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NRC Publishes Review of AFRI Program

Dear US ASPB members:

A very important report, “Spurring Innovation in Food and Agriculture: A review of the USDA Agriculture and Food Research Initiative (AFRI) Program,” was recently published by the National Research Council (NRC) of the National Academy of Sciences. A large portion of the researchers in our community are, have been, or will be funded through AFRI. Because it is the principal funding agency supporting plant science research and training in the agricultural space, we have a vested interest in its continued growth and success.

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In an effort to facilitate the improvement of AFRI and its ability to leverage cutting edge science to address societal needs with regard to the provision of food, fuel, and fiber, ASPB actively supported the NRC review of AFRI. Some of you may recall that we circulated a survey via the monthly Member Chatter to solicit your views and perspectives on the issues being considered by the NRC committee. The results of your feedback were then used to craft a presentation delivered by Peggy Lemaux, then serving as ASPB President, to the NRC committee. All of ASPB’s top concerns were addressed by this NRC report.

Briefly, some of the major issues articulated in ASPB’s comments that were addressed in the NRC review of the AFRI program were as follows:

  • Front and center in our remarks to the committee was the issue of the general lack of funding for research, especially plant research. In response, the NRC called for the increased “public investment in competitive agricultural R&D to ensure [the United States] continues its role of a global leader in the innovations and technologies that are needed to promote health and well-being and to feed growing worldwide populations sustainably.”
  • Second, we shared the ASPB community’s concern about the current generation of young scientists, especially assistant professors, who are in their first positions and need to launch their research programs in order secure tenure. The NRC concluded that “AFRI should carefully examine the causes of the decline in the numbers of applicants, awardees, and trainees and adjust its grant programs to ensure that future generations of young scientists are not lost inadvertently from food and agriculture R&D because of funding policies.”
  • A third area of concern was the unpredictable cycling of grant priorities. In response, the NRC report urges AFRI to 1) “develop a strategic plan that identifies priorities for its overall program goals…” and 2) “have a more consistent and predictable program portfolio and funding strategy to enable better planning by the food and agricultural research community.”

ASPB will continue to engage USDA around the concerns of our community and the recommended remedies proposed by the NRC. Further, we will use the report as an opportunity to advance the goals set forth by the “Plant Science Decadal Vision.” To learn more about the NRC review of the AFRI program, please click here to view the report prepared by Lewis-Burke Associates, ASPB’s government relations consultants, and click here to view the full report. As always, please feel free to share your comments and questions with ASPB’s director of legislative and public affairs, Tyrone Spady.

Sincerely,
Alan M. Jones, Ph.D.
President, American Society of Plant Biologists

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Charging ahead with plant nutrition

Teaching Tools in Plant Biology has released the first of a three-part series on the topic of Plant Nutrition, “Plant Nutrition 1: Membrane Transport and Energetics, K Nutrition and Na Toxicity”,  co-authored by Michael Blatt.

This lesson starts by describing the central role of membrane transport and energetics in plant nutrition. The proton-motive force needed for ions to be transported across membranes is generated by membrane-localized H+-ATPases and PPases, which can consume as much as a third of a cell’s metabolic energy.TTPB29Graphicsmall

The interplay between two similar but very different ions, K+ and Na+, is described to illustrate the connection between energetics and nutrition. Potassium is an essential nutrient and one of the elements most widely used in synthetic fertilizers to enhance yields, sodium is one of the elements that most limits plant growth, yet several transporters only poorly discriminate between them. Thus, in K-poor soils, plants are can be more susceptible to Na toxicity, whereas augmenting soils with K-containing soils can increase their tolerance. The genetics behind salinity tolerance has been studied intensively in close relatives of crop plants but also in extremely salt-tolerant halophytes, and the results of these studies are contributing to the development improved crop varieties.

In this lesson, the connection between ionic charge distribution across membranes and real-world food production challenges is made explicit; we hope you find it electrifying.

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Outreach is a Hybrid

What Transpires When Scientists Reach Out?

Broader Impacts and Community Service – compatible outreach options

Outreach matters. Good outreach advances science. Some folks conduct outreach through broader impact goals. Others get involved at the community level. What’s the difference? Where do you fit in?

Outreach-is-Hybrid

Broader Impacts Action Items:
1. Learn more about Broader Impacts from a recent summit here.
2. Share examples of successful plant biology broader impacts statements and reports. Send them to Katie@aspb.org to help populate an archive of quality sample statements and outcomes.

Community Service Action Items:
1. Nominate a US-based high school teacher or public librarian with whom you collaborate for free online access to ASPB’s journals.
2. Serve as a Science Fair judge or Career Day speaker.  Search here for a Career Day PPT & other resources to share.
3. Invite a local high school student into your lab for a month/semester/summer of hands-on experience and mentoring.

 

  Excellent input from Sarah Wyatt (Ohio University) aided in the creation of this post.

 

 

 


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Last but not least, as a very active member of the iConnect team, I went to the workshop regarding the funding opportunities available from three of the most important federal agencies in the United States: USDA (United States Department of Agriculture), DOE (Department of Energy) and NSF (National Science Foundation). It was very popular, as I could not find a place to sit at all. Well over 70 people attended! I am including a picture inside the room taken in a hurry, as the questions and answers were all so interesting I did not want to get distracted!

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As a Mexican early career faculty, currently sending proposals to different federal agencies in my country, I know how it feels to be in the ballgame. As my colleagues and collaborators in the U.S. have told me before, it was important to update my information on the state of funding in the United States, to know how I can help them, if it is the case. When I was a postdoc at Texas A & M University, economic crisis hit hard on our University system. It was difficult to see new and seasoned professors suffer a good deal of stress due to the lack of funding. Unfortunately the economy has improved but the amount of money destined to research has not increased. It is a bit depressing due to the great effort we invest preparing our proposals. It was the general feeling of many of the attendees to this workshop, I believe.

After listening the alarming numbers regarding population growth without control, I was wondering if a positive effect could be the increasing number of people dedicated to science. This is good news, right? But, what about lab space and funds? Well, I am an optimist and, as with many of my colleagues, a fighter. I think that these federal agencies are trying to help us but they have to support the best of the best, therefore the only thing we have to do is prepare our proposals until we reach excellence and keep trying until we get funded or drop dead!

The workshop was very complete as USDA‐NIFA, USDA‐ARS, DOE and NSF program staff discussed current research and education opportunities available in their agencies for Plant Biologists. Please visit each agency website to find which program fits better your interests and needs.

In addition, the speakers gave us useful advice on how to navigate the process. One key clue is to contact directly the program director and ask as many questions as might be needed. The process is very transparent as it is peer reviewed. However, the proposal to be successful has to pass several reviewing filters and be at the very top of the proposals to be recommended for funding. Nowadays we all are doing outstanding science and preparing our proposals as excellent as we can. As I said before, to be successful we will have to be the best of the best.

Below is the list of the staff members of each agency who presented a very complete view of the programs that they currently support.

Liang‐Shiou Lin, Shing Kwok and Pushpa Kathir, NIFA
Sharlene Weatherwax and Gail Mclean, DOE
Karen Cone and Diane Okumura, NSF

It was a useful workshop, but there were too many people interested that the time was not enough. I hope this kind of workshop continues during Plant Biology meetings as many more people will be looking for a place to obtain this kind of information.

Thanks to the organizers and the agencies staff members who were helping us with our questions and concerns.

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During the recent Plant Biology conference, editors from the ASPB journals The Plant Cell and Plant Physiology shared insights and fielded questions about how to publish in top journals, to an audience of about 100 early career researchers.

Mike Blatt (Editor-in-Chief of Plant Physiology) recognized the important contributions of the journals’ geographically diverse academic editorial boards (see http://www.plantphysiol.org/site/misc/edboard.xhtml and http://www.plantcell.org/site/misc/edboard.xhtml). He noted that both journals have very high impact and h-factors, and publish research of broad fundamental importance.

CoversMuch of what he and the next speaker, Leon Kochian (Editorial Board Plant Physiology, & Cornell University) spoke about can be found in the journal’s Instructions for Authors page, which is mandatory reading for anyone seeking to publish. In particular, they highlighted the importance of making sure that the article you submit fits the mandate of the journal, which is summarized:

“Research Articles must either present original findings that offer substantially new and fundamental insights into the biological processes of plants and/or set out novel and useful approaches, tools and resources that will enable scientific progress.”

They encouraged prospective authors to examine carefully the research areas covered by the journal, as well as the different types of article published, both of which are indicated in the Instructions for Authors. Mike urged authors to read the ASPB’s Ethics in Publishing statement and specific guidelines about how to manage image data.

Leon provided suggestions for good writing practices, including the importance of asking the right question, mastering the relevant literature, having a good story, and telling it in a clear, logical and interesting way (described later as “the 3 Cs: clear, concise and captivating”). He summarized by reminding us that “Writing a good paper is one of the hardest things you’ll ever do.”

The second half of the workshop was devoted to a question and answer session, led by two members of The Plant Cell’s editorial board, Blake Meyers (University of Delaware) and Bill Lucas (University of California, Davis). Several questions centered on how the review process works. Blake and Bill pointed out that top journals like The Plant Cell and Plant Physiology use a peer-review system that gets anonymous insights from top scientists (in contrast to some other journals that use professional editors for much of the decision making). Reviewer’s anonymity was discussed, with the majority sentiment being that anonymity can ensure the most useful reviews as well as protect reviewers from repercussion.

The question of having one’s work scooped by another group was raised repeatedly. Two points were made by the panellists: first, that it is extremely unlikely that identical experiments were done, and so your work still has value in its different approach, and second, that the journal editors and reviewers can often coordinate publication of two related papers as back-to-back articles, ensuring that both research groups get credit for their findings.

Finally, the issue of rejection was raised; Plant Physiology initially rejects 70% of its submissions. Learning to cope with rejection is one of the most important and challenging skills you need to acquire. Mike shared a useful guide to responding to rejection that includes the humorous retort “Your rejection was carefully reviewed by three experts in our laboratory, and based on their opinions, we find that it is not possible for us to accept your rejection.If you want to write an angry letter after reading your reviews, feel free to do so (it can be cathartic), but whatever you do, DON’T SEND IT! Deep breaths, discussion and sleep will help you respond more rationally. All of the panellists wanted to impart the message that the objective of the reviewers and editors is to support the scientist, to ensure that they get useful feedback, and ultimately to publish the best quality research.

And that’s really what makes science work, isn’t it?

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Next Generation Sequencing: Opportunities and Resources

As part of the iConnect team, I had the good fortune to go to several workshops during the conference Plant Biology 2014 organized by the American Society of Plant Biologists.

 

ASPB offers a diverse set of venues to acquire new skills and improve our careers by encouraging networking and initiation of collaborations. This year, for the Next Generation Sequencing workshop, ASPB organizers invited seven (the magic number?) experts with different levels of experience on bioinformatics. The event was sponsored by the ASPB Membership Committee and the speakers were Jason Williams and Christos Noutsos  from Cold Spring Harbor Laboratory, Nicole Hopkins from University of Arizona who is also working on iPlant Collaborative initiative (support@iplantcollaborative.org), Todd Mockler from Donald Danforth Plant Science Center, Kranthi Mandadi from Texas A&M University, Pankaj Jaiswal from Oregon State University and David Horvath from ARS-USDA. I have included a picture of them. They all are very photogenic!

Next Generation Sequencing Workshop Speakers

Next Generation Sequencing Workshop Speakers. (from left) Kranthi Mandadi, Pankaj Jaiswal, Christos Noutsos, Nicole Hopkins, Jason Williams, Todd Mockler, and David Horvath.

David Horvath, the workshop organizer, welcomed us, introduced all the speakers, mentioned each one’s expertise, and talked about iPlant Collaborative initiative, a National Science Foundation supported project aiming to provide “a place at the cyberspace where the power of high performance computing and data resources are available for life scientists”, therefore deep analysis of large sets of bioinformatics data is now possible in one place that is constantly curated and improved.

 

The common feeling among my colleagues and I was that due to the increasing availability of platforms, software and tools for bioinformatics analysis, it can be very confusing and challenging if you do not have a place where to start and have advice. iPlant Collaborative initiative offers several means of support to the very beginner and the more advanced user. It contains contact information of experts and places to put your questions and obtain answers from a community willing to help. Also, it contains confidentiality and security settings and links to other databases as GenBank and European Nucleotide Archive, in addition to the most trusted tools and software that are currently validated for use and publication.

 

The objective of the workshop was basically to know where the resources were and how to start and continue learning. We were around 50 people attending the workshop, with broad interests and projects but with the common goal to apply bioinformatics to the analysis of our data. We sat in groups of around six people, to allow a very dynamic round table discussion driven by one of the speakers, who changed table every 15 minutes. Each one of the speakers provided a unique perspective about the use of different tools and their own experiences. At the end, we concluded that we should not be overwhelmed for the large set of data to analyze, because there are places where to look and ask for help. iPlant Collaborative initiative is a very good place to go as it contains a complete set of settings to help us.

 

At the end I would like to thank the organizers and the speakers for a very helpful workshop. I hope to see you again in the near future.

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Thank You WORLD!

Looking back, we can all agree that it was a fantastic conference in Portland, full of exciting talks, eye-catching posters, motivated scientists, stimulating workshops, committee meetings, etc.

So foremost, Thank You to the organizers, to all who came out to Portland, a special Thank You to the iConnect Team, and of course to the sponsors, for making this meeting possible.

Unfortunately, we are left with some mind boggling stats. For example, there is the fact that the human population is increasing exponentially, whereas the food we produce grows merely arithmetically.

And so as the conference progressed, a defining question was posed: How can we achieve a reliable, sustainable, equitably-produced supply of nutritious food for a growing and increasingly urbanized world population within the context of climate change?

We are now most certainly aware that a sustainable agricultural intensification will be inevitable because maintaining current per capita food consumption with no increase in yield and no decrease in post-harvest and food waste will require almost doubling of the world’s cropland area within 40 years. This is not a viable approach to food security.

The present technologies in research are no doubt improving rapidly. We can all agree on that, but while, for example, next generation sequencing-based approaches are helping to improve the efficiency of breeding crops adapted to specific environments, we simultaneously need to provide farmers with information about the newest cultivars, technologies, etc.

As a result, immerging translational research and reduction in losses due to pests, pathogens, and environmental stresses could, and likely will, be equivalent to creating more land and more water! And that is purely thanks to the plant research being carried out globally.

The critically important basic discoveries being made in plant epigenetics, immunity, pathogen genomics, plant-environment interactions, structural biology, and metabolic engineering; discoveries will remain a driving force in agricultural innovation.

Ultimately, the continued translation of basic research into tangible agricultural and crop improvements will rely not only on the research itself but also on communicating the vital role that agriculture and plant genetics plays in all of our lives.

We were exposed to the social, economic, biological, environmental, and ethical aspects of food production.

We have been taking notes, growing our To Do lists. So if at least of few of those aims are realized before the next meeting, we will be in great shape.

Such a stance along with the growing population of plant scientists should no doubt translate into beneficial yields. I feel it’s time to move on beyond the GM debate, beyond the natural/unnatural argument, beyond the dualism of good versus bad and move toward adopting a continuum perspective that will allow for useful policies to be implemented.

I will be looking forward to seeing everyone in Minneapolis.

And for Goodbye a reminder

Ode to a Cluster of Violets
Pablo Neruda

Crisp cluster
plunged in shadow.
Drops of violet water
and raw sunlight
floated up with your scent.
A fresh
subterranean beauty
climbed up from your buds
thrilling my eyes and my life…

Read on

For more information and inspiration about worldwide impacts of plant biology, see the Decadal Vision report and related blog posts.

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I was eagerly waiting to write a post on this topic. This workshop attracted a lot of conference attendees, since current day plant biology research cannot move forward without these resources. Unfortunately it was kind of an effort to pack too many eggs in one basket within a limited time which could not meet expectations of many attendees. However a short note on the tools and resources described might be helpful for our readers.

Tanya Beraradini introduced the audience with the past and future of The Arabidopsis Information Resource (TAIR) which collects information and maintains the genetics and molecular biology data for the model plant Arabidopsis thaliana. It is managed by Phoenix Bioinformatics Corporation and is supported through institutional, lab and personal subscriptions. You can search and view the data using Gbrowse or interactive sequence viewer and they also have some tools like Mapviewer, AraCyc pathway, Patmatch, Motif search etc. for different analysis. The datasets can be downloaded as bulk.

Next, Chris Town from J. Craig Venter Institute (JCVI) talked about the first release of the Arabidopsis Information portal (AIP). This is an NSF and BBSRC-funded collaborative project between the JCVI, the Texas Advanced Computing Center (TACC) at the University of Texas at Austin and the University of Cambridge, with technical assistance from TAIR. The aim was to make a flexible community – extensible portal to enhance the next generation of Arabidopsis research. It has the enhanced search retrieval and display capabilities. It also enable community participation in functional annotation and own a language- and region-specific presentation of scientific content.

Next talk was on the iPlant Collaborative. Jason Williams from CSHL talked about the initiative in a title “Scalable Cyberinfrastructure for life science.” CI or CyberInfrastructure provides technological and sociological solution for the high throughput computational biology which consists of the hardware, software and people. The iPlant Collaborative is a dynamic virtual organization. The project is led by scientists at the University of Arizona (UA), the Texas Advanced Computing Center (TACC), Cold Spring Harbor Laboratory (CSHL) and University of North Carolina at Wilmington (UNCW). It includes a data storage facility, interactive web based analytical platform, cloud infrastructure for storage, computational data analysis. They provide support for scaling computational algorithms to run on large, high speed computers. They also have programs for education and training on how to use the CI for scientist at all levels.

Pankaj Jaiswal from Oregon State University delivered the next talk entitled “Gramene: A resource for comparative plant Genomics.” Gramene mainly deals with the grass genomes. As an information resource Gramene facilitates researchers by providing added value to the existing data of grass genomes. It takes advantage of genomic sequence known in one species to identify and understand the corresponding genes, pathways and phenotypes in the other related species. It contains information on Taxonomy ontology, Gene ontology, plant ontology, trait ontology and environment ontology. The genome module used here is adopted from Ensembl. It has cMAP and BLAST options. Literature supporting all data provided are also organized in the Literature database. It has a completely new look from the earlier version which is user friendly. And informative.

Peifen Zhang, from Carnegie Institution for Science talked about “PMN: metabolic pathway databases of 17 viridiplantae species, an introduction and demo of use cases.” PMN (Plant Metabolic Network) focuses on bringing the biochemical pathway databases focuses on plant metabolism. There is a growing need to place the sequenced and annotated genomes in a biochemical context in order to facilitate discovery of enzymes and engineering of metabolism. PMN, first made public in June 2008, generates an infrastructure for drawing together diverse sources of plant metabolism information.

The next talk was on Medicago truncatula genome resources at JCVI, Chris Town talked about the project which was initiated with a generous grant from Samuel Roberts Noble Foundation to the University of Oklahoma. Beginning in 2003 (and renewed in 2006), the National Science Foundation and the European Union’s Sixth Framework Programme provided funding to complete sequencing of the euchromatic genespace.

Asher Pasha, from University of Toronto, delivered a talk on the title “Data Sets, Web services and Visualization Apps from the Bio-Analytic Resource for use in the Arabidopsis Information Portal and other Cyberinfrastructure Assets.” As part of a Genome Canada grant, the Bio-Analytic Resource for Plant Biology (BAR) is providing seven modules to the Arabidopsis Information Portal: two modules for gene expression (transcript abundance and transcript structure) based on publish microarray and RNA-seq data sets, a module covering 90,000 conserved sequences in the Brassicaceae from Mathieu Blanchette and collaborators via the VEGI Project in a novel sequence conservation viewer (GeneSlider), a module for a database of almost 100k protein-protein interactions plus a viewer app, a module for viewing protein structures for ca. 500 experimentally-determined protein structures and predicted structures covering ~70% of the Arabidopsis proteome, an Expressolog/Synteny module and a zoomable user interface app to navigate between the biological organizations by the Arabidopsis Information Portal (AIP). Progress on these and other potential modules were discussed.

Doreen Ware and Sunita Kumari, from CSHL talked about “The DOE Systems Biology Knowledgebase: An integrated knowledgebase for biofuel research.” In 2011, DOE Office of Biological and Environmental Research (BER) launched KBase (KBase.us), an open-source, open-architecture software and data environment for systems biology research. It provides a computational framework for integrating and analyzing large datasets. High-level data types currently supported by KBase include genomes (of bacteria, archea, and eukaryotes), metagenomes, transcriptomes, proteomes (mapped to genomes), interactomes, phenotypes, 16s amplicons, expression data, enzymes, ontologies, pathway data, protein annotations, protein-protein interactions, regulons, and ribosomes. KBase pulls these data types from existing international repositories. So in future, data submitted to these standard resources wil be automatically integrated into the Kbase system. Because KBase pulls these data types from existing international repositories, future data submitted to these standard resources ultimately will be integrated into the KBase system. Powerful tools in Kbase allow users to analyze an simulate data for generating and testing hypotheses, designing biological functions or proposing new experiments.

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#plantbiology14 Wrap Up

I didn’t get much of a chance to sit down and write a post for the last two days of the conference. The schedule called for a party at the end of day 4 and a half-day day 5 that I’ll talk about here as well as my own take-aways from the conference. 

Day 4

The major symposia was on Plant Signaling, which is something I am very interested in, and yet I wasn’t very engaged with the speakers or their content; Ykä Helariutta had some truly gorgeous microscopy images of roots from a new type of SEM called SBF-SEM that allowed for 3-D rendering of root tissues as well as from a confocal microscope; I would love to learn to generate images like those. But his work on determining just how plant cells differentiate their vascular tissues was fascinating (at least in roots; shoot tissues may be different). A lot of it comes down to the spatial differentiation of two hormones: cytokinin and auxin, though the fine details rely on some very fine tuning of gene expression to specify phloem cells (that carry things long distance) and their companion cells that onload/offload things to be transported. The fine level microscopy needed is incredible.

around lunch time, I talked to Mike Sussman, my postdoc advisor’s Ph.D. advisor who told me about his bias against microscopy because ‘the molecule is the thing’ (he’s a biochemist that works on phosphorylation) to which I said, it’s best to marry the two together; the molecules and the microscopy; link the individual proteins to the cells where they’re acting, where they’re modified and if they move around or not.

I got to see examples of this in the root biology minisymposium where 3 of the 5 talks were from disciples of the Benfey lab that have gone on or are going on to start their own labs (don’t get me wrong, they all do great work; it confirms something I saw recently that 60% of postdocs from ‘elite’ or ‘rock star’ labs go on to found their own labs and become proto-rock stars of their own often times; so if you can get into one of those labs…you’ve got a good shot at successfully doing so; I’ll come back to this below). The upshot of the session (I sat through all the talks) was developing tools for studying roots more than actual root biology, though there was some of that too. From microscopy to track the properties of moving transcription factors (Sozzani lab), to realistic soil conditions to enable studying root growth (Ruben Rellan Alverez; starting his own lab soon) to studying the ROS pathway that’s independent of hormonal regulation of primary root establishment (Iyer-Pascuzzi lab), to ethylene formation of adventitious roots (Amanda Rasamussen), and how rice roots store nutrients after stress or ABA treatment (Wan-Chi Lin).

And I caught most of Keith Slotkin’s talk on epigenetics and how DNA methylation is established upon the plant first seeing a transposon it doesn’t currently possess in its genome; it was really interesting though I got lost a bit because he talked quickly and I’m not an epigenetics expert. The question was interesting and one I hadn’t thought of before.

Then there was a poster session (I talked to some people but left early to get my things ‘home’ to get myself to the closing party at the World Forestry Center which was great. And the iConnect team, responsible for digital coverage of the conference got together for a picture:

iConnect Team

Back: Ruben, Carl, Ian, Phil, X, Erin. Front: Molly, Susan, Maria, Kranthi. Photo by Naim, official photographer for the conference using @scato’s phone. Not pictured: (@PlantTeaching, #DaHorvathdp)

Day 5—President’s Symposium

Day 5 is just the president’s symposium where the president of the society each year gets to choose a theme for a symposium, find speakers for it and there you go. This year being the 25th anniversary of The Plant Cell (@ThePlantCell) being published as well as the 90th anniversary of ASPB’s (@ASPB) founding, the theme was ‘Firsts in plant biology’ (did you put an event on ASPB’s time line of historic plant discoveries? It’ll be online too).

Although one speaker had to cancel, the three that did speak were fantastic. It was well balanced with 2/3 being women or 2/4 if all 4 scheduled speakers had been speaking; plant biology doesn’t have anything close to parity when it comes to higher levels of academia (Ph.D.s and postdocs are near 50/50 though it’s been awhile since I’ve checked the numbers; someone can correct me if that’s not accurate) though I think it is better than many fields– a long way to go, for sure, but progress is being made, although the funding crunch scientists are presently under may really harm progress on this front, if only because there are fewer Tenure Track jobs out there. It’s something to be constantly vigilant about, as that seems to be the best way to ensure diverse voices are heard.

There were two epigenetics talks, the first by David Baulcombe (@dcb40) talking about some of his work on post-transcriptional gene silencing, and what underlies it and talked about how plants were the first systems where such RNA silencing was first observed. And took us through his modern day work which is also showing some firsts in plant biology, which ideas and mechanisms first described in plants being also discovered in animal cell systems. Julie Law from The Salk Institute continued on the theme of epigenetics talking about her work on the selective methylation mechanisms plants have and talked about how the first ‘methylome’ ever published was from Arabidopsis. I don’t follow it, but I wonder if there are prokaryotic systems that have epigenetic marks.

The final talk was given by Pamela Ronald (@pcronald), giving her second talk of the conference; this one about her lab’s research into a rice bacterial pathogen and the response to it in rice and the difficult process of tracking down a receptor ligand. The first in plant biology that she cited was the fact that the potato blight of the 1840′s was determined to be caused by a phytopthora species of fungus and Koch, of Koch’s postulates learned of this link and figured out that microbes can cause disease in animals (and came up with assays to determine just that). She talked about how the peptide that the rice pathogen produces that is the suspected ligand is modified post-translationally by sulfination that turns out to also be important for the mechanisms of HIV infection in humans. It was really fascinating and a great way to end the meeting.

Both Baulcombe and Ronald talked about how plant scientists tend to have an inferiority complex when it comes to our work and said that we shouldn’t hide the fact that we work on plants that they’re inherently great systems to work on and have some of the most cutting edge science in the world that has implications for not just mechanisms in all of biology, but also for overall human health. I have experienced this inferiority conference.

Final Impressions

Education matters. How we tell the story of plant science matters. And the community really matters.

Plants are indeed fascinating systems to work on and the modern tools of science are making the exciting biology of plants more and more discoverable; from whole genome approaches to better imaging technologies to populations that allow very fine mapping of markers for desired traits of interest. Of course, I’m not so short-sighted as to say there’s no interesting biology to be uncovered in other systems, even ones not yet explored.

Plants do offer a lot of unique opportunities as they provide things we rely on every day from ecosystem services to food, shelter, clothing, and energy; a list that’s only likely to grow over time as plants can be synthesis factories for a lot of things as well. Some of this conference was devoted to the debate between basic and applied science; a decision I don’t think any science enterprise should have to distinguish; both matter. Basic research, as Marcelo Gleiser (@marcelogleiser) argues in his recent book ‘the island of knowledge’ is to define the shores of our ignorance in order to push them out even further (we’ll likely always be pushing); there’s an ebb and flow of that shoreline as we slowly learn things, correct ourselves and yes, apply what we’ve learned.

The initial discovery phases of any product are underpinned by basic research. And of course, applied projects can make significant basic science discoveries (e.g. Cosmic microwave background). Anyone reading this is likely a plant scientist and knows all of this; yet Arabidopsis is still the only model organism that is up for the chopping block as far as I know (I am all for smarter use of the model; a lot of experiments may not hold true for other plants because we grow Arabidopsis under utterly false conditions often).

We currently live in a very short-term world; nothing should take a long time to develop. Basic research takes a painfully long time to mature into something that could be applied; on the order of 30-50 years. Should scientists be on the lookout for contributions they can apply from their discoveries? Absolutely, but there is nothing wrong with knowledge for the sake of knowledge. The frustration with that as an approach is that it is hard to feel like you’re making a difference in the world; ideally, any project has both applied and basic components, even if it is split 10/90. You never know when someone will come upon your work and make a brilliant discovery because of it (likely, it’ll only be a small piece of that breakthrough, but still, every bit helps; it’s useless knowledge until suddenly, it isn’t).

In the current funding environment, it’s likely that things that can be applied quickly will take priority, and that is kind of a shame. Both Pam Ronald and David Baulcombe talked about pursuing systems you are passionate about; I don’t think I’ve found my applied system yet that I feel I can make a contribution to. Maybe coffee? I am very interested in saving coffee.

Education Matters

To continue from my comments above, It also seems true that postdocs from amazing labs will be the ones to get funded and go on to be successful. In a way, that’s as it should be; success breeds success. Lots of research bang for the buck, which is what we want. As well as very talented people doing science (or people we can train to become talented; growth mindset!). However, if only people from a top few labs are able to get hired, the focus and scope of research may be limited. And schools that serve primarily undergraduates, currently a large supplier of grad programs may have an ever harder time getting funding for their mostly less ambitious research programs; I’m sure the people at the funding agencies do their best to balance research and education; the two shouldn’t be mutually exclusive to begin with, but it just seems like we’re living in an increasingly tiered world where a very few top labs produce the most research and leave the rest of us out in the cold (great if you’re one of those labs; or a lab that can collaborate with them). Competition is good; but I feel like what we have now is too competitive and may end up in what a cell biologist might call an apoptotic event for the entire scientific system. Again, I have no trouble with great labs doing amazing things that we end up often hearing about at conferences like Plant Biology. I just worry about the crowding out of smaller research programs, especially those form PUIs. Big science, is, well, big these days; and we’ll likely all be doing it at some level sometime soon, but I’m not so sure the resources are there for every lab, independent of its size, to do that RNAseq experiment (the crash in sequencing costs/base may continue, but to do a full on experiment is still expensive). I know that these are more systemic concerns within academia as a whole, but they affect us in the plant biology world too. Competition is good. Hyper-competition I’m not so sure is. I don’t know where that balance point is, but it seems like science as a whole is moving towards the latter.

The two major symposia sponsored by Monsanto, The Plant Cell and, Plant Physiology all highlighted messages of public education and awareness (which is necessary, but not sufficient as Nathanael Johnson (@SavorTooth) pointed out). The speakers weren’t there to tell us that feeding the world would be a challenge; we know that; but to give us data and perhaps a narrative to help communicate that message to others who aren’t so aware. Robb Fraley (@RobbFraley) talked about some of Monsanto’s latest projects/products and vision and Pam Ronald talked about how to integrate ecologically minded farming with GM technology. Like it or not, GM is controversial (even though it’s far from the only thing Monsanto produces). Part of the controversy is just that Monsanto is a large company. Robb Fraley flew into Portland on a private jet and flew out again soon after his talk. That’s some Bond Villain level activity right there. Or he has a demanding job that likely takes place in many cities all at the same time and Monsanto can afford a jet to enable him to do the work he’s obviously passionate about (I would love to tour Monsanto to see what it’s like; I’ve never been despite living in St. Louis for my Ph.D.). However, as a large and resourced company, Monsanto might have an even bigger responsibility to being environmentally friendly and encouraging farming practices that leave a lighter footprint on the planet (the scientists there, at least, are on board with this, I’m almost certain). Things like the two symposia really are important for getting the message of plant biology out to the world, it broadens our scope.

The Community Matters—iConnect with Plant Biology

Covering the conference on Twitter was great. The core group of us, the iConnect team tweeted up a storm. But that was only half the point. ASPB is embarking on a digital futures initiative to provide tools and connections to other plant scientists. Right now, even though we’re a community of mutual interest in plants, the links seem fairly loose and there’s still a lot of ivory towers/silos that exist. I envision a tighter community that will connect in real life as always, but also digitally. The end goal is to create a much better megaphone to communicate plant science as a whole to fellow plant scientists and build the membership, but to communicated it other audiences as well (various segments of the public, government, industry, etc.). It’s a new project and a big undertaking, but we’ve planted the seeds at least.

Final, Final Thoughts

I had a good time at #plantbiology14 even if I felt like I missed a lot and maybe could have done some things better (networking, getting noticed). I hope all the attendees did. There are some truly amazing plant scientists doing great work at all levels with projects at all stages of completion. Talking to a friend, she was saying plant biologist’s inferiority complex actually harms us because we’re a lot harsher on one another’s work; it has to be perfect before any of those animal people even get a glance at it. Perfectionism is no way to go about life, I’ve found. I’m still fighting those tendencies (I want to be excellent, but not to wait for perfection because it will never happen). I don’t know if that’s the case in the entire plant world, but from what I’ve seen, there’s a lot of good work being done. And the world needs a strong plant science community to work towards agricultural and environmental solutions to the world’s problems. It’s great to do the work and apply it, but two other keys are education and communication about plant science to relevant communities. And of course, paying for all of this won’t be easy, but I think a lot of it starts with a strong, diverse, and large community that has strong links to one another.

The World Domination Summit (WDS) coincided with Plant Biology this year in Portland. WDS is a conference of largely small business owners/startups that are trying to create socially/environmentally responsible companies that are going to be the next big thing (their founders think so anyway and most really do seem to want to put all the effort they can into creating a successful business). I follow it a bit though have never been (they are a community of people with positive voices that work for me, something I needed to hear a few years ago), and one thing they did one year was have everyone sing Journey’s “Don’t stop Believing”; something the band (The Nines, from Seattle, they were great) at the Plant Biology closing party played too, by request. The challenges we face are huge, but together, we can create a better Earth to live on.

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The “Flipped” Classroom Teaching Strategy

A key benefit of being a member of ASPB, at least for me, is that we have access to several activities to enhance career skills. One of my favorites is the Education Committee workshop. I’ve had the privilege to attend several by now. As a result, my teaching tools box has improved a lot and helped me to be successful in my job hunt. This year, along with several others, I was able to share my experience as a member of the iConnect team.

Workshop participants.

Workshop participants.

The workshop this year, sponsored by the Education Committee, was about a teaching strategy called “The Flipped Classroom,” by Adrienne Williams (University of California–Irvine). She is a project specialist and expert on biology education, particularly developmental and cell biology courses. She is doing outstanding work. On her Twitter account @BioTeaching, she describes her interests as “moving undergraduates from memorizing to thinking in gigantic lecture halls.” In addition, she has a lot of information online regarding what the flipped classroom strategy is, the different combination of activities she has applied, reports about the level of success, and her recommendations depending on the results obtained. You can read one of Adrienne’s recent reports on Introductory Biology and find  more of her tips on flipped classrooms on the UC Irvine website.

Adrienne is a very engaging instructor. During her presentation I was able to share experiences and obtain a lot of feedback from her and colleagues. These colleagues are from different institutions in the United States and other countries, with different class loads and experience. To make our learning experience more entertaining, we sat in groups and discussed our present strategies and why we wanted to flip our class. We concluded that our main concern was the size of the class and how to make it more dynamic and entertaining for our students. We also realized the extra time we would have to spend, but concluded that the benefits outweighed the costs.

One of the key points Adrienne mentioned is that students should be able to use any material and independently learn from them. One example is the use of interactive videos that encourage students to look for information before the class, therefore we could do other activities in class and ideally the material would be covered more thoroughly.

Basically we learned the basics of flipping, Adrienne’s tips for success (she gave us her contact info, so we can contact her directly for advice), the scale of flipping we want to apply, and how to evaluate student performance and success.

Finally, it was also great to see friends met in other workshops. We had a very good time exchanging experiences, advice, and encouragement, as we continue to work to improve our teaching skills.

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