Weeding the Gems - Page 45 of 67 - the GARNet community blog

Plant science at the RHS Chelsea Flower Show

Categories: something fun

Tags: Fera, RHS Chelsea Flower Show, Rothamsted

Comments: No Comments

Published on: May 30, 2014

Last week was the RHS Chelsea Flower Show, the biggest event in the horticulture calendar. I’m not sure it counts as a plant science event (unfortunately – I would love to be able to go for GARNet!) but it is a good opportunity to communicate some great plant science to an interested public. This year Rothamsted Research and Fera sprung into action and produced Award-winning exhibits.

The exhibit from Rothamsted, designed by Nicky Seymour and inspired by work on oilseed rape flowers by Sam Cook and Jason Baverstock, was awarded a Silver Medal in the Discovery category. Sam and Jason’s research shows that some oilseed rape pests are put off by different colour flowers, and others can be controlled by reservoirs of natural predators in field margins full of wild flowers. Sam explained her work, which received coverage from the BBC and Farmers Weekly, on the UKBRC website last year.

Images courtesy of Rothamsted Research

The Fera exhibit, Plants Need Passports Too, used the idea that plants are under threat from pests, diseases and invasive species. It explains some of the ways threats can creep into the country, and the regulations that aim to limit the damage. This video from Fera gives a guided tour of the Bronze Medal-winning garden.

Goldenbraid 2.0: A Standardised DNA Assembly Framework

by Guest Blogger

Categories: guest blogger, methods, resource, synthetic biology

Tags: guest blogger

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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 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

Sarrion-Perdigones A, Falconi EE, Zandalinas SI, Juarez P, Fernandez-del-Carmen A, Granell A and Orzaez D (2011) GoldenBraid: an iterative cloning system for standardized assembly of reusable genetic modules. PloS one 6:e21622.
Sarrion-Perdigones A, Palaci J, Granell A and Orzaez D (2014) Design and construction of multigenic constructs for plant biotechnology using the GoldenBraid cloning strategy. Methods Mol Biol 1116:133-151.
Sarrion-Perdigones A, Vazquez-Vilar M, Palaci J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A and Orzaez D (2013) GoldenBraid 2.0: a comprehensive DNA assembly framework for plant synthetic biology. Plant Physiol 162:1618-1631.

Plant synthetic biology in Europe

by Charis Cook

Categories: GARNet, synthetic biology

Tags: GARNet, meeting report, synthetic biology

Comments: 1 Comment

Published on: May 20, 2014

On 8-9 May I attended a meeting hosted by PlantEngine to discuss the idea of a synthetic biology repository in Europe. The presentations were varied and interesting, and hopefully the other delegates enjoyed mine (PDF) too,

The meeting was at VTT in Espoo, a city very close to Helsinki. The local host Heiko Rischer gave a brief introduction to VTT, which is a Finnish institute but has bases all over the world. VTT is very separate from the university system, and although fundamental research gets done there it has a big commercial focus and strong links to Finnish industry. For example, VTT developed Arctic cloudberry stem cell technology for cosmetics with the R&D team from Finnish skincare company Lumene Oy.

PlantEngine itself was introduced by lead PI Heribert Warczecha. It is a European network focused on enhancing capacity in plant metabolic engineering by activities like defining target pathways, disseminate new technologies, and setting standards. There are currently over 70 labs in 23 EU countries in the network. They run training schools and workshops, and fund short-term scientific missions – check it out if you’re looking for funding for a short research trip to another lab.

One of PlantEngine’s aims is to explore synthetic biology for engineering plant products, which is the reason for the meeting I attended. (more…)

Golden Gate cloning: Tips and resources

by Charis Cook

Categories: resource, synthetic biology

Tags: resources, synthetic biology

Comments: 2 Comments

Published on: May 14, 2014

Last week I was in Helsinki for a plant synthetic biology meeting, and I learned a lot about existing European synbio tools, resources and research. There’s a short Storify of Tweets from the meeting here, and I’ll do a round-up post very soon. But today I’m highlighting a tool presented at the workshop, which was also presented at our SynBio workshop last year and at PlantSci 2014 but still hasn’t really featured on this blog (rather remiss of me, I know).

The Golden Gate cloning and related MoClo systems were presented (PDF) by one of its inventors, Sylvestre Marillonnet, at our synbio workshop last year. Sylvestre has worked with Nicola Patron, Head of Synthetic Biology at The Sainsbury Laboratory, to make a MoClo toolkit and set of parts available on Addgene. The toolkit includes 39 parts encoding promoters and 5′ untranslated regions; antigenic tags; sub-cellular localisation signals; reporter genes; selectable marker genes; terminators; 3′ untranslated regions; a suppressor of silencing; and two linkers.

Unfortunately the paper describing the toolkit is behind a paywall, but I’ve been tipped off as to where to find all the practical information you need:

1. The supplementary data is accessible to anyone, and it is very informative. SD 2 and 4 list modules in the toolkit and parts kit respectively.

2. Nicola’s website, Synbio@TSL, has pages on how Golden Gate cloning works, making modules, and an assembly protocol.

3. Nicola presented the toolkit at PlantSci 2014 in May and her poster gives a good overview of the paper’s content: GG_Plant_Kit_Poster

Nicola has generated many other parts, which are listed on her website. Some of them can be obtained from Addgene, while others have to be requested from her lab. Synbio@TSL also has a nice introduction to synthetic biology, synthetic biology news, links to online resources and synbio centres, and guides to the major genome editing and DNA assembly techniques.

GoldenBraid is another modular cloning technique which has its own web resources and toolkit available. There’s a guest post coming up soon about that one though so no spoilers here!

The Golden Gate Toolkit is published in: Engler C, Youles M, Grüetzner R, Ehnert T-M, Werner S, Jones JDG, Patron N, Marillonnet S. (2014) A Golden Gate Modular Cloning Toolbox for Plants. ACS Synthetic Biology DOI: 10.1021/sb4001504

The MoClo system is published in: Weber E, Engler C, Gruetzner R, Werner S, Marillonnet S (2011) A Modular Cloning System for Standardized Assembly of Multigene Constructs. PLoS ONE 6(2): e16765. doi:10.1371/journal.pone.0016765

The GoldenBraid system was most recently published as: Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. (2013) GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. Plant Physiol. 2013 162: 1618-1631. doi:10.1104/pp.113.217661

Image credit: Nicola Patron

GARNet 2014 Early Career Researcher Bursaries

by Charis Cook

Categories: Arabidopsis, funding, GARNet

Tags: No Tags

Comments: No Comments

Published on: April 29, 2014

The Easter conference season is over and some of our readers will be planning flights, talks and posters for ICAR, ASPB, MPMI or another summer conference abroad. But if that isn’t you this year, don’t worry – GARNet 2014 is much closer to home! And if you’re a student or post-doc, you might be able to win a bursary to cover all your expenses.

Arabidopsis: The Ongoing Green Revolution is in Bristol, so it doesn’t have the glamour of ICAR 2014 in Vancouver, but Bristol does have a Banksy on nearly every corner and lots of good places to eat and drink (like this bar with in-house magicians!). For two days only the city will also be able to boast our great plenary speakers Rob Martienssen, Maarten Koornneef, Andrew Millar and Paul Schulze-Lefert. Our fifth plenary speaker is Bristolian Alistair Hetherington.

Registration is only £120 for students and post-docs, but we’re offering 10 bursaries for GARNet 2014 to early career researchers. These bursaries will cover the registration fee, reasonable UK travel expenses and one night’s accommodation in Bristol. They will be awarded to 5 students or early career researchers invited to give talks, and 5 students who submit excellent abstracts but are not selected for presentations. To register and/or to apply for a bursary, go to: http://garnet2014.org/call-for-abstracts/

banksy for bursaries

Image: ghostly Banksy graffiti on the Thekla by Libby

A sweet surprise: Revealing new roles for sugars in plants

by Guest Blogger

Categories: Arabidopsis, Celebrating Basic Plant Science, guest blogger, Summary for non-specialists

Tags: Arabidopsis, guest blogger

Comments: No Comments

Published on: April 23, 2014

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).

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 our 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…)

Novel tools for reducing bias in Next Generation Sequencing of small RNAs

by Guest Blogger

Categories: guest blogger, methods, resource

Tags: guest blogger, methods, resources

Comments: No Comments

Published on: April 15, 2014

Tamas Dalmay, Professor of RNA Biology at the University of East Anglia (Norwich), has developed a robust, simple method of profiling small RNAs using next generation sequencing. Here he explains his novel HD adapters and why they are more reliable than existing commercial adapters.

Figure 1c from Sorefan et al., 2012: The structure of miR-29b with the Illumina adapters (top) and some of the structures formed by HD adapters (bottom).

Small RNAs (sRNAs) are key regulators of gene expression, and accurate representation of sRNA in sequencing experiments is critical to the interpretation of biological data. Next generation sequencing (NGS) is now the gold standard for profiling and discovering new sRNAs, so it is essential that the tools and protocols used in NGS generate accurate, reliable sequence data.

RNA ligases are essential in creating cDNA libraries prior to NGS sequencing. However, a number of recent publications reported that RNA ligases used in cDNA preparation actually mediate sequence specific ligation, so NGS approaches using these RNA ligases do not represent all sRNA present in biological samples. These publications highlighted the limitations associated with RNA ligases, questioning the reliability of currently widely used NGS approaches and the data generated from them.

Sequence specific ligation occurs because the ligases preferentially ligate ends that are more likely to be close to each other. This means that sRNAs that can efficiently anneal to the adapters have a higher chance of being ligated (Jayaprakash et al. 2011, Hafner et al. 2011 and Sorefan et al. 2012).

While identifying that cloning bias in sRNA libraries is RNA ligase dependent, our group at the School of Biological Sciences, University of East Anglia (Norwich), developed a novel, simple, robust solution to overcome this problem (Sorefan et al. 2012).

We developed a set of adapters (High Definition or HD adapters) that contain degenerated nucleotides, meaning they are a pool of many sequences instead of one fixed sequence. Consequently, many different sRNAs can form a stable duplex with them, leading to better coverage and more quantitative libraries. We have shown that using the HD adapters: (more…)

In pictures: Software Carpentry for Plant Scientists

by Charis Cook

Categories: GARNet, something fun, Workshops

Tags: GARNet workshop

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.

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