Mycosmo

Links to selected world microbial webpages 

Mycology - links to: 

Index fungorum: http://www.indexfungorum.org (/names/names.asp)

Mycobank: http://www.mycobank.org/

Black yeast working group: http://www.blackyeast.org/

Microbiological garden: http://www.pmbio.icbm.de/mikrobiologischer-garten/ 

Bacteriology (bacteria and archaea) – links to: 

Todar´s Online Textbook of Bacteriology: http://www.textbookofbacteriology.net/

List of bacterial names with their standing in the nomenclature:

http://www.bacterio.net/

The Taxonomic Outline of Bacteria and Archaea:

http://www.taxonomicoutline.org/index.php/toba

Arcahea:

http://www.ucmp.berkeley.edu/archaea/archaea.html

Collaborations of Mycosmo with other centres of excellence 

Centre of Excellence for Environmental Technologies

The applied value of the extremophilic microorganism research within the IC Mycosmo has been demonstrated with the involvement with the Centre of Excellence for Environmental Technologies (Center Odličnosti Okoljske Tehnologije; COOT; http://sl.coot.si/). Within this framework, the IC Mycosmo was involved in the solving of the problem of salinisation of water in the waste water plant in Koper (Slovenia), which was due to either tidal fluctuations or the salting of roads in winter.

Centre of Excellence fo Integrated Approaches in Chemistry and Biology of Proteins

The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (Center Odličnosti za Integrirane Pristope v Kemiji in Biologiji Proteinov; CIPKeBip; http://www.cipkebip.org/) has brought together the most important Slovenian experts and laboratories in the field of protein science, with emphasis on the biomedical and natural sciences, and collabration with medium and large companies. The CIPKeBip is coordinated by the Department of Biochemistry, Molecular and Structural Biology of the Institute Jozef Stefan, and it has three main areas of activity: 

1. Mechanisms and pathways in immune responses.

2. Intracellular and intercellular communication;

3. Adaptation mechanisms of extremophiles to extreme parameters in the environment;

Link to further information for the CIPKeBiP. 

The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP)

Jamova cesta 39 (based at the Jozef Stefan Institute, Ljubljana, Slovenia)

SI-1000 Ljubljana, Slovenia

http://www.cipkebip.org 

The Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins (CIPKeBiP) is a non-profit research organisation that brings together researchers with expertise in light microscopy, cell, molecular and structural biology, mass spectrometry, biochemistry, biotechnology, bioinformatics, and chemistry. The goal of the CIPKeBiP is to provide scientific platforms for conducting internationally competitive, cutting-edge research in the area of life sciences, with a focus on the study of proteins in ex-vivo, in-situ, and in-vitro environments.

At the CIPKeBiP, the following research infrastructure/ scientific platforms have been established:

High resolution and super-resolution light microscopy, for visualisation of molecules and their interactions in cells or in tissues and organisms.

Mass spectroscopy for analysis of protein compositions in complex samples, and for the analysis and identification of individual biological molecules and their modifications.

Protein and structure analysis, with a high-throughput platform for the analysis of molecular mechanisms in biochemical to atomic resolution studies (3D crystal structures, kinetics of interactions, properties of biologically active molecules, including proteins and small organic molecules).

Platform for development of biologically active organic molecules, based on biological and chemical synthesis.

Computational analysis of complex biological and other experimental data, for descriptive and predictive modelling, knowledge extraction and integration, and optimisation of experimental approaches and technological processes.

The biomedical research topics of interest that have been implementing within these research platforms include:

1. Mechanisms and pathways in immune responses

(i) Adaptive immune response mechanisms and their molecular components

(ii) Structural biology of endosomal/ lysosomal and pathogen proteins

(iii) Interactions of pathogenic microorganisms and human/ mouse cell components (Staphylococcus aureus, Clostridium difficile)

(iv) Surface proteins of pathogens as potential vaccines, and those involved in biofilm formation

(v) Gut microbiota, including gut pathogens

(vi) Identification and validation of physiologically relevant protease substrates and their implications in the identification of molecular signalling pathways during inflammation-associated diseases

(vii) Development of computational tools for systems biology in the area of pathogenic microorganisms

2. Intracellular and intercellular communication

(i) Role and specificity of endosomal hydrolases (proteases and carbohydrate hydrolases)

(ii) Post-translational protein modifications 

(iii) Proteomics-based biomarker discovery 

(iv) Cytosolic Ca2+ changes and the late steps in regulated exocytosis

(v) Systems biology of endocrine pancreas, to tackle diabetes mellitus and related metabolic diseases

(vi) Cell physiology and pathophysiology

(vii) Alzheimer’s disease, cognitive impairment, neuro-inflammation, astrogliosis, intellectual disability

(viii) Development of targeted drug delivery systems based on active and passive targeting

(ix) Data analysis for predicting gene function, gene response, and drug target identification

(x) Computational modelling of dynamic cell processes

(xi) Development of computational tools for systems biology

3. Adaptation mechanisms of extremophiles to extreme parameters in the environment

(i) Extremophiles as pathogens at our home environments

(ii) Development of computational tools for systems biology in the area of extremophiles 

International activities:

CIPKeBiP is involved in the European research infrastructure initiative INSTRUCT (http://www.structuralbiology.eu/) for structural biology, and the European GRID initiative - the network of clusters.

An agreement for cooperation has been signed with SP Minimax Ltd. (St. Peterburg, Russia), represented by General Manager Marina Girina.

Scientific contact: 

Prof.Dr. Dušan Turk, 

Scientific Director

Phone: +386-1-4773857

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.

Business contact: 

Dr. Livija Tušar, 

General Director

Phone: +386-1-4773856, +386-1-4773962

E-mail: This email address is being protected from spambots. You need JavaScript enabled to view it.