Dr. Šafránek from the Department of Information Technologies, Faculty of Informatics, Masaryk University in Brno is organising the 16th International Conference on Computational Methods in Systems Biology from the 12th to 14th September 2018. The conference forms a well-focused international community in-between biology and computer science. Interesting and strong speakers that represent cutting-edge research at the borders of biology and other disciplines have been invited.

CMSB 2018 solicits original research articles, tool papers, posters, and presentations on the modelling and analysis of biological systems and networks as well as the analysis of biological data. The conference brings together computer scientists, biologists, mathematicians, engineers, and physicists interested in a system-level understanding of biological processes. It covers the broad field of computational methods and tools in systems and synthetic biology and their applications.

Paper abstract pre-submission: 20.4.2018
Paper and original poster submission: 27.4.2018
Author notification: 8.6.2018
Final version: 15.6.2018
Poster/oral presentation submission: 22.6.2018

Further information can be found here: 
https://cmsb2018.fi.muni.cz


poster

Prof. RNDr. Rudiger H. Ettrich, Ph.D., Department Head for the Center for Nanobiology and Structural Biology, Institute of Microbiology Academy of Sciences of the Czech Republic Nové Hrady, and director of the Center for Systems Biology in the Czech Republic C4SYS (the national distributed research infrastructure for systems biology research) visited Larkin University in Miami, Florida, USA, as an invited Guest Speaker to give a talk on “Using Computational Modeling and Simulation in Understanding Gene Mutations” on November 10th-17th, 2017. During this visit the University Provost also held meetings with Dr. Ettrich and signed affiliation agreements with the Center for Systems Biology in the Czech Republic C4SYS (the national distributed research infrastructure for systems biology research) and the Institute of Microbiology of the Czech Academy of Sciences of the Czech Republic.

In addition, Dr. Ettrich visited the College of Medical Sciences of Nova Southeastern University in Ft. Lauderdale, Florida, USA, to conduct collaborative research together with Prof. Dr. Venkatachalam, discuss possible future collaborations and give a seminar.

 

(L-R): Dr. Joshua Caballero, Chair of Clinical and Administrative Sciences (DCAS) in the
College of Pharmacy, Dr. Rudiger Ettrich, Department Head at the Center for Nanobiology
and Structural Biology, Institute of Microbiology Academy of Sciences of the Czech Republic,
Dr. Cecilia Rokusek, Larkin University Provost, and Dr. Gary M. Levin, Dean of the College of Pharmacy.

Supported by the International Visegrad Fund, the scientific and research Summer School in Molecular Biophysics and Systems Biology, was jointly organized by the University of South Bohemia, the Czech National Infrastructure for Systems Biology C4Sys and the Center for Nanobiology and Structural Biology of the Institute of Microbiology, Academy of Sciences of the Czech Republic. In partnership with the University of Miskolc, Hungary, the University of Warsaw, Poland and Comenius University in Bratislava, Slovakia, the summer school provided Czech and foreign university students with an opportunity to work with experienced scientists and tutors in internationally respected research teams for a month. During their time in Nové Hrady the students did not only concentrate on research but they also attended an excellent series of lectures that gave them a broad view on cutting-edge methodologies and research.

The 5th Summer School 2017 was attended by 21 distinguished students from Poland, Hungary, Czech Republic, Ukraine, Belarus, Russia, and Slovakia. 10 students were sponsored by the Visegrad Fund and the additional eleven were funded by the University of South Bohemia and the Academy of Sciences of the Czech Republic. The summer school participants had gone through a highly competitive selection procedure and subsequently worked in first-rate fully-equipped laboratories on topics related to systems biology and molecular biophysics. At the end of the summer school, the research teams presented their results in a student conference, where the 3 best presentations got awarded by a scientific committee. All the participants received certificates and promotional gifts  in the final ceremony.

The awarded projetcs were as follows: “Non-Invasive Measurements of Ion Fluxes Across Cell Membranes in Sacchoromyces cerevisiae” by Lucia Kmecová, Tatsiana Kachatkova and Aleksandr  Kalashnikov; “In-Silico Study of a Voltage-Sensitive Transmembrane Protein” by Ibolya Tóth and David Roesel; and “Modelling Interactions in Biomolecules Using Methods of Quantum and Molecular Mechanics” by Weronika Lidwin and Andrea Guljas.

Besides research activities and lectures, the students also enjoyed several social events, such as “80 Minutes around the World” Food Festival, rafting trip down the Vltava River, tour of Budweiser Budvar Brewery and a typical Czech barbeque.

 

      

 

From 27th to 30th June 2017, Prof. Dr. Cecilia Rokusek, Ed.D., M.Sc., R.D., Provost and Vice-President of Academic Affairs, Larkin University, Miami, Florida, visited the Center for Nanobiology and Structural Biology CAS in Nové Hrady, where she met the Center’s Director Prof. Rüdiger Ettrich, Ph.D.  He showed her how the Center works and introduced the C4Sys infrastructure, its development and the services offered. They discussed the possibility of education stays / internships of the Larkin university students at Nové Hrady as well as using the infrastructure by the students. A Memorandum of Understanding is currently being prepared for future signing.

Prof. Rokusek subsequently visited the grounds of the University of South Bohemia in České Budějovice, where she was warmly welcomed by the former rector Prof. Libor Grubhoffer.

 

           

From 21st to 24th June, the Center for Nanobiology and Structural Biology hosted the 7th Visegrad Symposium on Structural System Biology. The Scientific Organizing Committee consisted of Dr.Babak Minofar, prof. Rüdiger Ettrich and Dr. David Řeha from the Center for Nanobiology and Structural Biology, Academy of Sciences, Nové Hrady, Czech Republic; Prof. Ján Urban from Comenius University in Bratislava, Slovakia; Dr. Béla Viskolcz and Dr. Imre G. Csizmadia from the University of Miskolc, Hungary; and Dr. hab. Joanna Sułkowska from the University of Warsaw, Poland.

The symposium focused on various computational methods used in the study of biologically relevant macromolecules ranging from quantum calculations via atomistic models to coarse-grained molecular dynamics of biological systems. Furthermore, it dealt with experimental techniques (mainly spectroscopic methods) that complement the simulations or can be used for verification.

                

 

On Tuesday 20th June 2017 at 2 p.m., the seminar “Purification, Characterization, and Clinical Significances of Methionine Gamma Lyase Deaminase (Mgld) from Porphyromonas gingivalis” given by Dr. K.V. Venkatachalam, PhD. took place at the cinema auditorium of the Institute of Microbiology, CAS.  Prague – Krč.

Dr. Venkatachalam is a Professor of Biochemistry at the College of Allopathic Medicine, Nova Southeastern University, Ft. Lauderdale, Florida, where he has been active since 1999. His current research focuses on Methionine gamma lyase of Methionine metabolism and its impact on halitosis and cancer research.

After the seminar, he discussed the possibility of potential cooperation in the area of systems biology as well as regarding research infrastructures with the Institute of Microbiology’s scientists involved in the C4Sys infrastructure.

 

 

On Thursday 25th May 2017, the Center for Nanobiology and Structual Biology (CNSB) in Nové Hrady welcomed 48 students and their teachers from the Anglo-Czech High School in České Budějovice, the C4sys Research Infrastructure (C4Sys RI) being the main topic of their excursion.

First the students attended a speech by the director of the CNSB and the C4Sys RI – Prof. Rüdiger Ettrich. He introduced the infrastructure, talking about its development, purpose and objectives. He then explained what each research group involved in the infrastructure is focused on and what their main activities are, illustratively accompanying his speech with slides from his PPT presentation to clarify some difficult processes for the students. Since the C4Sys infrastructure is directly linked to the Infrastructure for Systems Biology in Europe (ISBE), prof. Ettrich also covered its role and the link between these two infrastructures. In the end, he compared data storing in the USA and in Europe.

The theoretical part was followed by a tour of laboratories at the CNSB. The students were divided in two groups and viewed the research premises of the Center with commentaries by their two “tour guides” – Prof. Ettrich and Dr. Lazar. They could see the scientific work as well as all the equipment used, in particular the Laboratory of Cell Biology, which focuses on the development and applications of two-photon polarization microscopy and related advanced optical microscopy techniques, and the Laboratory of Structure and Function of Proteins, with its central research issue being the relationship between the structure and function of the proteins and their complexes.

Finally, the students paid a brief visit to the Algatech Centre in Třeboň, whose Laboratory of Photosynthesis under the supervision of Prof. Josef Komenda is also part of the C4Sys infrastructure.

The ISBE Management Team Meeeting chaired by prof. Roel van Driel took place in Amsterdam on 25th April 2017.

On behalf of the C4Sys infrastrucure, the meeting was attended by the MT member prof. Rüdiger Ettrich. First, the present status of the ISBE project was discussed, as well as its challenges and next steps. Then the ISBE – ELIXIR relationship was outlined along with a future relationship ISBE – FAIRDOM. Finally, the members of the Management Team focused on ISBE Light services (the aims, timeline, module modelling & theory, module teaching & education and module stewardship).

The new ISBE website will be online as of 1st July . It will contain (i) the portal for the three classes of ISBE Light services, (ii) user access rules, and (iii) general ISBE information transferred from the old ISBE-Project website. The latter site will be terminated. The URL http://project.isbe.eu/ will be linked through to the new ISBE website.

 

 

The first meeting Intergovernmental Working Group took place in Amsterdam on Tuesday 10th January 2017.

The meeting was organised with support of the BBSRC and NOW, who together co-chaired the Legal and Governance work package of the ISBE’s Preparatory Phase.  The meeting was attended by the representatives of national European funding organisations, including two representatives from the Czech Republic.

Following the completion of the ISBE Preparatory Phase in July 2015, the ISBE partners have started to build a sustainable European research infrastructure. Two parallel tracks are being followed:

1) acquire start-up funding doe the interim phase

2) establish an initial portfolio of web-based services that are labelled ISBE light in three ISBE domains:

  • Modelling &Theory
  • Stewardship of research assets
  • Education & Training

At the meeting, the current progress as well as the process and the time line of building the ISBE was discussed and plans and activities in the context of national investments, priorities and roadmaps were considered.

A postdoctoral position is immediately available in the group of  Prof. Rudiger Ettrich at the Center for Nanobiology and Structural Biology, Institute of Microbiology of the Czech Academy of Sciences, Nove Hrady, Czech Republic.

Job description:

The job involves the use of computational methods, combined bioinformatics and molecular dynamics approach on translocation systems. This project will contribute to the understanding of different aspects of structure and function of cation translocation systems. These systems are either interconnected in function or structurally related. Studied systems will include non-selective cation channels as well as potassium- or calcium selective translocation systems. The study  shall also contributes to a clearer understanding of he evolutionary relationship between the  different groups of cation translocation systems and the the results will deepen the theoretical understanding of mechanisms behind cation translocation provided by these systems.

Qualifications:

The applicant must hold a Ph.D. degree in chemistry or physics. The applicant should also have solid experience with computational modeling of biomolecules and an overall strong motivation. The ability to work independently as well as to collaborate with an extended team of theoreticians and experimentalists is also crucial.

Applicants should send an e-mail containing their CV, motivation letter, brief summary of previous research, list of publications and names plus e-mail addresses of 2 references.

E-mail: ettrich@nh.cas.cz
Web: http://nh.cas.cz/index.php?node=691

Contact:
Prof. RNDr. Rudiger Ettrich, PhD.
Center for Nanobiology and Structural  Biology
Institute of Microbiology
Academy of Sciences of the Czech Republic
Zamek 136
CZ-37333 Nove Hrady
Czech Republic

 

Selected publications of our group related to the research topic:

Isabella Derler, Isaac Jardin, Peter B Stathopulos, Martin Muik, Marc Fahrner, Vaselina Zayats, Saurabh Pandey, Michael Poteser, Barbara Lackner, Marketa Absolonova, Klaus Groschner, Rüdiger Ettrich, Mitsu Ikura, Christoph Romanin (2016)  Cholesterol binding modulates Orai1 channel function Science Signaling 9 (412):  ra10. Jan 26.

Irene Frischauf, Vasilina Zayats, Michael Deix, Anna Hochreiter, Isaac Jardin Polo, Martin Muik, Barbara Lackner, Barbora Svobodova, Teresa Pammer, Monika Litvinukova, Amrutha Arumbakam Sridhar, Isabella Derler, Ivan Bogeski, Christoph Romanin, Rüdiger Ettrich, Rainer Schindl (2015)  A calcium accumulating region, CAR, in the Orai1 channel enhances Ca2+- permeation and SOCE-induced gene transcription Science Signaling 8 (408):  ra131. Dec 22.

Vasilina Zayats, Thomas Stockner, Saurabh K Pandey, Katharina Wörz, Rüdiger Ettrich, Jost Ludwig (2015)  A refined atomic scale model of the Saccharomyces cerevisiae K+-translocation protein Trk1p combined with experimental evidence confirms the role of selectivity filter glycines and other key residues. BBA-Biomembranes 1848 (5):  1183-1195.

Vasilina Zayats, Abdul Samad, Babak Minofar, Katherine Roelofs, Thomas Stockner, Rudiger Ettrich (2013)  Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain Journal of Molecular Modeling 19:  4689–4700.

Daniel Rozbeský, Žofie Sovová, Julien Marcoux, Petr Man, Rüdiger Ettrich, Carol V Robinson, Petr Novák (2013)  Structural model of lymphocyte receptor NKR-P1C revealed by mass spectrometry and molecular modelling Analytical Chemistry 85:  3.  1597–1604.

Azadeh Nikouee, Morteza Khabiri, Stephan Grissmer, Rüdiger Ettrich (2012)  Charybdotoxin and margatoxin acting on the human voltage-gated potassium channel hKv1.3 and its H399N mutant: An experimental and computational comparison Journal of Physical Chemistry B 116 (17):  5132-5140.

Morteza Khabiri, Azadeh Nikouee, Lukasz Cwiklik, Stephan Grissmer, Rüdiger Ettrich (2011)  Charybdotoxin unbinding from the mKv1.3 potassium channel: A combined computational and experimental study Journal of Physical Chemistry B 115:  39.  11490–11500.

 

 

 

 

 

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