SEB at Marseille 2008 - Tools for Systems Biology
8th July 2008
This workshop will showcase tools, technologies and methods for generating systems data and analysing complex interacting datasets and is embedded within the main systems biology session running 7-9th July [click here for info on main systems biology session]. Speakers have been recruited from a number of leading systems biology centres and associated manufacturers of software and equipment will be providing hands-on demonstrations. The workshop is aimed at helping researchers understand the range of cutting-edge techniques that are available for answering biological questions on a whole genome scale. The presentations will span a wide range of fields in which systems analysis is providing a deeper understanding of the problems and answers involved.
Programme - Tuesday 8th July
CSSW. Systems Biology Workshop: Tools for Systems Biology
Session organised by Dr Carol Wagstaff (Reading University) and Chris Trimmer (SEB)
Sponsored by BBSRC, European Science Foundation (ESF), Genetix, Corbett, Mathworks, BioRad, Centre for Plant Integrative Biology and Ingenuity Systems
Tools for Systems Biology is a workshop embedded within the main Systems Biology session and will showcase technologies and methods for generating systems data and methods for modelling complex interacting datasets.
Speakers have been recruited from leading Systems Biology centres and associated manufacturers of software and equipment will be providing hands-on demonstrations. The workshop is aimed at helping researchers understand the range of cutting-edge techniques that are available for answering questions on a whole genome scale. The presentations span a wide range of fields in which systems analysis is providing a deeper understanding of the underlying biology.
Each talk will be presented twice and the presentation times can be found next to each speaker. The first three presentations will run simultaneously at 2pm and 2.40pm. This will be followed by a break for refreshment at 3.20pm before three more simultaneous presentations starting at 3.40pm and 4.20pm. All talks take place on Level 1 of Les Palais de Congres, Parc Chanot.
Quick Reference Timetable
| Time | Speaker | Title of Presentation | Location |
| 2.00pm | Dr Alistair Middleton | Mathematical Modelling of the Aux/IAA Response to Auxin | Internet Café |
| 2.00pm | Dr Irene Bramke | High throughput post-genomic technologies | Endoume 1 |
| 2.00pm | Dr Carlos Marcelino Rodriguez Lopez and Dr Adam Croxford | High-Resolution Melt analysis for SNP discovery, Linkage Mapping and Analysis of DNA Methylation | Endoume 2 |
| 2.40pm | Dr Alistair Middleton | Mathematical Modelling of the Aux/IAA Response to Auxin | Internet Café |
| 2.40pm | Dr Irene Bramke | High throughput post-genomic technologies | Endoume 1 |
| 2.40pm | Dr Carlos Marcelino Rodriguez Lopez and Dr Adam Croxford | High-Resolution Melt analysis for SNP discovery, Linkage Mapping and Analysis of DNA Methylation | Endoume 2 |
| 3.20pm | Refreshment Break | ||
| 3.40pm | Dr Catalina Guerra | Ingenuity Pathways Analysis: software for discovering and modelling pathways and networks in your systems data | Internet Café |
| 3.40pm | Dr Max Bylesjo | Predictive modelling and integration of functional genomics data for applications in plant biology | Endoume 1 |
| 3.40pm | Dr Delphine Vincent | Hunting fungal secreted proteins down | Endoume 2 |
| 4.20pm | Dr Catalina Guerra | Ingenuity Pathways Analysis: software for discovering and modelling pathways and networks in your systems data | Internet Café |
| 4.20pm | Dr Max Bylesjo | Predictive modelling and integration of functional genomics data for applications in plant biology | Endoume 1 |
| 4.20pm | Dr Delphine Vincent | Hunting fungal secreted proteins down | Endoume 2 |
CSSW.1 Mathematical modelling of the Aux/IAA response to Auxin
Dr Alistair Middleton (Centre for Plant Integrative Biology, University of Nottingham)
2pm and 2.40pm in Internet Café on Level 1
This talk will utilise the 20-station ‘Internet Café’ allowing participants to manipulate example datasets provided by the speakers. This is designed to give delegates an interactive opportunity to fully understand the methodology being presented.
The hormone Auxin is implicated in regulating a diverse range of processes in developing Arabidopsis roots, including cell division, elongation and differentiation. Auxin functions in part by mediating the activation of the so-called Aux/IAA family of genes, comprising 29 members. We have developed a model of a single Aux/IAA gene's response to an Auxin stimulus. The model encompasses the time evolution of the following molecule concentrations: Aux/IAA protein and mRNA, ARF protein and components of the Aux/IAA ubiquitination pathway, including the interaction between SCF-TIR1 and Auxin. In this workshop we demonstrate how the model was developed using the available data and discuss the model predictions and how these can be tested in the lab.
CSSW.2 High throughput post-genomic technologies
Dr Irene Bramke (Genetix Ltd)
2pm and 2.40pm in Endoume 1 on Level 1
The post-genomic era has yielded an explosion of techniques and technologies for large-scale, high-throughput data generation. The challenge is to identify technologies that are best suited to address a particular question thus avoiding data collection for its own sake.
This presentation will focus on tools used in the investigation of protein interactions and biomarker identity. Examples include the use of CellReporter, a novel live cell imaging and analysis system for quantitative biomarker analysis, the development and characterisation of antibodies for mammalian systems using ClonePixFL technology and the generation of protein microarrays.
CSSW.3 High-Resolution Melt analysis for SNP discovery, Linkage Mapping and Analysis of DNA Methylation
Dr Carlos Marcelino Rodriguez Lopez (University of Wales, Aberystwyth), Adam E. Croxford and Michael J. Wilkinson (University of Aberystwyth)
2pm and 2.40pm in Endoume 2 on Level 1
High Resolution Melt analysis (HRM) is a closed-tube method of genotyping that does not require use of fluorescent probes, fragment fractionation or amplicon sequence information. Recent advancements in florescent-detection instruments (such as the Corbett Rotor-Gene 6000) and the use of fully saturating intercalating dyes have made HRM analysis considerably more sensitive. The flexibility of the system allows it to be adapted for a wide range of uses including SNP genotyping, mutation detection, screening for loss of heterozygosity, DNA fingerprinting, characterization of haplotype blocks, species classification, somatically acquired mutations studies, linkage and physical mapping, and DNA methylation analysis. Here, we describe the first use of high-resolution melt analysis to generate STS markers based on Single Nucleotide Polymorphisms (SNPs) and microsatellite length polymorphisms for use in linkage mapping, using white lupin (Lupinus albus, x = 25) as a case study. The described strategy is rapid and low-cost, and circumvents the need for labeled primers or amplicon fractionation. We also illustrate the use of HRM analysis for the detection and/or quantification of the presence of, and relative abundance of, methylated nucleic acid bases within the double-stranded molecule without any prior chemical modification of the target DNA.
3.20pm Refreshment Break
CSSW.4 Predictive modelling and integration of functional genomics data for applications in plant biology
Dr Max Bylesjo (Umeå University)
3.40pm and 4.20pm in Endoume 1 on Level 1
Tree biotechnology will soon reach a mature state where it will influence the overall supply of fiber and wood products. Through technological advancements, it may be possible to introduce trees that are optimized for faster growth or more efficient wood formation to grow more wood in managed plantation forests. To study and ultimately understand the underlying regulatory mechanisms of e.g. wood formation in trees, parallel profiling of molecular events are frequently utilized in functional genomics contexts. In practice, this implies that massive amounts of data are being generated from biological samples, e.g. the simultaneous measurement of tens of thousands of transcripts, proteins and metabolites at a current state or over time. This is not only creating logistical problems but also makes data integration and data mining one of the main challenges in post-genomics functional genomics studies. This presentation covers the integration of omics data sets using a predictive modeling approach. Based on the bi-directional, multivariate O2PLS method, it is possible to separate sources of variation that are overlapping across multiple analytical platforms as well as systematic sources of variation that are unique to each platform. This property can be highly beneficial for the biological interpretation of the results. Characteristics of the method as well as a conceptual comparison to related methods will be discussed. The main focus will be on the utility of the approach for studying simultaneous regulatory events in plant biology, exemplified by a study to reveal potential targets for optimization of the lignin biosynthesis.
CSSW.5 Hunting fungal secreted proteins down
Dr Delphine Vincent, Christophe Plomion (UMR1202 INRA BIOGECO), Marie-Hélène Balesdent, Françoise Blaise, Thierry Rouxel (UR256 INRA PMDV-Bioger), Julien Gibon, Francis Martin (UMR1136 INRA-UHP Interactions Arbres/Micro-Organismes), Stéphane Claverol, Marc Bonneu (Plate-forme Protéomique, Université Bordeaux 2), Marc-Henri Lebrun (UMR 2847 CNRS Bayercropscience)
3.40pm and 4.20pm in Endoume 2 on Level 1
Fungus-plant interaction is widely spread in most environments. The majority of tree species develop symbiotic relationships with fungi to enhance nutrient absorption. Many crop diseases originate from fungus attacks, which cause massive yield losses. Little is known about the molecular associations between fungi and the plant species they interact with, whether pathogenically or symbiotically. It is postulated that secreted proteins would play a key role in the interaction between an organism and its host. Secretomics, the study of all the gene products secreted from the cell, possibly into the environment, is an emerging field, involving a variety of techniques. In this study, we present the first secretomes of the rapeseed pathogen Leptosphaeria maculans and the tree symbiont Laccaria bicolor, using gel-based approaches combined to MS analyses. Initial tests were performed on fungi in vitro grown in specific liquid growth media, with or without plant extracts. Several protein extraction methods were tested in combination to various protein separation techniques. Improved 2-D gel resolution was achieved through an initial separation step of the secreted proteins contained in growth medium using liquid IEF (Rotofor Cell, Bio-Rad) followed by classic IPG-IEF/SDS-PAGE. Because of the variation in the secretion rate of each species, 1-D and 2-D patterns differed greatly from one fungus to another, highlighting changes due to growth media as well. MS results on both fungi, whose genome sequencing projects were recently completed, showed that most of the secreted proteins bore unknown functions while the cell localization of known proteins was ill-predicted.
CSSW. 6 Ingenuity Pathways Analysis: software for discovering and modelling pathways and networks in your systems data
Dr Catalina Guerra
3.40pm and 4.20pm in the Internet Café on Level 1
IPA is an all-in-one software application that enables researchers to model, analyze, and understand the complex biological and chemical systems at the core of life science research. IPA has been broadly adopted by the life sciences research community and cited in hundreds of peer-reviewed journal articles.
