www.ciisb.org  |  Newsletter 1/2019
Sent 25 Jun 2019, 10:11

Newsletter

Editorial

Dear colleagues,

CIISB Summer Newsletter summarizes the most important changes, events, and news from the past six month.

The Nanobiotechnology Core Facility has a new Head, Jan Přibyl, who replaced Petr Skládal. The upgrades of the CIISB instrumentation from the funds of the OP VVV project CIISB4HEALTH continues and is on time with the proposed planning.

Out of many meetings, I would like to highlight the 3rdCIISB User Meeting, which was organized as a part of the XVIth Discussions in Structural Molecular Biology in Nové Hrady, March 21-23, 2019. This traditional conference gathered more than 110 participants. Research highlights, recently obtained at the CIISB core facilities, have been presented and discussed. On May 29-31, 2019, the iNEXT workshop on Integrated Approaches and Methodologies for Structural Biology organized by CEITEC Masaryk University attracted 20 internationally recognized speakers and more 170 attendees.

Number of excellent papers published in high-quality journals is steadily increasing. Out of 34 papers published in 2019, 6 appeared in the journals listed in Nature index, and increased thus the total number since 2016 to 35. The most significant results are described in Research Highlights. Results of other important publications can be found in the section Publications written with support of CIISB on the CIISB web.

I wish you enjoyable summer and relaxing holiday season

Vladimír Sklenář

New instruments and laboratory modifications

New leader of CF nanobiotechnology

As of April 1, 2019, the CEITEC Nanobiotechnology Core Facility has a new Head. Jan Přibyl, PhD., has replaced prof. Petr Skládal who was a CF Leader since its establishment in 2011. Hereby, we thank Petr for his leadership, vision, and energy invested in founding and development of this core facility. As a CEITEC group leader of the Nanobiotechnology Research Group, he will supervise the core facility operation as a scientific advisor and will be involved in its further developments. You can find more information on page of CF.

Automatic sample changer and optic upgrade at the X-ray Diffraction and Bio-SAXS core facility at CEITEC

Since June 3rd the automatic sample changer for BioSAXS is available to the core facility users. Together with Xray optics upgrade (OptiSAXS, Rigaku) which allows to shorten the acquisitions times to ~15 min is the automatic sample changer big jump towards high-throughput SAXS measurements for biological samples. Temperature controlled sample storage area could be filled by samples in 96-well plate or in 8-well low profile PCR strips, what allows the users to benefit from extended number of examined samples by screen multiple samples, individual HPLC fractions or varying buffer conditions. More about X-Ray Diffraction and Bio-SAXS CF.

New grants

EU support to organize a workshop on sample quality for CF Biomolecular Interactions and Crystallization

Core Facility Biomolecular Interactions and Crystallization together with Cryo-electron Microscopy and Tomography succeeded in getting support to organize workshop: Analysis and optimisation of sample quality for cryo-electron microscopy and other structural techniques (February 11-13, 2020). This workshop was selected in an open call as an Instruct-ERIC & ARBRE-MOBIEU joint training course. More you can find here.

News

Wolfgang Baumeister received the 2019 Ivano Bertini Award

The Ivano Bertini Award is offered by Instruct to recognise a significant achievement in frontier research that utilises an integrative structural biology approach. The award is an independently reviewed competition and commemorates Ivano Bertini, who developed powerful new methods in NMR and founded CERM in Florence.

The award of €15,000 is endowed by Bruker BioSpin which is at the forefront of NMR instrument development with increasingly broad application and measurement sensitivity.

We are delighted to announce the 2019 recipient of the Ivano Bertini award is Wolfgang Baumeister, Director and Head of the Structural Biology department at the Max Planck Institute of Biochemistry and Honorary Professor of the Technical University in Munich. More about Wolfgang Baumeister you can find here.

Instruct-ERIC International Access Call

We are delighted to announce the opening of the Instruct access call for International users. In the last 4 years Instruct has been working to strengthen the collaboration with the international structural biology community, in particular with Latin America.  

In this context, we are starting Instruct-ERIC International Access Calls by offering the opportunity for scientists working in institutions that have signed Memoranda of Understanding (MOU) to apply to access the Instruct Research Infrastructure. You can find more information or registration here.

4th National Day of Large Research Infrastructures

The Ministry of Education, Youth and Sports of the Czech Republic and the Faculty of Mathematics and Physics of Charles University are honoured to invite you to take part in the 4th National Day of Large Research Infrastructures, to be held on 19th November 2019 in the premises of LINDAT/CLARIAH-CZ large research infrastructure. More about the event you can find here.

10th Call for proposals for Instruct Centre Training Courses

This call is for events planned, organised and implemented by Instruct Centres or in coordination with scientific representatives of Instruct members. Courses co-organised with industrial partners are encouraged. Courses can be organised in collaboration by more than one Instruct Centre or with other organisations, such collaborations should be included in the application. Courses may be funded up to 12000 Euros. Applications showcasing integrative approaches to structural biology are encouraged.  Please submit your application online,

Activities from the past six months

NanoTemper Technologies Symposium & Workshop

NanoTemper Technologies Symposium & Workshop was co-organized with NanoTemper Technologies company and was focusing on quality and stability of samples measured by nanoDSF and interaction with binding partner measured by Microscale thermophoresis. 2-day workshop was divided into theoretical and practical part. During theoretical part 31 participants could learn about various approaches and possible optimization of assays using MST, nanoDSF and Tycho. One lecture was also devoted to current reproducibility crisis in science and the necessity to characterize samples properly.  4 lectures were given by users themselves about their real samples and struggles on the road. Practical part was attended by 14 people who have 9 instruments available for their measurement. Intensive practical part lead to numerous interesting results which will be further developed. More about workshop you can find here.

The symposium was organized with the support of CIISB project.

iNEXT Workshop

The iNEXT workshop on Integrated Methodologies and Approaches for Structural Biology was attended by more than 170 participants, and hosted by CEITEC Masaryk University from 29-31 May 2019. The meeting was organised by Prof. Vladimír Sklenář, with a focus on providing a comprehensive overview of the state-of the-art integrative methodologies to existing and potential users of iNEXT facilities. 20 prominent speakers reported on recent advances and developments in modern structural biology methods. Please see the abstracts HERE

Instruct Biennial Conference - Structural Biology: Deeper into the Cell

Instruct is a distributed European Research Infrastructure, which provides scientists with access to all major cutting edge technologies that enable biomacromolecular structure determination at atomic resolution. The inaugural Instruct Structural Biology Meeting at Heidelberg in 2013 successfully showcased integrative structural biology and its impact on biological research and biomedicine. The second Biennial took place in Florence in 2015 continuing the integrative line with an increased focus on innovation. The last edition which took place in Brno in the Czech Republic included sessions representing recent structural biology highlights, emerging methods and technologies and results of biomedical importance. 4th edition took a place in Madrid, Spain from May 22 till May 24, 2019. The historical Alcalá de Henares was the original location of the Universidad Complutense, founded in 1293 and one of the oldest universities in the world, as well as being the birthplace of Miguel de Cervantes. On a meeting was invited outstanding speakers as you can see here.

Open Day of Research Infrastructures and Core Facilities

The event took place on the April 3rd 2019 at the BIOCEV centre. You can find page of the event here.

XVI. Discussions in Structural Molecular Biology

In March, 2019, the Czech and Slovak community of structural biologists met at the "XVI. Discussions in Structural Molecular Biology".  This year, the traditional conference was coupled with the 3rd User Meeting of the Czech Infrastructure for Integrative Structural Biology (http://cssb.structbio.org/program-xvi-discussions-structural-molecular-biology ). The conference took place at the venue of the Academic conference centre in Nové Hrady, South Bohemia between Thursday afternoon and Saturday lunch on March 21 - 23 2019.

The program was very intensive.  About 100 participants listened to 27 talks delivered mostly by young investigators or students and during the poster sessions 45 posters were displayed and discussed. The invited speaker, Marjolein Thunnissen from the Lund University (Sweden), was talking about structural biology at the synchrotron source MAX IV.  Six lectures were specifically devoted to the 3rd User meeting of the Czech Infrastructure for Integrative Biology, CIISB. The meeting of General Assembly of the Czech Society for Structural Biology was also organised. Abstracts of all presentations can be found at http://www.xray.cz/setkani/abst2019/abstracts.htm

At the end of the conference, three prizes were awarded for the best student posters, and three for the best student talks. The next XVII. Discussions are planned for mid-March 2020 again in Nové Hrady. For details see the web page structbio.org or contact the main organizer Jan Dohnálek at dohnalek007@gmail.com.

More information you can find here.

Save the date

Wed 26 – Fri 28 Jun 2019

4th Annual User Meeting of iNEXT 

All iNEXT Partners, together with the Scientific Advisory Board, the Executive Review Panel, the Industry Platform and the User Panel, will discuss the work that was performed during the project, including different essential technology developments that emerged from our Joint Research Activities. The iNEXT users will have a great platform to present their work, discuss the current access to the Facilities and make suggestions for improvements.

The 4th Annual Users Meeting of iNEXT will take place in Lund (Sweden) and is co-organized by the newly established synchrotron MAX IV and European Spallation Source (ESS).

Registration to the event is free of charge.

  • Scientific Sessions: 15:00 Wednesday 26 June - 16:00 Thursday 27 June
  • Facilities visits: 16:00 - 19:00 Thursday 27 June iNEXT
  • General Assembly: 09:00 - 11:00 Friday 28 June

Thu 27 – Fri 28 Jun 2019

EMBO Young Scientists Forum 2019 

Students, postdocs, and other early-career scientists are welcome to attend the upcoming EMBO Young Scientists' Forum that will take place in Prague, Czech Republic on June 27th and 28th 2019. This event is a unique opportunity for a close encounter with top-notch science by world-class rising star scientists, mostly affiliated with the EMBO Young Investigator Programme, combined with career sessions and social program encouraging networking. Excellent speakers, covering a wide range of life-science fields, have been invited to present their science and latest results.

Tue 10 – Wed 11 Sep 2019

BioSAXS practical course 2019 

Two days practical course on basics of biological small angle x-ray scattering (SAXS) is organised on September 10-11th, 2019 located in Brno, CEITEC (Central European Institute of Technology). Participants will be introduced to the practical aspects of SAXS experiment setup during laboratory practical and excursion to the Core Facility X-ray diffraction and BioSAXS.

Tue 8 – Thu 10 Oct 2019

Instruct-ERIC workshop: Computational approaches in integration of structural biology techniques 

The course will be focused on the growing need to combine computational tools in structural biology projects.

Sun 3 – Sat 9 Nov 2019

EMBO Course "Practical Integrative Structural Biology" 

We are happy to announce the upcoming EMBO practical course on “Practical Integrative Structural Biology” to be held from Nov 3-9, 2019 at EMBL and the Centre for Structural Systems Biology (CSSB), both on DESY campus in Hamburg, Germany. 

Research highlights

Nature Communication 2019

Viruses from the genus Enterovirusare important human pathogens. Receptor binding or exposure to acidic pH in endosomes converts enterovirus particles to an activated state that is required for genome release. However, the mechanism of enterovirus uncoating is not well understood. Here, we use cryo-electron microscopy to visualize virions of human echovirus 18 in the process of genome release. We discover that the exit of the RNA from the particle of echovirus 18 results in a loss of one, two, or three adjacent capsid-protein pentamers. The opening in the capsid, which is more than 120 Å in diameter, enables the release of the genome without the need to unwind its putative double-stranded RNA segments. We also detect capsids lacking pentamers during genome release from echovirus 30. Thus, our findings uncover a mechanism of enterovirus genome release that could become target for antiviral drugs. More about this topic you can find here.

Nature Communication 2019

Dishevelled (DVL) is the key component of the Wnt signalling pathway. Currently, DVL conformational dynamics under native conditions is unknown. To overcome this limitation, we develop the Fluorescein Arsenical Hairpin Binder- (FlAsH-) based FRET in vivo approach to study DVL conformation in living cells. Using this single-cell FRET approach, we demonstrate that (i) Wnt ligands induce open DVL conformation, (ii) DVL variants that are predominantly open, show more even subcellular localization and more efficient membrane recruitment by Frizzled (FZD) and (iii) Casein kinase 1 ɛ (CK1ɛ) has a key regulatory function in DVL conformational dynamics. In silico modelling and in vitro biophysical methods explain how CK1ɛ-specific phosphorylation events control DVL conformations via modulation of the PDZ domain and its interaction with DVL C-terminus. In summary, our study describes an experimental tool for DVL conformational sampling in living cells and elucidates the essential regulatory role of CK1ɛ in DVL conformational dynamics. You can find even more on our pages.

Selected publications

Abad, E. et al. Common Metabolic Pathways Implicated in Resistance to Chemotherapy Point to a Key Mitochondrial Role in Breast Cancer. Molecular & Cellular Proteomics 18, 231-244, doi:10.1074/mcp.RA118.001102 (2019).

Axmann, M. et al. Receptor-Independent Transfer of Low Density Lipoprotein Cargo to Biomembranes. Nano Letters 19, 2562-2567, doi:10.1021/acs.nanolett.9b00319 (2019).

Bokrova, J., Marova, I., Matouskova, P. & Pavelkova, R. Fabrication of novel PHB-liposome nanoparticles and study of their toxicity in vitro. Journal of Nanoparticle Research 21, 12, doi:10.1007/s11051-019-4484-7 (2019).

Bosakova, M. K. et al. Fibroblast growth factor receptor influences primary cilium length through an interaction with intestinal cell kinase. Proceedings of the National Academy of Sciences of the United States of America 116, 4316-4325, doi:10.1073/pnas.1800338116 (2019).

Buchta, D. et al. Enterovirus particles expel capsid pentamers to enable genome release.Nature Communications 10, 9, doi:10.1038/s41467-019-09132-x (2019).

Caluori, G. et al. Non-invasive electromechanical cell-based biosensors for improved investigation of 3D cardiac models. Biosensors & Bioelectronics 124, 129-135, doi:10.1016/j.bios.2018.10.021 (2019).

Harnos, J. et al. Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nature Communications 10, 18, doi:10.1038/s41467-019-09651-7 (2019).

Kaiser, K. et al. WNT5A is transported via lipoprotein particles in the cerebrospinal fluid to regulate hindbrain morphogenesis. Nature Communications 10, 15, doi:10.1038/s41467-019-09298-4 (2019).

Makki, A. et al. Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. Plos Biology 17, 32, doi:10.1371/journal.pbio.3000098 (2019).

Munster, L. et al. Selectively Oxidized Cellulose with Adjustable Molecular Weight for Controlled Release of Platinum Anticancer Drugs. Biomacromolecules 20, 1623-1634, doi:10.1021/acs.biomac.8b01807 (2019).

Trcka, F. et al. Human Stress-inducible Hsp70 Has a High Propensity to Form ATP-dependent Antiparallel Dimers That Are Differentially Regulated by Cochaperone Binding. Molecular & Cellular Proteomics 18, 320-337, doi:10.1074/mcp.RA118.001044 (2019).

Valkenier, H. et al. Fluorinated Bambusurils as Highly Effective and Selective Transmembrane Cl-/HCO3- Antiporters. Chem 5, 429-444, doi:10.1016/j.chempr.2018.11.008 (2019).

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