XV Cell Wall Meeting 2019

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Published on: July 23, 2019

By Christian Donohoe (@donohoho), University of Edinburgh

For my first conference since starting this PhD I attended the triennial XV Cell Wall Meeting, which in its latest iteration was at the University of Cambridge, with Professor Paul Dupree as the chair of the local organising committee. Along with my lab the Edinburgh Cell Wall Group and my supervisor Professor Stephen C. Fry, we came down for the week to present posters on our work and for Stephen to give a talk.

Stephen C. Fry showing Thuryya Al Hinai’s work studying  the enzymes behind fruit ripening

The meeting covers all disciplines related to plant cell wall research so there was a diverse mix of expertise in attendance, ranging from physicists studying secondary cell wall structure in poplar wood using atomic force microscopy, to geneticists over-expressing or supressing genes to uncover the effect of certain enzymes on cell wall structure. Even though I come from a mainly chemistry background this was of no hindrance as the 15-minute talks were all well designed and approachable for anyone with a scientific background.


Posters were hung and left standing all week to allow for casual browsing/lurking during lunches and coffee breaks. This relaxed ambiance carried across into the poster presentations, allowing for easy introductions and bustling halls of conversation throughout each session. I managed to engage with many posters and their presenters, mainly focusing on cell wall structure but the posters themselves were again were well written, so even the mass spec analysis posters that spared no detail were understandable when guided by the author.

Christian proudly presents his poster @donohoho

Throughout the years the meeting has been running there have been certain themes as the field has progressed, and currently it is said to be the ‘practical age’ of plant cell wall research – taking the tools and discoveries from the past 40 years and applying them in fields such as modifying cotton cell walls for physical improvements of the collected fibres, or the genetic optimisation of crop development for biofuel production. A particular highlight was from PhD student James Cowley from the University of Adelaide, looking the utilisation of seed mucilage of the plantago for better gluten-free bread.


Another highlight for me was the focus on personal workplace responsibility, equalities, and ethics that were discussed in busy well-attended sessions. Starting with Dame Professor Athene Donald and keeping pace from there, the talks covered a wide range of important issues that are usually only quietly acknowledged, and it was good to see open challenges to the biases of today people face, with clear instructions for how to help those around you. #just1action4WIS

From a early postgrad perspective, the diversity at the senior levels of research does not reflect the broad range of PhD students currently studying or graduating – by discussing these issues, putting in the time to listen, and vigilant self – criticism we can all work to improve this.

Edinburgh Cell Wall Group
Back: Marie Rapin, Ninni Nuorti, Stephen C. Fry
Front: Christian Donohoe, Thuryya Al Hinai, Lenka Frankova, Rifat Ara Bergum
Photo @donohoho

In all, it was a pleasure and a privilege to attend such a meeting, special thanks to the GARNet travel grant for helping me afford to attend the meeting. For the next meeting I am greatly looking forward to presenting my entire PhD work in 2022, when the meeting will be held in beautiful Malaga, Spain.   

John Innes Centre Gene Editing Workshop.

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Published on: July 22, 2019

Professor Wendy Harwood leads a team of researchers and technicians at the John Innes Centre who have expertise in tissue-culture based plant transformation techniques (BRACT- Biotechnology Resources for Arable Crop Transformation).

            Transformation is often considered a dark-art of plant science, as history informs that it requires an established set of protocols that have been well-tested for local experimental conditions. It takes significant time and expertise to set up an effective and reliable transformation pipeline, which is why few places around the UK undertake this type of work. These challenges can provide a significant bottleneck in the establishment of high-throughout transformation platforms.

            The BRACT expertise in transformation was aligned with gene editing technology to successfully gain UKRI-BBSRC Bioinformatics and Biological Resources Funding (BBR) funding in 2016 with a grant entitled ‘Targeted gene knockouts in crops using RNA-guided Cas9 nucleases’. Professor Harwood shares Co-I status on this grant with Dr Nicola Patron who is an expert on synthetic biology and genome editing based at the Earlham Institute.

Professor Harwood introduces the workshop. Photo @SadiyeHayta

Expanding UK capability in gene editing of crops

            This BBR funding is absolutely community-facing and included the provision for 50 genes, selected from open applications, to be targeted by CRISPR-Cas9 gene editing. Initially successful applicants would benefit from BRACT expertise in guide RNA (gRNA) design after which the optimised gRNAs and Cas9 would then be introduced into either barley or Brassica oleracea. However, the success of the BRACT service meant that over 60 genes were ultimately selected for targeted knock-out and in the second round of applications the available crops were expanded to include wheat, Brassica napus and tomato.

            This grant allowed users throughout the UK to take advantage of expertise in gene editing and transformation, which is beyond the capabilities of most individual research departments. The grant also included a requirement to provide training for new users and a training event was successfully delivered between July 10-12th at the JIC. On days 1 and 3, 12 successful applicants worked with the BRACT team to learn how to design CRISPR guides, assemble constructs, screen edited plants and perform the basics of plant transformation. In between these two days was a day of scientific talks that included talks from successful community applicants as well as updates on the latest technical developments at BRACT. The day 2 workshop was attended by 62 participants from across the UK.  The demand for training was significantly higher than the number of spaces available, with the course being 3x oversubscribed. Hopefully this may encourage the course organisers to consider running similar training events again.   


Demonstrating a clear community need.

During the two rounds of applications, researchers from 43 UK research groups across 26 institutions applied to have one or more genes of interest targeted by this resource. Due to high demand ultimately 61 genes were selected for targeting from a total of 126 requested genes. Multiple guide RNAs were designed and primary transformation conducted at BRACT before transgenic and potentially edited plants were sent out to users. The users then screen these plants for Non-homologous end joining (NHEJ)-editing events and, if needed, identified transgene-free germplasm. BRACT provided help with screening and growing on the selected plants as required.

Success Stories

            Mikhaela Neequaye presented the most complete study of those that have used the BRACT facility through this BBR funding. She works with Richard Mithen, formally from the Quadram Institute and Lars Ostergaard at the JIC on the Brassica oleracea MYB28 transcription factor, which is involved in glucosinolate biosynthesis. In collaboration with BRACT she has identified plants with edited MYB28 that show altered glucosinate levels and has even successfully gone through the onerous process of applying to DEFRA to conduct a field trial with these edited plants. An impressive output from a PhD project!

            Kate Henbest is a PhD student who works with Lorraine Williams at the University of Southampton on the challenge of developing plants with altered capacity to transport zinc. She targeting two loci encoding bZIP transcription factors in barley and had successfully identified the predicted double ‘CRISPR mutants’. In addition she also found a surprising triple mutant that also contained a mutation in a related bZIP family member. These multi-mutants were identified from a relatively small number of edited lines, which so far is a very satisfying result.

            However the appearance of the triple mutant highlights that we have an incomplete understanding of the editing events that will occur after NHEJ and demonstrate the importance of users feeding back this information to BRACT. This will allow them to build a valuable database about the particular editing events observed by users. The handful of users who presented their research at the workshop documented both small deletions as well as single nucleotide substitutions and deletions.


Growing plants can be surprisingly challenging!

            Early user feedback indicates that obtaining full-value from this BBR grant might rely on the extent of post-editing support that the BRACT team is able to provide (and how this might be financially supported). Some applicants had previously only worked with Arabidopsis, so after a successful application they will be confronted with the challenge of growing much larger (transgenic) plants that will require more space and different growth conditions. This might seem like a trivial problem but in order for the BRACT team to show that their project has been successful (in terms of follow-on publications or future grants) then this relies on end-users being able to correctly grow plants in order to obtain useful data. The BRACT team has been able to provide some advice on these issues without impinging on the time they must devote to other projects, but as is often the case, these additional requirements are often hidden time constraints that aren’t always factored into grant funding.

            Somewhat related to these issues was a talk from Gustaf Degen from Lancaster University who had received Brassica oleracea plants with edits within a gene involved in photosynthesis. His progress in this project has been delayed as all of the edited plants died during a particularly (surprisingly) hot summer in Lancaster! Fortunately, the plants were saved by returning to the original tissue-culture and although this was a fluke event, it does rather highlight that users need to be able to grow the plants that they intend to work with!

Penny Hundleby overseeing the Brassica transformation practical Photo @MarkSmedley15

Overcoming the challenges of HDR.

            Tufan Oz had recently joined the Patron lab at the Earlham Institute but gave a talk about his previous research conducted in Florida. He worked with sugarcane and had successfully targeted the acetolactate synthase (ALS) gene using homology-directed repair (HDR). He explained that sugarcane provides an excellent model for HDR as the tissue-culture transformation frequency is very high.

            One of the BRACT CRISPR-experts is Tom Lawrenson and he gave an informative update about his work aiming to undertake HDR in barley. HDR uses a ‘conventional’ gRNA/CRISPR system along with an additional DNA template with homology arms to a specific pre-selected region within the genome. Although HDR results in the insertion of a ‘foreign’ gene unlike conventional GMOs that rely on random insertion, HDR allows targeted insertion to a chosen place in the genome.

            A particular challenge of using HDR is ensuring that there is a sufficiently high quantity of the DNA template in the vicinity of the Cas9 cut site. Poor transformation frequencies will also be an impediment to this work as with fewer transformations there is less chance of obtaining a line with sufficient high levels of the template. Tom reported that overall this means that successful HDR occurs 10-100x times less efficiently than NHEJ.

            A major strength of this BBR grant is that it complements other funded work [wh(1] aiming to troubleshoot challenging protocols (such as HDR) precluding the need for replicated efforts in labs around the country. In these HDR experiments Tom is attempting to directly knock-in a N-terminal mCherry fusion and his primary advice is to ensure that you use very efficient gRNAs. Due to the low efficiency of HDR in order to obtain a correctly edited plant a researcher has the choice to either a) look at more primary transformants, b) to use a viral vector to improve expression or c) to screen a lower number of transformants over multiple generations. Tom has experimented with viral-derived components but found that this wasn’t necessary for successful HDR. As with NHEJ, the requirements for efficient HDR will vary on a plant-to-plant basis but the BRACT team are working out the basics so that the entire community will benefit from using this powerful technique in the future.


Future technologies

            The latter stages of the workshop focused on future technologies that could be of use to the community. The BRACT team discussed their recent work on:

1. Use of Cpf as an alternative to Cas9 (it doesn’t work as well in their hands)

2. On their testing of base-editing and epigenome editing techniques (work in progress)

3. Strategies to obtain multiple knock-outs from a single transformation (use different promotors to ensure even expression of all gRNAs in a single construct).

            Workshop participants were invited to suggest what they needed to improve their research using CRISPR-based technologies. The consensus amongst those few people I talked to was that more hands-on training would be very useful and that nothing is too simple to be taught. This type of training requires a significant commitment in time and space so there needs to be a community discussion around the mechanisms that could be used to enable these opportunities. CRISPR-based gene editing techniques are clearly game-changing technologies but, as with anything, without correct use they can take a lot of time for little reward.

            During discussions Professor Harwood gave a comment on the ‘Freedom To Operate’ study that they have commissioned as part of this BBR grant. This suggests that they will have no difficulty using CRISPR-based technology for projects working with academic applicants. Interestingly it was positive to learn that whereas there may be complications when they work with for-profit companies, it should be possible for those companies to use the CRISPR technology without having to pay a prohibitive licensing fee. However as the legal battles over the CRISPR-patent have not yet been resolved any opinion given in this area might be liable to change.

Relaxing after the meeting. Photo @SadiyeHayta

            The day of presentations ended in traditional John Innes Centre fashion with some locally brewed beer and wine on the terrace in the summer sun! The three-day workshop / training course then concluded for the trainees with the third day allowing hands-on experience of tissue-culture transformation techniques. Hopefully the training course participants will take this knowledge back to their home institutions in order to allow more researchers to master one of the dark-arts of plant science!

European Plant Science Retreat 2019:

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Published on: July 15, 2019

University of Nottingham, July 8th-10th 2019

By Sophie Mogg, University of Manchester. @Mini_Moggy

The European Plant Science Retreat is an annual event hosted by PhD students for PhD students.

The fact that this event was orchestrated by my own peers was simply amazing and a feat not to be sniffed at.  As any PhD student knows, sometimes walking into those big society-led conferences can be daunting and even more so when you want to approach those in your field.

However, at the EPSR, it was a level playing field allowing for a more easy-going approach to networking – especially as those we were talking to could be potential collaborators in the near future.

The Organising Team!

The three days of proudly presented research was arranged in a series of talks and poster sessions to open the floor to like-minded students. Somewhat unusually only a few hours over the whole conference was dedicated to more experienced keynote speakers. This for me is what made the conference. Both new and more experienced PhD students were able to interact, share ideas and advice and feel free to ask questions that otherwise might not have been asked in a more ‘serious’ setting.

The keynote speakers themselves made quite the contribution, sharing with us their journey from being PhD students to their current revered positions! It was important for us to learn that each journey was DIFFERENT. What stuck with me was that there was no necessity to jump ship to another country, or even publish a single paper, in order to gain a post doc position.

Therefore as long as you persevere, remained passionate and show your worth, many doors will remain open for your future! It was great to hear their love for science in their voices as they told their tales.


Speaking with others at the conference, my experience wasn’t unique and I didn’t hear a single negative comment, no doubt owing to the great organisation and planning done by the EPSR2019 team.

Sadly, this was my first and only European Plant Science Retreat, but I hope that the tradition continues for many years, allowing students from across Europe to practice their networking skills, present their research and have a all round great experience at a conference designed especially for them.

Jason and Marty, part of the EPSR2019 team, offered words of wisdom for the 2020 organising team. They highlighted that although it may seem like a giant undertaking, especially in terms of sourcing funding from sponsors, that the entire team had improved their organisation and team-work skill sets, giving them invaluable experience that they will undoubtedly make use of in the future.

Finally they advised to keep it light and enjoy it! Because how often do you get to organise a conference?

Meeting attendees in the University of Nottingham Millennium Garden

Meeting Report from ICAR2019

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Published on: July 11, 2019

Gina Garzón Martínez, Aberystwyth University

Four days full of knowledge, innovative research, interesting culture this is what summarizes my time at the ICAR2019, Wuhan, China.

Thanks to the Gatsby foundation and GARNet, I had the opportunity to attend the ICAR2019 conference in Wuhan, China. The meeting was hosted by the Huazhong Agricultural University-a partnership University which I also managed to visit during my stay in Wuhan.

Mornings at ICAR2019 started with a plenary sessions leading by scientists from Asia, Australia, USA and Europe who delighted us with their latest work in Arabidopsis. In particular, I found interesting a plenary session called “From Models to Crops”, where Barry Pogson from Australia showed us the importance of translational genetics. As an example, he showed us drought stress regulators discovered in Arabidopsis that also play a role in a range of crop plants such as wheat.

Barry Pogson gave a fantastic talk!

Every afternoon, there were concurrent sessions and more interesting talks given by PI researchers and early career scientists from all around the world. Of particular interest to me were the talks on the use of Arabidopsis to elucidate biotic and abiotic interactions. As an example, Lin Li from Fudan University gave a good talk about how the transcription factor PHY7 is involved in shade avoidance response when plants compete with their neighbours. Also, Ling Li from Mississippi State University shared with us her work in a starch gene with great potential to improve protein and disease resistance in other crops such as rice, soybean and corn, using innovative strategies.

Poster Session

At the end of the day, there was a poster session and a range of different workshops. I really enjoyed the workshop called “Communicating your science to the broader community” organized by Isabel Mendoza (Global Plant Council) and including Geraint Parry (GARNet) and Mary Williams (ASPB). This workshop gave me ideas of how I can increase the impact of my work by using social media and how to share my work not only to the scientific community but also to the regular public. Thanks to this workshop I gained more encouragement to be more active in social media, considering the importance of sharing my work with others at this stage of my PhD.

I really encourage all PhD students to not miss this kind of opportunities of networking, learning, sharing your work, along with having a cultural experience and making friends from other parts of the world. Next year, ICAR2020 will be held in the USA, followed by Belfast, UK in 2021, so I already recommend you to book some time off in your calendar and prepare for another productive and exciting week of science!

Gina with her poster

GARNet Research Roundup: July 5th 2019

This edition of the GARNet research roundup begins with a study from the University Leicester that investigates the rate of selection of genes expressed in Arabidopsis pollen.

The second and third papers focus on the function of members of the AP2 family of transcription factors. Sarah McKim’s lab in Dundee characterizes the role of APETALA2 during barley stem elongation whilst the other paper investigates the function of the Arabidopsis PUCHI gene and includes co-authors from the University of Nottingham.

The fourth paper is from Lars Ostergaard’s lab at the John Innes Centre and demonstrates the benefit of using models to understand developmental processes in crop plants. The next paper from the University of Glasgow investigates the plant response to low fluence rates of UV-B light.

The penultimate paper features authors from Oxford Brookes University and characterizes a novel LINC-KASH protein in maize whilst the final paper is from the University of Cambridge and investigates the novel function of two members of DUF579 family in methylation of glucuronic acid residues.


Harrison MC, Mallon EB, Twell D, Hammond RL (2019) Deleterious mutation accumulation in Arabidopsis thaliana pollen genes: a role for a recent relaxation of selection. Genome Biol Evol. doi: 10.1093/gbe/evz127

Open Access

This research from Hammond and Twell lab’s at the University of Leicester uses Arabidopsis to investigate the hypothesis that pollen genes evolve faster than sporophytic genes. This study is challenging to perform in Arabidopsis as for the past million years the plant has been self-compatible, which causes reduction in pollen competition, increased homozygosity and a dilution of masking in diploid expressed, sporophytic genes. This study has two main findings: firstly prior to becoming self-compatible pollen genes evolved faster than sporophytic genes. Secondly, since becoming self-compatible selection has relaxed causing higher polymorphism levels and a higher build-up of deleterious mutations.


Patil V, McDermott HI, McAllister T, Cummins M, Silva JC, Mollison E, Meikle R, Morris J, Hedley PE, Waugh R, Dockter C, Hansson M, McKim SM (2019) APETALA2 control of barley internode elongation. Development. doi: 10.1242/dev.170373

Open Access

Vrushali Patil leads his study from the lab of current GARNet committee member Sarah McKim at the James Hutton Institute in Dundee. They show that the APETALA2 (AP2) transcription factor is necessary for stem elongation in Barley. In addition they demonstrate that AP2 expression is controlled by the activity of the microRNA mi172 as well as jasmonate signaling.

https://dev.biologists.org/content/146/11/dev170373.long

Trinh DC, Lavenus J, Goh T, Boutté Y, Drogue Q, Vaissayre V, Tellier F, Lucas M, Voß U, Gantet P, Faure JD, Dussert S, Fukaki H, Bennett MJ, Laplaze L, Guyomarc’h S (2019) PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1906300116

Julien Lavenus, Ute Voß and Malcolm Bennett from University of Nottingham are co-authors on this French-led study that investigates the mechanism by which the AP2 family transcription factor PUCHI controls lateral root development. By performing a transcriptional analysis of developing lateral root cells they show that genes involved in very long chain fatty acid (VLCFA) biosynthesis enzymes are induced in a PUCHI dependent manner. Concomitantly they show puchi-1 mutant roots have reduced VLCFA content when compared with wildtype roots. They conclude that PUCHI regulates VLCFA biosynthesis as part of a pathway controlling cell proliferation during lateral root formation.


Stephenson P, Stacey N, Brüser M, Pullen N, Ilyas M, O’Neill C, Wells R, Østergaard L (2019) The power of model-to-crop translation illustrated by reducing seed loss from pod shatter in oilseed rape. Plant Reprod. doi: 10.1007/s00497-019-00374-9

Open Access

Pauline Stephenson and Lars Østergaard at the John Innes Centre lead this study in which they demonstrate that lessons learnt from understanding the genes involved in fruit ripening in Arabidopsis lead to an ability to adjust the pod-opening process in oilseed rape. They have combined two mutant alleles, first characterized in Arabidopsis, to develop OSR plants that have significantly increased yield. In addition they present a new software tool for the analysis of pod shatter data in other crops plants.


O’Hara A, Headland LR, Díaz-Ramos LA, Morales LO, Strid Å, Jenkins GI (2019) Regulation of Arabidopsis gene expression by low fluence rate UV-B independently of UVR8 and stress signaling. Photochem Photobiol Sci. doi: 10.1039/c9pp00151d

Open Access

This UK-Swedish collaboration is led by Andrew O’Hara from the Jenkins lab in the University of Glasgow. They continue the lab focus on the UV-B receptor UVR8, in this case performing a transcriptomic analysis of wildtype and uvr8 mutants grown under low UV-B fluence rates. They analyse one differentially expressed gene in more detail, the transcription factor ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN 13 (ANAC13), which was induced by UV-B but by the activity of any other photoreceptor.


Gumber HK, McKenna JF, Tolmie AF, Jalovec AM, Kartick AC, Graumann K, Bass HW (2019) MLKS2 is an ARM domain and F-actin-associated KASH protein that functions in stomatal complex development and meiotic chromosome segregation Nucleus. doi: 10.1080/19491034.2019.1629795

Open Access

Hardeep Gumber is first author on this US-led study that includes Joe KcKenna, Andrea Tolmie and Katja Graumann from Oxford Brookes as co-authors. They characterise the Maize LINC KASH AtSINE-like2 protein, MLKS2, whose targeting to the nuclear periphery requires its N-terminal armadillo repeats. Mutant mlks2 plants have pleiotropic plant phenotypes and on a nuclear level show defects in chromosome segregation and positioning. These findings support a model in which cytoplasmic actin is linked to chromatin through the LINC-KASH nuclear envelope network.

https://www.tandfonline.com/doi/full/10.1080/19491034.2019.1629795

Temple H, Mortimer JC, Tryfona T, Yu X, Lopez-Hernandez F, Sorieul M, Anders N, Dupree P (2019) Two members of the DUF579 family are responsible for arabinogalactan methylation in Arabidopsis. Plant Direct. doi: 10.1002/pld3.117

Open Access

Henry Temple is first author on this work from the University of Cambridge that characterizes two members of the DUF579 family (AGM1 and AGM2). These proteins are required for 4-O-methylation of glucuronic acid within highly glycosylated arabinogalactan proteins (AGPs).


Remember to download the latest edition of the GARNish newsletter.

GARNish Edition 31 available to download!

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Published on: July 2, 2019

The 31st edition of the GARNish newletter is now available for download.

Included in this edition is:

– Update from UKPSF and the Global Plant Council

– List of Upcoming Events

– Introducing the Shiny 3D RNA-Seq analysis App

– Reports from UK Plant Networks

– Update from UKRI-BBSRC including about transfers of responsive mode grants

– Stories from Fascination of Plants Day

– Report from ICAR2019

– The Future of Gene Editing in the UK

– Spotlight on the University of Liverpool

– Analysis of Arabidopsis Publications

If you like to suggest any articles to be included in future edition then please contact the GARNet coordinator, Geraint Parry.

https://www.garnetcommunity.org.uk/sites/default/files/newsltr/GARNish31_Online_.pdf

GARNet Research Roundup: June 12th 2019

In another big edition of the GARNet Research Roundup we cover many different areas of research that utilise a varied group of experimental organisms!

The first paper from the Feng lab at the John Innes Centre performs an assessment of the factors influencing heterochromatin activity in sperm companion cells. Second is work from the JIC and Cardiff University that looks at the role of an auxin minima during fruit valve margin differentiation.

The next two papers have authors from Edinburgh. Firstly the McCormick lab has developed a stereo-based 3D imaging system for plants while Steven Spoel is a co-author on a study that looks at the pathogen responsive gene NPR1.

Coming from across the M8 is a paper from the Christie lab in Glasgow that looks into using phototropin genes as potential targets for crop improvement.

The next paper is from Oxford Brookes University where they visualise the movement of protein nanodomain clusters within the plasma membrane. Elsewhere in Oxford is a paper from the van der Hoorn group that characterises the effect of a novel triazine herbicide.

Two papers from the University of Durham also identify and characterise the role of novel herbicides, in this case on the activity of inositol phosphorylceramide synthases.

The final five papers feature research that each use different experimental organisms. Firstly a paper from the Earlham Institute uses delayed fluorescence to investigate the circadian clock in wheat and OSR. Second is a paper from Warwick that assesses the role of nodulation during nitrogen uptake in Medicago. The next paper features the Yant lab at University of Nottingham looks at growth of two species of Arabidopsis in challenging environments.

The penultimate paper includes authors from the University of Oxford and provides a detailed analysis of the factors controlling leaf shape in Cardamine and Arabidopsis thaliana. The final paper uses the imaging facility at the Hounsfield facility in Nottingham to image the roots of date palms.


He S, Vickers M, Zhang J, Feng X (2019) Natural depletion of H1 in sex cells causes DNA demethylation, heterochromatin decondensation and transposon activation. Elife. doi: 10.7554/eLife.42530

Open Access

Lead author on his paper is Shengbo He from Xiaoqi Feng’s lab at the John Innes Centre. This work looks at activation of Transposable elements (TEs) in the sperm companion cell of Arabidopsis. This is catalyzed by the DEMETER-catalyzed DNA demethylation in regions depleted of histone H1, demonstrating a key role for H1 in determining heterochromatin activity.

https://elifesciences.org/articles/42530

Li XR, Vroomans RMA, Fox S, Grieneisen VA, Østergaard L, Marée AFM (2019) Systems Biology Approach Pinpoints Minimum Requirements for Auxin Distribution during Fruit Opening. Mol Plant. doi: 10.1016/j.molp.2019.05.003

Open Access

Xin-Ran Li and Renske Vroomans are co-lead authors on this work from the Ostergaard, Grieneisen and Maree labs from the John Innes Centre and (now) Cardiff University.They look at the role of an auxin minima in the control of valve margin differentiation in Arabidopsis fruit. They used a cycle of experimental-modeling to develop a model that predicts the maturation of the auxin minimum to ensure timely fruit opening and seed dispersal.


Bernotas G, Scorza LCT, Hansen MF, Hales IJ, Halliday KJ, Smith LN, Smith ML, McCormick AJ (2019) A photometric stereo-based 3D imaging system using computer vision and deep learning for tracking plant growth. Gigascience. doi: 10.1093/gigascience/giz056

Open Access

Gytis Bernotas from UWE and Livia Scorza from the McCormick lab at the University of Edinburgh lead this work that is the result of a 2+ year collaboration with the Melvyn Smith and others at the Computer Machine Vision (CMV) facility at UWE. The authors have developed hardware and software (including a deep neural network) to automate the 3D imaging and segmentation of rosettes and individual leaves using a photometric stereo approach.

https://academic.oup.com/gigascience/article/8/5/giz056/5498634

Chen J, Mohan R, Zhang Y, Li M, Chen H, Palmer IA, Chang M, Qi G, Spoel SH, Mengiste T, Wang D, Liu F, Fu ZQ (2019) NPR1 promotes its own and target gene expression in plant defense by recruiting CDK8. Plant Physiol. doi: 10.1104/pp.19.00124

GARNet chairman Steven Spoel is a co-author on this US-led study with Jian Chen as lead author. The paper investigates the interacting partners of NPR1 (NONEXPRESSER OF PR GENES 1), which is a master regulator of salicyclic signaling and therefore an important regulation of plant defense response.


Hart JE, Sullivan S, Hermanowicz P, Petersen J, Diaz-Ramos LA, Hoey DJ, Łabuz J, Christie JM (2019) Engineering the phototropin photocycle improves photoreceptor performance and plant biomass production. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1902915116

Open Access

Jaynee Hart is first author on this research from Christie lab at the University of Glasgow in which they target the phototropin blue light receptor as a candidate for crop improvement. They showed plants that engineered to have a slow-photocycling version of PHOT1 or PHOT2 had increased biomass under low light conditions, due to their increased sensitivity to low light.


McKenna JF, Rolfe DJ, Webb SED, Tolmie AF, Botchway SW, Martin-Fernandez ML, Hawes C, Runions J (2019) The cell wall regulates dynamics and size of plasma-membrane nanodomains in Arabidopsis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1819077116

Open Access

Joe McKenna from Oxford Brookes University leads this work that takes advantage of their superb imaging facilities to assess the dynamic regulation of specific protein clusters in the Arabidopsis plasma membrane. They show that the cytoskeleton (both actin and microtubule) and the cell wall play roles in the control of intra-PM moment of the pathogen receptor FLS2 and the auxin transporter PIN3.

https://www.pnas.org/content/early/2019/06/07/1819077116

Morimoto K, Cole KS, Kourelis J, Witt CH, Brown D, Krahn D, Stegmann M, Kaschani F, Kaiser M, Burton J, Mohammed S, Yamaguchi-Shinozaki K, Weerapana E, van der Hoorn RAL (2019) Triazine probes targeting ascorbate peroxidases in plants. Plant Physiol. doi: 10.1104/pp.19.00481

Open Access

Kyoko Morimoto is first author on this UK-German-Japanese collaboration led from the lab of GARNet committee member Renier van der Hoorn. They characterise the herbicidal effect of the small 1,3,5-triazine KSC-3 on ascorbate peroxidases (APXs) across a range of plant species.


Pinneh EC, Stoppel R, Knight H, Knight MR, Steel PG, Denny PW (2019) Expression levels of inositol phosphorylceramide synthase modulate plant responses to biotic and abiotic stress in Arabidopsis thaliana. PLoS One. doi: 10.1371/journal.pone.0217087

Open Access

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW (2019) The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Sci Rep. doi: 10.1038/s41598-019-44544-1

Open Access

Elizabeth Pinneh leads these two papers from the Denny lab in Durham. In the first paper they use RNAseq data and analysis of overexpression transgenic lines to define the role of inositol phosphorylceramide synthase (IPCS) during abiotic and biotic stress responses.

Secondly they screened a panel of 11000 compounds for their activity against the AtIPCS2 in a yeast two-hybrid assay. Successful hits from the screen were confirmed with in vitro enzyme assays and in planta against Arabidopsis.


Rees H, Duncan S, Gould P, Wells R, Greenwood M, Brabbs T, Hall A (2019) A high-throughput delayed fluorescence method reveals underlying differences in the control of circadian rhythms in Triticum aestivum and Brassica napus. Plant Methods. doi: 10.1186/s13007-019-0436-6

Open Access

Hannah Rees from Anthony Hall’s lab at the Earlham Institute leads this methods paper that introduces the use of delayed fluorescence to investigate the circadian rhythms in wheat and oil seed rape.

https://plantmethods.biomedcentral.com/articles/10.1186/s13007-019-0436-6

Lagunas B, Achom M, Bonyadi-Pour R, Pardal AJ, Richmond BL, Sergaki C, Vázquez S, Schäfer P, Ott S, Hammond J, Gifford ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula. Mol Plant. doi: 10.1016/j.molp.2019.03.014

Open Access

Beatriz Lagunas is lead author on this paper from the University of Warwick that investigates the role of nodulation in actual nitrogen uptake by the roots of Medicago truncatula. They use integrated molecular and phenotypic analysis to determine that the respond to nitrogen flux are processed on a whole plant level through multiple developmental processes.

https://www.cell.com/molecular-plant/fulltext/S1674-2052(19)30127-3?

Preite V, Sailer C, Syllwasschy L, Bray S, Ahmadi H, Krämer U, Yant L (2019) Convergent evolution in Arabidopsis halleri and Arabidopsis arenosa on calamine metalliferous soils Philos Trans R Soc Lond B Biol Sci. doi: 10.1098/rstb.2018.0243

Open Access

Veronica Preite is first author on this UK-German collaboration led by Ute Kraemer and Levi Yant in Nottingham. They performed whole genome resequenced of 64 individuals of two Arabidopsis species that grow on calamine metalliferous sites (which have toxic levels of the zinc and cadmium). They revealed a modest amount of gene and network convergence in plants that have colonised these challenging environments.


Kierzkowski D, Runions A, Vuolo F, Strauss S, Lymbouridou R, Routier-Kierzkowska AL, Wilson-Sánchez D, Jenke H, Galinha C, Mosca G, Zhang Z, Canales C, Dello Ioio R, Huijser P, Smith RS, Tsiantis M (2019) A Growth-Based Framework for Leaf Shape Development and Diversity. doi: 10.1016/j.cell.2019.05.011

Open Access

Claudia Canales and Carla Galinha from Oxford are co-authors on this German-led study from Miltos Tsiantis’ lab that performs a detailed dissection of the growth parameters that control differences in leaf-shape in Cardamine and Arabidopsis. They show critical roles for the SHOOTMERISTEMLESS and REDUCED COMPLEXITY homeobox proteins to define differences in shape determination.


Xiao T, Raygoza AA, Pérez JC, Kirschner G, Deng Y, Atkinson B, Sturrock C, Lube V, Wang JY, Lubineau G, Al-Babili S, Ramírez LAC, Bennett MJ, Blilou I (2019) Emergent Protective Organogenesis in Date Palms: A Morpho-devo-dynamic Adaptive Strategy During Early Development. Plant Cell. doi: 10.1105/tpc.19.00008

Open Access

Members of the Hounsfield CT Imaging Facility 
at the University of Nottingham are co-authors on this paper that is led by Tingting Xiao from KAUST in Saudi Arabia. The paper takes a detailed look at root morphology in Date Palm.

Monogram 2019 by Laure Forquet

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Published on: May 29, 2019

Monogram 2019 was my first conference attended as part of my master degree final year internship at NIAB. As it was my first conference, I was very excited to meet the UK cereal research community.

Being very new to wheat research and having focused mainly on model plants like ​Arabidopsis thaliana so far, I really enjoyed having such a complete overview of wheat research in the UK and abroad.
The talks were organized in clear sessions making the whole conference a lot easier to follow and connect between the talks.


The wide diversity of subjects covered was eye-opening. I was very interested in the bioinformatics session which opened the conference on the first morning as it relates to my project in quantitative genetic. It introduced me to the brilliant tools that are available for wheat genetic research such as the resources from the Designing Future Wheat program.

The plenary talk from Keith J. Edwards from the University of Bristol was a very nice introduction to the conference and was a good reminder of wheat hybridization history. He offered some new insight into the origin of the genetic variation in bread wheat resulting from the unaware side-by-side cultivation of the newly hybridized hexaploid wheat with the tetraploid wheat.

Opening keynote from Keith Edwards. Photo: @GuilleMendiondo

I also really enjoyed discovering about other subjects further away from my domain such as the quality and nutrition session. I especially liked the talk from Alison Lovegrove from Rothamsted Research. She presented insights on the way to improve the quality of cereals to increase the health benefits, with a focus on white versus brown rice. Brown rice has a higher quality for health but is not very popular with consumers who prefer the taste of white rice. Increasing the nutrient and fiber content and lowering the glycemic index of white rice, without altering the taste, would help improve global health, notably by reducing the risk of type 2 diabetes.


I was given the opportunity to present a poster on my project at NIAB on flowering time in wheat during the poster session. I enjoyed discussing the subject with other researcher and receiving outside perspective, advice and feedback. It was also a great occasion to have one-to-one conversation with the other people presenting their posters.

At the end of the second day there was a very interesting panel discussion covering the challenges that the breeding community. The panel discussed their points of view between and took questions from the audience.

Panel discussion. Photo @HuwJonesLabour

The conference was overall pretty intense so I really appreciated the opportunity to interact and meet professional researchers and students during the tea breaks, lunches and the formal conference diner.

I am very grateful to GARNet for offering me a travel grant to attend this exciting event and I hope I will be able to return next year to have updates on all these inspiring projects and meet the community again. I would recommend any students or early career researchers interested in cereals to go to the annual Monogram meeting!

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