Genomes to Systems 2008 – day 3
Today’s seminars began with a plenary lecture from James Ferrell of Stanford University on systems-level properties of the mitotic oscillator. The morning continued with systems biology in time: dynamic cellular processes, chemical genomics: small molecules with large effects, and pharmacogenomics. I chose to attend the systems biology in time lectures.
The lectures began with Mike White of Liverpool University on temporal and spatial information encoding by the NF-kB system and continued with Olivier Pourquié (Kansas City) on periodic patterns in embryonic development: the vertibrate segmentation clock. Following this lecture we had Andrew Millar of Edinburgh on unwinding the biological clock, and finally Béla Novák of Oxford on the systems biology of the cell cycle. Béla Novák’s lecture was of particular interest and delivered with great enthusiasm. It was clear that we must dispense with reductionist approaches if we are to understand the true essence of biological systems. It is the understanding of the interplay between the various components that defines the behaviour of the system, and not the individual key components. The reductionist approach to the components is still crucial to understanding the working of the component parts, but cannot be used to describe the emergent properties of cellular processes when working as part of their overall function in the cells life cycle.
The afternoon continued with seminars on systems biology from microbe to planet: understanding lots of data through comprehensive models, advanced concepts and techniques in array informatics, and clinical genomics of cancer.
I chose to attend the systems biology modelling lectures and we had Masaru Tomita (Keio) on multi-omics analysis and integrative systems biology, Steve Oliver (Cambridge) on yeast systems biology, and Matthias Reuss from Stuttgart on unravelling regulatory networks in hepatocytes on the basis of time-series data.
The afternoon finished with David Richardson of Norwich who presented an interesting talk on the global nitrogen cycle, detailing the effect of nitrogen fixing bacteria on the environment and how it fits into the current issues around the environment, particularly its under-reported importance next to the levels of carbon in the environment.
The conference was concluded by an excellent lecture from Hans Westerhoff of Manchester/Amsterdam entitled “from genomes to systems… dealing with the networks”. Professor Westerhoff presented some interesting theories on the future of systems biology, together with some new mathematics on fragility that went with his theories on control coefficients and robustness.
I found the conference very interesting, and it was a great opportunity to be immersed in the community of systems biology. It was inspiring to see so many people working in the field without the usual question of “what the heck is systems biology?”… although I don’t think anybody had a clear definition of what the heck it is anyway!
Genomes to Systems Conference 17th – 19th March 2008
March 18, 2008 by Steve · 2 Comments
This week I have been attending the Genomes to Systems Conference at the Manchester GMEX centre. The week has provided an outstanding series of lecturers from eminent scientists in the field of systems biology.
Monday began with an opening by Professor Hans Westerhoff, (pictured below) and followed with Nobel prize winner Robert Huber with Proteases and their regulation, from structures to mechanisms and application.
The opening day progressed with lectures on disease proteomics, metabolic markers of disease, and deep mining of genomes and was finished up with an outstanding lecture from John Mattick from Brisbane entitled “The eukaryotic genome as an RNA machine”.
The second day began with an opening lecture by Luis Serrano from Barcelona entitled “Evolvability and hierarchy in rewired bacterial gen networks”. The morning was then lectures on systems biology computational environments, single molecule imaging for analysis of biological processes, and “from structure to biology”. I personally attended the systems biology computational environments lectures after attending a number of proteomics lectures yesterday. I find the computational biology sections of systems biology most interesting after our first few months of taught courses. I attended some excellent lectures from Mike Hucka (Caltech) on SBML: present status and ongoing efforts for extensions, Nicolas Le Novére (EBI) on principled annotation or quantitative methods in systems biology, Ursula Kummer (Heidelberg) on COPASI, and finally an excellent lecture from Hiroaki Kitano (SBI, Tokyo) on SBGN: the systems biology graphical notation. We finished the morning with a technology showcase from Thermo Fisher Scientific and Roche diagnostics, who demonstrated the Genome Sequencer FLX system. Lunch included an EBI workshop on Ensembl and ArrayExpress.
For the afternoon, we had talks on emerging strategies for global proteomics, metagenomics approaches to biodeiversity and systems ecology, and facts from the flood: text mining for biomedicine. I attended the proteomics seminars as I have been finding this field interesting of late, and I feel it is of increasing importance in the post human genome project world as we can now link our genome data with the next level of expression – the proteins. I think that disease biomarkers will be crucially important in future disease diagnosis, and in delivering an application for the vast array of data from genome sequencing studies. Scientists have discovered the code, and now we need to understand the program. Anne Dell ( ICL) presented on high throughput glycomics and glycoproteomics, followed by Rob Beynon (Liverpool) on quantitative proteomics, and Simon Hubard (Manchester) on improved informatics for proteomics.
I particularly enjoyed the talks from Anne Dell discussing glycomics, as I had not heard about this field before, and it could be very useful in discovering and assaying biomarkers for cancer. I will be reading some more information on this subject in the future. The talk from Rob Beynon and Simon Hubard were also fascinating new incites in quantitative technique for the previously qualitative field of proteomics.
The day concluded with a plenary lecture from Ron Breaker (Yale) on gene control by metabolite-sensing riboswitches, and later an informal talk was given by Larry DeLucas on Space travel & genomics in space” !!
I am looking forward to tomorrow seminars on dynamic cellular processes, chemical genomics, and pharmacogenomics.
Rotation project 1
March 3, 2008 by Steve · Leave a Comment
Over the past 2 weeks our class has been undertaking training in the genetic engineering of yeast and E. coli cells with flourescent protein, which we have subsequently expressed and purified using chromatography, gel electrophoresis, and blotting techniques. We successfully cloned and purified green and red fluorescent proteins.
Next week we begin the first of our 12 week rotation projects. My project will involve the purification, kinetic assaying, and parameter fitting of a subgroup of enzymes that are involved in a so-far uncharted part of the yeast metabolic pathway. We will present a poster of our project to our colleagues in the systems biology program at Warwick University.