GARNet Research Roundup: June 12th 2019


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

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.

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

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.

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.

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

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

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

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.

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.

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.

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

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.

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

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.

The post GARNet Research Roundup: June 12th 2019 appeared first on Weeding the Gems.