http://onlinelibrary.wiley.com/doi/10.1002/bies.201400187/abstract

Óttar Rolfsson and Bernhard O. Palsson, Decoding the jargon of bottom-up metabolic systems biology, BioEssays, Article first published online: 11 MAR 2015, DOI: 10.1002/bies.201400187 

Bottom-up metabolic systems biology is of particular relevance to biochemists. The jargon of bottom-up metabolic systems biology however represents a major obstacle that needs to be overcome. Herein, we diminish this early hurdle by providing a lexicon of the most important terms.

http://pubs.rsc.org/en/Content/ArticleLanding/2014/MB/C4MB00335G#!divAbstract

 

Steinn Gudmundsson and   Juan Nogales, Cyanobacteria as photosynthetic biocatalysts: a systems biology perspective, Mol. BioSyst., 2015, Advance Article DOI: 10.1039/C4MB00335G
 
In this review we describe recent successes in biofuel and fine-chemical production using cyanobacteria. 
http://onlinelibrary.wiley.com/doi/10.1111/trf.12834/abstract
Giuseppe Paglia et al. Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat–derived platelet concentrates, Transfusion August 2014
 
This study demonstrated two discrete metabolic phenotypes in stored PLTs prepared with both apheresis and buffy coat methods. PLT activation occurs during the first metabolic phenotype and might lead to a low reproducibility of the apheresis PCs.
 
http://link.springer.com/article/10.1007/s11306-014-0721-3#page-1
Maike K. Aurich, et al. Prediction of intracellular metabolic states from extracellular metabolomic data, Metabolomics, August 2014
 
Our workflow is well-suited to the characterization of cellular metabolic traits based on extracellular metabolomic data, and it allows the integration of multiple omics data sets into a cohesive picture based on a defined model context.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098760

Rohatgi N,  Nielsen TN, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson BO, Rolfsson O, Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis, PLOS ONE,  June 2014 9 (6)

 Here we report the recombinant expression, purification and biochemical characterization of isoform I of human gluconokinase ...

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html

Thiele, I., Swainston, N., Fleming, R.M.T., et al. ''A community-driven global reconstruction of human metabolism'', Nat Biotech, doi:10.1038/nbt.2488 (2013).

Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling.

http://www.landesbioscience.com/journals/gutmicrobes/article/22370/?show_full_text=true

Heinken, A., Sahoo, S., Fleming, R. M. T., Thiele, I., "Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).

In this study, we assembled and validated a genome-scale metabolic reconstruction of Bacteroides thetaiotaomicron (iAH991)...

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http://onlinelibrary.wiley.com/doi/10.1002/bies.201400187/abstract

Óttar Rolfsson and Bernhard O. Palsson, Decoding the jargon of bottom-up metabolic systems biology, BioEssays, Article first published online: 11 MAR 2015, DOI: 10.1002/bies.201400187 

Bottom-up metabolic systems biology is of particular relevance to biochemists. The jargon of bottom-up metabolic systems biology however represents a major obstacle that needs to be overcome. Herein, we diminish this early hurdle by providing a lexicon of the most important terms.

http://pubs.rsc.org/en/Content/ArticleLanding/2014/MB/C4MB00335G#!divAbstract

 

Steinn Gudmundsson and   Juan Nogales, Cyanobacteria as photosynthetic biocatalysts: a systems biology perspective, Mol. BioSyst., 2015, Advance Article DOI: 10.1039/C4MB00335G
 
In this review we describe recent successes in biofuel and fine-chemical production using cyanobacteria. 
http://onlinelibrary.wiley.com/doi/10.1111/trf.12834/abstract
Giuseppe Paglia et al. Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat–derived platelet concentrates, Transfusion August 2014
 
This study demonstrated two discrete metabolic phenotypes in stored PLTs prepared with both apheresis and buffy coat methods. PLT activation occurs during the first metabolic phenotype and might lead to a low reproducibility of the apheresis PCs.
 
http://link.springer.com/article/10.1007/s11306-014-0721-3#page-1
Maike K. Aurich, et al. Prediction of intracellular metabolic states from extracellular metabolomic data, Metabolomics, August 2014
 
Our workflow is well-suited to the characterization of cellular metabolic traits based on extracellular metabolomic data, and it allows the integration of multiple omics data sets into a cohesive picture based on a defined model context.
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0098760

Rohatgi N,  Nielsen TN, Bjørn SP, Axelsson I, Paglia G, Voldborg BG, Palsson BO, Rolfsson O, Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis, PLOS ONE,  June 2014 9 (6)

 Here we report the recombinant expression, purification and biochemical characterization of isoform I of human gluconokinase ...

http://www.nature.com/nbt/journal/vaop/ncurrent/full/nbt.2488.html

Thiele, I., Swainston, N., Fleming, R.M.T., et al. ''A community-driven global reconstruction of human metabolism'', Nat Biotech, doi:10.1038/nbt.2488 (2013).

Here we describe Recon 2, a community-driven, consensus 'metabolic reconstruction', which is the most comprehensive representation of human metabolism that is applicable to computational modeling.

http://www.landesbioscience.com/journals/gutmicrobes/article/22370/?show_full_text=true

Heinken, A., Sahoo, S., Fleming, R. M. T., Thiele, I., "Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut", Gut Microbes, 4(1):1-13 (2013).

In this study, we assembled and validated a genome-scale metabolic reconstruction of Bacteroides thetaiotaomicron (iAH991)...

Photosynthetic Micro-Algae

The convergence of light-emitting diode technology, photobioreactor design, algal biotechnology and low energy processing costs make biological fixation of this CO2 into fine chemicals feasible. The Center for Systems Biology is working on projects that are aimed at:

  1. determining the key performance characteristics of a core unit of a photobioreactor-based factory,
  2. designing and initiating scale-up of these units into versatile modules,
  3. determining the spectrum of algal strains that can be cultivated with this system.

 

Human Metabolism

Metabolism is a foundational process in all living cells. In fact, the ability to metabolize is considered as one of the criteria for being considered a living organism. Metabolism is directly or indirectly involved in essentially all cellular functions and is implicated in all major human disease states. With the state of the annotation of the human genome, it has been possible to perform an initial reconstruction of the genome-scale metabolic network in Homo sapiens. This genome-scale reconstruction opens unprecedented opportunities for basic research in human physiology and disease. The Center for Systems Biology is focused on these newly emerging opportunities and deploys the rapidly developing discipline of systems biology.

Center for Systems Biology

CSBui

The Center for Systems Biology focuses on human metabolism. In addition, the Center will establish an industrial biotechnology focused program. The systems biology of thermophilic bacteria found in Iceland will be studied. Application of such knowledge will be deployed to develop processes that will lead to the fixation of CO2, H2 and H2S that comes from geothermal well in Iceland. When developed, such processing technology could be used on a worldwide basis as geothermal energy is likely to be a part of the world’s future energy solution.

Funding

The ERC's mission is to encourage the highest quality research in Europe through competitive funding and to support investigator-initiated frontier research across all fields of research.  

Rannis administers the main public competitive funds in the field of research and innovation in Iceland

 

http://ec.europa.eu/research/mariecurieactions/The Marie Curie Actions have long been one of the most popular and appreciated features of the Community Framework Programmes for R&D.

The objectives of the Georg Consortium is to create a platform for entrepreneurship and export of geothermal energy resources and education.

Systems Biology

Molecular systems biology represents an interdisciplinary field. To operate in this field a practitioner needs to know the basic life science disciplines (biochemistry, genetics, cell biology, physiology, etc), the genomic and high- throughput sciences, bioinformatics (statistics, algorithms and large-scale data analysis), and engineering sciences (numerics, modeling and simulation). Thus a molecular systems biology program will need participation from the natural sciences, engineering and medicine.

The Center for Systems Biology at the University of Iceland is indeed such an interdisciplinary effort. The University of Iceland will be significantly impacted by the establishment and growth of the Center and it will nucleate new research and education.

Resources

RECON X - Reconstruction of The Human Genome

 

 

The openCOBRA Project The COnstraints Based Reconstruction and Analysis (COBRA) 

 

Courses

 

 

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