New Phytologist Synthetic Biology Workshop: SynBio toolboxes for your lab!

Categories: synthetic biology
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Published on: June 28, 2012

Of more immediate practical use to the GARNet community than the technology described here are toolkits presented at the 4th New Phytologist Workshop by Susan Rosser (University of Glasgow) and Keith Saunders (John Innes Centre).


Susan Rosser presented a soon-to-be-published multi-gene assembly kit based on synthetic integrons – ‘Syntegron’. Like existing kits for manipulating DNA, it involves cassettes which top and tail each gene or section of DNA. Unlike other kits, it will be open source and allows for many genes, even a whole pathway, to be assembled, shuffled if required, and expressed. It has been demonstrated to work on the 5-gene violacein pathway which was put, complete and functioning, into E. coli in just 5 days. I’m pretty sure this protocol will be a hit, and it will be an excellent method for a group to use when they try out synthetic biology for the first time.

Keith Saunders presented another gene transfer method, the CPMV-HT expression system which won the BBSRC Innovator of the Year award for Professor George Lomonossoff and Dr Frank Sainsbury. Their system is based on empty virus-like particles (eVLPs), made from modified cow pea mosaic virus (CPMV). (more…)

New Phytologist Synthetic Biology Workshop: SynBio toolboxes for de novo peptide synthesis

Categories: synthetic biology
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Published on: June 26, 2012

As exciting as this research in this post is, to me as a humble traditional molecular biologist the most impressive ‘toolboxes’ were the truly synthetic ones involving no genes at all. Dek Woolfson (University of Bristol) and Samuel Stupp (Northwestern University, USA) presented astonishing work on custom peptides.

The Woolfson group is working towards making a toolbox for building proteins. They chose to work on α-helical coiled-coils because these peptide structures have that essential orthogonality built in – the correct peptides form coiled-coils irrespective of the surrounding domains, which can then be customised to fit the designer’s requirements. The group is now able to synthesise a number of structures using coiled-coils.

from Moutevelis and Woolfson (2009) JMB 385:726 (Click on image to go to paper)


Summary for non-specialists: Science paper on epigenetics

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Published on: June 21, 2012

One of the things I wanted to do on this blog was to highlight recent plant science journal articles, and when I found back-to-back papers on Arabidopsis research in Science I thought they would be a good place to start.

But when I started to read, I realised the obvious – my cell wall biochemistry background will be no help at all when trying to understand other areas of plant science research. But I still want to highlight high-impact articles like this on the blog, so I decided to have a Summary for non-specialists series. Please feel free to comment if I’ve got something horribly wrong, and of course if anyone would like to provide a Summary by a Specialist that would be great!

Highlighted article

Qian et al., June 2012. A Histone Acetyltransferase Regulates Active DNA Demethylation in Arabidopsis. Science 336: 1445-1447

Prior to this research, little was known about the regulation of DNA methylation, or how DNA and histone modifications were related. Here, Qian et al. define a process in which histone modification is an essential part of DNA methylation. This research opens the door to deeper understanding of the regulation and mechanism of DNA modification, and possible manipulation of epigenetic mechanisms.


4th New Phytologist Workshop: SynBio toolbox for secondary metabolite synthesis

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Published on: June 20, 2012

The objective of much of the work presented at the 4th Annual New Phytologist Workshop was a ‘SynBio Toolbox’. The intended aim is that these toolboxes can be used to make anything the user wants, be it a novel antibiotic, chemical cell, or micromachine. The most important characteristic of all the ‘toolboxes’ was that the components must be orthologous – the pieces, or tools, must be useful for a wide variety of end products, so interchangeable within certain parameters

Eriko Takano’s group at the University of Groningen have taken on the much-needed but unenviable task of making a ‘toolbox’ of antibiotic synthesis genes. Their oracle is an online tool they developed called antiSMASH, which finds and annotates secondary metabolite biosynthesis gene clusters in a DNA sequence. Once the genes are identified in silico, they can be found and manipulated in vivo. The Takano group successfully used this method to re-awaken the cryptic CPK gene cluster and discover two novel compounds with anti-bacterial activity.


Plant Sentinels and Robolobsters at the New Phytologist Synthetic Biology Workshop

Categories: synthetic biology
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Published on: June 15, 2012

In the rainy aftermath of last week’s Jubilee celebrations, a group of synthetic biologists gathered in Bristol for the 4th New Phytologist Workshop. Participants were treated to three days of stimulating talks on a wide range of topics all considered to be ‘Synthetic Biology.’ GARNet was there, and will be posting highlights, like the plant sentinel in the video below.

Video courtesy of the Medford Lab at Colorado State University.

So what is synthetic biology? The consensus definition of synthetic biology, or synbio, appears to be  ‘the design and construction of novel biologically based parts, devices and systems from first principles, or the re-design of existing natural systems for useful purposes.’

Synbio differs from traditional science by viewing biological systems as an engineer would view a machine – something to be created, not necessarily something that needs to be fully understood. The process consists of a cycle of hypothesis, computer aided design, production of molecule or system, analysis of results, repeat. Creating synthetic biology tools and resources (libraries of promotors, active sites, peptide sequences … the list is endless) of course involves a great deal of understanding of biological systems, but to an extent the unknown remains unknown, the most important thing is that you understand how the building blocks of your synthetic system work.


Bioscience and Innovation at the Plant Sci conference

Categories: funding, guest blogger, UKPSF
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Published on: June 14, 2012

Becky Nesbit was at the Plant Sci conference in April and reviews a talk encouraging academics to link with business.
Science and industry are unavoidably linked, so it is important for academics to have business knowledge and often beneficial to have a working relationship with commercial companies.

At the recent PlantSci conference, Dr Dan Godfrey from the BBSRC Bioscience and Innovation Unit was a speaker at the ‘Working with Business’ evening workshop.

His advice to the plant science community is to develop links with business. “Academic researchers can gain a huge amount from working with business, for example through sharing expertise and facilities and by establishing a dialogue on important research challenges. I would encourage all plant scientists to consider partnering with business. It can be a valuable source of funding and they may discover their research has commercial potential, which they hadn’t yet considered.”

The BBSRC operates a range of schemes designed to support academic partnerships with industry. (more…)

Welcome to the GARNet blog

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Published on: June 13, 2012

Welcome to the newest GARNet venture. If you don’t know much about GARNet, check out the About Us page.

This blog will have regular highlights of recent papers and events, as well as mentioning upcoming events and funding opportunities. We’ll try to keep you updated on new resources and methods, too.

Our first piece of news to share on the blog is that there is a new GARNet Officer – Charis Cook has taken over from Irene as Communications and Liasons Officer for GARNet.

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June 2012

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