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1000 Plants

By | Blog, Interviews

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!

Cassava brown streak: lessons from the field

By | Blog, GPC Community

This week’s post was written by Katie Tomlinson, a PhD student at the University of Bristol, UK, who spent three months as an intern at the National Crops Resource Research Institute in Uganda. She fills us in on the important research underway at the Institute, and how they communicate their important results to local farmers and benefit rural communities.  

Over the summer, I had a great time at the National Crops Resources Research Institute (NaCRRI) in Uganda. I’m currently in the second year of my PhD at the University of Bristol, UK, where I’m researching how the cassava brown streak disease (CBSD) viruses are able to cause symptoms, replicate and move inside plants. I was lucky enough to be given a placement at NaCRRI as part of the South West Doctoral Training Partnership Professional Internship for PhD Students (PIPS) scheme, to experience the problem for myself, see the disease in the field, meet the farmers affected and investigate the possible solutions.

 

Cassava brown streak disease

Cassava brown streak disease symptoms on tubers. Image credit: Katie Tomlinson.

 

Cassava is a staple food crop for approximately 300 million people in Africa. It is resilient to seasonal drought, can be grown on poor soils and harvested when needed. However, cassava production is seriously threatened by CBSD, which causes yellow patches (chlorosis) to form on leaves and areas of tubers to die (necrosis), rot and become inedible.

Despite being identified in coastal Tanzania 80 years ago, CBSD has only been a serious problem for Uganda in the last 10 years, where it was the most important crop disease in 2014–2015. The disease has since spread across East Africa and threatens the food security of millions of people.

NaCRRI is a government institute, which carries out research to protect and improve the production of key crops, including cassava. The focus is on involving farmers in this process so that the best possible crop varieties and practices are available to them. Communication between researchers and farmers is therefore vital, and it was this that I wanted to assist with.

 

Scoring cassava brown streak disease

Scoring cassava plants for Cassava brown streak symptoms. Image credit: Katie Tomlinson.

 

When I arrived I was welcomed warmly into the root crop team by the team leader Dr Titus Alicai, who came up with a whole series of activities to give me a real insight into CBSD. I was invited to field sites across Uganda, where I got to see CBSD symptoms in the flesh! I helped to collect data for the 5CP project, which is screening different cassava varieties from five East and Southern African countries for CBSD and cassava mosaic disease (CMD) resistance. I helped to score plants for symptoms and was fascinated by the variability of disease severity in different varieties. The main insight I gained is that the situation is both complex and dynamic, with some plants appearing to be disease-free while others were heavily infected. There are also different viral strains found across different areas, and viral populations are also continually adapting. The symptoms also depend on environmental conditions, which are unpredictable.

I also got to see super-abundant whiteflies, which transmit viruses, and understand how their populations are affected by environmental conditions. These vectors are also complex; they are expanding into new areas and responding to changing environmental conditions.

It has been fascinating to learn how NaCRRI is tackling the CBSD problem through screening different varieties in the 5CP project, breeding new varieties in the NEXTGEN cassava project, providing clean planting material and developing GM cassava.

 

Tagging cassava plants

Tagging cassava plants free from Cassava brown streak disease for breeding. Image credit: Katie Tomlinson.

 

And there’s the human element…

In each of these projects, communication with local farmers is crucial. I’ve had the opportunity to meet farmers directly affected, some of whom have all but given up on growing cassava.

 

Challenging communications

Communicating has not been easy, as there are over 40 local languages. I had to adapt and learn from those around me. For example, in the UK we have a habit of emailing everything, whereas in Uganda I had to talk to people to hear about what was going on. This is all part of the experience and something I’ll definitely be brining back to the UK! I’ve had some funny moments too… during harvesting the Ugandans couldn’t believe how weak I was; I couldn’t even cut one cassava open!

 

Real world reflections

I’m going to treasure my experiences at NaCRRI. The insights into CBSD are already helping me to plan experiments, with more real-world applications. I can now see how all the different elements (plant–virus–vector–environment–human) interact, which is something you can’t learn from reading papers alone!

Working with the NaCRRI team has given me the desire and confidence to collaborate with an international team. I’ve formed some very strong connections and hope to have discussions about CBSD with them throughout my PhD and beyond. It’s really helped to strengthen collaborations between our lab work in Bristol and researchers working in the field on the disease frontline. This will help our research to be relevant to the current situation and what is happening in the field.

 

Some of the NaCRRI team

Saying goodbye to new friends: Dr. Titus Alicai (NaCRRI root crops team leader), Phillip Abidrabo (CBSD MSc student) and Dr. Esuma Williams (cassava breeder). Image credit: Katie Tomlinson.

 

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

By | Blog, Interviews

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.

 

Plantwise – promoting and supporting plant health for the Sustainable Development Goals

By | Blog, Global Change, GPC Community
Andrea Powell

Andrea Powell, CABI

Promoting and supporting plant health will be an important part of how we achieve the United Nations’ Sustainable Development Goals (SDGs). Andrea Powell, Chief Information Officer of the Centre for Agriculture and Biosciences International (CABI) looks at how the CABI-led Plantwise programme is helping to make a difference.

By Andrea Powell

 

On 26th and 27th July 2016, CABI held its 19th Review Conference. This important milestone in the CABI calendar saw our 48 member countries come together to agree a new medium-term strategy. As always, plant health was a key focus to our discussions, cutting across many of CABI’s objectives. For CABI, with 100 years of experience working in plant health, it has become one of our most important issues, upon which our flagship food security program, Plantwise, has been built.

Plant health can, quite simply, change the lives and livelihoods of millions of people living in rural communities, like smallholder farmers. Human and animal health make headlines, while plant health often falls under the radar, yet, it is crucial to tackling serious global challenges like food security. Promoting and supporting plant health will be an important way to achieve the Sustainable Development Goals (SDGs).

Plant health and the SDGs

Take, for example, SDG 1, which calls for ‘no poverty’. The UN states that one in five people in developing regions still lives on less than $1.25 a day. We know that many of these people are smallholder farmers. By breaking down the barriers to accessing plant health knowledge, millions of people in rural communities can learn how to grow produce to sell to profitable domestic, regional and international markets.

Plantwise ReportSDG 2 focuses on achieving ‘zero hunger’. Almost one billion people go hungry and are left malnourished every day – and many are children. Subsistence farmers, who grow food for their families to eat, can be left with nothing when their crops fail. Access to plant health knowledge can help prevent devastating crop losses and put food on the table.

Interestingly, SDG 17 considers ‘partnerships for the goals’ and is critical to the way in which we can harness and share plant health knowledge more widely to help address issues like hunger and poverty. By themselves, individual organizations cannot easily resolve the complicated and interconnected challenges the world faces today. This is why partnership is at the heart of CABI’s flagship plant health programme: Plantwise.

What is Plantwise?

Plantwise Report 2015

Since its launch in 2011, the goal of Plantwise has been to deliver plant health knowledge to smallholder farmers, ensuring they lose less of what they grow. This, in turn, provides food for their families and improves living conditions in rural communities. Plantwise provides support to governments, helping to make national plant health systems more effective for the farmers who depend on them. Already, Plantwise has reached nearly five million farmers. With additional funding, and by developing new partnerships, we aim to bring relevant plant health information to 30 million farmers by 2020, safeguarding food security for generations to come.

Plantwise ‘plant clinics’ are an important part of the fight against crop losses. Established in much the same way as clinics for human health, farmers visit the clinics with samples of their sick crops. Plant doctors diagnose the problem, making science-based recommendations on ways to manage it. The clinics are owned and operated by over 200 national partner organizations in over 30 countries. At the end of 2015, nearly five thousand plant doctors had been trained.

Plantwise

A Plantwise plant clinic in action. Credit: Plantwise

Harnessing technology for plant health

The Plantwise Knowledge Bank reinforces the plant clinics. Available in over 80 languages, it is an online and offline gateway to plant health information, providing the plant doctors with actionable information. It also collects data about the farmers, their crops and plant health problems. This enables in-country partner organizations to monitor the quality of plant doctor recommendations; to identify new plant health problems – often emerging due to trade or climate change issues; and develop new best-practice guidelines for managing crop losses.

Plantwise

The first ever e-plant clinic, held in Embu Market, Kenya. Credit: Plantwise

The Plantwise flow of information improves knowledge and helps the users involved: farmers can receive crop management advice, and researchers and governments can access data from the field. With a new strategy for 2017–19 agreed, CABI will continue to focus on building strong plant health systems. We are certain that plant health is of central importance to achieving the SDGs and, together in partnership, we look forward to growing the Plantwise program and making a concrete difference to the lives of smallholder farmers.

“A few years ago, I would make ZMW 5000 per year. Last year I got 15 000. I have never missed any plant clinic session. I’ve been very committed, very faithful, because I have seen the benefits.”––Kenny Mwansa, Farmer, Rufunsa District, Zambia.

Take a look at Plantwise in action in Zambia (YouTube):

Plantwise in Zambia

Meet Linda, a Zambian plant doctor

Meet Kenny, a Zambian farmer

 

Learn more about Plantwise at www.plantwise.org.

Uncovering the secrets of ancient barley

By | Blog, Interviews

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 ($).

How do you grow a plant scientist?

By | Blog, GPC Community, Scientific Meetings

This week’s blog post is written by Sarah Blackford.

Plant scientists are generally very good at growing their plants, taking good care of them and making sure they’re well fed and watered. But what about their own development? Who’s growing them?

In a recent survey, Principal Investigators (PIs) were asked to rate areas of their work they perceived to be the most important. Research-related activities were valued the highest (Vitae, 2011), while conversely, “providing career development advice” and “continuing professional development” were rated as two of their lowest priorities, at around 5% (see figure). This, perhaps, is not surprising when you consider PIs need to prioritize a multitude of responsibilities on their ‘to do’ list.

PI Leaders report 2011

Figure reproduced from Principal investigators and research leaders survey, Vitae (2011) showing the importance of activities and functions for the development of research leaders, against their own confidence in those activities

 

From small shoots

Like the plant, overlooking the growth of the person could lead to plant scientists being held back from a flourishing career. So, taking responsibility for your own development is vital, especially since programs of professional and personal development are not always readily available to PhD students and researchers in many institutes and universities. Even if they are, the content and timing is not always relevant or convenient. I’ve been delivering bespoke career development workshops for bioscientists, including plant scientists, for over 10 years now and one of the main aims is to help people to help themselves. As well as providing practical information and advice on bioscience-related careers, job seeking strategies and career transition planning, I use interactive exercises and discussions to raise self-awareness. This involves recognizing the range of skills acquired through research, appreciating work values, linking interests with career choice and showing how personality plays a crucial role in effective communication and leadership. During the workshops, the participants complete a personal action plan identifying what they need to do to grow their own careers.

Firmly planted

Most people need to update and improve their CVs (even me!), hone their interview technique and perfect their self-presentation skills. But personal and professional development requires a range of different actions depending on career goals and intentions. Some PhD students want to continue on to do at least one postdoc and then decide whether to carry on after that. With quite a good number of posts available, and with some industry recruiters saying they prefer researchers with postdoc experience, this can be an excellent first step – but be careful to ensure you’re moving forward and building on your experience. Look at the career stories of early career researchers who were awarded this year’s prestigious SEB president’s medal – they relate strategies they have used to fill gaps in their expertise and to position themselves favorably to secure a permanent research leadership position. For researchers who are aspiring academics, their plans may include actions such as submitting an abstract to give a talk at a forthcoming conference, doing some strategic networking or finding a mentor to help them to apply for a fellowship.

Branching out

For those considering a non-academic career, their personal development will depend on which career sector they plan to move into. For example, arranging work shadowing or doing voluntary work can help shift your career towards your desired destination. I helped out at the career service during my job as assistant editor when I was based at Southampton University, giving me enough experience and a reference to break into this career. Internships can provide opportunities to spend time working in areas such as policy, outreach and publishing, and if you’re a budding science writer you can simply start up your own blog, or write on someone else’s – like this one! Everyone would benefit from setting up or improving their presence on social media, whether it’s Researchgate, LinkedIn or Twitter. These global networks help to raise your profile, provide information about companies and careers of interest, build relationships and even advertise jobs. Generic training in communication, networking, self-awareness and other personal effectiveness can help to improve everyone’s self-reliance and confidence.

A fertile future

So in answer to the question, “how do you grow a plant scientist?” I would say it depends on their field of interest and direction of growth. Never think of your PhD as the end of your learning – it’s another new beginning. Even PIs lack confidence in some important aspects of their work, such as securing research funding (see figure) and would likely benefit from training in this area, not to mention management and leadership. Growing plants is your business; without them you would make no progress, nor generate results on which to write your publications and build a career. Ignore your own personal growth and you might be in danger of going to seed!

This blog is a summary of the career workshop, organized and delivered by Sarah Blackford, at the recent FESPB/EPSO Congress 2016 in Prague.


Sarah Blackford

Dr Sarah Blackford

 

Sarah Blackford started her career in plant science research at York University, moved into journal publishing with the Journal of Experimental Botany and then trained to be a professional higher education careers adviser. She is currently the Head of Education and Public Affairs at the Society for Experimental Biology (SEB) and writes a regular blog for bioscience PhD students and postdocs: www.biosciencecareers.org

Let’s get Plantae!

By | Blog, GPC Community, Plantae

So you’re hearing good things about the new plant science networking platform Plantae and want to get involved? You’ve come to the right blog post! Read on to learn how to set up your profile, find friends and get involved with the community.

Who are you?

Plantae profile

Filling in your profile is easy!

Plantae is a great place to network with researchers around the world, so you’ll want your profile to be as detailed as possible.

As a minimum, add your name, a profile photo, your professional affiliations and a summary of who you are and what you do. This will help your colleagues and friends to find you, and break the networking ice with new connections!

What makes a good bio? Give the reader a little information about your fields of interest, background, plant science outreach, new papers, favorite plant, whatever you like (related to plants and plant science, of course!). Remember that Plantae is a professional networking site, so don’t put anything on there that you wouldn’t want your boss (current or future!) to see!

Where can I find out more about this interesting person?

Plantae social media

Don’t forget to add your social media and researcher profiles

A great feature of the Core Profile is the ability to add your social media profiles, website, and enhance the visibility of your research by adding researcher profiles, for example your ORCID, Mendeley, or ResearchGate account. To ensure that the accounts connect properly, add the full URL of each profile, not just your account name.

 

Will you be my friend?

From the Community homepage you can choose to see the recent activity of your friends, but only if you’ve added them first!

Add a friend on Plantae

How to add a friend on Plantae

To find colleagues, click on ‘Members’ and you can search for a name, or filter all members by city, state or country. Click on your friend’s name to go to their profile. On the left sidebar, you’ll see a button named ‘User Actions’, which when clicked brings up the option to add them as a friend. After they accept your request, you’re officially friends. Congratulations!

Branching out

Plantae groups

Join a group to continue networking

Now you’ve added everyone you know, it’s time to connect with people that you don’t! Get over to the Discussion boards and let everyone know how you feel about the latest hot paper or public engagement scheme. Or you could join a Group of users who share your interests, location, or love of plant-themed poetry (disclaimer: the latter is currently not a Plantae group – feel free to start it!). It’s easy to join conversations or start one of your own.

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A typical day for PhD students in Japan

By | Blog, GPC Community
Akiko Nakazaki

Akiko Nakazaki, PhD student at Kyoto University

Kon-nichiwa! (Hello!) I am Akiko Nakazaki, a PhD student studying plant molecular cell biology at Kyoto University in Japan.

I’m interested in plant defense – specifically the glucosinolate-myrosinase defense system, which is specific to Brassicales such as Arabidopsis thaliana. Glucosinolates are a group of secondary metabolites stored in separate cells to myrosinases, the enzymes that break them down. Upon tissue damage, the glucosinolates and myrosinases are released from their cells and combine. The glucosinolates are hydrolyzed to volatile repellent compounds such as isothiocyanates and nitriles.

Glucosinolate myrosinase defense system

When damaged, cells containing glucosinolate and myrosinase are ruptured, releasing their contents. The glucosinolate is broken down by the myrosinase into volatile compounds that repel herbivores

I was impressed by this ingenious and rational survival strategy! I want to reveal this defense system at the cellular level, and am researching it in Arabidopsis thaliana by performing microscopic observations, bioassays with insects, and so on.

A day in the lab

Are you interested in how PhD students from other countries spend their day in the laboratory? I am! Let me tell you about my typical day in the lab.

I wake up at 8:30am, and have morning coffee and toast for breakfast while reading a newspaper. Then, I get dressed and ride on my bicycle to the University. During the ride (about 10 minutes), I remind myself of the day’s schedule. I get to the lab at 10am and take my seat. All the members of the lab have their own desk and workbench. I turn on my computer and check my emails.

In the daylight, I basically do experiments and read papers. I start doing microscopic observations and lose track of time until I hear my stomach growling and realize that it is almost 2pm. I have lunch at the eating space in lab. In this room, there are always some lab members who are eating, discussing their research, playing social games, etc. After lunch, I report the result of my microscopic observations to my boss and we have a brief discussion about it.

Microscopic_observations

Then, I return to my seat and realize the primers I ordered yesterday have arrived. I perform a PCR and prepare an agarose gel for electrophoresis. While I am waiting for the PCR to end, I search PubMed and Google Scholar for new papers to read. I load the PCR products to the gel and check that the PCR worked. In the evening, I allocate myself free time for doing more experiments, reading more papers, preparing research presentations, discussions, etc.

I’ve sought a more effective way to advance my research through trial and error. For example, when I started researching in the lab I was a little too ambitious, and planned my schedule too tightly. I sometimes felt tired and depressed when my research was not right on schedule, as is often the case. In these negative moods I couldn’t enjoy my work, so I adopted a schedule with more free time. Because of this change, I’ve come to be able to work flexibly and keep a positive frame of mind.

I’m home between 10pm and midnight. At home, I have a late dinner and take a good long soak in the bath (my favorite time of day!). I go to bed at 2am.

Free weekends!

On weekends I enjoy playing badminton, learning traditional Japanese dance and shopping. I try to make plans without lab work as much as I can, however I’m not able to do avoid it sometimes when I am struggling to get new data before academic conferences and progress reports. Leaving the lab allows me to get rid of stress and feel refreshed for a healthy next week. Furthermore, I devise ways to work more efficiently on weekdays, because I am required to take time off at the weekends.

Treasure every encounter

My boss always says, “It is important to value encounters with people and things.” It wasn’t until recently that I finally understood that message! I have found that experiments may not always work well, but when I look at it from a different angle, even experiments that haven’t gone the way I’d wanted could make me aware of something new and interesting. This awareness could also be brought about through discussions with others.

I am grateful for being able to receive this opportunity. Thank you.


Akiko Nakazaki is in the first year of her doctoral program in the Department of Botany, Graduate School of Science, Kyoto University, Japan.

 

Lessons from the oldest and most arid desert on Earth

By | Blog, Global Change, GPC Community
Atacama Desert

Image credit: Center for Genome Regulation

The Atacama Desert is a strip of land near 1000 km in length located in northern Chile. With an average yearly rainfall of just 15 mm (close to 0 in some locations) and high radiation levels, it is the driest desert in the world. Geological estimates suggest that the Atacama has remained hyperarid for at least eight million years. Standing in its midst, one may easily feel as though visiting a valley on Mars.

Despite these harsh environmental conditions, it is possible to find life in the Atacama. At the increased altitudes along the western slopes of the Andes precipitation is slightly increased, allowing plant life.

Convergent evolution

The driest and oldest desert in the world acts as a natural laboratory where for 150 million years plants adapted to and colonized this environment. These adaptations are likely present in multiple desert plant lineages, thus providing an evolutionary framework where these traits can be associated with a signature of convergent evolution.

Surviving a nitrogen-limited landscape

Plant in the Atacama Desert

Image credit: Center for Genome Regulation

The interplay of environmental conditions in the transect of the Atacama, ranging from 2500 to 4500 meters above sea level, results in three broad microclimates; Pre Puna, Puna, and High Steppe. These microclimates have different humidities, temperatures, levels of organic matter and even different pH levels, but share one common feature: low nitrogen levels.

To engineer crops with higher nitrogen use efficiency, it is very useful to first learn how plants adapt to growth in low nitrogen environments. Here the Atacama Desert enters into the game. Plants growing in the desert can survive 100-fold less nitrogen below optimum concentrations. Using phylogenetics it is possible to uncover novel genes and mechanisms related to adaptation to these extreme conditions, which have not been discovered through traditional genetic approaches.

Currently, nitrogen fertilizers are widely employed to increase crop yield. In 2008 100 million tons of this fertilizer were used and it is projected that for 2018 the demand for nitrogen will rise to 119 million tons. Regretfully, the production and over-usage of this type of fertilizer has an enormous impact in the environment and human health. Around 60% of the nitrogen introduced to the soil for agricultural purposes is leached and lost. Moreover, nitrogen runoffs to the water cause eutrophication in both freshwater and marine ecosystems, leading to algae and phytoplankton blooms, low levels of dissolved oxygen, and finally the migration or death of the present fauna, forming dead zones such as the one in the Gulf of Mexico.
 

Plants in the Atacama Desert

Image credit: Center for Genome Regulation

Nitrogen fertilizers are not the only major concern in modern agricultural procedures. The co-localization of drought and low nitrogen levels is especially detrimental for plant growth and development. We need to support not only the nutritional requirement of an expanding global population but also new energetic strategies based on production of biomass for biofuels on marginal nutrient poor soils. In order to increase crop yields while reducing the environmental impact of nitrogen fertilizers, it is necessary to develop new agricultural strategies and cutting edge technologies.

Learning from the desert

What if we could profit from the extraordinary plants that have had thousands of years to learn how to cope with nitrogen scarcity, drought and extreme radiation? Specifically, can we unravel the genes and mechanisms that allow them to survive in such a barren place?

Atacama Desert

Image credit: Center for Genome Regulation

Over the past three years our group has identified 62 different plant species that inhabit the Atacama Desert, and established a correlation between their habitat attributes and biological characteristics. Using tools such as whole transcriptome shotgun sequencing or RNA-Seq complemented with different bioinformatics approaches, we have identified over 896,000 proteins that are expressed in these conditions.

In this way we aim to learn which processes are highly utilized in these “extreme survivors” compared to similar species that are present in the deserts of California, where the climatic conditions are similar but there is no nitrogen scarcity. That is how we expect to find new mechanisms (or, more precisely, very old mechanisms) that enable plants to survive and grow efficiently in extreme environments.


 

Susana Cabello

Dr Susana Cabello

Written by Dr Susana Cabello, Center for Genome Regulation, Millennium Nucleus for Plant Systems and Synthetic Biology, Chile. Susana would like to acknowledge Maite Salazar & Rodrigo Gutierrez for their suggestions and edits.

The Secrets of Seagrass

By | Blog, Future Directions
Zosteramarina

Zostera marina. Public domain, via Wikimedia Commons.

It’s the ancient story of plant evolution: photosynthetic algae moved to damp places on land, eventually evolving more complex architecture, and spreading across almost all terrestrial habitats. To cope with the drier conditions, plants developed roots to absorb water, and vascular tissue to transport it; a waxy cuticle coating their surfaces to prevent evaporation; and microscopic pores called stomata that open to allow carbon dioxide to diffuse in for photosynthesis but close to prevent excessive water loss.

How, then, does eelgrass (Zostera marina) fit in to this tale? It’s a monocot descended from the flowering plants, but it has turned its back on dry land and returned to the sea; a rare feat that only appears to have happened on three occasions. The recent sequencing of the eelgrass genome has revealed several interesting insights into the dramatic genetic changes that have allowed it to adapt to what lead author Professor Jeanine Olsen described as, “arguably the most extreme adaptation a terrestrial (and even a freshwater) species can undergo.”

Sayonara to stomata

If you live in the sea, conserving water isn’t your main concern. Eelgrass was known to lack stomata, but genetic comparisons to other species, including its freshwater relative Spirodela polyrhiza, revealed the first surprise of the study: eelgrass has lost not only its stomata but also the genes involved in their development and patterning. “The genes have just gone, so there’s no way back to land for seagrass,” said Olsen.

A difference in defense

When angiosperms are attacked by herbivores or pathogens, their defense response typically involves the release of volatile secondary metabolites through their stomata. How can eelgrass release these compounds without stomata? The answer is: it doesn’t. The genome study found that eelgrass is missing crucial genes involved in making ethylene (an important hormone release in times of stress), as well as those responsible for producing non-metabolic terpenoids, which act to repel pests.

Selective pressures of the marine environment differ greatly from those of terrestrial habitats, so different pathways may be involved. Second, eelgrass has a wide repertoire of pathogen resistance genes, which suggests that it is exposed to a very different set of pathogens that may not respond to typical immune responses. Third, volatile secondary metabolites are often involved in attracting pollinators; this is not believed to be necessary in eelgrass, where submarine pollination occurs using the water itself.

Zostera marina. Public domain, CC0 1.0.

Zostera marina – National Museum of Nature and Science, Tokyo. Public domain, CC0 1.0, via WikiMedia Commons.

Changing the cell wall

Eelgrass is subject to extremely salty conditions, and it’s had to adapt to osmotic stress. Unlike typical plant cell walls, eelgrass has engineered its cell wall matrix to retain water in the cell wall, even during low tide. This involves depositing sulfated polysaccharides and low methylated pectins in the cell wall matrix, but until its genome was sequenced no-one knew exactly how. It turns out that eelgrass has rearranged its metabolic pathways: “They have re-engineered themselves,” Olsen explains.

Living with a lack of light

Some species of Zostera can grow in water 50m deep, where light levels are reduced and shifted into a narrow wavelength range; ultraviolet (UV), red and far-red light have particularly low penetration after the first 1–2m of seawater. In a classic eelgrass ‘use it or lose it’ response, it has lost the UVR8 gene, which is responsible for sensing and responding to UV damage, as well as the phytochromes associated with red and far-red receptors. It does, however, retain the photosynthetic machinery, including photosystems I and II.

Unravelling angiosperm evolution

The recent eelgrass publication has revealed how this plant has either lost or adapted typical angiosperm traits to suit its needs, by ditching its stomata, volatile secondary metabolites and certain light sensing genes, or by altering the structure and function of the cell wall. It also developed adaptations that enable gas exchange, help pollen stick to submerged stigmas, and promote nutrient uptake.

Could these adaptations be useful in crop breeding? While a lack of defense compounds would probably be a step backwards, it would be extremely useful to understand how eelgrass copes with biotic stresses without them. Removing light receptors would also be problematic, but could eelgrass help us to develop crops that can grow in shaded conditions, perhaps in intercropping systems? What can we learn from eelgrass’ nutrient uptake and salt-tolerant adaptations?

Now that we have seen some of the secrets of eelgrass, how can we best make use of them?

 

Read the paper: The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea (Open Access)

Read the editorial: Genomics: From sea to sea (paywall)

Read the press release: Genome of the flowering plant that returned to the sea