Arabidopsis Research Roundup

This week roundup features a wide range of research topics from two current members of GARNet Advisory board as well as two papers featuring work from the lab of Laszlo Bogre at Royal Hollaway. The studies range from an investigation into the similarity between the barley and Arabidopsis circadian clocks, the role of MYR3R during regulation of organ growth, documenting a novel interaction of a MAPK protein and the development of new fluorescent probes for study of cysteine proteases.

 

Kusakina J, Rutterford Z, Cotter S, Martí MC, Laurie DA, Greenland AJ, Hall A, Webb AA (2015) Barley Hv CIRCADIAN CLOCK ASSOCIATED 1 and Hv PHOTOPERIOD H1 Are Circadian Regulators That Can Affect Circadian Rhythms in Arabidopsis. PLoS One. 10(6):e0127449. http://dx.doi.org/10.1371/journal.pone.0127449

This publication is the result of a multi-site collaboration between the Alex Webb at Cambridge, GARNet Advisory board member Anthony Hall at Liverpool, Andy Greenland at NIAB and David Laurie at the JIC. The focus of this study are the barley CIRCADIAN CLOCK ASSOCIATED 1 and PHOTOPERIODH1 genes, which are involved in regulation of the circadian clock. The authors investigated the circadian rhythms in barley whilst using heterologous expression in Arabidopsis to show that the barley CCA1 is functionally equivalent to AtCCA1 and that barley PHOTOPERIODH1 functions similar to AtPRR7.

 

Kobayashi K, Suzuki T, Iwata E, Nakamichi N, Suzuki T, Chen P, Ohtani M, Ishida T, Hosoya H, Müller S, Leviczky T, Pettkó-Szandtner A, Darula Z, Iwamoto A, Nomoto M, Tada Y, Higashiyama T, Demura T, Doonan JH, Hauser MT, Sugimoto K, Umeda M, Magyar Z, Bögre L, Ito M (2015) Transcriptional repression by MYB3R proteins regulates plant organ growth. EMBO J. http://dx.doi.org/10.15252/embj.201490899

GARNet advisory board member John Doonan and Royal Hollaway-based Laszlo Bogre are collaborators on this multi-nation publication that looked at the role of three MYB2R3 proteins in cell cycle control. Arabidopsis plants that have mutations in three repressor type-myb3r genes display enlarged organs. In addition, MYB3R3 binds to G2/M-specific genes and associates with the repressor-type E2F and RBR proteins. The authors perform a range of pair-wise interaction studies to identify components of multiprotein complexes, that have also been identified in other organisms. Ultimately they show that these MYC3R genes are important for periodic expression during the cell cycle and for establishing a post-mitotic quiescent state that determines organ size.

 

Kohoutová L1, Kourová H1, Nagy SK2, Volc J1, Halada P1, Mészáros T2,3, Meskiene I4,5, Bögre L6, Binarová P1 (2015) The Arabidopsis mitogen-activated protein kinase 6 is associated with γ-tubulin on microtubules, phosphorylates EB1c and maintains spindle orientation under nitrosative stress New Phytologist. http://dx.doi.org/10.1111/nph.13501

Laszlo Bogre also features as a collaborator in this East European-led study that investigated the interaction of the MAPK-protein MPK6 with microtubules. Immunoprecitations showed that the active form of MPK6 interacted with γ-tubulin, sedimenting with in vitro polymerised microtubules. In addition they identified a novel substrate for MPK6, the microtubule plus-end protein, EB1c. Overall the authors propose that MPK6 plays a significant role in maintaining regular planes of cell division, particularly during stress conditions.

 

Lu H, Chandrasekar B, Oeljeklaus J, Misas-Villamil JC, Wang Z, Shindo T, Bogyo M, Kaiser M, van der Hoorn RA (2015) Subfamily-specific Fluorescent Probes for Cys proteases Display Dynamic Protease Activities During Seed Germination. Plant Physiology http://dx.doi.org/10.1104/pp.114.254466

Renier Van De Hoorn who works in the Department of Plant Chemetics at the University of Oxford, leads this study that investigates the activity of plant cysteine proteases. They developed a novel set of fluorescent probes that specifically target different subfamilies of Cys proteases. In order to test these probes they used Arabidopsis mutant lines alongside transient expression studies in tobacco. In addition they show that these probes have broad applicable across 8 plant species. Finally they use these new tools to reveal the dynamic properties of different protease sub-families during remobilization of seed storage proteins in Arabidopsis.

Arabidopsis Research Roundup: June 3rd 2015

We are unashamedly biased in this weeks Arabidopsis Research Roundup which firstly features work from the group of GARNet PI Jim Murray about the genetic interactions that define growth of lateral organs. Elsewhere we highlight papers that investigate a different role for CYCD3 genes in vascular development, the role of TFL1 in the shoot meristem and the ability of Arabidopsis seedling to tolerant a high light environment during ontogenesis.

Randall RS, Sornay E, Dewitte W, Murray JA (2015) AINTEGUMENTA and the D-type cyclin CYCD3;1 independently contribute to petal size control in Arabidopsis: evidence for organ size compensation being an emergent rather than a determined property Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv200

Jim Murray and Walter Dewitte (Cardiff) lead this study that investigates the relationship between the AINTEGUMENTA (ANT) transcription factor and cyclin CYCD3;1 during lateral aerial organ (LAO) formation. LAO growth is determined by the both the number and size of cells that comprise the organ. During petal development, ant mutants have reduced cell number but increased cell size, demonstrating a ‘compensatory mechanism’ of growth. In contrast cycd3;1 mutants have increased cell size that results in larger petals, showing no compensatory mechanism. Interestingly ant cycd3;1 double mutants do show growth compensation in the same tissue. The authors propose that occurrence of the compensatory mechanism depends on at which time-point during distinct phases of cell division and cell expansion the growth defect occurs.

 

C Collins, Maruthi M.N and C Jahn (2015) CYCD3 D-type cyclins regulate cambial cell proliferation and secondary growth in Arabidopsis. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv218

Another study that investigates a different role of D-type cyclins is led by former Murray lab member, Carl Collins working at the Natural Resources Institute at the University of Greenwich. The factors that control cambial cell growth are poorly understood but the authors provide a link between the cell cycle and cambial differentiation by showing that CYCD3 subgroup of genes play a role in the process. Three CYCD3 genes are expressed in cambial tissue and the equivalent triple mutant has reduced hypocotyl and stem diameter, which is linked to a reduction in mitotic activity. Conversely, mutant xylem cells increased in size. This shows that CYCD3 genes provide a mechanism for controlling the correct proportions of cell growth during vascular development. This might provide a useful tool in the future study of this important process in woody plants.

 

Carvalho FE, Ware MA, Ruban AV (2015) Quantifying the dynamics of light tolerance in Arabidopsis plants during ontogenesis Plant Cell Environment http://dx.doi.org/10.1111/pce.12574

The group of Professor Alexander Ruban at Queen Marys University London utilise a novel methodology to measure the ‘intactness’ of photosystem II (PSII). In this paper they assess the amount of light required to inhibit PSII activity through the life cycle of Arabidopsis plants grown in short days. They show that maximum light tolerance occurs in 8-week old plants. Interestingly the light tolerance correlates with rates of electron transport yet did not coincide with the chlorophyll a/b ratios or anthocyanin content.

 

Baumann K, Venail J, Berbel A, Domenech MJ, Money T, Conti L, Hanzawa Y, Madueno F, Bradley D (2015) Changing the spatial pattern of TFL1 expression reveals its key role in the shoot meristem in controlling Arabidopsis flowering architecture. Journal Experimental Botany http://dx.doi.org/10.1093/jxb/erv247

The TFL1 gene is a repressor of flowering in the Arabidopsis shoot meristem. Researchers from the UK, USA, Spain and Italy, led by Desmond Bradley at the JIC show that ecoptocally expressed TFL1 can repress flowering outside of its normal expression domain. By comparing the expression of TFL1 with genes that determine floral identity (APETALA, LEAFY) the authors conclude that the shoot meristem is more sensitive to TFL1, allowing the maintenance of a vegetative state in this tissue.

Great British Success in ERA-CAPS

The ERA-CAPS funding call was a major EU initiative that was focused on plant sciences. Recently the second set of successfully funded projects were announced, even though the funding levels have not been confirmed. Amongst these twelve successful bids, eight feature UK plant scientists (including four from the JIC). These successful projects are highlighted below:
logo-era-caps
Project Name: DesignStarch, Designing starch: harnessing carbohydrate polymer synthesis in plants

The UK representative Rob Field is a biochemist based at the John Innes Centre. The objective of this project is to ‘gain a profound understanding of the regulation and control of the biophysical and biochemical processes involved in the formation of the complex polymeric structure that is the starch granule’, which will involve in vitro analysis of the enzymology of starch formation with the ultimate aim of transferring their findings back into plants.

EfectaWheat: An Effector- and Genomics-Assisted Pipeline for Necrotrophic Pathogen Resistance Breeding in Wheat

James Cockram (NIAB) is the project leader on this grant that proposes to investigate the economically important wheat leaf spot group (LSG) of necrotrophic pathogens. The project will use a range of techniques such as high-density genotyping, pathogen re-sequencing and advanced virulence diagnosis to deliver a genomics- and effector-based pipeline for the genetic dissection of LSG host-pathogen interactions across Europe.

EVOREPRO: Evolution of Sexual Reproduction in Plants

Both David Twell (Leicester) and Jose Gutierrez-Marcos (Warwick) are included in this seven-group consortium that aims to investigate the origin of the mechanisms that predate double fertilization in plants. The project will take a comparative gene expression-based approach to investigate gametogenesis across Marchantia, Physcomitrella, Amborella, Arabidopsis and a range of crop species. The expected findings will allow the identification of specific mechanisms that are targeted by environmental stresses during sexual reproduction in crops and will assist in the selection of stress-resistant cultivars.

INTREPID: Investigating Triticeae Epigenomes for Domestication

GARNet advisory board member Anthony Hall (Liverpool) leads this group which includes long time collaborator Mike Bevan (JIC). This project will look at variations in the epigenome across eight diverse wheat lines with the aim of determined how epigenetic marks are re-set and stabilized during the formation of new wheat hybrids and how they might influence gene expression.

MAQBAT: Mechanistic Analysis of Quantitative Disease Resistance in Brassicas by Associative Transcriptomics

John Innes Centre scientist Chris Ridout leads this six PI consortium that will look at pathogen resistance in Brassica napus, where diseases are a major limiting factor in growth success. Almost 200 lines of B.napus will be screened against a range of specific and general pathogens in the aim of discovering important disease resistance loci. One proposed aspect of the work will look at the role of glucosinolates in both disease resistace and seed quality. The project also includes UK B.napus expert Bruce Fitt (Hertfordshore).

PHYTOCAL: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae crops

Karen Halliday (Edinburgh) leads this three-PI group that will investigate the link between phytochrome signaling and resource allocation in both Arabidopsis and B.rapa. One aim of the project will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production.

RegulaTomE: Regulating Tomato quality through Expression

Cathie Martin (JIB) leads this largest successful consortium of 8 labs that aim to link transcriptional regulation of metabolic pathways with tomato quality. Loci contributing to abiotic stress tolerance will also be identified toward the combined goals of obtaining more nutritious, stable and sustainable crops. The project will lead to regulatory gene identification (an important advance in terms of fundamental understanding), and provide new tools for metabolic engineering of fruit quality.

SOURSI: Simultaneous manipulation of source and sink metabolism for improved crop yield

Lee Sweetlove (Oxford) leads this group that aims to understand the linkages between source and sink tissues in the assimilation of carbon and nitrogen. The project claims to implement a metabolic engineering strategy of unprecedented scale in plants exploiting the new technique of biolistic combinatorial co-transformation.

Software Carpentry Bootcamp: An organiser’s story

Categories: resource, Workshops
Comments: 1 Comment
Published on: November 27, 2014

Lisa and I have been involved in two Software Carpentry Bootcamps this year: firstly the hosts of a Bootcamp in April at the University of Warwick, and the second, just last week, at a Bootcamp co-organised with the Centre for Genomic Research at the University of Liverpool. A few people at the Liverpool event expressed interest in organising their own workshops, so we thought we would talk you through the stages of hosting a bootcamp and share our experiences to help you decide whether you want to run one of your own.

 

1. Early planning: Decide where the event will be, who will pay, who your audience is and what topics you want to be covered.

It is (now) not free to host a Software Carpentry event. When we organised the Warwick Bootcamp, Software Carpentry was subsidised by the Mozilla Foundation, but since the recent move to its own Software Carpentry Foundation, events now command a fee (TBC) – it’s still a non-profit organisation though.

Software Carpentry trainers are volunteers but you will need to be able to reimburse their travel, food and accommodation expenses. They can come from anywhere in the world, so budget for transatlantic flights!

Other costs you will need to think about include venue hire, and travel, food and accommodation for the workshop participants. It is also up to you whether you want to charge people to attend the workshop to recoup some or all of your costs. For our first bootcamp at Warwick we had sufficient funding to make the event free for attendees, and we paid for one nights’ accommodation too. Because it was free, we did get some last-minute drop-outs, but we had a long waiting list to fill the empty spaces. At the Liverpool event, trainees paid a small registration fee, and paid for their accommodation themselves. Both events booked up quickly and were oversubscribed, so either model works.

We provided lunch and refreshments during both workshops (caffeine breaks are definitely recommended!), and also organised a dinner on the first night of the workshop.

Both of our bootcamps were for complete beginners, but if there are specific topics you need to cover, Software Carpentry can tailor a programme to your needs.

 

2. First contact with Software Carpentry: If you’re in the UK, the Software Sustainability Institute (SSI) in Edinburgh is your point of contact for organising Software Carpentry events. There is information and an email address on the Software Carpentry website.

Discuss your ideas for the bootcamp with Software Carpentry. We worked with Aleksandra Pawlik and Giacamo Peru from SSI over Skype and via email. Software Carpentry requires core topics to be covered, so there may be some negotiating as you work it out. As our bootcamps were for absolute beginners, unlike most Software Carpentry events, this took some time but was not at all difficult to sort out.

Decide on a date, making sure to consider other events that might limit both trainees and instructors.

The Software Carpentry website suggests being flexible with the dates to make finding instructors easier. I think this would mean pulling a bootcamp together very quickly, which might be ok for an institutional event but was impossible for us.

(more…)

Data Mining with iPlant: Published

Categories: GARNet
Comments: No Comments
Published on: October 20, 2014

Data mining with iPlant

We have a new paper published! Lisa is first author on the report from last year’s Data Mining with iPlant workshop, published last week in the Journal of Experimental Botany.

As noted in the abstract, the paper ‘provides an overview of the workshop, and highlights the power of the iPlant environment for lowering barriers to using complex bioinformatics resources, furthering discoveries in plant science research and providing a platform for education and outreach programmes.’

The full reference for the paper is: Martin L, Cook C, Matasci N, Williams J and Bastow R (2014) Data Mining with iPlant: A meeting report from the 2013 GARNet workshop ‘Data Mining with iPlant’, Journal of Experimental Botany, DOI: 10.1093/jxb/eru402

You can view the paper via this toll-free link.

Don’t forget, all the tutorials from the workshop are available for anyone to use on the iPlant Wiki pages.

GARNet and CGR Liverpool present Software Carpentry

Categories: GARNet, Workshops
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Published on: September 9, 2014

SWC Liverpool v1

 

On 17th-18th November 2014, GARNet and the University of Liverpool’s Centre for Genomic Research are teaming up with Software Carpentry in Liverpool for the second Software Carpentry for Plant Scientists bootcamp.

Software Carpentry teaches principles of good programming applicable to any coding language or application, whether sequencing data, phenotypic trait analysis or biochemical assays. Tutorials will start from first principles and cover using Command Line, Python programming including data manipulation with Python, and version control using Git and GitHub. Teaching will be a combination of live coding guided by the trainer and independent practical exercises.

Although the content is suitable for complete beginners, researchers with some experience of programming will also benefit from being taught good practice like version control and test-driven development. These practices will make your programs more sustainable, vastly reducing replication in your code over time, and make them easier to share with team members, collaborators and even in publications.

The programme and tutorials from the first Software Carpentry for Plant Scientists bootcamp is here. This information is to give potential delegates an idea of what the Liverpool event will be like – please be aware that the upcoming bootcamp event will be run by different trainers and therefore will not be exactly the same as the previous one.

To apply for a place on the bootcamp, email charis@garnetcommunity.org.uk between 9th and 23rd September 2014. In your email, please include:

  • Your name
  • Whether you are a student, post-doc, PI or hold another position
  • A brief description of your research interests (less than 50 words)
  • Why you would like to attend the bootcamp (less than 50 words)

Successful applicants will then be invited to register for the workshop from 29th September.

In pictures: Software Carpentry for Plant Scientists

Comments: 1 Comment
Published on: April 11, 2014

Over 30 plant scientists gathered at the University of Warwick this week for our Software Carpentry for Plant Scientists bootcamp. Together we learned to move through space and time using Git, how to make, explore and delete files and directories, how to use Version Control and how to program defensively. As ever we encouraged everyone to Tweet about the event and we’ve collected the tweets in a Storify, which you can access here: sfy.co/ffpW

Some photos from the event are below – enjoy! The photo on the second row is the team that made the event such a success. From left to right: Jason Piper, Charis Cook, Leonor Garcia Gutierrez, Aleksandra Pawlik, Christina Koch and Lisa Martin. Thanks especially to our trainers Aleksandra (sent to us from the Software Sustainability Institute, UK) and Christina, who came all the way from Vancouver.

GARNETSWC

Report launch: Developing Plant Synthetic Biology in the UK

Categories: GARNet, synthetic biology
Comments: No Comments
Published on: March 31, 2014

plant synthetic biology

 

We’ve been working on the meeting report from last year’s An Introduction to Plant Synthetic Biology workshop for months, so we’re delighted that GARNet Chair Professor Jim Murray is going to launch it tomorrow during his talk at PlantSci 2014!

You’ll be able to download the report, Developing Plant Synthetic Biology in the UK: Opportunities and Recommendations tomorrow on the GARNet website, or if you’re at the conference come and see Jim, Lisa or Charis to get a printed version.

To keep up with all the news from PlantSci 2014, follow #PlantSci2014

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