Reduced models of circadian clocks: Dr Ozgur Akman

Dr Ozgur Akman is a Senior Lecturer in the Mathematics department at the University of Exeter, and will be visiting WISB as part of our seminar series on Wednesday 8th November.

Ozgur will speak about his research which could lead to the reverse-engineering of large-scale biochemical networks. If you would like to attend, please email wisb@warwick.ac.uk.

The full abstract for Ozgur’s talk is as follows:

The gene networks that comprise the circadian clock modulate biological function across a range of scales, from gene expression to performance and adaptive behaviour. In recent years, computational models of these networks based on differential equations have become useful tools for quantifying the complex regulatory relationships underlying the clock’s oscillatory dynamics. However, optimising the large parameter sets characteristic of these models places intense demands on both computational and experimental resources, limiting the scope of this approach. In this talk, a complementary approach based on combining Boolean logic with evolutionary optimisation will be introduced that dramatically reduces the parametrisation and computational load, making the state and parameter spaces more tractable. Through the construction of Boolean models fitted to both synthetic and experimental time courses, it will be shown that logic models can reproduce the complex responses to environmental inputs generated by more detailed differential equation formulations. In particular, it will be demonstrated that logic models have sufficient predictive power to identify optimal regulatory structures from experimental data. This suggests that the capacity of logic models to provide a computationally efficient representation of system behaviour could facilitate the reverse-engineering of large-scale biochemical networks.

More information on Ozgur’s research. 

Successful meet at WISB’s International Workshop

The WISB International Workshop ran from Tuesday 19th – Thursday 21st September 2017 and was hosted at the picturesque Palazzo Pesaro Papafava, the University of Warwick’s conference facility in Venice.

Over the course of the three days, delegates experienced many informative and insightful talks from both WISB members and invited speakers. There were many discussions had over the banquet meal on Wednesday evening!

Special thanks are to be extended to Dr Sarah Bennett who coordinated the entire workshop, and to those who travelled great distances to join us.

To see some highlights from the workshop, search Twitter for #WISBinVenice

Prof Barbara Ann Halkier: Pathway and transport engineering

Visiting WISB from the DynaMo Center in the Department for Plant and Environmental Sciences at the University of Copenhagen on Wednesday 1st November, Prof Barbara Ann Halkier will be speaking about pathway and transport engineering when using glucosinolates as case study.

If you are interested in attending Barbara’s talk, please email wisb@warwick.ac.uk.

Abstract of Barbara’s talk:

Cruciferous vegetables are unique in synthesizing the natural products glucosinolates. Substantial attention is given to particularly the glucosinolate glucoraphanin that is present in broccoli, as it is generally thought to be the major bioactive compound associated with the cancer-preventive effects of broccoli. The health-promoting effects have resulted in a strong desire to increase the intake of glucoraphanin. Establishment of a microbial production of glucoraphanin will provide a stable, rich source of this compound and enable intake of well-defined doses. Using transient expression in tobacco, we have shown the feasibility of engineering in a heterologous plant the seven genes pathway of indole glucosinolate, and the 12 genes pathway of the glucosinolate glucoraphanin. In yeast and E. coli, we have successfully engineered the benzyl glucosinolate pathways. However, engineering of the 12 genes glucoraphanin pathway poses challenges. Latest development in our goal towards microbial production of glucoraphanin will be discussed. Transport engineering is receiving increased attention as a novel means to control accumulation of specific metabolites. In Brassica crops, glucosinolates are anti-nutritional factors that reduce the nutritional value of the high-quality protein-rich seed meal that is a byproduct in the oil production. Recently, we showed that by mutating two glucosinolate transporters it was possible to eliminate glucosinolates from seeds of the model plant Arabidopsis. As an example of translational biology, we have successfully translated the gtr loss-of-function phenotype from the Arabidopsis model plant to Brassica crops, – a novel and potentially generic transport engineering approach for reducing seed glucosinolate content in other oilseed crops.

Nour-Eldin HH et al. (2017) Reduction of antinutritional glucosinolates in Brassica oilseeds by mutation of genes encoding transporters. Nature Biotechnology, 35, 377

Further information about Barbara’s research can be found here. 

Dr Ross Anderson at next seminar series

Visiting WISB from the University of Bristol, Dr Ross Anderson will be speaking on Wednesday 11th October at 1pm (MRI room) about the design of new proteins and enzymes and how this remains one of the great challenges in biochemistry.

Ross will explain how our fundamental understanding of both the nature of protein as a material and the principles of enzymatic catalysis is currently being tested and remoulded.

Dr Munehiro Asally will be hosting lunch with Ross beforehand for those interested in speaking with him.

Full details of Ross’s talk can be found in the Seminar Series.

WISB International Workshop taking place in Venice

The WISB International Workshop will take place next week from Tuesday 19th – Thursday 21st September 2017 in Palazzo Pesaro Papafava, the University of Warwick’s conference facility in Venice.

The workshop will see WISB members come together with external speakers to discuss advances in their research, the latest global advances in Synthetic Biology, and will also see plans being made for future exploitation of these technologies.  This workshop will focus on multiple themes in the burgeoning field of synthetic biology, including predictive design, biological circuitry, biosynthetic pathways and cell communities. There will be oral and poster presentations on a range of synthetic systems, featuring computational modelling as well as experimental research on microbial, mammalian and plant cells. The workshop will also include a session on ethical and societal aspects of synthetic biology.

Guest speakers will be travelling from as far afield as the USA and South Korea with Josh Leonard and John Coley (Northwestern University, USA), Virginia Cornish (Columbia University, USA), Ahmad Khalil (Boston University, USA) and Haseong Kim (Korea Research Institute of Bioscience and Biotechnology, South Korea) in attendance.

Speakers travelling from Europe include:

  • Kobi Benenson (ETH Zurich, Switzerland)
  • Victor de Lorenzo (Centro Nacional de Biotecnologia, Spain)
  • Irina Borodina (Technical University of Denmark)
  • Jordi Garcia Ojalvo (Universitat Pompeu Fabra, Spain)
  • Philip Shapira (University of Manchester, UK)
  • Stefaan Blancke (Ghent University, Belgium)
  • Anke Becker (Philipps-Universitat Marburg, Germany)

You can follow updates from the workshop on Twitter #WISBinVenice

Warwick’s iGEM students take on E.coli

Warwick’s 2017 iGEM team, Blueprint 361, is determined to make E.coli work in their favour. The team is made up of 5 engineering undergrads, 4 students from the School of Life Sciences and a chemist, and are supervised by Dr Alfonso Jaramillo. To meet the team, check out their video.

Their project is going to use E.coli to produce a biopolymer, which will then in turn be used as the bio-ink for their 3D printer. Over the course of the summer months, the team have been relentlessly working away in many labs around the campus to use this system for the creation of surface coatings with improved biocompatibility and osseointegration. If successful, the team could see revolutionary increase in both the strength and versatility of artificial joints and dental implants.

Excitingly, further development could even see this technology lead to the 3D printing of biological structures, such as trachea frameworks or even organ scaffolds.

The Blueprint 361 team will be taking their project to Boston in November 2017 to compete in the iGEM Jamboree against over 300 other teams from around the world. The team are urgently seeking additional funds in order to allow them to further develop their project. Can you help them? If so, please email igem@warwick.ac.uk.

iGEM is an international synthetic biology competition, which was established by MIT in 2003. Each iGEM team works over the summer to produce a new genetically engineered biological system, and competes in the following categories: the environment, manufacturing, diagnostics, therapeutics and food.

Keep up to date with the team here:

Facebook               @warwickIGEM

Twitter                    @warwickigem

Instagram              @igemwarwick

Review 2017

The 2017 WISB review workshop will take place on the 7th of June in the Oculus building at the University of Warwick.

The programme will primarily showcase the work of our PDRAs, Research Fellows and SynBio CDT PhD students. For those of you who are already familiar with WISB, these presentations will provide a valuable update on all of our science and technology development activities. For those of you who are relatively new to this community, these presentations will reveal the breadth of excellent work that is being done in the centre.

 

 

 

Great new employment opportunity!

Applications are now closed for this position. Keep an eye out for more opportunities in the future.

We are looking for a WISB Research & Outreach Manager

This post will suit a candidate with a background in research who wishes to develop a career in research programme management, learning and/or applying skills in financial oversight, grant proposal writing, research communication and outreach activities.

Apply now for a PhD starting in October 2017

Applications can be made to the SynBio CDT programme for the remaining two PhDs starting in October 2017. The 4-year studentships cover UK/EU Tuition Fees in full and pay an annual stipend. The next application deadline is 30th April 2017.

The SynBioCDT draws upon the breadth and depth of multidisciplinary expertise within the research environment at the Universities of Oxford, Bristol and Warwick to offer comprehensive training in the design and engineering of biologically based parts, devices and systems as well as the re-design of existing, natural biological systems across all scales from molecules to organisms.

Students from a wide range of backgrounds are encouraged to apply.

For more details see the SynBioCDT website.