Matthew Parker, Kasia Knop and Anya Sherwood talk to the GARNet community podcast

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Published on: February 12, 2020

This research team from the Simpson lab at the James Hutton Institute, University of Dundee discuss a recent paper published in elife entitled ‘Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification.

Apologies for the poor sound quality of the transmission coming down the line from Dundee!

GARNet Research Roundup: February 7th 2020

This latest edition of the GARNet Research Roundup begins with two studies that look at different aspects of lateral root formation and include members of Malcolm Bennett’s lab in Nottingham. The first investigates a critical role for hydropatterning in the control of lateral root initiation whilst the second looks at how cell death in overlying tissue layers plays an active role in the control of lateral root emergence.

The third paper is from the John Innes Centre and investigates the mechanism through which a small number of noncoding SNPs can alter chromatin dynamics at the FLC locus. The fourth paper is from Glasgow and assesses a link between auxin signaling and proteins involved in membrane trafficking.

The next paper is from Rothamsted Research and looks at how aerial differences in wheat cultivars can affect the root-associated microbiome. The sixth paper is from the James Hutton Institute and investigates the relationship between phosphate and zinc signaling during the growth of Brassica oleracea.

The final three papers focus on some aspect of plant mechanical strength. The first paper is from Aberystwyth and looks at the how mechanical stress impacts growth of Brachypodium. The next two papers are led from the US and Sweden respectively and include UK co-authors from Leeds, the JIC and York. The first looks at how lignin modifications illicits defence responses whilst the second begins to demonstrate how xyloglucan modifications alter secondary cell wall growth.


von Wangenheim D, Banda J, Schmitz A, Boland J, Bishopp A, Maizel A, Stelzer EHK, Bennett M (2020) Early developmental plasticity of lateral roots in response to asymmetric water availability. Nat Plants. doi: 10.1038/s41477-019-0580-z Open Access with link.

This brief communication is led by Daniel von Wangenheim, who worked with Malcolm Bennett and colleagues at the University of Nottingham. They use light sheet fluorescence microscopy to investigate how the local water environment controls the initiation of lateral root primordia. They show that this response is extremely plastic and that the initiation of pericycle cell files is linked to the external hydrological landscape. This study reveals a potential adaptive advantage when roots forage under heterogeneous soil conditions, which of course exists in all ‘real-world’ situations.

BotanyOne has written a nice blog about this paper and Daniel von Wangenheim has produced a superb explanatory video.


Escamez S, André D, Sztojka B, Bollhöner B, Hall H, Berthet B, Voß U, Lers A, Maizel A, Andersson M, Bennett M, Tuominen H (2020) Cell Death in Cells Overlying Lateral Root Primordia Facilitates Organ Growth in Arabidopsis. Curr Biol. doi: 10.1016/j.cub.2019.11.078 Open Access

Ute Voss and Malcolm Bennett from Nottingham are co-authors on this Finnish-led study in which Sacha Escamez is first author. They show that cell death occuring in advance of emerging lateral roots is an active developmental process rather than a passive effect of lateral root initiation. Plants with a cell-death-deficiency show delayed lateral root development, which is rescued through physical or genetic removal of outer cell files.


Qüesta JI, Antoniou-Kourounioti RL, Rosa S, Li P, Duncan S, Whittaker C, Howard M, Dean C (2020) Noncoding SNPs influence a distinct phase of Polycomb silencing to destabilize long-term epigenetic memory at Arabidopsis FLC. Genes Dev. doi: 10.1101/gad.333245.119 Open Access

This research from the John Innes Centre is led by Julia Qüesta and Rea Antoniou-Kourounioti. They show that four noncoding SNPs in the Lov-1 Arabidopsis accession are responsible for the reactivation of FLC after only a short cold treatment. They combine experimentation and modelling to also propose that the control of FLC reactivation is linked to the extent of DNA replication during the cold period.

Rea discusses this paper on the GARNet Community podcast. Look out for it on February 19th.


Xia L, Marquès-Bueno MM, Karnik RA (2020) Trafficking SNARE SYP132 Partakes in Auxin-associated Root Growth. Plant Physiol. doi: 10.1104/pp.19.01301 Open Access

This short communication is led by Lingfeng Xia in the Karnik lab at the University of Glasgow and looks at the role of auxin in the control of expression of the SNARE protein SYP132 during root growth and the gravitropic response. This linkage is indicative of an important role for membrane trafficking during the auxin response.


Kavamura VN, Robinson RJ, Hughes D, Clark I, Rossmann M, Melo IS, Hirsch PR, Mendes R, Mauchline TH (2020) Wheat dwarfing influences selection of the rhizosphere microbiome. Sci Rep. doi: 10.1038/s41598-020-58402-y
Open Access

Vanessa Kavamura is first author on this study led from Rothamsted Research that looks at how the aerial phenotypes of different wheat cultivars impacts root traits and the soil microbiome. Interestingly they show that taller wheat varieties are predicted to have a more connected bacterial network, which might lead to a more favourably rhizosphere for plant growth.


Pongrac P, Fischer S, Thompson JA, Wright G, White PJ (2020) Early Responses of Brassica oleracea Roots to Zinc Supply Under Sufficient and Sub-Optimal Phosphorus Supply. Front Plant Sci. doi: 10.3389/fpls.2019.01645 Open Access

Paula Pongrac is the first author on this study led from the James Hutton Institute in which they investigate how plants respond to their access to environmental phosphate and zinc. They assess gene expression of Brassica oleracea plants grown under different mineral conditions and reveal important relationships between the response to phosphorous and zinc that will inform future nutrient supply strategies and identification of novel germplasm.


Gladala-Kostarz A, Doonan JH, Bosch M (2020) Mechanical stimulation in Brachypodium distachyon: implications for fitness, productivity and cell wall properties. Plant Cell Environ. doi: 10.1111/pce.13724.

Agnieszka Gladala‐Kostarz who works with Maurice Bosch at Aberystwyth University is the first author on this research that looked at the effect of both wind- and mechanical- treatments on growth of two accessions of Brachypodium distachyon. They catalogue the physical changes that occur in this important base-line study that tracks the relevance of these environmental factors on the multiple growth traits.


Gallego-Giraldo L, Liu C, Pose-Albacete S, Pattathil S, Peralta AG, Young J, Westpheling J, Hahn MG, Rao X, Knox JP, De Meester B, Boerjan W, Dixon RA (2020) ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) releases latent defense signals in stems with reduced lignin content. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1914422117 Open Access

Lina Gallego-Giraldo is the first author on the US-led paper that includes Paul Knox and Sara Pose-Albacete from the University of Leeds. In this work they look at the link between lignin modifications and the inappropriate initiation of plant defence responses. They show that cell wall pectin remodeling mediated by the ARABIDOPSIS DEHISCENCE ZONE POLYGALACTURONASE 1 (ADPG1) protein releases defence elicitors and as such provides important information on the link between these processes.


Kushwah S, Banasiak A, Nishikubo N, Derba-Maceluch M, Majda M, Endo S, Kumar V, Gomez L, Gorzsás A, McQueen-Mason S, Braam J, Sundberg B, Mellerowicz EJ (2020) Arabidopsis XTH4 and XTH9 contribute to wood cell expansion and secondary wall formation. Plant Physiol. doi: 10.1104/pp.19.01529 Open Access

Sunita Kushwah leads this Swedish-study that has co-authors from the JIC and York. They investigate a novel role for the XTH4 and XTH9 xyloglucan endo-transglycosylase/ hydrolases during secondary growth in Arabidopsis. The activity of these enzymes has a significant effect on cell wall composition and in the control of wood formation

https://www.nottingham.ac.uk/biosciences/people/ute.voss

Zaigham Shahzad on the GARNet Community podcast

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Published on: February 5, 2020

Zaigham Shahzad who works with Anna Amtmann at the University of Glasgow chats to GARNet about a paper published in Nature Communications entitled ‘Cryptic variation in RNA-directed DNA-methylation controls lateral root development when auxin signalling is perturbed‘.

COST Programmes support Training and Collaboration: Get involved!!

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Published on: February 4, 2020

Take home Message: COST Activities are open for everyone*

Since its inception, the European COST programme has operated according to one main instrument, the COST Action.

COST Actions are organised by a range of networking tools, such as meetings, conferences, workshops, short-term scientific missions, training schools, publications and dissemination activities. Funding supports COST Action networking tools but does not provide support for research projects (aside from within STSMs).


A COST Action is open to all:

– researchers, policy makers and innovators

– across all fields of science and technology (including trans-, and interdisciplinary, new and emerging fields)

– Most type of institution (academia, public institutions, SME/industry, NGO, European/international organisations, etc.)

– all career stages (both young and experienced)

COST Actions provide funding for meetings that bring together researchers from around Europe and the world. These face-to-face meetings reduce barriers to form important collaborative relationships.


The other main instruments that COST Actions use to support training are

1) Training Schools are up-to week-long events that offer instruction in a relevant topic for the Cost Action. These are usually fully supported by the Cost Action.

2) Short Term Scientific Missions (STSMs) provide funding for a participating (usually early career) researcher to perform research in a different country for up to 3months. This period of research is supported with a maximum of ~€2500.

Both Training schools and STSMs represent essentially FREE support to train the next generation of researchers. These are particularly useful for countries where the research infrastructure is being developed.

Importantly researchers in ANY MEMBER COUNTRY are eligible to participate in training schools or STSMs as well as to apply to attend Action conferences. Most researchers will be unaware of these opportunities but they are a real option to support your own or your lab member’s research.


CA16212: Impact of Nuclear Domains On Gene Expression and Plant Traits (INDEPTH) Active until 27/11/2021

https://www.brookes.ac.uk/indepth/

CA18111 – Genome editing in plants – a technology with transformative potential (PlantEd) Active until 24/4/2023

https://plantgenomeediting.eu/

CA15223 – Modifying plants to produce interfering RNA Active until 26/10/2020

https://iplanta.univpm.it/

CA16110 – Control of Human Pathogenic Micro-organisms in Plant Production Systems Active until 5/3/2021

https://huplantcontrol.igzev.de/

CA16107 – EuroXanth: Integrating science on Xanthomonadaceae for integrated plant disease management in Europe Active until 15/3/2021


CA18201 – An integrated approach to conservation of threatened plants for the 21st Century Active until 14/10/2023

https://www.cost.eu/actions/CA18201/#tabs|Name:overview

*- Currently UK researchers are only eligible until the end of 2020 depending on pending Brexit negotiations. We remain confident that these will be successgfully resolved.

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