Putting Big Data to Work with ARPA-E’s TERRA Program

This week we spoke to Dr. Joe Cornelius, the Program Director at the Advanced Research Projects Agency – Energy (ARPA-E). His work focusses on bioenergy production and conversion as a renewable and sustainable energy source, transportation fuel, and chemical feedstock, applying innovations in biotechnology, genomics, metabolic engineering, molecular breeding, computational analytics, remote sensing, and precision robotics to improve biomass energy density, production intensity, and environmental impacts.

 

What is ARPA-E? How are programs created?

The Advanced Research Projects Agency-Energy (ARPA-E) is a young government agency in the U.S. Department of Energy. The agency is modeled on a successful Defense Department program, the Defense Advanced Research Projects Agency (DARPA). Both agencies target high-risk, high-reward research in early-stage technologies that are not yet ready for private-sector investment.

Program development is one of the unique characteristics of the agency. ARPA-E projects are in the hands of term-limited program directors, who develop a broad portfolio of concepts that could make a large impact in the agency’s three primary mission areas: energy security, energy efficiency, and emissions reductions. The agency motto is “Changing what’s possible”, and we are always asking ourselves, “if it works, will it matter?”. Getting a program approved is a lot like a doing a PhD; you survey the field, host a workshop, determine key points to research, define aggressive performance metrics, and finally defend the idea to the faculty. If the idea passes muster, the agency makes a targeted investment. This flexibility was recently noticed as one of the great aspects of ARPA-E culture and is an exciting part of the job.

 

What is TERRA and how is it new for agriculture?

TERRA stands for Transportation Energy Resources from Renewable Agriculture, and its impact mission is to accelerate genetic gains in plant breeding. This is an advanced analytics platform for plant breeding. Today, significant scientific progress is possible through the convergence of diverse technologies, and TERRA’s innovation for breeders comes through the integration of remote sensing, computer vision, analytics, and genetics. The teams are using robots to carry cameras to the field and then extracting phenotypes and performing gene linkages. It’s really awesome to see.

 

This is run by the U.S. Department of Energy. How does TERRA tie into energy?

The United States has a great potential to generate biomass for conversion to cellulosic ethanol, but the crops useful for producing this biomass have not seen the improvement that others, such as soybeans or maize, have had. TERRA is focused on sorghum, which is a productive and resilient crop with existing commercial infrastructure that can yield advanced biomass on marginal lands. In addition, sorghum is a key food and feed crop, and the rest of the world will benefit from these advancements.

 

How does TERRA address the challenge of phenotyping in the field?

The real challenges that remain are in calibrating the sensor output and generating biological insight. A colleague from the United Kingdom, Tony Pridmore, captured the thought well, saying “Photography is not phenotying.” It’s generally easy to take the pictures — unless it’s very windy, the aerial platforms can pass over any crop, and the ground platforms are based on proven agricultural equipment. To get biological insights however, each team requires an analytics component, and a team from IBM is contributing their analytics expertise in collaboration with Purdue University.

 

 

What is most exciting about the TERRA program?

We commissioned the world’s biggest agricultural field robot, which phenotypes year-round. The six teams have successfully built other lightweight platforms involving tractors, rovers, mini-bots, and fixed and rotary wing unmanned aerial vehicles. It’s exciting to see some of the most advanced technologies move so quickly into the hands of great geneticists. The amazing thing is how quickly the teams have started generating phenotyping data. I expected it to take years before we got to this point, but the teams are knocking it out of the park, and we are entering into full-blown breeding systems deployment.

 

Who’s on the TERRA teams? How did you build the program?

ARPA-E system teams include large businesses, startups, and university groups. The program was built to have a full portfolio of diverse sensor suites, robotic platform types (ground and aerial), analytics approaches, and geographic breadth. Because breeders are working for a particular target population of environments, different phenotypes are valued differently across the various geographies. For that reason, each group is collecting its own set of phenotypes. Beyond that, we’ve worked very hard to encourage collaboration across the teams and have an exciting GxE (genotype x environment) experiment running, where several teams plant the same germplasm across multiple geographies. By combining this with high-throughput phenotyping, the teams are in a good position to determine key environmental inputs to various traits.

 

Once we achieve rapid-fire field phenotyping, what’s next?

We’re going underground! ARPA-E has made another targeted investment, this time in root phenotyping. We’re really excited about this one. It’s a very similar concept, but the sensing is so much harder. The teams have collaborated with medical, mining, aerospace, and defense communities for technologies that can allow us to observe root and soil systems in the field to allow breeders to improve crops.  Ask us again next year—we will have some cool updates to both programs!

The Regulator’s perspective: Why some gene-edited plants are not GM-regulated in Sweden

Staffan Eklof

Dr. Staffan Eklöf, Swedish Board of Agriculture

At July’s New Breeding Technologies workshop held in Gothenburg, Sweden, Dr. Staffan Eklöf, Swedish Board of Agriculture, gave us an insight into their analysis of European Union (EU) regulations, which led to their interpretation that some gene-edited plants are not regulated as genetically modified organisms. We speak to him here on the blog to share the story with you.

 

Could you begin with a brief explanation of your job, and the role of the Competent Authority for GM Plants / Swedish Board of Agriculture?

I am an administrative officer at the Swedish Board of Agriculture (SBA). The SBA is the Swedish Competent authority for most GM plants and ensures that EU regulations and national laws regarding these plants are followed. This includes issuing permits.

 

You reached a key decision on the regulation of some types of CRISPR-Cas9 gene-edited plants. Before we get to that, could you start by explaining what led your team to start working on this issue?

It started when we received questions from two universities about whether they needed to apply for permission to undertake field trials with some plant lines modified using CRISPR/Cas9. The underlying question was whether these plants are included in the gene technology directive or not. According to the Swedish service obligation for authorities, the SBA had to deliver an answer, and thus had to interpret the directive on this point.

 

Arabidopsis thaliana

Image credit: INRA, Jean Weber. Used under license: CC BY 2.0.

 

Could you give a brief overview of Sweden’s analysis of the current EU regulations that led to your interpretation that some CRISPR-Cas9 gene-edited plants are not covered by this legislation?

The following simplification describes our interpretation pretty well; if there is foreign DNA in the plants in question, they are regulated. If not, they are not regulated.

Our interpretation touches on issues such as what is a mutation and what is a hybrid nucleic acid. The first issue is currently under analysis in the European Court of Justice. Other ongoing initiatives in the EU may also change the interpretations we made in the future, as the directive is common for all member states in the EU.

 

CRISPR-Cas9 is a powerful tool that can result in plants with no trace of transgenic material, so it is impossible to tell whether a particular mutation is natural. How did this influence your interpretation?

We based our interpretation on the legal text. The fact that one cannot tell if a plant without foreign DNA is the progeny of a plant that carried foreign DNA or the result of natural mutation strengthened the position that foreign DNA in previous generations should not be an issue. It is the plant in question that should be the matter for analysis.

Arabidopsis thaliana

Image credit: Frost Museum. Used under license: CC BY 2.0.

Does your interpretation apply to all plants generated using CRISPR-Cas9, or a subset of them?

It applies to a subset of these gene-edited plants. CRISPR/Cas9 is a tool that can be used in many different ways. Plants carrying foreign DNA are still regulated, according to our interpretation.

 

What does your interpretation mean for researchers working on CRISPR-Cas9, or farmers who would like to grow gene-edited crops in Sweden?

It is important to note that, with this interpretation, we don’t remove the responsibility of Swedish users to assess whether or not their specific plants are included in the EU directive. We can only tell them how we interpret the directive and what we request from the users in Sweden. Eventually I think there will be EU-wide guidelines on this matter. I should add that our interpretation is also limited to the types of CRISPR-modified plants described in the letters from the two universities.

 

Crops

Will gene-edited crops be grown in Europe in the future? Image credit: Richard Beatson. Used under license: CC BY 2.0.

We are currently waiting for the EU to declare whether CRISPR-Cas9 gene-edited plants will be regulated in Europe. Have policymakers in other European countries been in contact with you regarding Sweden’s decision process?

Yes, there is a clear interest; for example, Finland handled a very similar case. Other European colleagues have also shown an interest.

 

What message would you like plant scientists to take away from this interview? If you could help them to better understand one aspect of policymaking, what would it be?

Our interpretation is just an interpretation and as such, it is limited and can change as a result of what happens; for example, what does not require permission today may do tomorrow. Bear this in mind when planning your research and if you are unsure, it is better to ask. Moreover, even if the SBA (or your country’s equivalent) can’t request any information about the cultivation of plants that are not regulated, it is good to keep us informed.

I think it is vital that legislation meets reality for any subject. It is therefore good that pioneers drive us to deal with difficult questions.

The Global Plant Council visits the Australian Plant Phenomics Facility

This post is republished with the kind permission of the Australian Plant Phenomics Facility (APPF). 

We at the APPF love visits from our global plant science community, so it was a treat to host Ruth Bastow, Executive Director of the Global Plant Council (GPC), this week.

While she was here, we took the opportunity to ask a few quick questions:

Ruth Bastow at the Australian Plant Phenomics Facility

Ruth Bastow, Executive Director of the Global Plant Council in high-throughput phenotyping Smarthouse™ at the Australian Plant Phenomics Facility’s Adelaide node

Ruth, could you tell us a little bit about the GPC?

The GPC is a not-for-profit coalition of national, regional, and international societies and affiliates representing thousands of plant, crop, agricultural, and environmental scientists. We bring together all those involved in plant and crop research, education and training, to provide a body that can speak with a single, strong voice in the policy and decision-making arena, and to promote plant science research and teaching around the world.

What do you do there?

As Executive Director of the GPC I am responsible for the day to day management of the organisation.

What is the reason for your visit here?

To meet up and discuss GPC initiatives with colleagues here at the University of Adelaide, to further develop current collaborations and hopefully initiate new ones.

For example the Australian Plant Phenomics Facility (APPF) is partner of the Diversity Seek Initiative (DivSeek). DivSeek is a global community driven effort consisting of a diverse set of partner organisations have voluntarily come together to enable breeders and researchers to mobilise a vast range of plant genetic variation to accelerate the rate of crop improvement and furnish food and agricultural products to the growing human population. DivSeek brings together large-scale genotyping and phenotyping projects, computational and data standards projects with the genebanks and germplasm curators. The aim is to establish DivSeek as a hub to connect and promote interactions between these players and activities and to establish common state-of-the-art techniques for data collection, integration and sharing. This will improve the efficiency of each project by eliminating redundancy and increasing the availability of data to researchers around the world to address challenges in food and nutritional security, and to generate societal and economic benefit.

So, whilst I am here, I will be learning about how the APPF team collate and analyse their data and try and understand how the approaches here could be translated into solutions for the wider community. For example, the Zegami platform used in the high-throughput phenotyping Smarthouses™ at the Adelaide node is a useful visualisation tool that could benefit others.

Where else have you visited?

Whilst I am here in Australia I have been working with colleagues in Canberra including Prof Barry Pogson who is currently the chair of the Global Plant Council, Dr Xavier Sirault (APPF node based at CSIRO), Prof Justin Borevitz (APPF node based at ANU), and Dr Norman Warthmann. I will also be taking time to visit friends in Sydney and on the Central Coast.

Where do you see plant phenomics research in 5-10 years time?

High throughput and field based phenotyping has seen huge transformational change in the last decade and in the next 5-10 years I hope that it will start to become part of the everyday toolkit of plant science researchers in the way that genomics has.

If you could solve one plant science question what would it be?

I would actually like to try and solve a social/conceptual problem that effects science rather than an actual biological question and that is the sharing of data, information, knowledge and best practice. The sharing of scientific theories, including experimental data and observations has been a core concept of the scientific endeavour since the enlightenment. Sharing allows others to evaluate research (peer review), to identify errors, and allow ideas to be corroborated, invalidated and built upon. It also facilitates the transmission of concepts and theories to a wider audience and that will hopefully inspire others to get involved in science, contribute ideas and further our understanding of the world around us.

However, the current systems of reward and evaluation in science; lack of appropriate mechanisms, standard and infrastructures to easily share and access information; and in some cases the debilitating effects of ‘IP thickets’ can act as a barrier to ‘open science’. It is not all bad news. In the last decade a number of changes at the government, funder, publisher and institutional level have promoted and facilitated the concept of open science. However, if science is to be a truly open endeavour it will require a change in mind-set at many levels to migrate towards a culture where open data is the norm. Without this we will not be able to fully realise the investment in research, in terms of both finance provided and the time and intellectual contribution of the individual involved, and contribute to developing solutions that will help ameliorate current global problems.

When I am not working I am?

Walking the dog or gardening and generally enjoying the beauty of my home in South Wales in the UK.

If you could have one super power what would it be?

For my work it would probably be telepathy or omnilinguism, as most problems seems to arise from lack of understanding or miscommunication at some level, so these would be very helpful superpowers. From a personal perspective perhaps the ability to predict the future would be good.


Thanks again to the APPF for giving us permission to republish this blog post!


About the APPF

The APPF is a national facility, available to all Australian plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sectors anywhere else in the world. The APPF is based around automated image analysis of the phenotypic characteristics of extensive germplasm collections and large breeding, mapping and mutant populations. It exploits recent advances in robotics, imaging and computing to enable sensitive, high throughput analyses to be made of plant growth and function. New technologies are being developed to ensure that the APPF remains at the international forefront of plant science. Research networks and established pathways to market ensure outcomes are delivered for the long-term benefit for Australian scientists and primary producers.

Using plants to convert explosives to fertilizers: an interview with Neil Bruce

Neil Bruce

Professor Neil Bruce

This week we spoke to Professor Neil Bruce, whose research at the University of York (UK) focuses on metabolic pathways. His insights into the detoxification of pollutants by plants and microorganisms has led to promising new solutions to help clean up polluting explosives from military testing.

 

Could you begin by telling us a little about your research interests?

I have very broad research interests that often revolve around finding enzymes for biotechnological applications. A particular focus of my lab is the biochemistry and molecular genetics of plant and microbial metabolism of xenobiotic (foreign) compounds, such as environmental pollutants. Elucidating these metabolic pathways often results in the discovery of new enzymes that catalyze interesting chemistries. Being a biologist at heart, I’m interested in the evolutionary origin of these enzymes, but also by studying their structure and function I’m exploring how these enzymes can be engineered to further improve their properties for a particular application, such as environmental remediation or biocatalysis.

 

 

You spoke at the GARNet 2016 meeting about engineering plants to remediate explosives pollution. Could you explain what this problem is and how it affects both people and the environment?

Explosive compounds used in munitions are highly toxic and the potential for progressive accumulation of such compounds in soil, plants, and groundwater is a significant concern at military sites. It is estimated that in the US alone, 10 million hectares of military land is contaminated with components of munitions. The explosives mainly used in artillery, mortars and bombs are 2,4,6-trinitrotoluene (TNT) and Composition B (containing TNT and hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX)). The US Department of Defense estimated that the clean-up of unexploded ordnance, discarded military munitions and munition constituents on its active ranges would cost between $16 billion and $165 billion. Explosives pollution is, however, a global problem, with large amounts of land and groundwater contaminated by TNT and RDX, including polluted sites in the UK that date back to the First and Second World Wars. Explosives pollution will continue to be a pressing issue while there is a requirement for military to train and the existence of armed conflict requires munitions to be manufactured. There is an urgent need to develop sustainable in situ technologies to contain and treat these pollutants.

 

TNT toxicity in plants

TNT is toxic to plants because of the actions of an enzyme called monodehydroascorbate reductase, which breaks TNT down into a toxic form. Plants lacking this enzyme, such as the mdhar6 mutant plants on the right, can grow very well on TNT-polluted soil. Credit: Johnston et al. (2015).

 

How did you develop the idea of using plants to remove explosives pollution? What benefits do plants have over the microorganisms from which the enzymes are obtained?

We have worked closely with the UK Ministry of Defence and US Army to understand the fate of explosives in the environment. Knowledge of their effects on biological systems is important, as this information can be used to support the management of contaminated sites. We have, therefore, been uncovering the molecular mechanisms behind these detoxification processes in plants, and have used this knowledge, in combination with studies on the bacterial degradation of pollutants, to successfully engineer transgenic plants able to remediate toxic explosive pollutants in a process called ‘phytoremediation’.

An innovative aspect of our work has been the use of genetic engineering to combine the biodegradative capabilities of explosives-degrading bacteria with the high biomass, stability and detoxification systems inherent in plants. While it is possible to find explosives-degrading bacteria on polluted land, they do not degrade the explosives fast enough to prevent leaching into the groundwater. Our engineered transgenic plant systems, however, can efficiently remove toxic levels of TNT and RDX from contaminated soil and water.

 

You mentioned that you are currently testing transgenic switchgrass to remove RDX and TNT pollution in the US. Why did you choose this species and have you considered developing other species suited to different environments?

Plants appropriate for the phytoremediation of explosives need to be adaptable to conditions on military ranges, for example, they need good fire tolerance, and to be able to grow over a wide geographical range. Switchgrass meets these criteria, and is also deep-rooting, can be grown on marginal lands, and researchers can benefit from established methods for genetically engineering switchgrass. We have also been engineering other grass species and have considered fast-growing deep-rooting trees such as poplar.

 

Turning explosives into fertilizers

In a poetic twist, rather than turning fertilizers into explosives, Professor Bruce’s phytoremediating plants convert explosives into fertilizer. Credit: Neil Bruce.

 

How quickly can engineered plants remove this pollution?

In the lab these plants can remove levels of explosives pollution found in the environment within a matter of days. We are currently carrying out field trials with our transgenic plants on a military site in the US, to observe their phytoremediation effectiveness in the real world. If these trials are successful, a number of demonstration studies on contaminated sites will be required to convince end users of the benefits of phytoremediation for remediating and maintaining military land. These demonstration studies will also allow us to evaluate any risks, which will be important to obtain further approval from the US Department of Agriculture to be able to use these plants on a larger scale.

 

What other projects are you working on? Could you elaborate on any recent discoveries?

As well as explosives, we are also working on the use of plants to extract platinum group metals (PGMs) from mining waste. PGMs are used in an ever-expanding array of technologies and demand is spiralling upwards; however, these are rare and expensive to mine. It is essential that these metal reserves are utilized and recycled responsibly, not dispersed and lost into the environment. Plants can take up metals from their environment and, in the case of PGMs, can deposit them as nanoparticles within their tissues. Importantly, we have recently shown that plants containing palladium nanoparticles can also be used to make efficient biocatalysts, and we are currently using synthetic biology in plants to improve palladium uptake and nanoparticle formation.

 


More information:

Johnston, E.J., Rylott, E.L., Beynon, E., Lorenz, A, Chechik, V. and Bruce, N.C. (2015) Monodehydroascorbate reductase mediates TNT toxicity in plants. Science. 349: 1072-1075.

Gunning, V., Tzafestas, K., Sparrow, H., et al. (2014) Arabidopsis glutathione transferases U24 and U25 exhibit a range of detoxification activities with the environmental pollutant and explosive, 2,4,6-trinitrotoluenePlant Physiol. 165: 854-865.

Rylott, E.L.. Budarina, M.V., Barker, A., Lorenz, A., Strand, S.E. and Bruce, N.C. (2011) Engineering plants for the phytoremediation of RDX in the presence of the co-contaminating explosive TNT. New Phytologist, 192: 405-413.

Farming Futures: integrating plant research and industry in the agri-food supply chain

This week we speak to Tim Williams, the Business Manager of Farming Futures and Research Fund Development Manager at Aberystwyth University, UK.

Could you give a brief introduction to Farming Futures and its mission?

Farming Futures is an independent, UK-based, inclusive agri-food supply chains alliance. Our mission is to work with researchers and industry to share knowledge, with the aim of improving the sustainability and productive efficiency of agriculture, all within the context of healthy, high-quality food.

 

What is the history of the organization?

Farming Futures started with an idea by Professor Wayne Powell in 2009 (then the director of the Institute of Biological, Environmental and Rural Sciences (IBERS) at Aberystwyth) in discussion with Mark Price, who was the Managing Director of British supermarket chain Waitrose. It was launched in 2010, starting out as the Centre of Excellence for UK Farming (CEUKF). Waitrose seed-funded Farming Futures, and since then we have received support from the Agriculture and Horticulture Development Board (AHDB) and Innovate UK.

 

Farming Futures

The inauguration meeting of Farming Futures in 2009, then known as the Centre of Excellence for UK Farming. Left-Right: Tim Williams, Wayne Powell, Heather Jenkins, David Davies, Philip Morgan, Jamie Newbold.

 

How has plant and crop research been integrated into the recommendations presented by Farming Futures?

Plant science is the fundamental driver for agri-food development. We work closely with industry, as well as the AHDB and other farm advisory bodies across the UK to inform them about new developments. Accelerated, directed breeding programs using genomic and phenomic technologies are helping us to develop new varieties that offer more productive, more resilient, environmentally friendly plants – not just as food crops, but also for soil quality, nutrient retention, flood reduction, energy biomass, renewable chemistry, and a host of other desirable characteristics.

Historically, to paraphrase a fellow botanist, we have bred ‘needy, greedy plants’ that deplete resources and need lots of nasty chemicals to keep them growing. Now scientists are mining the genomes of crop ancestors to rediscover the genetic traits we unwittingly threw away on the route to increased yield.

 

What roles do research partners such as universities play?

We work together in a pre-competitive way to enable research, and to represent farming within agri-food policy – researchers from different organizations can collaborate thanks to our partners’ trusting relationships with each other. Collaborations in science are vital because the problems our global society faces are multi-factorial, non-linear and multi-disciplinary. They are far too complex for the typical university research team, working alone, to address efficiently. We need the equivalent of the CERN Large Hadron Collider project for agri-food.

In addition to helping researchers to bring in millions of pounds worth of applied research projects (at least £12 million, but it is notoriously difficult to find out what industry is funding), Farming Futures helped to establish the government-funded Agri-Food Tech Centres of Innovation for a total of around £90 million, bringing in industry to co-fund and support three of the four: the Agrimetrics Centre, Agri-Epi-Centre and Centre of Innovation Excellence in Livestock. In time, these Centres will catalyze a lot of collaborative research and will help stimulate innovation and technology uptake by industry.

 

What climate change challenges will farmers face? Are there any specific challenges that Farming Futures can address?

Farming Futures and its network brings together scientists from different disciplines to discuss these problems and potential solutions. For instance, people from the UK’s national weather service (the Met Office) and some of the biggest food retailers and processors in the world come together at our conferences and workshops to think through scenarios and solutions. These solutions include breeding crops for increased resilience, not just peak yield. We are running out of fungicides that work efficiently, in the same way that we are running out of antibiotics; however, some very clever scientists have worked out some potential solutions that are more environmentally sound, so I am an optimist.

This problem solving is best done at the supply-chain level as it brings in a wider expertise. As I repeat often, a colleague once said to the board of one of the world’s biggest brewers, “No barley = no beer = no business”, inferring the question, “What are you doing to ensure that barley growers are going to be able to supply you in the future?”

 

Your website has an interesting study from 2011 highlighting six potential jobs of the future, including geoengineer, energy farming, web 3.0 farm host, pharmer, etc. How can students direct their skill development to meet the needs of the future?

There are many emerging jobs and skills, but each of these named jobs from 2011 are actually in practice now. The web 3.0 has now become web 4.0, which is the “internet of things”, with data collection from lots of devices including drones for precision agriculture and robots for weeding and picking crops.

The future of agri-food is in big data, including consumer behavior, weather forecasting, genomics, phenomics, and real-time analysis of the growth progress of plants and animals on-farm. We need more electronic and mechanical engineers with an understanding of biology, as well as more biologists who work within the agri-food industries and in government policy development.

 

Farming Future exhibition

The Farming Futures exhibition stand at the Livestock Event, NEC Birmingham, 2012.

 

What are you currently working on?

We are currently working with partners on a number of projects across the Agri-Food Tech Centres and trying to form more research collaborations. One of our big projects is The National Library for Agri-Food. I am currently working with web developers and experts from Jisc and the British Library to scope the requirements and to build a demonstration web site.

Finally, I would just like to add that we are open to collaborations across agri-food supply chains and will work to foster them, either openly or privately as appropriate.

 


In addition to IBERS, Farming Futures has four founding members (Northern Ireland’s Agri-Food and Biosciences Institute (AFBI), Harper Adams University (HAU), NIAB with East Malling Research (NIAB-EMR), and Scotland’s Rural College (SRUC)) and an influential Steering Board, chaired by Lord Curry of Kirkharle, who is very well known and respected in UK government and farming.

 

1000 Plants

The 1000 plants initiative (1KP) is a multidisciplinary consortium aiming to generate large-scale gene sequencing data for over 1000 species of plants. Included in these species are those of interest to agriculture and medicines, as well as green algae, extremophytes and non-flowering plants. The project is funded by several supporters, and has already generated many published papers.

Gane Wong is a Professor in the Faculty of Science at the University of Alberta in Canada. Having previously worked on the Human Genome Project, he now leads the 1KP initiative. Dennis Stevenson, Vice President for Botanical Research, New York Botanical Garden, and Adjunct Professor, Cornell University (USA), studies the evolution and classification of the Cycadales. He became involved in the 1KP initiative as an opportunity to sample the breadth of green plant diversity.

We spoke to both Professor Stevenson (DS) and Professor Wong (GW) about the initiative. Professor Douglas Soltis from Florida Museum of Natural History also contributed to this blog post with input in editing the answers.

What do you think has been the biggest benefit of 1KP?

DS: This has been an unparalleled opportunity to reveal and understand the genes that have led to the plant diversity we see around us. We were able to study plants that were pivotal in terms of plant evolution but which have not previously been included in sequencing projects as they are not considered important economically

The 1KP project presented a fantastic opportunity to explore plant biodiversity. Photo by Bob Leckridge. Used under Creative Commons 2.0.

The 1KP project presented a fantastic opportunity to explore plant biodiversity. Photo by Bob Leckridge. Used under Creative Commons 2.0.

GW: The project was funded by the Government of Alberta and the investment firm Musea Ventures to raise the profile of the University of Alberta. Notably there was no requirement by the funders to sequence any particular species. I was able to ask the plant science community what the best possible use of these resources would be. The community was in full agreement that the money should be used to sample plant diversity.

Hopefully our work will change the thinking at the funding agencies regarding the value of sequencing biodiversity.

What techniques were utilized in this project to carry out the research?

GW: Complete genomes were too expensive to sequence. Many plants have unusually large genomes and de novo assembly of a polyploid genome remains difficult. To overcome this problem, we sequenced transcriptomes. However, this made our sample collection more difficult as the tissue had to be fresh. In addition, when we started the project, the software to assemble de novo transcriptomes did not work particularly well. I simply made a bet that these problems would be solved by the time we collected the samples and extracted the RNA. For the most part that’s what happened, although we did end up developing our own assembly software as well!

The 1KP initiative is an international consortium. How has the group evolved over time and what benefits have you seen from having this diverse set of skills?

GW: 1KP would not be where it is today without the participation of scientists around the world from many different backgrounds. For example, plant systematists who defined species of interest and provided the tissue samples worked alongside bioinformaticians who analyzed the data, and gene family experts who are now publishing fascinating stories about particular genes.

 DS: One of the great things about this project is how it has evolved over time as new researchers became involved. There is no restriction on who can take part, which species can be studied or which questions can be asked of the data. This makes the 1KP initiative unique compared to more traditionally funded projects.

GW: We continually encouraged others to get involved and mine our data for interesting information. We did a lot of this through word of mouth and ended up with some highly interesting, unexpected discoveries. For example, an optogenetics group at MIT and Harvard used our data to develop new tools for mammalian neurosciences. This really highlights the importance of not restricting the species we study to those of known economic importance.

According to ISI outputs from this research, two of the most highly cited papers from 1KP are here and here.

You aimed to investigate a highly diverse array of plants. How many plants of the major phylogenetic groups have now been sequenced, and are you still working on expanding the data set?

DS: A lot of thought went into the species selection. We aimed for proportional representation (by number of species) of the major plant groups. We also aimed to represent the morphological diversity of those groups.

GW: Altogether, we generated 1345 transcriptomes from 1174 plant species.

Has this project lead to any breakthroughs in our understanding of the phylogeny of plants?

DS: This will be the first broad look at what the nuclear genome has to tell us, and the first meaningful comparison of large nuclear and plastid data sets. However, due to rapid evolution plus extinction, many parts of the plant evolutionary tree remain extremely difficult to solve.

Hornworts are non-vascular plants that grow in damp, humid places. Photo by Jason Hollinger. Used under Creative Commons License 2.0.

Hornworts are non-vascular plants that grow in damp, humid places. Photo by Jason Hollinger. Used under Creative Commons License 2.0.

One significant breakthrough was the discovery of horizontal gene transfer from a hornwort to a group of ferns. This was unexpected and very interesting in terms of the ability of those ferns to be able to accommodate understory habitats.

GW: With regard to horizontal gene transfer, there are papers in the pipeline that will illustrate the discovery of even more of these events in other species. We have also studied gene duplications at the whole genome and gene family level. This is the most comprehensive survey ever undertaken, and people will be surprised at the scale of the discoveries. However, we will be releasing our findings shortly as part of a series and it would be unwise for us to give the story away here! Keep a look out for these!

Interview with Dr. Winfried Peters: Bringing forgotten ideas on plant biomechanics into the 21st century

This week we spoke to Dr. Winfried S. Peters from Indiana University/Purdue University Fort Wayne (IPFW). His research mainly focuses on the biomechanics of plant cells, which led him to take a second look at some of the ideas of botanists in the 19th and early 20th century and use modern techniques to make exciting new discoveries.

Winfried Peters

Dr Winfried S. Peters, Indiana University/Purdue University Fort Wayne (IPFW), next to several tons of land-plant sieve elements!

 

Could you begin by describing your research interests?
I am interested in the biophysical aspects of the physiology of plants and animals. In plants, my research focuses on the mechanics of growth and morphogenesis, and on the cell biology of long-distance transport in the phloem. For both topics, a solid background in the history of the field can be quite helpful – I love studying the old literature to reconstruct the ideas botanists had a century or two ago regarding the functioning of plants.

At the recent New Phytologist Symposium, entitled “Colonization of the terrestrial environment 2016”, you presented fascinating work on the sieve tubes of kelp, which resemble the phloem tubes of vascular plants. What is the purpose of these tubes?
In large photosynthetic organisms, not all parts of the body are truly autototrophic. Some tissues produce more material by photosynthesis than they need, while others produce less than they require or none at all– think of green leaves and growing root tips. Over-producing tissues can act as sources and export photoassimilates to needy sink tissues. Sieve tubes are arrays of tubular cells that mediate this exchange, enabling the rapid movement of photosynthate-rich cytoplasm between sources and sinks.

What techniques did you utilize to investigate the function of these tubes, and what did this reveal?
During my recent sabbatical, I became involved in this project in the lab of my friend and long-term collaborator, Professor Michael Knoblauch. Michael heads the Franceschi Microscopy and Imaging Center at Washington State University, where we studied sieve tubes of the Bull Kelp (Nereocystis luetkeana) using a variety of state-of-the-art microscopy techniques. Most importantly, we employed fluorescent dyes to visualize transport in sieve tube networks. To do this, one needs to work with intact kelp, which is demanding given a thallus size of 12 meters and more. So we moved to Bamfield Marine Sciences Centre on Vancouver Island, where Bull Kelp is a ‘common weed’.

A particularly important result was the pressure-induced reversal of the flow direction in sieve tubes and across sieve plates. This was in line with Ernst Münch’s (1876-1946) theory, who suggested that sieve tube transport was driven by osmotically generated pressure gradients.

 

Nereocystis wounding

An intact Nereocystis luetkeana is kept in a tank (right) while sieve tube transport is studied using a fluorescence microscope. Photo credit: Michael Knoblauch.

How do the biomechanics of the kelp sieve tubes differ from the phloem tubes of higher plants?
Regarding cytoplasmic translocation, there doesn’t seem to be a difference – in higher plants as in kelps, the contents of the sieve tubes move in bulk flow – but wounding responses differ drastically. After wounding, we found that kelps have a massive swelling of the walls, which reduced the sieve tube diameter by more than 70%. By injecting silicon oil into severed kelp sieve tubes we demonstrated that wall swelling was fully reversible, and that the swelling state of the walls depended on intracellular pressure.

Wounding response in kelp

Sieve wall tubes swell after wounding due to changes in intracellular pressure. (Images taken from video below).

Have reversible wall-swelling reactions been observed in other species, and what are the implications of this finding?
We have observed the wall-swelling response in all kelp species examined. Ironically, there is no shortage of drawings and photographs of kelp sieve tubes with swollen walls in the literature over the last 130 years; however, the dynamics of cell behavior remained hidden in plain sight because fixed tissue samples rather than fully functional, whole organisms were studied. Consequently, sieve tubes with swollen walls were misinterpreted as senescent cells. There also are publications on turgor-dependent cell wall swelling in red and green algae, but these ceased around 1930.

Afterwards, wall swelling was completely forgotten, judging from the textbooks. This is remarkable, as Wilhelm Hofmeister (1824-1877), often celebrated as a founding father of plant biomechanics, denied a significant role for osmotic processes in the generation of turgor, the hydrostatic pressure within plant cells. Rather, he maintained that living cells were pressurized by the swelling of their walls. The example of the kelp sieve tube shows how easy it is to remain unaware of wall swelling when it happens right before our eyes. Maybe we should take Hofmeister’s idea seriously once again?

What are the evolutionary implications of your work?
Brown algae and vascular (land) plants are only remotely related, and their sieve tube networks certainly evolved independently of each other. It seems surprising that such sophisticated structures, which serve a complex function that integrates the physiology of the entire organism, have evolved at least twice, but think again. Real cells are not embedded in a totally homogeneous environment, and neither is the cytoplasm within the cell a homogeneous solution. Thus every cell experiences gradients of solute concentrations along its inner and/or outer surface. As a consequence, differential water fluxes across the plasma membrane will occur, resulting in movements of the cell contents. In other words, Münch flow, the cytoplasmic bulk flow driven by osmotically generated pressure gradients, is not a peculiar process operating specifically in sieve tubes, but a ubiquitous phenomenon. Sieve tubes consist of cells that simply do the things cells do, just a little more efficiently as usual. In this view, the repeated convergent evolution of sieve tube networks is not really unexpected.

But kelps resemble land plants in other ways too. As in land plants, kelp cell walls are made of cellulose (at least partly), kelp cells are connected through plasmodesmata, and the kelp life-cycle is a sporophyte-dominated alternation of generations. Evidently, none of these features represents a specific adaptation to life on dry land.


Wound responses including wall swelling in a sieve tube of Nereocystis luetkeana. (Watch for the rapid cell wall swelling between 11 and 14 seconds in!) This video was taken by Professor Michael Knoblauch in collaboration with Dr Winfried S. Peters.
 


If you’d like to know more about this fascinating work, it was been published in the following articles:

Knoblauch, J., Peters, W.S. and Knoblauch, M., 2016. The gelatinous extracellular matrix facilitates transport studies in kelp: visualization of pressure-induced flow reversal across sieve platesAnnals of Botany117(4), pp.599-606.

Knoblauch, J., Drobnitch, S.T., Peters, W.S. and Knoblauch, M., 2016. In situ microscopy reveals reversible cell wall swelling in kelp sieve tubes: one mechanism for turgor generation and flow control? Plant, Cell and Environment39(8), pp.1727-1736.

 

Uncovering the secrets of ancient barley

This week we speak to Dr Nils Stein, Group Leader of the Genomics of Genetic Resources group at the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK). We discuss his recent work on the genomes of 6000-year-old cultivated barley grains, published in Nature Genetics, which made the headlines around the world.

Nils Stein

Dr Nils Stein, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)

Could you describe your work with the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)?

The major research focuses of my group, the Genomics of Genetic Resources, are to continue sequencing the genomes of barley and wheat, perform comparative genomics on the Triticeae tribe, isolate genes of agronomic interest, and investigate the genomics of wild barley relatives.

We are currently leading the work to generate the barley reference genome, and we are also partners in several wheat genome sequencing projects. We are genotyping-by-sequencing (GBS) all 20 000 barley accessions in the IPK Genebank, as well as 10 000 pepper accessions as part of a Horizon 2020 project (G2P-SOL) investigating the Solanaceae crop species.
Your recent collaborative paper on the genomic analysis of 6,000-year-old barley grains made headlines around the world. What did this study involve?

This was an interdisciplinary study to sequence the DNA of 6000-year-old barley grains. The grains were excavated by a team of Israeli archaeologists and archaeobotanists led by Prof. Ehud Weiss, Bar-Ilan University, the DNA was extracted and sequenced by ancient DNA specialists Prof. Johannes Krause and Dr. Verena Schünemann in Germany, and the data were analyzed by Dr. Martin Mascher in the context of our comprehensive barley genome diversity information. This allowed the resulting sequence information to be put into a population genetic and ecogeographic context.

Ancient barley

Preserved remains of rope, seeds, reeds and pellets (left), and a desiccated barley grain (right) found at Yoram Cave in the Judean Desert. Credit: Uri Davidovich and Ehud Weiss.

What led you to the realization that barley domestication occurred very early in our agricultural history?

The genome of the analyzed ancient samples was highly conserved with extant barley landraces of the Levant region, which look very similar to today’s high-yielding barley varieties. Although suggestive and tendentious, this told us that the barley crop 6000 years ago looked very similar to extant material. The physical appearance and the archaeobotanical characters of the analyzed seeds also very much resembled modern barley.

 

These barley grains contain the oldest plant genomes reconstructed to date. Did you find any differences between the samples that might give us an insight into the traits that were first selected in the early domestication of the crop?

We have only scratched the surface so far. The major domestication genes controlling dehiscence, brittleness or row-type of the main inflorescence had the same alleles in the ancient samples that are found in extant barley, confirming that these traits were selected for early in domestication. Additional analyses on other genes controlling different traits in barley are still ongoing – bear in mind that many of the genes controlling major traits in barley are still unknown, which complicates the selection of targets for analysis.

Modern barley

Modern barley cultivar. Credit: Christian Scheja. Used under license: CC BY 2.0.

 Do these grains have any genetic variation that we lack at key loci in modern barley lines, for example in stress or disease resistance?

This is matter of ongoing analysis. So far it is obvious that the most genetically similar extant landraces from the Levant region have accumulated natural mutations over the last 6000 years, resulting in additional variation that we don’t find in the ancient sample.

 

What can we expect from the barley genome projects in the future?

The International Barley Genome Sequencing Consortium is preparing a manuscript on the reference sequence of barley. This will allow further analysis of the ancient DNA data with a more complete, genome-wide view, including the consideration of a more complete gene set than has been available so far. Our Israeli collaborators (Professor Ehud Weiss and Professor Tzion Fahima) have more ancient samples of similar quality. We hope we will be able to generate a more comprehensive view of the ancient population genomics of barley in the future, to better address the question of novel ancient alleles and lost genetic diversity.

The Barley Pan-Genome analysis will soon give us a better understanding of the structural variation in the barley genome. Putting the ancient DNA information into this more comprehensive genomic context will be very exciting. We also hope to be able to compare a variety of ancient samples of different ages to more precisely date the event of barley domestication.


You can read the paper here: Genomic analysis of 6000-year-old cultivated grain illuminates the domestication history of barley ($).

Professor Stefan Jansson on what makes a GMO, and the Scandinavian Plant Physiology Society

This week we speak to Professor Stefan Jansson, Umeå University, Sweden, who is the President of one of the Global Plant Council member organizations, the Scandinavian Plant Physiology Society (SPPS). He tells us more about his fascinating work, his prominent role in the GM debate, and his thoughts on the work of the SPPS and GPC, both now and in the future.

Stefan_Jansson

Could you tell us a little about your areas of research interest?

I have worked on (too) many things within plant science, but now I am focused on two subjects: “How do trees know that it is autumn?”, and “How can spruce needles stay green in the winter?” We use several approaches to answer these questions, including genetics, genomics, bioinformatics, biochemistry and biophysics.

 

Your ground-breaking work on CRISPR led to you being awarded the Forest Biotechnologist of the Year award by the Institute of Forest Biosciences. Could you tell us more about this work, and the role you have played in the GM debate?

In our work on photosynthetic light harvesting, we have generated and/or analyzed different lines lacking an important regulatory protein; PsbS. PsbS mutants resulting from treatment with radiation or chemical mutagens can be grown anywhere without restriction, but those that are genetically modified by the insertion of disrupting ‘T-DNA’ are, in reality, forbidden to be grown. For years, I, and many other scientists, have pointed out that it does not make sense for plants with the same properties to be treated so differently by legislators. In science we treat such plants as equivalents; when we publish our results we could be required to confirm that the correct gene was investigated by using an additional T-DNA gene knock-out line or an RNAi plant (RNA interference, where inserted RNA blocks the production of a particular protein), but in the legislation they and the ‘traditionally mutated’ plants are opposites.

This has been the situation for many years, but it has been impossible to change. To challenge this, we set up an experiment using a targeted gene-editing approach called CRISPR/Cas9 to make a deletion in the PsbS gene, which resulted in a plant with a non-functional PsbS gene but no residual T-DNA. We asked the Swedish competent authority if this would be treated as a GM plant or not, arguing that it is impossible to know if it is a ‘traditional’ deletion mutant or a gene-edited mutant. In the end, the authority said that, according to their interpretation of the law, this cannot be treated as a GMO.

If this interpretation is also used in other countries, plant breeders will have access to gene-editing techniques to aid them in their work to generate new varieties, which would otherwise not be a possibility. The reason we did this was to provide the authorities with a concrete case, and one which was not linked to a company or commercial crop but rather something that everyone would realize could only be important for basic science. Therefore most of the arguments that are used against GMOs could not be used, and this should be a step forward in the debate.

 

Check out Stefan’s fantastic TEDxUmeå talk to hear more on the GM debate:

spps_logoYou are the President of the Scandinavian Plant Physiology Society, one of the Global Plant Council member organizations. Could you briefly outline the work of the SPPS?

We support plant scientists – not only plant physiologists – in the Nordic countries, organize meetings, publish a journal (Physiologia Plantarum), etc.

 

What are the most important benefits that SPPS members receive?

This is an issue that we discuss a lot in the society right now. Only a limited fraction of Nordic plant scientists are members – obviously are the benefits not large enough – and this is something that we intend to change in the coming years. We think, for example, that we need to be a better platform for networking between researchers and research centers, and have a lot of ideas that we would like to implement.

 

How does the GPC benefit the SPPS?

Although there are country- and region-specific issues important for plant scientists, the biggest issues are global. The arguments why we need plant science are basically the same whether you are a plant scientist in Umeå or Ouagadougou, therefore we all benefit from a global plant organization.

 

What do you see as important roles for the future of the GPC, both for SPPS and the wider community?

This is quite clear to me: we will contribute to saving the planet.

 

What advice would you give to early career researchers in plant science?

Your curiosity is your biggest asset, so take good care of it.

 

Is there anything else you’d like to add?

The challenge for the GPC is clearly to get enough resources to be able to fulfil its very worthwhile ambitions. GPC has made a good start: the vision is clear and the roadmap is there, which are two prerequisites, but additional resources are needed to employ people to realize these ambitions, build upon current successes, and perform the important activities. It is easy to say that if we all contribute with a small fraction of our time that would be sufficient, but we all have may other obligations and commitments, and a few dedicated people are needed in all organizations.

Women in Plant Science, Part II

Tuesday 13th October was Ada Lovelace Day, an international celebration of women in science, technology, engineering and maths (STEM) in honor of Ada Lovelace, the first computer programmer.

To highlight the achievements of women in STEM we’ve spoken to female plant scientists around the world about their careers and experiences. Read on for Part II of the series (for Part I, click here):

 

Professor Kalunde Sibuga

Professor Kalunde Sibuga

Professor Kalunde Sibuga

Sokoine University of Agriculture, Tanzania

What are you working on?

I have always been interested in working with farmers who have limited resources and coming up with production technologies that can help reduce their workload (particularly for women) and dependence on purchased inputs such as fertilizers, herbicides and other pesticides. These interests led to a research career focusing on weed management and agronomy of legumes, vegetable crops and cereals.

 

Have you ever faced any specific challenges as a female scientist in Tanzania?

Not particularly, because policies in Tanzania encourage girls to go to school and do whatever they are able to do. Women in science in my country are not targeted for discrimination, but until recently, certain sections of science such as engineering were considered a male domain. The government aims for gender equality and funds various projects to encourage girls to take science subjects, which have assisted in increasing enrolment of girls in universities.

 

What are your hopes and goals for the future?

I have always believed that whatever we do, our aim should be to increase productivity, reduce drudgery and increase household income. This can only be achieved if governments, particularly African governments, would take a serious look at mechanization, timely delivery of inputs, marketing, and value addition aspects. Our work in agronomy is of no great benefit if the other components are not properly and appropriately addressed.

Weed Science and Management are not as well staffed as other branches of crop protection such as entomology and plant pathology. My goals for the future are therefore to continue to train and encourage young scientists to engage in weed research.

 

 

Associate Professor Siobhan Brady

Associate Professor Siobhan Brady

Associate Professor Siobhan Brady

University of California, Davis, USA

Could you give a brief overview of your research into root development?

My lab explores the development of root cell types, and the gene regulatory mechanisms and networks that are responsible for producing them. We are also interested in how different species and stresses have different networks in order to adapt to different environments. We love to utilize genome-scale data and systems approaches to understand how these systems are organized.

 

Have you faced any specific challenges as a woman in science?

Yes. Finding the right time to have a baby is one example. I ended up having my first child five months into my position as a PI and the experience was one of the most challenging in my life. I was trying to find my feet being a new mum at the same time as being a new lab leader, writing grants and teaching. I even felt “guilty” (purely self-imposed) for starting my position by having a baby and felt that I had so much to prove by being able to get this position at a time when getting faculty positions was incredibly challenging. I went back to work full time after six weeks. Nursing, working, and travelling was very hard, but I made it. I had the support of my partner and of an incredibly wonderful lab and colleagues. Looking back in fact, I wish I’d opened up to them a little more.

I now have two beautiful boys. I have had to cut some of my work responsibilities (for instance, picking and choosing which weekly meetings are really the most important to attend). It has changed our lives, but learning to be flexible (not always easy for me!) and finding the unique advantages in each challenge that faces us has been a tremendous learning experience.

 

What would you say is the general experience of women in science in the US?

So much better than it once was. When I started in science I knew of very few female faculty members with children. Now there are many more incredible mentors who have families, are very successful and maintain a good work-life balance.

That being said, given the current funding situation in the US and the general economy there are fewer and fewer faculty jobs available. Many graduate students and postdocs have presented their concerns to me that raising a family and having a successful career are inherently incompatible in this era – that is, that you will always be so busy that something will fail.

It is hard to figure out when to have children. If you have a grant, there is no allowance for your graduate students or postdocs to take leave, but you are mandated to take some leave (as you should be). This is a real challenge, both for PIs and for students/postdocs, as there is really only a limited amount of time to get a project done and to have a mother stay with an infant. I don’t know of a good way to handle this other than to always have open communication with people in your group and to let them know (if a PI) that you support them in their life goals, no matter what they are, while encouraging them to be the best they can be.

 

What are your goals for the future?

Raise happy, well-adjusted children, continue to train amazing scientists, learn different fields of research and ask new and creative biological questions. And of course, publish well and get funded sufficiently so that our work can make a difference in science and the world in general!

 

 

Thank you to both Professor Kalunde Sibuga and Associate Professor Siobhan Brady for taking the time to discuss their experiences with us.

Please leave a comment below and describe any challenges or opportunities you have observed for women in science in your country!