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.

(more…)

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:

http://sfy.co/ppQS

Image credit: Charis Cook

Optimising photosynthesis

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Published on: September 25, 2014
Perennial grass Alloteropsis semialata (image c/o Marjorie Lundgren)
Perennial grass Alloteropsis semialata (image c/o Marjorie Lundgren)

Angela White (University of Sheffield) spoke to some photosynthesis researchers at the SEB annual conference in July – this is what she found out! Find Angela on Twitteronline and at the blog.

This post was originally published on the UK Plant Sciences Federation blog

Photosynthesis is a major target area for crop improvement. In July 2014, I caught up with three plant scientists researching photosynthesis to discover their latest findings, which were presented at the Society for Experimental Biology’s annual main meeting in Manchester.

Understanding evolutionary intermediates between two photosynthetic pathways

Marjorie Lundgren, a PhD student at the University of Sheffield, is researching how different photosynthetic mechanisms evolve. She works on the grass Alloteropsis semialata, which is unique in having both C3 and C4 photosynthetic pathways within this single species. Excitingly, her work has discovered populations of this species with intermediate photosynthetic phenotypes (known as C2 plants), helping us to understand how C4 evolves from the C3 pathway.

Marjorie’s research has three main findings. Firstly, she’s confirmed the existence of intermediate photosynthetic states using a range of physiological techniques.  Secondly, she’s established that this intermediacy arose in Central Africa.  And finally, Marjorie has elucidated clear links between environment, leaf anatomy and physiology. Together, her preliminary work suggests that leaf anatomical traits which are important for the C3 to C4 transition respond to environmental changes. This responsiveness is known as phenotypic plasticity and may affect the evolution of photosynthetic types.

“There’s a huge amount of variation within this species,” says Marjorie. “It’s a brilliant system.” Marjorie hopes that her research will inform the multinational C4 rice consortium, which aims to introduce the efficient C4 photosynthetic pathway into rice. She is working to identify important anatomical turning points in the evolutionary process which leads from C3 to C4 photosynthesis.

The next challenge is to use this wild grass species to identify the genetic variation that underpins evolution of the C4 photosynthetic pathway, and see how it affects physiology. This understanding is crucial if we are to successfully engineer C4 traits into C3 plants to improve crop efficiency and yield.  (more…)

Publication trends in Arabidopsis

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Published on: September 18, 2014

Pete McQuilton and Richard Smith of Nowomics have pulled a load of information on Arabidopsis trends for us to write this fascinating guest blog post. Nowomics is a new website that fetches data from many biological databases every day and works out what’s changed, and finds genes and species names mentioned in new PubMed abstracts. This lets users (this can be anyone – it’s free!) to follow genes and gene ontology terms to create a personalised news feed of new papers and data. 

Arabidopsis thaliana, the humble model organism for flowering plants, has been studied for over 140 years. Discovered by Johannes Thal (hence the name thaliana), the mouse-ear cress is a member of the mustard family (Brassicaceae), alongside such luminaries as cabbage and radish. With it’s relatively small sequenced genome (114.5mb/125Mb total), rapid life cycle (about 6 weeks from germination to mature seed), prolific seed production and many genetic tools and mutants, Arabidopsis is a wonderful model organism for basic research in genetics and molecular biology.

As part of a series of blog posts at Nowomics we have examined the publication trends in Arabidopsis-related research. We’ve extracted data on primary research papers from PubMed (excluding reviews and clinical trials) for a ten year range from 2004-2013 and have identified those that mention Arabidopsis in the title or abstract. These papers are defined as Arabidopsis papers (further details of the method are given below).

From this analysis, it is clear that the Arabidopsis community is thriving, having produced just over 3500 papers in 2013, up from 1847 in 2004. This represents a 91% increase in article number, keeping pace with the overall rise in number of journal articles published, which has grown by 95% since 2004.

Journals

Figure 1. The top Arabidopsis-publishing journals 2004-2013.
Figure 1. The top Arabidopsis-publishing journals 2004-2013.

From 2004 to 2011, Plant Physiology (Plant Physiol.), Plant Journal (Plant J.) and Plant Cell made up the top three journals publishing Arabidopsis research (see figure 2). Plant Signal Behaviour (Plant Signal Behav.) has risen rapidly from it’s inception in 2006 to join the top five in 2008. By far the strongest trend, however, is the rise of PLoS ONE from outside the top ten in 2010 with just 66 Arabidopsis papers, to topping the chart with 315 in 2013. That figure represents 9% of all Arabidopsis articles in 2013. The meteoric rise of PLoS ONE can be seen for other organisms, such as in Drosophila, as described in a previous blog post. (more…)

ADAS Boxworth Open Day

Categories: guest blogger
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Published on: June 26, 2014

Charlotte White, crop physiologist at environmental and agricultural consultancy ADAS, reports from the ADAS Boxworth Open Day where science from ADAS is showcased alongside work funded by Defra and HGCA as well as private enterprises. It is a great opportunity for scientists, agronomists, farmers and seed/agrochemical representatives to network and discuss their needs and current work.

adas boxworth

On the 3rd of June ADAS Boxworth in Cambridgeshire opened its fields to welcome around 200 visitors. The rather wet morning, which made the behind the scenes setup soggy, dissipated in time for the mid-day opening and the afternoon was lovely and sunny. Visitors included farmers, agronomists, members of the seed and agrochemical industry, students and the farming press.

On arrival visitors were welcomed with a complementary hog roast and could register for BASIS and NRoSO points. At reception there was a demonstration of electrical weeding, which had a lot of interest, along with updates on the SCEPTRE project, the fertiliser value of anaerobic digestate and the HGCA stand. There were then two routes: wheat followed by oilseed rape or oilseed rape followed by wheat. The majority took the latter.

The oilseed rape field had a number of Defra, HGCA and commercially funded project demonstration plots. These included optimising seed rates/row widths, and the project I was demonstrating, which looks at precision applications of late foliar nitrogen fertiliser to increase yield and feed value of the rape-meal (CC: described in this UKBRC factsheet). Dr Steve Ellis spoke about pollen beetle thresholds and neonicotinoids, while Dr Faye Richie was on hand to answer questions on oilseed rape diseases relevant to this season and give updates on the latest findings from the pathology group. The industry variety and product demo plots appeared to have a high yield potential and formed the perfect environment to catch up with sponsors and collaborators. As you turned the corner in the field it was a surprise to find Ken Smith stood in a soil pit promoting good soil management on behalf of HGCA, a topic which always generates a lot of interest and gets people talking!

The wheat field was across the farm road and had a similar mix of government, levy and industry funded project demonstration plots, industry stands and variety and product plots. Prof Roger Sylvester-Bradley explained the yield enhancement network (YEN), an innovation competition to help growers break existing cereal yield records. The demonstration plots, testing ‘innovative ideas’ to maximise grain filling, included irrigation, reflective soil strips and plot cooling (if you are interested in entering the YEN competition, visit the website). The triticale demo plots also received a lot of attention and Dr Sarah Clarke and Dr Daniel Kindred were on hand to discuss the benefits of triticale – it out-yields wheat as a second cereal – and to promote the LearN project, which is using a novel on-farm approach to investigate nitrogen monitoring and management. Jonathan Blake was there to discuss the HGCA Fungicide Performance work, and had some interesting demonstration plots to show yellow rust and septoria tritici control. In addition to these and other interesting research demonstration plots, national ADAS experts in weed, pest and disease management were around to answer all manner of questions. Visitors were kept lingering long after the 4pm close.

For me, it was a long and invigorating day and great to talk to farmers and agronomists about their experiences with late application of foliar nitrogen and to provide an update on the latest project findings, as well as seeing what everyone else in ADAS has been working on. Don’t worry if you missed it, keep your eye out for flyers for future open days!

Image credit: Charlotte White

Adjusting the Circadian Clock

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Published on: June 3, 2014

As highlighted in Lisa’s excellent weekly Arabidopsis Research Round-up two weeks ago, a paper on the feedback loop mechanisms that give the circadian clock flexibility was recently published in New Phytologist Early View (DOI: 10.1111/nph.12853Open Access) by GARNet 2014 speaker Andrew Millar. Here first author Laura Dixon, post-doctoral researcher in flowering regulation in the Department of Crop Genetics at the John Innes Centre, explains the research.

Dixon May2014
Arabidopsis thaliana (left) and single celled green alga Ostreococcus tauri

The circadian clock is an innate time-keeping mechanism found in most organisms, and has a period of about 24 hours. The circadian rhythm syncs to the environment as the clock mechanism adjusts to long or short photoperiods, or environmental summer and winter, and so co-ordinates many biological processes with respect to time of day and season. How quickly these adjustments can occur varies between species, and is believed to be a property of how many interlocking feedback loops the circadian clock mechanism is comprised of.

To empirically test the idea that clock flexibility is linked to the number of interlocking feedback loops within the circadian clock mechanism, we compared the fairly complex Arabidopsis thaliana clock to the very reduced clock of the smallest free-living eukaryote, unicellular green alga Ostreococcus tauri. We use A. thaliana as a plant model as it is a simple system relative to often very complex crop species. Many crop species are polyploid and so have very complicated signalling pathways; Arabidopsis is simpler but still contains complex regulation which can inform crop research. The Arabidopsis clock is a network of interlocking feedback loops. Groups of gene families encode clock components and at least 10 photoreceptor proteins.

We switched photoperiod conditions directly between short day and long day and observed what happened in the two systems. In combination with network analysis through mathematical modelling of the proposed possible clock structures, we showed that flexibility of entrainment to environmental conditions is a property of both the number of interlocking loops and the number of light inputs to the clock mechanism. Our research highlights one of the mechanisms through which circadian clock transcriptional and translational loops are flexible and adaptable in response to environmental conditions.

Images: A. thaliana from GARNet; TEM of Ostreococcus from Eikrem and Throndsen University of Oslo

Goldenbraid 2.0: A Standardised DNA Assembly Framework

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Published on: May 27, 2014

As promised in my posts about the Plant Engine meeting I attended a couple of weeks ago (1, 2), here is Diego Orzaez to explain his GoldenBraid cloning method and online DNA assembly framework. Diego co-leads the Plant Genomics and Biotechnology Lab at the Instituto de Biología Molecular y Celular de Plantas in Valencia, Spain. 

goldenbraid

GOLDENBRAID 2.0: A STANDARDIZED DNA ASSEMBLY FRAMEWORK FOR MULTIGENE ENGINEERING IN PLANTS

Engineering large multigenic constructs for Plant Synthetic Biology, such as complex metabolic pathways or intricate gene networks, requires efficient, flexible DNA synthesis and assembly technologies. Although custom gene synthesis is becoming increasingly affordable, the direct synthesis of large multigenic constructs remains prohibitive for most labs. Moreover, custom gene synthesis gives little room for combinatorial engineering, something that is highly valued by biotechnologists.

An alternative “building” strategy for multigene engineering is Modular Construction, that is, the fabrication of new devices by combination of prefabricated standard modules. Modular DNA Construction brings a number of advantages as speed, versatility, lab autonomy, combinatorial potential and often lower cost. As in any standardized methodology, the more users adopt the standard, the bigger the advantages.

GoldenBraid is a Modular DNA Construction method developed at the Plant Genomics and Biotechnology lab (IBMCP-Spain), especially designed for building exchangeable multigenic constructs for Plant Synthetic Biology. Routinely, 15-20 Kb constructs comprising 4-6 transcriptional units made of dozens of individual pre-fabricated modules (GBparts) can be created in few days. Longer constructs can be assembled with little additional effort.

To facilitate the process of genetic design using GoldenBraid, and to stimulate the exchange of genetic modules among laboratories, we have recently launched GoldenBraid2.0 (GB2.0), a web-based DNA assembly framework available at www.gbcloning.org site. The GB2.0 webpage hosts the public GB2.0 database, an increasingly populated collection of pre-made “GBparts” that conform to the GB standard. An embedded software tool named GBdomesticator provides users with personalized lab protocols for creating their own collection of standard genetic parts. Users can always combine their own parts with those deposited in the public GB2.0 database. Moreover, building new GB2.0 multigenic constructs is highly facilitated by the GB assembler tool, a software package that assists in the design of new multigenic constructs.

We believe that adopting common standards and creating of public repositories of exchangeable genetic parts will speed up progress in Plant Biotechnology. If you are interested in this field, we encourage you to explore the gbcloning.org webpages. The details of GB assembly system are described in the publications listed below, and there are tutorials online.

Comments on how to enhance community efforts towards the development of public repositories of standard DNA parts are most welcome, and can be addressed to goldenbraid@ibmcp.upv.es

 

References

A sweet surprise: Revealing new roles for sugars in plants

The fifth post of our Celebrating Basic Plant Science series comes from Mike Haydon, a lecturer at the University of York. He and his research group work on understanding signalling in plants. Here he explains some of his work on integrating sugar metabolism with light signals. You can see more about Mike and his group on his website. The work he discusses below was published in the journal Nature last year (Haydon et al. Nature 502:689-692).

 

sugar
Sucrose

A life based on sugar

Most of us think about sugar every day, be it consciously as we consider our calorie intake, or unconsciously when our brain tells us it’s mealtime. Sugars are among the simplest of carbohydrates and they are the raw material for cellular respiration, which produces energy for almost all living cells. Glucose, a monosaccharide, is the preferred sugar for cellular respiration. Sucrose, most familiar to us as the granulated sugar in our kitchens, is a disaccharide made of glucose and fructose. These, and other simple carbohydrates, are used to build complex carbohydrates such as starch and cellulose in plants, and glycogen and chitin in animals. Sugars are the foundation of cellular metabolism, and produce the wide array of molecules that sustain our carbon-based existence.

 

The most important process on the planet

Plants, along with algae and some species of bacteria, use photosynthesis to convert carbon dioxide in the air into glucose using energy from sunlight, while producing oxygen as a by-product. Photosynthetic bacteria were responsible for the Great Oxidation Event, which occurred from about 2.5 billion years ago and led to the life-sustaining atmosphere we now live in. Photosynthetic organisms are called autotrophs, because they produce their own sugars to use in cellular metabolism. All other organisms, called heterotrophs, must somehow get their sugars from their environment. For animals, this is ultimately through the plant-based component of their diet. So essentially all the carbon in DSC_0010 smallour bodies was, at some point, converted from carbon dioxide into glucose by photosynthesis. Thus, photosynthesis is probably the most important metabolic process on the planet.

You might think that something so fundamental in biology would be completely understood, and we certainly do know a lot about carbohydrate metabolism. We also know that sugars have functions outside of this basic metabolism. For example in plants they can act as hormones, regulating processes such as cell growth, cell division, flowering time and disease resistance. But there is still a lot we don’t know about how plants regulate carbohydrate metabolism, and sometimes we still find entirely new functions for sugars in biological processes.

 

How time matters in sugar metabolism (more…)

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