“Molecular and functional genomic approaches to novel antibacterial target discovery”


Antibiotarget University of Groningen
The University of Groningen
(The Netherlands)
Partner 3

Group Leader:

Professor Wim Quax
(Head Department of Pharmaceutical Biology, University Centre for Pharmacy)
Antibiotarget

Research Centre Hosting EST Fellows: Department of Pharmaceutical Biology, University Centre for Pharmacy

The University of Groningen
Antibiotarget

The University of Groningen http://www.rug.nl being one of the oldest research universities in Europe is an active member of the Coïmbra Group. Since its inception in 1614 more than 100,000 graduates have been trained. Some 21,000 students are currently enrolled in more than 160 bachelor and master programs, and some 775 students are studying for their PhD. Every year, about 2,500 students graduate from the University, and some 250 PhD-students defend their doctorate thesis.
As their students and staff come from the Netherlands and from at least 90 other countries, the University of Groningen is truly international. Furthermore, with 5,000 employees and an annual budget of Euro 445 million, the host is able to create a perfect climate for scientific investigation, educational renewal and personal development.
The University is an active participant in the Socrates and Erasmus programmes aimed at building up a Europe of knowledge by cooperation in education. In response to the Bologna treaty Groningen was among the first at the European mainland to adapt to the Bachelor/Master system in 2002.
At present the very successful PhD training programmes, hitherto organised in Research Schools, are being evolved into Graduate schools allowing a smoother entrance of international students. The share of international students enrolling in 2004 in the Faculty Bachelor and Master programmes was 18.7 % with a 40 % share of female students. At the level of PhD the share of international students is 25.6% with a share of 45% for female students.

The graduate school GUIDE:The GUIDE Training Program accommodates a large population of PhD-students with various backgrounds (a.o. medicine,medical biology, molecular biology, pharmacy). The average yearly flow of PhD-students into GUIDE is around 50. The school offers a specific scholarship program for foreign PhD students, the Ubbo Emmius program. At this moment, 30% of the PhD-students are from outside the Netherlands. Therefore, an extensive, English-spoken-training program, with accompanying capacity is offered. Parts of this program will be integrated into the Antibiotarget research training (see section B2.2).
A further indicator of the international orientation of GUIDE is the active participation in two European Graduate Schools, bilateral collaborations with a German university by the German Research Community (DFG) and the Dutch Organisation of Scientific Research (NWO). EGCs have been created to foster exchange of PhD training programs at an international level. GUIDE participates in the following European Graduate Colleges:
(i) European Graduate College ‘Regulatory Systems’, partner: Ruhr Universität Bochum, Germany.
(ii) European Graduate College ‘Vascular Medicine’, partner: Ruprecht Karls Universität in Heidelberg and Mannheim, Germany.

Prof. Quax is the co-founder and vice-speaker of the 1st EGC with the full title: "Regular circuits in cellular systems: fundamentals and biotechnological applications". This PhD training program is jointly executed by the Ruhr-University Bochum, the University of Düsseldorf (IMET), and the University of Groningen, The Netherlands, with partner 4 of this EST proposal (Prof. Jaeger) being an active member.

The infrastructure for the specific research training in this host institution is described above (Point B3.1 under the University of Groningen). In addition the University of Groningen and the Graduate School GUIDE have a well established support infrastructure for complementary training offering the following:

  • International Service Desk of The University of Groningen, Broerstraat 5, Groningen, couples foreign Ph.D students to their contact persons within the university, gives support on visa procedures, registration, work permits, taxes, finances, scholarships, medical care, housing, facilities, travel information and matters concerning daily life:
    www.rug.nl/prospectiveStudents/intro/index

  • The Faculty coordinator helps with daily practicalities such as language courses, schools, kindergardens, driver licences and access to University sport facilities (ACLO). Most importantly the faculty coordinator arranges the initial housing for the foreign students:
    www.rug.nl/prospectivestudents/contact/faculteitsCoordinatoren/index

  • University Guest House temporary apartments for guest researchers and teachers at low prices:
    www.rug.nl/ufb/productendiensten/guesthouse/index?lang=en

  • The International Housing Office is a non-profit organisation, which acts as an intermediary in finding furnished accommodation for international guests of the University of Groningen. The Housing Office provides suitable accommodation for a reasonable price. For temporary housing of international PhD students an especially build apartment complex is available via the faculty coordinator:
    www.housingoffice.nl/

  • Language training courses are offered by “The Language Centre” of the University Groningen at 4 different levels for all international guests as well as preparatory courses for the state examination:
    www.rug.nl/fwn/informatievoor/internationalstudents/incomingstudents/organisation/languagePreparation?lang=en

Antibiotarget
       Department of Pharmaceutical Biology

For additional support and student mentoring the PhD students can use facilities of the University of Groningen as well as of the Graduate School GUIDE. The main offices to contact are:

Groningen Team
  • WINGS-ESN stands for Workgroup Internationalization Groninger Students. They organize many different social and cultural activities to help the international students have an unforgettable stay here in The Netherlands (www.wings-esn.nl/). Every Sunday an activity is organised including the preparation of a joint meal:
    www.wings-esn.nl

  • The Global Club. The aim of the Global Club is to contribute to a warm social environment for researchers (PhD-students and postdocs) who often spend most of their time on research, and to assist international guests in getting to know Groningen and the Netherlands. The Global Club organises a monthly Tea Hour, excursions and other get-togethers. It publishes an electronic newsletter that contains announcements, information about Dutch life and an agenda of cultural events in Groningen in the English or French languages.

  • The USVA. The University’s Cultural Student Centre organises courses on dance, music, drawing, painting and drama. Besides the courses they house their own theatre in which 4 to 5 times a week a variety of performances is to be seen:
    www.usva.nl

  • Grasp! is the organization of Groningen PhD-students and stands up for the rights and interests of all PhD-students at the University of Groningen. This means that Grasp! is also intended for international PhD-students:
    www.grasp.name

Professor Wim Quax, Head of the Department of Pharmaceutical Biology http://www.farmbio.nl (The Netherlands), aims at the exploitation of novel routes for drug biosynthesis. Their major research topics are: (i) functional analysis of protein secretion factors in Bacillus and Pseudomonas species (ii) enzyme engineering through directed molecular evolution and phage display selection, (iii) regulation, maturation and transport of exoenzymesP.aeruginosa . Recently this has resulted in the identification of quorum quenching enzymes that interfere with P. aeruginosa virulence. Inhalation apparatus for studying drug delivery in a cystic fibrosis mouse model is available. His Department is well equipped for the proposed training with excellent facilities for DNA, protein and drug analysis. They are also actively involved in collaborative research with industry on antibiotics. The Department was rated “excellent” in the recent international peer review of research www.qanu.nl (13/10/2004).

National and international collaborations: The department of pharmaceutical biology has close and on-going collaborations with the leaders of the other institutions from this EST project funded by one EU Framework V project and a College. In addition to the international collaboration with the EST members, various aspects of protein folding, secretion and virulence of enzymes from Pseudomonas aeruginosa are being studied with Prof J.Tom Utrecht and Prof. B. Dijkstra Groningen. Other international collaborators include Prof.L. Serrano (EMBL), Prof. L. Wyns Brussels), Dr. Msadek (Institut Pasteur), Prof.D. Ehrlich (INRA), Prof. D. Haas (Lausanne, Prof. Schumann (Bayreuth) and Prof. C. Harwood (Newcastle). Our industry partners include DSM bv (Delft, Solvay Pharmaceuticals (Amsterdam), Genencor International (Leiden), Lonza Ltd. (Visp, Switzerland), Symrise GmbH; Co. KG (Holzminden), and Novozymes (Copenhagen, Denmark). Our SME partners include IQ Corporation and IMEnz Bioengineering (Groningen, Zebra Biosciences (Enschede) and Signalomics (Münster). These industrial partners collaborate with us in the fields of microbial genomics, enzyme gene expression, and optimisation, directed evolution and biotechnological applications and they have agreed to host PhD students working in the framework of the EST project.


All the fellowships allocated to the University of Groningen have now been appointed.

Work packages associated with these Fellowships as indicative of the type of postgraduate research training to be provided is:

                WORKPACKAGE 4
TITLE: Construction of ‘designer’ organisms to increase the production of proteins and chemical compounds that can be used therapeutically to treat Pseudomonas infections.

Deliverables:
1. Construct specific pseudomonas isogenic mutant strains that will enable the production of high levels of active therapeutic products.
2.Construction of potent quorum quenching variants of HSL acylases. Directed evolution and expression will be used to provide purified variant proteins that can be used to interfere with quorum sensing.
3. Demonstration of efficacy of HSL deacylation for interference with virulence of P. aeruginosa in model system.

Milestone:
To develop tools for the large scale production of therapeutic agents that can be exploited by biotechnology companies