Computational image analysis for microscopy (by Adrienne Roeder).

plantcell;31/10/tpc.119.tt0819/FIG1F1fig1The age of big data includes sophisticated imaging datasets. Computational image processing is essential for extracting quantitative information from these large image datasets. Computer scientists have been working for decades to build image analysis tools. It is critical for biologists to understand the concepts in image processing so that they can communicate with computer scientists in designing image processing pipelines and applying these tools to their own images. We focus on microscopy images, but the principles apply to other types of images as well. Furthermore, it is important to understand what manipulations are appropriate in preparing images for publication, what manipulations must be disclosed in the methods and the figure legends, and what manipulations are unacceptable. Here we introduce computational image analysis concepts and terms and illustrate them with Fiji and the COSTANZA (COnfocal STack ANalyZer) plugin. We provide a step by step, hands-on workshop with a sample image so that students can try some of these functions themselves.(Posted September xx, 2019)Click HERE to access Teaching Tool ComponentsRECOMMENDED CITATION STYLE:Roeder, A. (September xx, 2019). Computational image analysis for microscopy. Teaching Tools in Plant Biology. The Plant Cell doi/ 10.1105/tpc.119.tt0819.

Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations.

plantcell;31/12/tpc.119.tt1219/FIG1F1fig1Structural biology has provided valuable insights and high-resolution views of the biophysical processes in plants, such as photosynthesis, hormone signaling, nutrient transport, and toxin efflux. However, structural biology only provides a few "snapshots" of protein structure, whereas in vivo, protein function involves complex dynamical processes such as ligand binding and conformational changes that structures alone are unable to capture in full detail. Here, we present all-atom molecular dynamics (MD) simulations as a "computational microscope" that can be used to capture detailed structural and dynamical information about the molecular machinery in plants and gain high-resolution insights into plant growth and function. In addition to the background information provided here, we have prepared a set of tutorials that allow students to run and explore MD simulations of plant proteins.(Posted December 10, 2019)Click HERE to access Teaching Tools ComponentsRECOMMENDED CITATION STYLE:Feng, J., Chen, J., Selvam, B., and Shukla, D. (December 10, 2019). Computational microscopy: Revealing molecular mechanisms in plants using molecular dynamics simulations. Teaching Tools in Plant Biology: Lecture Notes. The Plant Cell (online), doi/ /10.1105/tpc.tt1219.

Genetics of Floral Development (By Christine Fleet).

Summaryplantcell;29/11/tpc.117.tt1117/FIG1F1fig1A basic model for floral organ identity has been developed using model systems such as Arabidopsis thaliana, snapdragon (Antirrhinum majus), and petunia (Petunia hybrida). In this model, different combinations of proteins known as ABCDE proteins, mostly MADS-domain transcription factors, activate the transcription of target genes to specify the identity of each whorl of floral organs. Changes in the regulation or activation of these target genes contribute to the wide variety of floral forms that we see within and across species. In addition, duplications and divergence of these genes in different groups of flowering plants have resulted in differences in gene function and expression patterns, contributing to differences in flower form across species. Posted December 8, 2017.Click HERE to access Teaching Tool Components.

A really useful pathogen, Agrobacterium tumefaciens.

Bacteria of the genus Agrobacterium are very useful and unusual plant pathogens. Through a rare inter-kingdom DNA transfer, the bacteria move some of their genes into their host's genome, thereby inducing the host cells to proliferate and produce opines, nutrients sources for the pathogen. Agrobacterium's ability to transfer DNA makes can be adapted to introduce other genes, such as those encoding useful traits, into plant genomes. The development of Agrobacterium as a tool to transform plants is a landmark event in modern plant biology. This lecture provides an introduction to Agrobacterium tumefaciens and related species, focusing on their modes of pathogenicity, their usefulness as tools for plant transformation, and their use as a model for the study of plant-pathogen interactions.

The Gatsby Plant Science Summer School: inspiring the next generation of plant science researchers.

We provide evidence from a 5-year study to show that a single concerted effort at the start of undergraduate study can have a clear and lasting effect on the attitudes of students toward plant science. Attendance at a week-long residential plant science summer school in the first year of an undergraduate degree resulted in many students changing courses to include more plant science and increased numbers of graduates selecting plant-based PhDs. The evidence shows that the Gatsby Plant Science Summer School has increased the pool of high-quality plant science related PhD applicants in the UK and has had a positive impact on students' career aspirations. The results are discussed within the context of enhancing the pipeline of future plant scientists and reversing the decline of this vulnerable and strategically important subject relevant to addressing food security and other major global challenges. We have shown that a single well-designed and timely intervention can influence future student behavior and as such offers a framework of potential use to other vulnerable disciplines.

Visual plant anatomy: From science to education and vice versa.

Plant biology, mainly plant anatomy, is a less attractive area for students at high school and university, but not much research has been devoted to improve this field. We therefore researched into the teaching of root, stem and leaf anatomy combined with the preparation of native microscopic slides and histochemical reaction using two selected dyes (classic phloroglucinol test combined with textile dye 'Duha green' to visualize xylem and phloem, respectively). The use of reagents in teaching had a positive effect on students' knowledge (control/ experimental class) of root (+70%), stem (+70%) and leaf anatomy (+130%) as well as vascular and mechanical tissues (+170%), leading to an overall improvement of knowledge by ca. 100%. Students' ability to identify individual tissues on microscopic slides increased and they also understood the functions of individual tissues after self-preparing and staining slides. However, we identified that some aspects were still problematic for students after the experimental education (e.g. identification of tissue providing secondary growth, significance of sclerenchyma and transpiration). We also attach correct answers for the anatomy test and worksheets used for practical exercises as motivation for wider use to improve students' knowledge of plant anatomy.

Photosynthesis-related quantities for education and modeling.

A quantitative understanding of the photosynthetic machinery depends largely on quantities, such as concentrations, sizes, absorption wavelengths, redox potentials, and rate constants. The present contribution is a collection of numbers and quantities related mainly to photosynthesis in higher plants. All numbers are taken directly from a literature or database source and the corresponding reference is provided. The numerical values, presented in this paper, provide ranges of values, obtained in specific experiments for specific organisms. However, the presented numbers can be useful for understanding the principles of structure and function of photosynthetic machinery and for guidance of future research.

The role of botanic gardens in the science and practice of ecological restoration.

Many of the skills and resources associated with botanic gardens and arboreta, including plant taxonomy, horticulture, and seed bank management, are fundamental to ecological restoration efforts, yet few of the world's botanic gardens are involved in the science or practice of restoration. Thus, we examined the potential role of botanic gardens in these emerging fields. We believe a reorientation of certain existing institutional strengths, such as plant-based research and knowledge transfer, would enable many more botanic gardens worldwide to provide effective science-based support to restoration efforts. We recommend botanic gardens widen research to include ecosystems as well as species, increase involvement in practical restoration projects and training practitioners, and serve as information hubs for data archiving and exchange.

Authentic Research in the Classroom Increases Appreciation for Plants in Undergraduate Biology Students.

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 (PAD) (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. The 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. However, quantitative gains in self-efficacy and scientific identity 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 PAD, implementing multiple CUREs per course, or focusing more on final CURE products, could promote larger and more consistent gains in student affect across institutions.

Good for a national cemetery: questions of land use and an 1888 Botanical Expedition across Northern Michigan.

In the second half of the nineteenth century, lumbermen logged the virgin pine forests of northern Michigan. The assumption was that the "plow would follow the axe," and agriculture would dominate the region as it did in the southern half of the state. When farming did not quickly take root, William James Beal and Liberty Hyde Bailey led an expedition of scientists and journalists on a trip across northern Michigan in June 1888 to collect botanical samples, to find a site for a state forest reserve, and to recommend appropriate farming enterprises. This essay contends that without a key reforestation advocate in charles Garfield the explorers focused too much on the questions related to botany and agriculture.While agriculture would ultimately thrive in some parts of the cutover, much of the region was unsuitable for intensive farming. The failure of the scientists to convey these limits adequately in newspaper articles and subsequent reports allowed for their work to be used by agricultural boosters throughout the region. The result was a cycle of erosion, fire, and farm abandonment that proved to be a political problem in Michigan for the first three decades of the twentieth century.

Finding the Gaps: An Assessment of Concepts, Skills, and Employer Expectations for Plant Pathology Foundational Courses.

Foundational plant pathology courses, taught at the undergraduate level, serve students from a wide array of disciplines, and for most will be the only plant pathology course taken. This work examined the content, skills, and delivery modes of undergraduate plant pathology courses at a national scale, and assessed employer expectations for these courses and for students entering the workforce with degrees in plant science-related disciplines. While content knowledge coverage among plant pathology courses was generally consistent and aligned well with employers' knowledge expectations, delivery modes and skill development components were more variable and less aligned. Significant gaps were found between skills expected by employers and those emphasized by instructors, particularly in the areas of general laboratory skills (e.g., media preparation, molecular techniques, microscopy, and competence with other lab equipment) and recognition of plant problems that are not caused by pathogens. Employers also emphasized the value of (and frequent lack of) critical soft skills, such as teamwork, adaptability, communication, writing, and critical thinking. Results of this study will provide a foundation for course and curriculum development and evaluations. Recommendations are also discussed for enhanced interactions among educators and employers outside of academia.