Have a holly jolly Christmas

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Published on: December 22, 2014

holly 1

In Europe holly is a spiky, festive plant that gets an annual spotlight in wreaths and garlands at Christmas. But taxonomically holly is a genus, Ilex, of 400-600 species. Ilex aquifolium (‘holly’) is the dominant species in the UK and Europe but worldwide the genus includes evergreens, deciduous trees, shrubs and climbing plants.

holly 2
Ilex asprella

One holly species, I. asprella, is known locally in its native southern China as Gang-Mei. Tea made from the roots and leaves is a traditional medicine for influenza, bacterial infections and lung abscess. Several studies have shown that extract from I. asprella contains bioactive compounds; this recent systems biology paper profiled the biosynthetic pathway for Ilex triterpinoid saponins. Others have demonstrated that root extract can inhibit flu viruses and sooth inflammation, and this year a team of researchers at the Guangzhou University of Traditional Chinese Medicine showed that I. asprella root extract is also fairly effective at reducing the impact of acute respiratory distress syndrome in mice.

A slow invasion of English holly (the festive kind), I. aquifolium, is causing a bit of a stir in the North West USA. This paper in the rather niche Northwest Science journal sampled holly in a forest in Washington state. The authors looked at spatial distribution and age data to estimate that both vegetative and seed-based spread are increasing exponentially. The paper states that the population doubling time is about 5 years, and individual holly trees grow slowly, so hopefully the situation will be controlled quite easily.

For more varied Christmas plant science, check out my Christmas post from 2012, which features frankincense, mistletoe, fir trees and more holly.


Dai WP, Li G, Li X, Hu QP, Liu JX, Zhang FX, Su ZR, Lai XP. 2014. The roots of Ilex asprella extract lessens acute respiratory distress syndrome in mice induced by influenza virus. Journal of Ethnopharmacology 155 (3): 1575–1582

Zheng X, Xu H, Ma X, Zhan R, Chen W. 2014. Triterpenoid saponin biosynthetic pathway profiling and candidate gene mining of the Ilex asprella root using RNA-Seq. International Journal of Molecular Sciences 15(4): 5970-87

Stokes DL, Church ED, Cronkright DM and Lopez S. 2014. Pictures of an Invasion: English Holly (Ilex aquifolium) in a Semi-Natural Pacific Northwest Forest. Northwest Science 88(2): 75-93.

Image credits: holly after by Allie Edwards冬青科 Ilex asprella (Hook. et Arn.) Champ. 燈稱花 98特生 by 潘立傑 LiChieh Pan. Both via Flickr, shared under Creative Commons. 

Memory of seasons past controls germination

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Published on: December 18, 2014

Arabidopsis seedling germinating JIC

In research published this week in PNAS, Steve Penfield (formerly Exeter, now John Innes Centre) and Ian Graham (CNAP, York) and collaborators have shown that ‘mother’ plants remember seasons and use this memory to program germination time into their seeds.

Working on Arabidopsis thaliana, Penfield found that the mother plant plays an important role in sensing temperature and forms a long term temperature memory, which she uses to control the behaviour of her progeny seeds. These temperature memories enable seeds to determine time of year and modify their germination rates to ensure that their growth and development is coordinated with the seasons.

If the mother experiences warmer temperatures, it produces more of a protein called Flowering Locus T (FT) which in the fruit of the plant, represses production of tannins, making seed coats thinner, increasing their permeability, meaning they will germinate more quickly.

Conversely if the mother plant experiences cooler temperatures prior to flowering it will produce less FT protein in its fruit and therefore produce more tannins. Seed coats will be thicker and less permeable and will germinate later. In this way the mother plant can manipulate seed germination to be optimal for the time of year.

If the environment during seed production is not optimal this can result in poor germination. With climate change making suboptimal conditions more frequent, having a better understanding how plants program progeny dormancy and germination will help researchers optimise seed quality for crops and domestic use.

Steve Penfield said: “By understanding how the mother plant uses temperature information to influence the vigour of her seeds we can begin to develop strategies for breeding seeds with more resilience to climate change.”

Highlighted paper: Min Chen, Dana R. MacGregor, Anuja Dave, Hannah Florance, Karen Moore, Konrad Paszkiewicz, Nicholas Smirnoff, Ian A. Graham, and Steven Penfield. 2014. Maternal temperature history activates Flowering Locus T in fruits to control progeny dormancy according to time of year. PNAS published ahead of print December 16, 2014, doi:10.1073/pnas.1412274111.

This article is adapted from a news release from the John Innes Centre. The image is c/o John Innes Centre. 

GARNish Issue 22 is Hot off the Press!

Categories: Arabidopsis, GARNet, Global
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Published on: December 12, 2014


GARNish cover large

Your December issue of GARNish is now available to download from the GARNet website!

Edition 22 is full of news and views from the UK Arabidopsis and plant science community, including a round-up of some exciting new Arabidopsis projects recently funded by BBSRC. There are also reports from our GARNet 2014 conference in September, and from the second of our sold-out Software Carpentry bootcamps.

In our Plant Science Resources section you can find out more about PlantRegulome.org, and if you weren’t able to be there yourself, you can read all about what happened at the BBSRC Great British Bioscience Festival in London in November.

Finally, we caught up with plant science group leaders at The Genome Analysis Centre and the University of York to find out what’s new.



Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 10, 2014

Lots of new and interesting papers from the UK Arabidopsis research community this week! New papers have been published by scientists from Rothamsted Research and the Universities of Warwick, Leicester, Aberdeen and Manchester.


  • Brewer HC, Hawkins ND and Hammond-Kosack KE. Mutations in the Arabidopsis homoserine kinase gene DMR1 confer enhanced resistance toFusarium culmorum and F. graminearum. BMC Plant Biology, 29 November 2014. DOI: 10.1186/s12870-014-0317-0. [Open Access]

It was already known that mutations to the DMR1 gene affect Arabidopsis’ resistance to the biotrophic pathogens Hyaloperonospora arabidopsidis and Oidium neolycopersici. In this BMC Plant Biology paper, Nelly Brewer, Nathaniel Hawkins and Kim Hammond-Kosack from Rothamsted Research instead investigate the effects of these mutations on resistance to the ascomycete pathogens Fusarium culmorum and F. graminearum.


  • Footitt S, Müller K, Kermode AR and Finch-Savage WE. Seed dormancy cycling in Arabidopsis: Chromatin remodelling and regulation of DOG1 in response to seasonal environmental signals. The Plant Journal, 1 December 2014. DOI: 10.1111/tpj.12735.

Working with collaborators in Canada, Bill Finch-Savage and Steven Footitt from the University of Warwick’s Crop Centre present the findings of a study to investigate natural variation in the expression of genes involved in chromatin remodeling in two Arabidopsis ecotypes. Several key observations were made, including changes detected in the histone modifications H3K4me3 and H3K27me3 of the DOG1 gene during dormancy cycling, leading to the proposal that these histone marks serve as a thermal sensing mechanism during dormancy cycling in preparation for light repression of dormancy.


  • Hoedemaekers K, Derksen J, Hoogstrate SW, Wolters-Arts M, Oh S-A, Twell D, Mariani C and Rieu I. BURSTING POLLEN is required to organize the pollen germination plaque and pollen tube tip in Arabidopsis thaliana. New Phytologist, 1 December 2014. DOI: 10.1111/nph.13200.

David Twell from the University of Leicester was involved in this study with Dutch colleagues from Radboud University Nijmegen. The group explored the processes taking place during pollen hydration in Arabidopsis; the step in pollination before emergence of the pollen tube. Expression of the gene BURSTING POLLEN (BUP) was found to be essential for the correct organisation of a ‘germination plaque’ – an intine-like structure consisting of cellulose, callose and party de-esterified pectin – which provides passage for the emerging pollen tube.


  • Chao D-Y, Chen Y, Chen J, Shi S, Chen Z, Wang C, Danku JM, Zhao F-J and Salt DE. Genome-wide association mapping identified a new arsenate reductase enzyme critical for limiting arsenic accumulation in plants. PLOS Biology, 2 December 2014. DOI: 10.1371/journal.pbio.1002009. [Open Access]

In a collaboration with scientists based in China, Fang-Jie Zhao and Yi Chen (Rothamsted Research), and new GARNet Chair David Salt (University of Aberdeen) carried out genome-wide association mapping in Arabidopsis in order to learn more about natural variation in the genetic control of the reduction of arsenate to arsenite. Understanding the control of this chemical reaction, and the extent to which inorganic arsenic accumulates in crops such as rice, is key to reducing the carcinogenic risk to human health. Analysis revealed a new arsenate reductase enzyme, High Arsenic Content 1 (HAC1).


  • Dyson BC, Allwood JW, Feil R, Xu Y, Miller M, Bowsher CG, Goodacre R, Lunn JE and Johnson GN. Acclimation of metabolism to light in Arabidopsis thaliana – the glucose 6-phosphate/phosphate translocator GPT2 directs metabolic acclimation. Plant, Cell & Environment, 4 December 2014. DOI: 10.1111/pce.12495.

When transferred from low light conditions to high light conditions, mature plant leaves typically increase their photosynthetic capacity via expression of GPT2. In this study, researchers from Germany and the University of Manchester used wild type and GPT2 knockout plants to try and work out how and why this happens.

Funding and networking opportunities from BBSRC plant science NIBBS

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Published on: December 9, 2014

Early this year, BBSRC announced 13 new Networks in Industrial Biotechnology and Bioenergy (NIBBS). Their aim is to foster collaborations between the academic research base and industry in order to drive new ideas in specific areas of focus. Four NIBBS have plant science themes:

•   A Network of Integrated Technologies: Plants to Products: http://www.nibbp2p.org/

•   High Value Chemicals from Plants Network: https://hvcfp.net/

•   Lignocellulosic Biorefinery Network (LBNet): http://lb-net.net/

•   PHYCONET: unlocking the IB potential of microalgae: http://www.phyconet.org.uk/

Each BBSRC NIBB organises free residential networking events and awards funding in the form of Business Interaction Vouchers and Proof-of-Concept funds. You need to be a member of the NIBB to access any of these resources, but they are all free to join.

Business Interaction Vouchers are worth up to £5000 and are intended to support research done by an academic partner for an industrial partner of the NIBB. Depending on the NIBB, there are deadlines throughout the year or applications are accepted at any time.

Proof-of-concept funds are more flexible in scope and amount awarded, but have stricter deadlines. Each NIBB is dealing with their awards differently: The HvCFP deadline is 19 January 2015; and the LB-Net has organised Challenge Workshops in 2015, which will lead to funding for multi-disciplinary teams formed at the workshops. The other networks do not currently have proof-of-concept calls open.

First Arabidopsis Information Portal developer workshop a success

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Published on: December 4, 2014

The Arabidopsis Information Portal (AIP) was funded in 2013 by NSF, and co-funded this year by BBSRC. The UK team is led by Gos Micklem at the University of Cambridge. AIP provides the Arabidopsis thaliana Col-0 reference genome sequence with associated annotation, including gene structure, gene expression, protein function, and interaction networks. It is much more than this however: an open-access online community resource for Arabidopsis research. AIP is intended to be full of resources and tools to navigating the genome, all built by community developers as part of their own research and shared with the rest of the community via AIP. 

Here Makeda Easter blogs about the first AIP developer workshop, which was hosted by TACC, JCVI, and the University of Cambridge. This post was originally published on the news pages at the Texas Advanced Computing Centre


AIP dev workshop 1000

Last month, a group of 20 plant scientists from the U.S. and Europe convened at the Texas Advanced Computing Center (TACC) in Austin to participate in the Arabidopsis Information Portal (AIP) Developer Workshop.

“Our key goal with this workshop was to onboard a group of developers with varying degrees of experience with web technologies to contribute web apps and APIs to our platform,” said TACC Life Sciences Computing Director Matthew Vaughn, co-PI of the project. “With the growing number and diversity of data types available for Arabidopsis, effective developer engagement is crucial to making it all available in a single place. No one group can do it all.

The Arabidopsis Information Portal is an open-access, community extensible, online resource for Arabidopsis research. AIP is an international effort from collaborators TACC, J. Craig Venter Institute (JCVI), and Cambridge University and is powered by cutting edge technologies such as InterMine, Jbrowse, Drupal, and the iPlant Agave API.

The portal not only provides users access to genomic information, but it also allows researchers to contribute their own data through developing scientific applications.


Arabidopsis Research Round-up

Categories: Arabidopsis, Global, Round-up
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Published on: December 3, 2014

It’s all about the Institutes in today’s UK Arabidopsis Research Round-up! New work this week comes from the John Innes Centre, the Sainsbury Laboratory, Rothamsted Research – and theEuropean Bioinformatics Institute, part of the European Molecular Biology Laboratory (EMBL-EBI) based in Cambridge, makes an appearance too.

  • Wirthmueller L, Roth C, Fabro G, et al. Probing formation of cargo/importin-a transport complexes in plant cells using a pathogen effector. The Plant Journal, 17 November 2014. DOI: 10.1111/tpj.12691.

With collaborators in Germany, researchers from the John Innes Centre and the Sainsbury Laboratory in Norwich deduce that complexes between the adapter proteins importin-a, and the cargo proteins they recruit for active nuclear transport, are formed dependent upon cargo specificity, variation at the importin-a nuclear localisation sequence-binding sites, and tissue-specific expression levels of importin-a.

  • Hsiao A-S, Haslam RP, Michaelson LV, Liao P, Chen Q-F, Sooriyaarachchi S, Mowbray SL, Napier JA, Tanner JA and Chye M-L. Arabidopsis cytosolic acyl-CoA-binding proteins ACBP4, ACBP5 and ACBP6 have overlapping but distinct roles in seed development. Bioscience Reports, 21 November 2014. DOI: 10.1042/BSR20140139.

This Bioscience Report included a number of researchers from Rothamsted Research, and explores the previously poorly understood roles of three cytosolic acyl-CoA-bding proteins (ACBPs). Microarray data revealed that all three are expressed in seeds, but further analysis in transgenic Arabidopsis revealed overlapping, but differing physiological effects on seeds.

  • Cubillos FA, Stegle O, Grondin C, Canut M, Tisné S, Gy I and Loudet O. Extensive cis-regulatory variation robust to environmental perturbation in Arabidopsis. The Plant Cell, 26 November 2014. DOI: 10.1105/tpc.114.130310.

Led by a French team, this study also involved Oliver Stegle from EMBL-EBI in Cambridge. Using drought stress as an example of environmental variation, the aim here was to produce a detailed map of the ways in which cis- and trans-acting factors affect gene expression and responses to environmental conditions in Arabidopsis thaliana.

Guest post: Software Carpentry for Plant Scientists bootcamp

Categories: guest blogger, Workshops
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Published on: December 2, 2014
Software Carpentry Liverpool
Photos from the Bootcamp. Instructors and helpers shown in the bottom photo: Bert Overduin, Marios Isaakidis, Kwasi Kwakwa, Fatima Silva.

Thanks to Robyn Drinkwater from the Royal Botanic Garden Edinburgh for this guest post about the Software Carpentry Bootcamp we ran with CGR Liverpool a couple of weeks ago. This piece was first published on Botanics Stories, the RBGE blog. 

Programming is becoming an increasingly useful skill as it can aid in the execution of large, repetitive tasks, and in running analyses of large data sets. Four staff from RBGE recently attended a workshop set up by GARNet and the University of Liverpool’s Centre for Genomic Research along with Software Carpentry, to help them learn and improve their use of some simple tools and programming.

During the workshop they explored the principles of good programming, which can be applied to any programming language, the use of the Command Line, version control using Git and GitHub, and Python, a widely used programming language, which can be used for data manipulation, as well as other programming tasks.

The workshop led us from first principles through each tool, building our understanding of how it works, and showing us examples of how it could be used. During the workshop we started to explore how we could use these tools to look at our own data, and for some of us, we were still seeing what we could do on the train home!

The next step for all of us is to keep practicing and looking at how we can use Python, Git and the Command Line in our work and keep building on the good foundation the bootcamp gave us.

Tweets from participants and organisers of the event have all been brought together by the organisers:


Image credit: Charis Cook

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