional Development, Equity, Diversity, and Inclusion||Our Lab': Building an Inclusive Lab Culture||In this workshop, participants from all career stages and unit types will come together to learn about inclusion, discuss what inclusion means together, and gain hands-on experience with strategies to create an inclusive lab culture. Examples may include: Group Agreement Building, Humanizing STEM, Hierarchy Analysis of Lab Structure, Developing Projects Inclusively, Community Drive Lab Meetings|
|Technical Development and Innovation||Impact of climate change on plant-pathogen interactions||At this workshop, we will discuss how rapidly rising global atmospheric carbon dioxide concentration and the accompanying abiotic stresses alter plant-pathogen interactions and pose a significant threat to global food safety and security. Impending climate conditions are predicted to directly impact the productivity of staple crops and increase the frequency and severity of plant disease outbreaks. Plant pathogens are responsible for more than a third of all of crop losses. Furthermore, crop losses are often compounded due to abiotic stresses, which are also predicted to become more severe in the future. Abiotic factors drive plant-pathogen interactions, and the individual and combined abiotic stress factors associated with climate change, including rising atmospheric CO2, temperature, and extreme precipitation events, can all influence crop susceptibility and disease severity. Finally, industrialized agricultural practices that rely on homogeneous and standardized control strategies have led to more virulent and pesticide resistant pathogens. To fully understand the complex plant-pathogen-environment interactions in future climate conditions, a combined interdisciplinary research approach is needed. This workshop aims to highlight innovative research approaches in addressing this topic, from early career researchers and established scientists alike.|
|Technical Development and Innovation||FlowerNetPheno: Detection of Flowers based on Spatio-Temporal Image Sequence Analysis using Deep Learning Techniques for Event-based Plant Phenotyping||FlowerNetPheno: Detection of Flowers based on Spatio-Temporal Image Sequence Analysis using Deep Learning Techniques for Event-based Plant Phenotyping
With the ease of digital image capturing facility and enormous increase in the processing power of the computers, computer vision and artificial intelligence have gained immense popularity in order to meet current and emerging issues in agriculture relating to future food security under dwindling natural resources and projected climate variability. Imaging techniques facilitate the measurement of observable traits of plants as a result of complex interaction between genotype and environment (referred to as phenotypes) by analyzing a large number of plants in short time interval with precision, nullifying the need for time-consuming physical human labor. The timing of important events in plant's life, e.g., germination, emergence of new leaf, flowering, fruiting and onset of senescence, is crucial in the understanding of the overall plant’s vigor, which is likely to vary with the interaction between genotype and climate, and are referred to as event-based phenotypes. Unlike the visual tracking of rigid bodies, e.g., vehicles and pedestrians whose movements are merely characterized by the change in location, the emergence timing detection of new organs and tracking its growth over time in plants requires a different problem formulation with a completely new set of challenges. Phyllotaxy, the plant’s mechanism to optimize light interception by re-positioning the leaves, adds another layer of complexity in growth tracking of flowers due to self-occlusions. The newly emerged organs, e.g., buds, are often occluded by leaves and assume color of the leaves, which makes their detection challenging. The workshop will provide discussion on the application of deep neural networks, e.g., You Only Look Once (YOLO), Region-based Convolutional Neural Networks (R-CNN), Long Short-Term Memory (LSTM) and U-Net, in event-based plant phenotyping by proposing FlowerNetPheno which detects flowers in a multi-view image sequence. YOLO frames object detection as a regression problem, where a single convolutional neural network is used to simultaneously predict the coordinates of the bounding boxes enclosing the objects and the associated class probabilities. Following flower detection, a set of new phenotypes are computed, e.g., the day of emergence of first flower in a plant’s life cycle, the total number of flowers present in the plant at a given time, the highest number of flowers bloomed in the plant, the growth of individual flowers and blooming rate. To develop a new algorithm and facilitate performance evaluation based on experimental analysis, a benchmark dataset is indispensable. Thus, we introduce a benchmark dataset called FlowerPheno which consists of image sequences of a variety of flowering plants including sunflower, canna, greenbasil, purplebasil and okra, captured by a visible light camera in a high throughput plant phenotyping platform from multiple view angles. The experimental analysis shows the efficacy of using deep learning for event-based flower phenotypes.
|Technical Development and Innovation||The biotechnology of HIGS and SIGS for plant pest resistance: What works, what doesn’t, what’s next?||In this workshop we will convene experts, including advanced graduate students and postdocs, who are working on HIGS (host induced gene silencing by transgenes) and SIGS (spray induced gene silencing by chemical application) to critically assess the state of the technology and its underlying science. We will invite diverse speakers who will present case studies in a variety of crops and pathosystems where one or both of these methods has succeeded or failed, or are under active development. We will also consider the mechanisms of RNA transfer and cross-kingdom function in relation to technology design. Speaking slots will be a combination of long and short talks and discussions, selected after making a general solicitation and inviting active laboratories to take part.|
|Technical Development and Innovation||Full Stack Innovation @ Inari||New companies generally take a technology or science-focused approached to product design and market entry. Not surprisingly, the same technologies are used to facilitate innovation. This framework typically requires specialized teams that are focused solely on creation for the organization, with little interaction with the broader company. This ultimately leads to siloing as the company grows and is the bane of innovation. In this workshop, we will discuss our multi-pronged approached to structured innovation at all levels in a growing organization.|
|Technical Development and Innovation||Plant Bioinformatics Resources||This workshop will introduce attendees to a variety of digital research resources, particularly online bioinformatics websites and knowledgebases, that are valuable for plant biologists to gather background information, generate hypotheses, design experiments, and analyse data. There will be a combination of resource overview talks and application talks which illustrate the use of specific online resources with real-world examples, and a live Q & A.|
|Technical Development and Innovation||Workshop and hackathon on improving orphan crops to foster bio-economies||Most of the research pursued by plant scientists in low- and lower-middle-income countries(LMIC) addresses challenges that directly affect people and local livelihoods, such as climate change, food security and preservation of biological diversity. Yet, these research efforts have often received limited attention by the scientific community, industry, and governments. This is even more evident in research involving neglected or underutilized crop species, also known as orphan crops. Orphan crops are crops that are locally or regionally grown, with less international trade and therefore see little or no attention in terms of research, agricultural training, and extension. These crops are highly nutritious and possess nutraceutical properties. Despite their key roles in the food/ nutritional security and livelihood of resource-poor farmers, especially women, and consumers in the regions they are cultivated, these crops have lagged behind conservation and improvement efforts compared to major crops. With little attention, orphan crops produce inferior yields, a threat to food security. At ASPB ARN, we believe that the inclusion of underrepresented scientists working on marginalized, yet impactful, research themes is key to diversify plant science and to foster thriving bioeconomies in LMIC. The workshop has the following objectives: increasing awareness on research conducted by scientists in LMIC, highlighting ongoing research/breakthrough and potential avenues for product/commodity processing with these crops and promoting collaborations among workshop participants. In particular, the workshop will feature an agricultural technology hackathon to foster innovation and collaboration with the goal of expanding technology development of orphan crop research in LMIC. Over a 72-hour period, multiple teams (including plant scientists, students, and farmers, among others) will be asked to hack possible solutions to a series of given challenges in marginalized agricultural systems leveraging orphan crops.
Overall, the workshop and Hackathon promises to bring together a cohort of international and local scientists, as well as farmers, agriculture extension specialists and other players in the orphan crops league.
|Technical Development and Innovation||The International Weed Genomics Consortium: how you can contribute and what it can do for you.||The International Weed Genomics Consortium (IWGC) are academic and industrial scientists interested in undertaking technical development and innovation for the genomics of weedy species. It currently includes industrial members and 21 academic institutions from 11 countries. We not only recognize that our knowledge of weed genomes lags significantly behind other plant species, but that this lack is more than just a knowledge gap, it is a major obstacle to our understanding these globally impactful plant species. Weeds are an important biotic factor hindering the Bioeconomy and their unique genomes underpin the distinct suite of traits weeds exhibit, setting them apart from model, crop or wild plant species. The IWGC aims to enable technical development and innovation in Weed Science through public-private research that creates weed-specific genomic resources and training partnerships that generate a workforce able to analyze these and implement the innovations generated from them.
A PB21 workshop would enable the IWGC to 1) highlight Weed Genomics Science to the global PBD21 audience, 2) demonstrate our analytical and training resources to a new, more diverse audience, and 3) advertise IWGC opportunities for personal development within weed genomics. We request a 1.5-hour slot to allow time to update our audience on the current state and engage in co-development and sharing of best practice. 1) We would highlight research that has used IWGC innovations and technical developments in sequencing and annotation to demonstrate how weed genomics can provide a mechanistic understanding of how weeds impact the agri-environment (e.g. Kochia scoparia’s rapid evolution of resistance to glyphosate in response to high levels of environmental stress). 2) We would showcase the user-friendly databases and training material IWGC are developing. For instance, we will discuss the functionalities of our first main training resource, the WeedPedia website, which is a home for weed genomics resources, tools, and networking. 3) Attracting new talent across the range of learning and career possibilities in Weed Genomics is fundamental to IWGC’s purpose and supported by dedicated funding to enable research experience visits to IWGC academic and industry labs for students. The details for this and other efforts to expand the diverse and inclusive community of scientists in weed genomics can be explained further at PB21.
An IWGC workshop at PB21 would not be one-directional knowledge transfer. Instead, IWGC would engage and interact with a wide range of scientists outside of our predictable weed-centric research communities, from students to established genomicists. We would actively recruit participants and presenters from across disciplines and career stages to this workshop supported by IWGC resources. We have much that could be gained from interacting with the global, high-quality plant science community at the ASPB Plant Biology conferences. Although our weed-focused questions are different from crop, model or wild plant research, we can learn from others’ triumphs and tribulations and share our own. Therefore, we predict this workshop would provide mutual benefit for the PB21 audience and the IWGC.
|Technical Development and Innovation||A KBase Case Study: Investigating the reconfiguration of plant metabolism in response to pathogen invasion using SRA data.||In this workshop, we will demonstrate the use of Narratives and Apps in The Department of Energy Systems Biology Knowledgebase (KBase) to create reproducible, flexible workflows for the analysis of next generation sequencing (NGS) data in both model plants and crops. We will present a case study using SRA data and also lead a hands-on session in which users can create their own Narratives, import data, run Apps, and analyze the results.
Case Study: Plant metabolism is reconfigured in response to invasion by pathogens. When mediated by transcriptional changes, this metabolic reconfiguration can be detected by comparing genome-wide mRNA sequence (mRNA-seq) data between infected and control plants. By integrating transcript abundances with a model of primary metabolism, we can then identify biochemical reactions where transcription is altered upon infection in both model and crop species. This approach can be extended to study the responses of plant metabolism to a variety of environmental conditions.
KBase: The Department of Energy Systems Biology Knowledgebase (KBase) is a knowledge creation and discovery environment designed for both biologists and bioinformaticians. KBase integrates a large variety of public data and analysis tools into Narratives, an easy-to-use graphical user interface that leverages DOE computational infrastructure to perform sophisticated systems biology analyses.
Narratives and Apps: Narratives are dynamic, interactive documents that promote collaboration and reproducibility of the scientific results generated by Apps. Apps are analysis tools you use in KBase. Apps interoperate seamlessly within a Narrative to enable a range of scientific workflows. A finished Narrative is persistent and represents a complete record of the methods for a computational experiment. Public Narratives serve as resources for the user community by capturing valuable datasets, associated computational analyses, and scientific context describing the rationale behind a scientific study. The Narrative structure simplifies the re-purposing, re-application, and extension of scientific techniques, thereby supporting reproducible and transparent research in KBase.
Presentation: The KBase tools featured in our case study are broadly applicable for profiling plant gene expression using NGS data. We will demonstrate the following workflow: In a KBase Narrative, we import public mRNA-seq data from susceptible Arabidopsis thaliana and Solanum lycopersicum (tomato) samples treated with either the bacterial pathogen Pseudomonas syringae DC3000 or sterile buffer as a control. Using KBase Apps, we process the Illumina reads to obtain consistent length, depth, and quality across datasets. We align the reads to reference genomes and assemble transcripts using a customized combination of KBase Apps running published, open-source software. We then generate tables with normalized, average transcript abundances for infection and control conditions.
Our case study also features user-friendly tools for building metabolic models from plant genomes in KBase. Transcript abundances are integrated with genome-scale networks of primary metabolism to find the reactions with the largest expression changes between conditions.
Hands-on session: In the second part of the workshop, users will receive guidance on importing their own NGS data to a KBase Narrative and selecting from among the Apps described above to analyze gene expression or construct metabolic models.
|Technical Development and Innovation||Accessing Genomes and Plant Ecosystems – One SMRT Cell at a Time||The advent of single-molecule sequencing technology dramatically changed access to genomic resources for all species. PacBio Sequel II and Sequel IIe system delivers highly accurate reads (HiFi reads) that enables assembly of high-quality genomes and transcriptomes with a single SMRT Cell 8M. PacBio sequencing has been used to sequence the highly complex and repetitive genomes and transcriptomes such as California redwood, Norway spruce, Scots pine, to agriculturally important crops including maize, rice, barley, wheat, and quinoa. Continued technical advances have led to increasing outputs, lower cost, and greater access. Recently, HiFi reads have ushered in new assembly tools that enables directly phased genome assemblies. Using long reads, we now not only have the ability to sequence full-length transcripts for genome annotation, but also look at tissue- and allele-specific isoform expression, under different conditions, in many individuals. Furthermore, long reads can be applied to look at transcriptome at the single cell level, to monitor allele specific expression single cell level. In this workshop, we will cover applications of long read sequencing for the purpose of genome and transcriptome sequencing for plants and their associated microbiome.|
|Technical Development and Innovation, Professional Development||Plant stem anatomy: what cells can tell us||Over 300 years of wood anatomical exploration underlined the minute details of the structures supporting plant life on Earth and its modification due to external factors. But this knowledge is still not widely applied. Therefore, this workshop will combine theoretical and practical learning experiences on selected case studies at local, regional, and global scales. The workshop will introduce absolute beginners into the fascinating world of plant stem anatomy of herbs, shrubs, trees and lianas. During the workshop, we will discuss field sampling and sample preparation techniques for anatomical studies. Then we will observe anatomical images to understand the processes of wood and bark formation, and to gain insight into the evolution of xylem structures. The workshop will further focus on the ecological significance of selected anatomical features in response to climate adaptation. This will open new possibilities for future studies in bioeconomy, ecology and evolutionary biology, global change biology and the carbon cycle.
− Crivellaro, A. & Schweingruber F.H. (2015). Stem Anatomical Features of Dicotyledons. Xylem, phloem, cortex and periderm characteristics for ecological and taxonomical analyses. Kessel Publishing.
− Crivellaro, A., & Büntgen, U. (2020). New Evidence of Thermally Constrained Plant Cell Wall Lignification. Trends in Plant Science. 25 (4): 322-324.
− von Arx, G., Crivellaro, A., Prendin, A. L., Čufar, K., & Carrer, M. (2016). Quantitative wood anatomy—practical guidelines. Frontiers in plant science, 7, 781.
− Piermattei, A., Crivellaro, A., Carrer, M., & Urbinati, C. (2015). The “blue ring”: anatomy and formation hypothesis of a new tree-ring anomaly in conifers. Trees, 29(2), 613-620.
|Technical Development and Innovation, Professional Development||Author-Driven Computable Data and Ontology Product for Taxonomists||It takes great effort to manually convert free-text phenotype narratives (e.g. morphological descriptions in taxonomic works) to a computable format before they can be used in large-scale analyses. We argue that this manual curation approach is not a sustainable solution to produce computable phenotypic data for three reasons: 1) it does not scale to all of the biodiversity; 2) it does not stop the publication of free-text phenotypes that will continue to need manual curation in the future and, most importantly, 3) It does not solve the problem of inter-curator variation (curators interpret/convert a phenotype differently from each other). Our empirical studies have shown that inter-curator variation is as high as 40% even within a single project. With this level of variation, it is difficult to imagine that data integrated from multiple curation projects can be of high quality. The key causes of this variation have been identified as semantic vagueness in original phenotype descriptions and difficulties in using standardized vocabularies (ontologies). We argue that the authors describing characters are the key to the solution. Given the right tools and appropriate attribution, the authors should be in charge of developing a project’s semantics and ontology. This will speed up ontology development and improve the semantic clarity of the descriptions from the moment of publication. In this workshop, we will introduce a web-based, ontology-aware software application called 'Character Recorder' that provides authors with the flexibility of using their preferred terminology in recording characters for a set of specimens, yet at the same time facilitates semantic clarity and consistency across species descriptions. Participants will experience this software prototype with hands-on exercises. The workshop will start with an intro where we report the findings from a recent survey on the need for a tool like Character Record, followed by a set of short and carefully structured hands-on sessions, and end with participants filling out a user experience questionnaire and a free discussion. The final outcome of the workshop will be a manuscript with all participants as authors summarizing the user experience with this tool.|
|Technical Development and Innovation, Professional Development||Improving Crop Nitrogen Use Efficiency for Sustainable Nitrogen Management||Even as carbon continues to dominate the global conciousness on pollution and climate change, reactive nitrogen compounds like ammonia, nitrates, NOx and nitrous oxide have been menacingly growing in the global environment and agriculture is one of their major contributors. Nitrous oxide has 265 times higher global warming potential than carbon dioxide (IPCC AR5). The UNEP annual Frontiers Report (2018-19) co-authored by me identified reactive nitrogen as one of the 5 emerging threats to planet earth and the 4th UN Environment Assembly (2019) has unanimously adopted the first ever resolution on “Sustainable Nitrogen Management”. Our ongoing global nitrogen assessment under the GEF-UNEP-INI project “Towards the establishment of an International Nitrogen Management System” clearly indicates that most of the solutions to N pollution must come from agriculture. We must enhance fertilizer N-use efficiency (NUE) of crops from the present global average of 30%. This is not only an economic loss of fertilizers worth billions of dollars, but also environmental losses worth many fold more, as they cascade into adverse impacts on our health, biodiversity, climate change and much more.
This workshop aims to bring together the best plant biologists engaged in this field to share the latest developments in phenotyping and genotyping for NUE, candidate genes/loci and the meeting points for forward and reverse genetics for innovative selection and breeding. Some of our own recent work on some of these aspects is in press. This field itself has witnessed impressive growth in the recent past and is ideal for professional development of young scientists as well as for fostering technical development and innovation among practitioners. Many journals like Frontiers, Environmental Research Letters, Sustainability etc., have announced special issues on NUE (being coedited by me) to be completed by the 2nd quarter of 2021, just in time for the Plant Biology 2021 conference. In my capacity as the current Chair of the International Nitrogen Initiative and a steering committee member of the UNEP Global Partnership on Nutrient Management, I have been closely interacting with the “International Society for Nitrogen Nutrition of Plants (ISNNP) and “International Conference on Nitrogen Fixation (ICNF)” which are the main international bodies working on plant biological aspects of NUE. Their last triennial conferences were held in 2019 and I hope to galvanize them to this workshop (apart from other independent scientists of the field) to share their latest findings for the benefit of the larger community. Some of them may already be planning to participate in PB21, but being a part of this workshop will bring a strong focus for the presenters as well as the participants interested on NUE. If possible, I would be glad to give a plenary talk on the opportunities and challenges to improve NUE, to highlight the ongoing transition of the field from Arabidopsis to crop plants and invite wider participation in the workshop.
It may also be possible to work towards a special issue/section of Plant Physiology on this theme as a follow up activity after this workshop, hopefully co-edited by the chairs of all the 3 above international scientific bodies on nitrogen.
|Technical Development and Innovation, Professional Development||Enhancing Plant Science Education through the NSF National Research Traineeships (NRT)||In 2014, the National Science Foundation formed National Research Traineeships (NRT) to encourage innovation in graduate education and research. NRTs are interdisciplinary in nature and tap into convergent themes in other disciplines such as data sciences and engineering to provide deep training in trainees’ chosen fields and broad training in adjacent disciplines. These programs also include training in teamwork, communications skills, entrepreneurship, and professional development. The NRT has funded projects for the last six years, many of which focus on plant science and agriculture. The purpose of this proposed special ASPB session is to demonstrate the diverse training activities that are currently implemented by NRT programs in the Plant Sciences, and to discuss how these programs are training the next generation of plant scientists to address important issues in foundational plant research and agriculture. The goal is to generate discussion about how these novel innovations in graduate training can be extended on a national level, to equip emerging plant scientists who are poised to address challenges in a changing world.
We propose a special session at the 2021 ASPB conference focused on NRTs and the unique interdisciplinary training opportunities they provide in plant science graduate education. Some potential topics to be discussed in this session include:
• Cross-disciplinary graduate education in plant science and other disciplines.
• Assessment, evaluation and continuous improvement of graduate programs.
• Creating diverse, inclusive and supportive graduate student communities.
• Professional development of graduate students with diverse skill sets in communications and entrepreneurship.
• The impact of educational disruptions on graduate students and graduate education.
The presenting NRTs include:
Predictive Plant Phenomics at Iowa State University (Julie Dickerson, PI)
Plants3D at UC Riverside (Julia Bailey-Serres, PI)
Digital Plant Sciences at Cornell University (Michael Scanlon, PI)
IMPACTS at Michigan State University (Shin-Han Shiu, PI)
These NRTs represent a variety of approaches to next-generation graduate education, and comprise different stages of program development. All four programs focus on methods to successfully bridge the divide between plant sciences and quantitative disciplines such as data science and engineering.
Topics to be discussed and demonstrated in this session include:
• Cross disciplinary graduate education in plant science and quantitative analysis.
• Assessment, evaluation and continuous improvement of graduate programs
• Professional development of graduate students with diverse skill sets in communications and entrepreneurship.
• Teamwork skills.
|Technical Development and Innovation, Professional Development, Equity, Diversity, and Inclusion||Marine farming - biotech for the oceans||UN decade for ocean science for sustainable development is from 2021-2030.
The workshop will be focused around the importance of ocean primary producers for the future bioeconomy. Marine sources contributes only some 2% of the global food/feed production. This is because we harvest at high trophic levels and very little at the primary producers level. Microalgae and seaweeds and have a huge potential to contribute to a sustainable food and feed production. This is also due to the potential of serious targeted breeding and the technology developments opening for all kinds of trait improvement. The field is underexploited and have been give far to little attention up to now. But there is many exciting things in the pipeline and the toolbox is growing fast. Technology developments, new models and a range of potential applications together with the strong focus on saving some wild terrestrial areas from agriculture point to future marine farming. At the same time the development of marine farming and the technology opportunities raises many governing and moral philosophic questions.
|Technical Development and Innovation, Professional Development, Equity, Diversity, and Inclusion||Advances in Plant Biology and Sustainable Agriculture across the Middle East and North Africa|