Lorentz Center - Microbes in ecosystems: weaving intracellular processes into ecological networks from 12 Oct 2009 through 15 Oct 2009
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    Microbes in ecosystems: weaving intracellular processes into ecological networks
    from 12 Oct 2009 through 15 Oct 2009

 
The day to day programme will be as follows:

The day-to-day program will be as follows:

 

Monday October 12, 2009

General introduction to the workshop and introduction to topics 1 and 2.

Each lecture will be 30-35 minutes with 10-15 minutes for specific questions.

 

09.15 – 10.15         Arrival of participants, coffee/tea

10.15 – 10.30         Welcome by Lorentz center and organizers, Outline of the workshop

 

Lectures on topic 1 “Quantitative understanding of community functioning from molecular data”

 

10.30 – 11.15         Raes: From metagenomics to microbial community function

11.15 – 12.00         Kowalchuk: Meta-transcriptomics, Meta-proteomics and meta metabolomics

12.00 – 13.30         Lunch break

13.30 – 14.15         Teusink: From metabolic networks to cellular functioning

 

Lectures on topic 2 “Analysis of fluxes through ecosystems”

 

14.15 – 15.00         de Ruiter: Fluxes through ecological networks

15.00 – 15.30         Coffee break

15.30 – 16.15         Lueders: Tracking the fate of (labeled) substrates through microbial

                                 networks

16.15 – 17.00         Kleerebezem: Fluxomics

17.00 – 17.30         Plenary discussion

17.30 – 19.30         Wine & cheese party

 

 

Tuesday October 13, 2009

Introduction to subjects 3 and 4. Each lecture will be 30-35 minutes with 10-15 minutes for specific questions. Assignment of participants to discussion groups.

 

Lectures on topic 3 “Community assembly and structure”

 

09.00 – 09.45         VandenKoornhuyse: Community assembly and structure

09.45 – 10.30         Curtis: Estimating microbial diversity

10.30 – 11.00         Coffee break

11.00 – 11.45         Fierer: From community structure data to functioning

11.45 – 12.15         Plenary discussion

12.15 – 13.45         Lunch break

 

Lectures on topic 4 “Microbial controls on ecosystem processes”

 

13.45 – 14.30         Röling: Control and regulation of fluxes at the ecosystem level

14.30 – 15.15         Bruggeman: Flux balance analysis at the community level

15.15 – 15.45         Coffee break

15.45 – 16.30         De Graaf: Flux analysis in complex microbial ecosystems

16.30 – 17.30         General plenary discussion on the topics for the four workgroups and

                                 assignment to workgroups

18.00                       Departure (walking, cycling or by public transport) to Restaurant

                                 Scheltema (Marktsteeg 1) in Leiden.

18.30 – 21.00         Dinner in Restaurant Scheltema.

 

 

Wednesday October 14, 2009

Each working group will work on one particular topic

 

09.00 – 10.30         Working groups

10.30 – 11.00         Coffee break

11.00 – 12.30         Working groups

12.30 – 14.00         Lunch break

14.00 – 15.30         Plenary presentation (15 minutes per topic) and discussion of current

                                 workgroup (15 minutes per topic)

15.30 – 16.00         Coffee break

16.00 – 17.30         Preparation of final presentations per topic, within work group

18.00                       Departure (walking, cycling or by public transport) to Restaurant

                                 De Branderij / de Gaanderij in Leiden.

18.30 – 21.00         Dinner in Restaurant De Branderij / de Gaanderij

 

 

Thursday October 15, 2009

Integration of workgroup visions

Wrap up and conclusions:

09.00 – 10.00         Preparation of final presentations per topic, within work group.

10.00 – 10.30         presentation on topics 1

10.30 – 11.00         Coffee break

11.00 – 12.30         Presentation on topics 2, 3 and 4 (about half an hour each)

12.30 – 14.00         Lunch break

14.00 – 14.30         Final conclusions, identifying the links and preparing an outline/central

                                 scheme for the perspective paper

14.30 – 15.30         Closing lecture by Ian Head

 

The workshop will be centered about four major, interrelated, topics:

 

1. Quantitative understanding of community functioning from molecular data. Large scale sequencing (metagenomics) is rapidly providing information on the microbial gene content of many environments. Meta-transcriptomics, meta-proteomics and meta-metabolomics reveal which genes are active. However, these experimental approaches lose the connectivity between genes, mRNAs and proteins (~ the parts) on the one hand and species in which they resided on the other hand. Does deriving the understanding on ecosystem functioning from the part lists require the ability to determine the connectivity between the parts and the involved species? How to determine this connectivity in a quantitative way? May approaches to determine and model part-to-part interactions at the cellular level be extended to microbial ecology?

 

2. Analysis of fluxes through ecosystems. An important component of ecosystem functioning is the flux of material through an ecosystem and its resistance and resilience to perturbations. Detailed analysis of fluxes through cellular networks of individual species is well possible using fluxomics. Also in ecology, various modeling approaches are available to determine the flux of matter through tropic levels. In ecological models, bacteria are often lumped into a few compartments at most. Nowadays it is possible to track the fate of labeled substrates in microbial communities and through this identify ecological networks to substrate usage. How to integrate these approaches on ecosystems fluxes such that quantitative determination of fluxes through functional groups or even individual microbial species may be obtained?

 

3. Community assembly and structure. Ecologists put large effort in determining the species abundance and distribution and on the relative importance of species interactions versus selection by the environment. For microorganisms this task is still tremendous and relies on the application of cultivation-independent molecular techniques, targeting informative marker genes. Ideally, we would like to understand what determines the assembly of microbial community structure. We will explore which theoretical and modeling approaches are around in ecology and systems biology to understand the composition of communities.

 

4. Microbial controls on ecosystem processes. Understanding which species, and which of their intracellular metabolic activities, are relatively important with respect to fluxes through ecosystems and in determining the concentrations of metabolites will allow for rationale engineering of ecosystems such that they provide better services (e.g. enhanced bioremediation, energy production) and for selecting species for environmental conservation. Tools in systemsbiology/molecular biology such as metabolic control analysis and hierarchical regulation analysis have allowed for insight into which enzymes are important and how changes in fluxes are regulated at the metabolic and hierarchical level. First steps to extend these tools to ecological applications have been made. We will explore how these tools can be applied practically. May we specifically modulate and measure the abundance and activity of particular species at the field scale. How to deal with growth of microorganisms? How to explore which processes within relatively important microorganisms contribute to this importance?

 



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