| 14/1 |
End of the year 2007 report is given by Karin Klinga Levan, chairperson of the systems biology management group. |
| Speaker: Zelmina Lubovac |
| Title: Identifying Functionally and Topologically Cohesive Modules in Protein Interaction Networks |
Abstract: Systems biology offers a holistic perspective where individual proteins are viewed as elements in a network of protein-protein interactions, in which the proteins have contextual functions within functional modules. In order to facilitate the identification and analysis of such modules, we here propose novel approaches that combine knowledge, in terms of Gene Ontology annotation with network topology information. The majority of previous methods for identifying modules in protein interaction networks are based solely on analysing topological features of the networks. In contrast, we propose the use of integrated functionally informed clustering coefficients to identify biologically plausible network modules. The main part of the thesis is focused on the method named SWEMODE (Semantic WEights for MODule Elucidation), which uses a weighted clustering coefficient to identify network modules. We demonstrate that the proposed methods are able to identify the key functional modules in protein interaction networks. We also investigate the functional and topological features of the proteins that are involved in multiple modules, as well as their role in the interconnectivity between modules. |
| 28/1 |
| Speaker: Maria Svensson |
| Title (Swedish): Ärtrotröta - Molekylärbiologiska metoder kan undvika skördeförluster |
Abstract (Swedish): Ärtrotrötan är en allvarlig växtsjukdom som orsakas av att flera jordburna svampar angriper ärtplantornas rötter. Detta leder slutligen till att ärtplantorna gulnar, vissnar ihop och dör. De sjukdomsframkallande svamparna kan överleva åtskilliga år i marken och kan tillväxa nästa gång ärtplantorna odlas på fältet. För jordbrukaren är det väldigt viktigt att kunna undvika odling på infekterade fält så att de inte förlorar stora delar av sin skörd. I mitt projekt (som bland annat är ett samarbete med Analysen i Lidköping) så försöker jag utveckla molekylärbiologiska analysmetoder (real-tids PCR) för att detektera och kvantifiera de sjukdomsframkallande svamparna för att på så sätt kunna förutsäga den potentiella risken för sjukdomsangrepp. |
| 11/2 |
| Speaker: Jonas Gamalielsson |
| Title: Developing Semantic Pathway Comparison Algorithms for Systems Biology |
Abstract: Systems biology is an emerging multi-disciplinary field in which the behaviour of complex biological systems is studied by considering the interaction of all cellular and molecular constituents rather than using a "traditional" reductionist approach where constituents are studied individually. Systems are often studied over time with the ultimate goal of developing models which can be used to predict and understand complex biological processes, such as human diseases. To support systems biology, a large number of biological pathways are being derived for many different organisms, and these are stored in various databases.
There is a lack of and need for algorithms for analysis of the vast amount of biological pathways.
In this thesis we propose methods for semantic comparison of different kinds of biological pathways. We use Gene Ontology (GO), documented pathways or sets of gene products, GO annotation databases, various algorithms from computer science, and statistics. These methods are meant to be useful for biologists in order to assess the biological plausibility of derived pathways, compare different pathways for semantic similarities, and to derive putative pathways using a query set of gene products and documented pathways as input. |
| 25/2 |
| Speaker: Diana Karlsson |
| Title: Molecular Mechanisms for Evolution and Spread of Antibiotic Resistant Streptococcus pneumoniae |
Abstract: The bacterium Streptococcus pneumoniae (pneumococcus) is the leading cause of community-acquired infections and is responsible for diseases ranging from mild upper respiratory infections to life-threatening invasive diseases like septicemia and meningitis. Worldwide, this human pathogen is a major contributor to mortality causing millions of deaths each year, especially among children and the elderly. Traditionally, antibiotic therapy has been a successful treatment for pneumococcal diseases. However, in recent years has the therapeutic effect been compromised by the growing prevalence of resistant pneumococci. This leads to an increasing need for interventions that minimize the opportunities for the evolution and spread of resistance. The purpose of the studies within this project is therefore to investigate mechanisms contributing to antibiotic resistance in pneumococci. The research is carried out by an interdisciplinary approach where mathematical and computational modeling is combined with more traditionally molecular biological methods. |
| 10/3 |
| Speaker: Malin Setzer |
| Title: Integrating size-structure modeling with food web dynamics to study the decline of Arctic char (Salvelinus umbla) in Lake Vättern |
Abstract: As many other ecosystems worldwide, Lake Vättern has changed significantly during the last century and one example is the dramatic decline in the stock of large-bodied Arctic char (Salvelinus umbla). The cause for the decline and what to do about it is hotly debated. Most suggested causes are in some way linked to human activity, such as overexploitation, decreased nutrient loading, competition from introduced salmon, predation from introduced crayfish, decreasing frequency of winters with ice cover and increasing water temperature. To investigate this further one can use different approaches. The Swedish Fishery Board (Fiskeriverket) together with Sweden’s County Administrative Boards (Länsstyrelser) is conducting empirical investigations and experiments, such as fish stock surveys and crayfish predation experiments. This theoretical research project tries to develop a size structured food web model and analytical tools to analyze such a model. These different approaches could be linked together to render the work to understand the causes for the decline of Arctic char in Lake Vättern more effective. This is also the aim of this project, to link these approaches to gain a better understanding of ecosystem changes in Lake Vättern. |
| 31/3 |
| Speaker: Sofia Berg |
| Title: Sensitivity analysis of food webs |
Abstract: Mankind is affecting our planet in several ways. Fragmentation, habitat loss, diseases and introduction of foreign species are some of the ways. Today, species extinction rate is far over what conservative define to be "normal" and it is now of highest importance to understand more about how ecosystem responds to changes in their environment. One approach to understand ecological communities and how they respond to a change in their environment is to apply sensitivity analysis on community level. Such an analysis would illustrate how the stability of an ecosystem is affected when there is a change in some important variables of some species. Two concepts that are important in community stability and sensitivity analysis are resilience (the potential to return to equilibrium state after a temporary perturbation) and resistance (the reciprocal to the degree of change in species equilibrium abundances after a temporary perturbation). Sensitivity analyses of the Baltic Sea and Lake Vättern show that there is a significant decrease in the dynamical resistance (resilience) and structural resistance (resistance) with increasing trophic height of the affected species for both Lake Vättern and the Baltic Sea. Thus, a change in the mortality rate of predators results in the largest effect on resilience and resistance in the communities. |
| 28/4 |
| Speaker: Peter Sögård |
Abstract (Swedish): Att studera skeenden i omvärlden innebär att vi oftast måste skapa ett förenklat system som, förhoppningsvis, ger oss en insikt i hur vårt studieobjekt fungerar. Viktigt är att vi har en förståelse för vad vi tar bort, och om de egenskaperna påverkar vårt förenklade system. Inom diabetesforskningen används djurmodeller där specifika vävnader inkuberas i en lämplig lösning. Det förfarandet är vida använt även inom andra discipliner. Vi har utvecklat en matematisk modell med syfte att analysera data från inkubering av muskler från möss. Vidare så försöker vi att med hjälp av modellen förstå om de antaganden som görs, både implicit och explicit experimentellt påverkar tolkningen av data. Våra resultat visar att några av datapunkterna ej är relevanta att mäta då en kompensatorisk mekanism går in och påverkar dem, vilket leder till att felaktiga slutsatser har dragits. Turligt nog så kan de omätbara komponenterna beräknas med modellen. Experimentell validering av våra slutsatser är gjorda. |
| 12/5 |
| Speaker: Lina Nolin |
| Title: Information Fusion in Precision Agriculture – decision support for variable-rate nitrogen application, based on sensor data, databases and model simulations |
Abstract: In recent decades the term precision agriculture (PA) has emerged in the agricultural discipline. The basic idea of PA is to adjust treatments in the field according to within-field spatial variability, aiming at site-specific rather than average agricultural management to satisfy both economic and environmental interests. The objective of this project is to combine field background data, i.e. historical data about previous yield, soil type, soil water content, soil nutrients etc., with sensor estimation of the current nitrogen (N) status in crop, to result in a real-time variable N fertiliser application system that adds fertiliser according to within-field differences in the soil and in crop demand. In order to facilitate the background data handling, a soil-and-crop model is thought to operate in conjunction with the crop sensor. In the present study, a handful of soil-and-crop models (COUP, SUNDIAL, SIRIUS and DAISY) are being evaluated according to criteria that examine the potential suitability of these models to be applied in PA for real-time fertilizing. The seminar will give a short introduction to PA and information fusion and thereafter focus on the current status of the project, preliminary results and coming work. |
| 9/6 |
| Speaker: Simon Wetterlind |
| Title: Biological models and the Kalman filter |
Abstract: The talk will consist of:
1) An introduction to state-space models and to how they relate to ordinary difference/differential equation systems
2) A brief introduction to the Kalman filter
3) An example of the implementation of a biological model that is fitted to data using the Extended Kalman filter. |