European Consortium of Microbial Resource Centres - EMbaRC
Training and Outreach Programme - Transnational Access Grants
List of opportunities
-
High Throughput Screening of food bacteria (CIRM-BIA), France
- Strain identification on pathogenic bacteria (CIRM-BP1), France
- Initiation to handling of microorganisms of group 3 (CIRM-BP21), France
- Taxonomy of pathogenic bacteria relevant in food safety (CIRM-BP22), France
- High Throughput Screening of filamentous fungi (CIRM-CF), France
- Management of microbial strains in ex situ collections (CRBIP), France
- State of the art techniques in Bacteriology (DSMZ), Germany
- Preservation and storage of micro-organisms (CABI Bioservices), United Kingdom
- Taxonomy, identification and preservation of prokaryotes, filamentous fungi and yeasts (CECT), Spain
- Fungal identification, preservation techniques and collection management (MUM), Portugal
- Preservation, collection management, databasing, identification (CBS), Netherlands
- Theoretical, practical and regulatory aspects of a plasmid collection management (BCCM/LMBP), Belgium
- Operation of a bacterial collection & preservation of samples through freeze-drying (BCCM/LMG1), Belgium
- Taxonomy, identification and typing of prokaryotes (BCCM/LMG2), Belgium
- In vitro Culture of Arbuscular Mycorrhizal Fungi (BCCM/MUCL), Belgium
INRA - Institut National de la Recherche Agronomique
CIRM - Centre International de Ressources Microbiennes
The CIRM is a well-equipped recent infrastructure; technical staff are experienced and used to research partnership and to welcome users from many countries to use facilities of the four sites of CIRM as described above.
Each user is placed under the responsibility of one technical permanent staff and scientific results are discussed with INRA scientists and experts of the field, inside the CIRM or more widely inside INRA.
In each location, users will have access to all equipment and the routine service of the facility. This equipment notably comprises L2 and L3 containment laboratories and high throughput screening facilities. Scientific data issued from the collaboration with the users led to common publications.
The CIRM was created in 2005. The four sites have been first involved in obtaining certification ISO9001 version 2000 for the activity of microbial resources preservation and delivery. It provides to customers
Some of these abilities are offered under the grant agreement as described below.
More info on this partner: www.international.inra.fr/crb-cirm |
1. High Throughput Screening of food bacteria (CIRM-BIA)
Organisation:
INRA - CIRM
Location of work: CIRM-BIA Rennes, France
Duration: 1 week (5 working days), with the option of prolonging to 2 weeks
Programme:
Access is organised for up to 2 users simultaneously. It typically consists of a welcome, visit of the laboratory, definition of the work plan and inoculation of the strains (day 1). Screening of the properties exhibited by the strains using the high throughput robot (days 2 – 4). Final day: interpretation of the results and writing of a final report. As it is quite likely that the screening work will take more than 3 days users will have the opportunity to extend their stay to 2 weeks (i.e. 2 units of access).
Type of equipment/service used: high throughput screening robot and other equipment from the facility.
Expected output/deliverables for users: comparison of technological properties of a large number of bacterial strains, owned by the users or part of the CIRM collections.
More info on this opportunity: http://www.rennes.inra.fr/cirm_bia
Contact person: Dr Florence Valence-Bertel |
2. Strain identification on pathogenic bacteria (CIRM-BP1)
Organisation:
INRA - CIRM
Location of work: CIRM-BP Tours, France
Duration: 1 week (5 working days), with the option of prolonging to 2 weeks
Programme:
Day 1: welcome, visit of the laboratories, definition of the work plan and inoculation of the strains in broth media. From day 2 to 5, culturing and phenotypic identification of the strains.
Type of equipment/service used: strain/species molecular typing, L2 and L3 containment laboratories, and other equipment from the facility.
Expected output/deliverables for users: identification of pathogenic strains
More info on this opportunity:
http://www.tours.inra.fr/cirm_bp_eng/
Contact person: Dr Emmanuelle Helloin |
3. Initiation to handling of microorganisms of group 3 (CIRM-BP21)
Organisation:
INRA - CIRM
Location of work: CIRM-BP Tours, France
Duration: 1 week i.e. 5 working days.
Initiation to handling of microorganisms of group 3: example of Brucella. (5 days, 6 users max. per unit). Theoretical, practical and regulatory aspects. Technical part will be made in group of 2 persons. The phenotypical characterisation is divided in 4 sequences A, B, C and D.
Day 1: AM theoretical part on Pathogenic bacteria of type 3 (2 h); PM phenotypical characterisation technical part A (2 groups).
Day 2: AM theoretical part on the case of Brucella and (2 h) and the regulatory aspects (1 h); PM phenotypical characterisation technical part A (1 group) and B (2 groups).
Day 3: AM phenotypical characterisation technical part B (1 group) and C (2 groups); PM Visit of different L3 laboratories and A3 high security animal units.
Day 4: AM molecular characterisation technical part (3 groups); PM phenotypical characterisation technical part C (1 group).
Day 5: AM phenotypical characterisation technical part D for 3 groups; PM Debriefing.
Type of equipment/service used. L2, L3 laboratory
Expected output/deliverables for users: expertise in pathogenic microorganisms holding
More info on this opportunity:
http://www.tours.inra.fr/cirm_bp_eng/
Contact person: Dr Emmanuelle Helloin |
4. Introduction to taxonomy of pathogenic bacteria relevant in food safety (CIRM-BP22)
Organisation:
INRA - CIRM
Location of work: CIRM-BP Tours, France
Duration: 1 week i.e. 5 working days
Programme:
Introduction to taxonomy of pathogenic bacteria relevant in food safety (4 days, 4 users max per unit). Theoretical, practical and regulatory aspects.
Day 1: AM theoretical part on Handling in sterile condition; PM practical part on handling in sterile conditions (Techniques of inoculation and isolation, Gram staining and microscope observation).
Day 2: AM theoretical part of bacterial identification (3 h); PM Practical part on bacterial identification first step: example of the enterobacteria.
Day 3: AM theoretical part on bacterial identification (1 h), on different containment levels of laboratory and on the regulatory aspects (2 h); PM Practical part on bacterial identification second step.
Day 4: AM Practical part on bacterial identification last step; PM Visits of L1, L2 and L3 laboratories. Debriefing.
Type of equipment/service used. L2, L3 laboratories
Expected output/deliverables for users: expertise in pathogens microorganisms holding
More info on this opportunity:
http://www.tours.inra.fr/cirm_bp_eng/
Contact person: Dr Emmanuelle Helloin |
5. High Throughput Screening of filamentous fungi (CIRM-CF)
Organisation:
INRA - CIRM
Location of work: CIRM-CF Marseille, France
Duration: 1 week i.e. 5 working days
Programme:
Access is organised for up to 2 users simultaneously. It typically consists of a welcome, visit of the laboratory, definition of the work plan and inoculation of the strains in culture media (day 1). Screening of the properties exhibited by the strains using the high throughput robot (days 2 – 4). Final day: interpretation of the results and writing of a final report. As it is quite likely that the screening work will take more than 3 days users will have the opportunity to prolong their stay to 2 weeks (i.e. 2 units of access)
Type of equipment/service used: high throughput screening robot and all other equipment from the facility.
Expected output/deliverables for users: screening of a large number of filamentous fungi strains, owned by the users or part of the CIRM collections.
More info on this opportunity: http://cirm.esil.univ-mrs.fr/crbmarseille/
Contact person:
Dr Laurence Lesage-Meessen
|
Centre de Ressources Biologiques de l’Institut Pasteur (CRBIP)
The CRBIP is the first BRC which keeps bacterial and fungal strains, as well as risk 3 viruses, to be certified according to the ISO 9001 standard. Services currently offered by the CRBIP are the following:
More info on this partner: www.crbip.pasteur.fr
|
6. Management of microbial strains in ex situ collections (CRBIP)
Organisation:
Institut Pasteur - CRBIP
Location of work: Laboratories of Institut Pasteur, in Paris
Programme:
Duration: as 1 week i.e. 5 working days, for up to two users.
Day 1: - Welcome
- Visit of the CRBIP
- Validation of the work plan
- Inoculation of strains in broth media (if necessary)
- Introduction to the quality system of a BRC
- Discussion with the CRBIP computer scientist concerning the CRBIP software of the management of the collection
From day 2 to 5: - Culturing and identification of the strains
- Analysis of the results
Type of equipment/service used: The CRBIP can provide to the trainees/ host scientists the possibility of working on fungi, bacteria (except anaerobic bacteria, Archaea and extremophiles) and viruses (except class 3 viruses)
Several options can be provided and will be finalized with the users.
Expected output/deliverables for users
- expertise in identification and preservation of strains
- knowledge in BRC management: - quality system of BRC
- software of collection management
The scientific data issued from the collaboration with the users led to common publications
More info on this opportunity: www.crbip.pasteur.fr
Contact person: Dr Chantal Bizet |
DSMZ - German Collection of Microorganisms and Cell Cultures
Between 2002 and 2004 the DSMZ has been listed as a large scale facility within the EU program “Improving Human Potential”. Within the project BIOREMAT (BIOlogical REsource Centre MAnagement and Training” (Contract HPRI-CT-2001-00166) access was offered to scientists and technical staff from 10 European countries.
Training in individual analytical methods used in characterization of biological material, such as the use of:
This access was both personnel-, and equipment- intense and lasted a few days to several weeks.
Taxonomic descriptions
Access (in general a few days to several weeks) was offered to users performing a thorough characterisation of microbial isolates and plant viruses that often lead to a taxonomic description of novel taxa. The DSMZ is unique in that staff is not only in the position to apply state-of-the-art taxonomic methods but also to interpret the data in the light of modern polyphasic systematics. It can be assumed that most users will actually request this range of expertise. Location: Braunschweig, Germany
More info on this partner: www.dsmz.de
Modality of access and support under this proposal
Before entering laboratories, users will be informed about national safety rules. They will then be taught in the use of individual equipment by the DSMZ staff responsible for this very facility until independence from guidance of DSMZ staff is guaranteed. Use of new equipment require introduction into its appropriate handling.
Each user or user group will have a scientific contact person and this person and the associated technical staff will be responsible for the scientific progress. Each user will be allowed to work independently and to move freely between the floors, contacting and discussing problems with DSMZ staff members of any Department. Within the framework of the polyphasic approach to taxonomy, covering multiple methods and a diverse range of equipment, located at different floors, this point is extremely important for the progress of the project. All users will take part in meetings and seminars and during their stay they are considered members of the DSMZ. DSMZ staff understands that the success of a user’s stay at the facility will be measured by the independent successful implementation of the methods and use of equipment in the home country.
|
|
7. State of the art techniques in bacteriology (DSMZ)
Organisation:
DSMZ
Location of work: Laboratories of the DSMZ, in Braunschweig, Germany
Programme (example)
Duration:
5 working days
Access is organised for up to 2 users simultaneously. It typically consists of:
Day 1: Safety instruction, familiarization with the facility. Collection management. DNA extraction of cell mass provided and PCR. Cycle sequencing reactions. Inoculation of strains on specific media.
Day 2: Fatty acid analysis. Sequencing of PCR products. BIOLOG and API tests. Base composition of DNA.
Day 3: Riboprinter. Thin layer chromatography for cell wall analyses.
Day 4: MALDI-TOF. BLAST analysis of sequences. Reading of physiological tests. Sequence alignment and determination of similarities
Day 5: Polyphasic evaluation of data. Determination of the phylogenetic and taxonomic position. Interpretation of data, discussion on publication strategy and additional steps.
Type of equipment/service used:
All DSMZ equipment used daily in research and service is open to use. This includes equipment for molecular, chemotaxonomic and phenotypic testing and analyses.
Expected output/deliverables for users:
It is the goal to teach users in techniques and strategies not available in their own facilities. Emphasis will be placed on sustainable use. These components should complement the spectrum of techniques needed to improve either taxonomic descriptions and validation regimes or quality control mechanisms.
More info on this opportunity: www.dsmz.de
Contact persons: Dr Vera Weihs / Dr Rüdiger Pukall
|
CABI Microbiological Services
Relevant services currently offered by the infrastructure
A service to develop optimal preservation and storage of microorganisms: a patent deposit service as an International Depositary Authority (IDA); a Safe Deposit service, offering customers a higher degree of service and reassurance for the long term storage of valuable isolates. Stability checking, a service to ensure the stability of production cultures by checking them against cultures in long-term storage.
CABI offers advice on the best way to store and maintain specific microorganisms, as well as providing a regular supply service to ensure that only the best cultures are used in production.
CABI provides pharmaceutical, agricultural biotech companies and related industries with lead natural products. CABI offers a range of testing and consultancy services for customers at our UKAS accredited facilities.
Identification of species and strains, training in mycological techniques, identification, preservation and biological resource collection management; In addition to the above consultancies CABI provides assistance in management of invasive species, improved production in commodities, knowledge for development opportunities and study visits.
More info on this partner:
http://www.cabi.org/microbiologicalservices
Modality of access under this proposal
CABI has over 80 years experience working with its users from study visits to tailored training programmes. The user is fully supervised and supported by technical and administrative staff: Access is given to the scientists, technologists and the equipment delivering the microbiological service the user is interested in, for example looking at the molecular integrity of an organism utilising PCR sequencing and fingerprinting facilities and where appropriate studying the production of specific metabolites, products or properties. The technologies and facilities used would include liquid handling robotics to equipment such as the ABI sequencer. The testing services would utilise the ISO 17025 facilities and appropriate test chambers; consultancies would be charged at the daily rate for consultants used. Users are appointed a supervisor and scientific results discussed in our research forum. |
8. Preservation and storage of micro-organisms (CABI Bioservices)
Organisation:
CABI Microbiological services
Location of work: Services listed above will be provided at CABI’s laboratories based in Egham, UK; Consultancies can be delivered at the user/customers premises and training courses are generally run at CABI but can be undertaken at the users venue depending on the need for access to CABI’s facilities and equipment
Programme:
Duration: 5 working days
Access is organised for up to 4 users simultaneously. It typically consists of:
Day 1: Use of facilities to develop optimal preservation and storage for a strain or species of microorganism.
Day 2: Introduction to and use of technologies to investigate the stability of preserved microorganisms.
Days 3-5: Introduction to the principles of the operation of an International Depositary Authority; Background and technologies for the identification of species and strains; Elements of establishing: a) a natural product discovery programme OR b) testing and consultancy accredited facilities OR c) assistance in management of invasive species OR d) improved production in commodities OR e) knowledge for development opportunities
The identifications will utilise the morphological or molecular technologies as appropriate/requested.
Type of equipment/service used: Equipment: microscopes; freeze driers; liquid nitrogen tanks and apparatus; programmable cooler; liquid handling robots; ABI sequencer; PCR; Services: Identification; Preservation; Challenge testing; various consultants services
Expected output/deliverables for users: Users will get optimally preserved materials; Training to high skill level compliant with OECD Best Practice; Materials tested to meet ISO 17025; Experience in the use of CABI equipment and techniques of identification and characterisation of bacteria and fungi.
More info on this opportunity:
http://www.cabi.org/default.aspx?site=170&page=1528
Contact person: Dr David Smith |
Universitat de València Estudi General (UVEG)
Colección Española de Cultivos Tipo (CECT)
The CECT, Spanish Type Culture Collection, is the only collection of microorganisms that is official and of public nature in Spain. It maintains and supplies bacteria, filamentous fungi and yeasts and since 1992 it is recognized as an International Depositary Authority (IDA) for storing microorganisms for patent purposes in accordance with the Budapest Treaty.
The main services offered are:
The CECT offers as well tailor made services if they can be tackled and fall under the expertise of its staff. Registered users of CECT account for almost 50 different countries.
More info on this partner: www.cect.org
Modality of access and support under this proposal
CECT has the capacity to accept guests for short stays, be it students or scientists, to perform tasks according to a previously agreed program under the supervision of an appointed responsible staff member of CECT. The user will be allowed to move freely within the CECT, and other facilities of the University of Valencia, such as the Department of Microbiology and Ecology, campus library, etc. The users are welcome to participate in CECT meetings and discuss their progress with the staff of CECT.
|
9. Taxonomy, identification and preservation of prokaryotes, filamentous fungi and yeasts (CECT)
Organisation:
CECT
Location of work: Research Building at the Burjassot Campus, which is one of the three main locations of the University of Valencia, Spain.
Duration: 2 weeks i.e. 10 working days for 1 user at each time
Programme:
Day 1: welcome, visit to CECT and relevant places of the campus. Theoretical explanations on taxonomy and phylogeny of prokaryotes or fungi (the combination of both is also possible). Review of the work plan.
Days 2-9: laboratory work on phenotypic characterization (biochemical, nutritional and physiological tests) and/or molecular methods (sequence analysis of 16S rRNA or other ribosomal rRNA fractions, housekeeping genes, etc.) The later may include the computerized analysis of the sequences and training on software packages such as Arb.
Day 10: interpretation of results and preparation of a draft report to be completed by the user at his/her home institution. When necessary, a list of other post-stay tasks can be prepared in order to make it the access more profitable for the user.
If requested by the user one or both of the following modules can be included as part of the unit of access: Collection management (1 day), Preservation technologies (2 days). They would be run in short sessions from day 2 to 9 together with the laboratory work mentioned above.
Type of equipment/service used: we offer our own equipment and public strain holdings as well as the access to the same services we regularly obtain from the University of Valencia (DNA sequencing, ribotyping, MALDI-TOF, electron microscopy …).
Expected output/deliverables for users:
The main goal is the training of scientists but users may also obtain as part of their stay crucial results and/or material for their research.
More info on this opportunity: www.cect.org
Contact person: Dr Esperanza Garay |
Micoteca da Universidade do Minho (MUM)
Location: Braga, Portugal
The Universidade do Minho is the fifth largest university in Portugal, with about 17000 students, and courses in almost all disciplines. The MUM was established in 1996 and is hosted by the Biological Engineering Research Centre, which is a centre of excellence integrated in the Institute for Biotechnology and Bioengineering. The Mycology and Molecular Biology Laboratory is one of the working groups of this centre. This laboratory has a long experience in applied mycology studies, namely in food and drink mycology and, in recent years efforts have also focused on mycotoxins and others secondary metabolites as well as in molecular mycology. Furthermore, in this laboratory is located the MUM. The main mission is maintain and provide fungal strains for research and teaching and wish act as a centre of expertise, information and training (MSc and PhD) in mycology. Nowadays in the Universidade do Minho the training atmosphere is related with lifelong education, e-learning, long-distance training which using new educational technologies and platforms. MUM is also involved in these new educational programmes and teaching approaches.
More info on this partner: www.micoteca.deb.uminho.pt
Services currently offered by the infrastructure
Access to our strains with on-line access to the relevant information. MUM supports technical courses, MSc and PhD students which research on mycology or use fungal material. The collection offers services for the industry (identification and consultancy). |
10. Fungal identification, preservation techniques and collection management (MUM)
Organisation:
MUM
Location of work: Micoteca da Universidade do Minho, Braga, Portugal
Programme
Duration: 1 week i.e. 5 working days for 1 user.
The visit of laboratory includes the definition of the work plan, the tutorial of the theoretical and experimental work and the final interpretation of the results. Access typically consists of:
Day 1: Introduction to the laboratory work, safe procedures and preparation of the material to be used (media, sterilization of material and introduction how to work with equipments).
Day 2: Preparation of strains to be preserved using different techniques (cryopreservation, lyophilisation, and other alternative methods).
Day 3: Theoretical part on how to identify fungal strains and use different techniques in polyphasic approach to identify, characterise and authenticate the preserved strains using classical (morphological, biochemical) and modern (molecular biology and spectral analysis using MALDI-TOF MS) methods.
Day 4: Practical part on how to identify fungal strains and use different techniques in polyphasic approach to identify, characterise and authentication of the preserved strains using classic methods (morphological, biochemical) and modern methods (molecular biology and spectral analysis using MALDI-TOF MS).
Day 5: Organization of the results and how to use them to build up databases and create management systems quality control of strains preserved in culture collections.
Type of equipment/service used: databases and culture collection management system, preservation equipment (e.g. freeze-drying), training facilities for fungal strain identification and authentication, confocal and other microscopes, MALDI-TOF MS.
Expected output/deliverables for users: collection management, fungal identification, preservation techniques.
More info on this opportunity: www.micoteca.deb.uminho.pt
Contact person: Dr Nelson Lima |
Centraalbureau voor Schimmelcultures Utrecht, The Netherlands
The Centraalbureau voor Schimmelcultures (KNAW-CBS), Utrecht, The Netherlands is an institute of the Royal Netherlands Academy of Arts and Sciences (RNAAS). It maintains a large collection of micro-organisms (60.000 fungal strains, 10.000 bacterial strains), which is embedded in the research projects of the institute. The collection is also an IDA for patented strains and is ISO 9001 certified.
The institute is a two-storey building. The Collection is located on the ground floor and contains:
-
an access-protected store area in which 10 360 l LN tanks are stored, each provided with a dynamic vapour system and connected with an automatic filling device and also with the institutes Equipment Control System, which records malfunctions and immediately warns technical people; it is also connected with an electrical aggregate in case of power failures.
- an access-protected, fire-protected area containing the freeze-dried collection at 6°C.
- An air-conditioned 17°C area for the active agar cultures. This area also contains 6°C cold-storage chests
- A medium preparation area with a destruction autoclave, glass cleaners which also open in the clean area where the media are prepared, two fully controlled medium preparation autoclaves
- A freeze-drying area with two professional fully controlled freeze dryers
- two inoculation rooms each with 2 biohazard laminar flow cabinets
- laboratory space for technicians
There are also rooms for the identification service and the database managers (bioinformatics).
The top floor contains the laboratories for the 3 project groups. They are equipped for molecular work and contain all the preparation devices. A sequencer is shared with a neighbour lab (NIOB) and is located there.
Back-up of the collections is realized in a different location.
More info on this partner: www.cbs.knaw.nl
Description of work and role of participants
KNAW has a long tradition in collaboration with guests, be it students or visiting scientists. They have to make themselves known with the KNAW safety instructions. According to an agreed program a qualified staff member is given the responsibility for the guest(s), meaning he/she has to make sure that the guest is familiar with the equipment, regulations and protocols; this scientist will remain the contact, also when the guest has demonstrated his ability to work independently. The working language usually is English.
Modality of access and support under this proposal
One staff member will be assigned to guide the participant during his/her visit.
A tailor made program optimised to the specific needs of the visitor can be arranged. |
11. Preservation, collection management, databasing, identification (CBS)
Organisation:
CBS
Location of work: CBS building, Utrecht, the Netherlands where all facilities are located.
Programme
Duration: 2 weeks i.e. 10 working days for 1 user.
Access typically consists of:
Day 1: AM: Welcome, introduction to the Collection and research programmes of the CBS; introduction to house-rules and security regulations of the institute. PM: First tour around the facilities; discussion and scheduling of the work and training programme for the visit.
Day 2: AM: introduction to principles of long-term preservation, techniques and equipment (freeze-drying and cryopreservation) by scientific staff (curators); PM: Phenotypic characterization, of cultures and, if required, other aspects of taxonomy.
Day 3-4: hands-on training in preservation of cultures by experienced technicians Part 1 (Cryopreservation or freeze-drying).
Day 5: introduction to molecular facilities and tools; genomic DNA extraction and preservation; start of work on molecular characterization of cultures for own research of the visitor.
Day 6-7: hands-on training in preservation of cultures by experienced technicians Part 2 (Cryopreservation or freeze-drying).
Day 8: molecular work continued; PCR, sequencing.
Day 9: introduction to database systems used for culture collection management; database managers will explain the design, functionality and applications of the software.
Day 10: Sequence analysis; Biolomics software for multi-character analysis.
Depending on the wishes and research topic of the visiting scientist, the programme parts can be changed in order and duration. Training may only constitute a small part of the visit.
However, topics in courses on general mycology, medical mycology and food mycology can be part of the visit. Incidentally, tailor-made courses (e.g. collection management) of up to three days long can be provided during the time of the visit.
Type of equipment/service used: databases, preservation equipment, training facilities, software.
Expected output/deliverables for users: skills in preservation, collection management, databasing, identification, results on molecular or phenotypic characterization and identification of CBS cultures in CBS and/or material of the visiting scientist.
More info on this opportunity: www.cbs.knaw.nl
Contact person: Dr Gerard Verkleij |
Belgian Coordinated Collections of Micro-organisms
The BCCM are a multi-site national microbial resource centre, offering biological materials and research-based public services in bacteriology, mycology and molecular biology.
The BCCM have the IDA statute (WIPO) and are ISO 9001:2000 certified for all aspects of accessioning, preservation, quality control, storage and supply of the biological materials and associated information of their public collections, and their patent- and safe deposit collections. The infrastructure allows the extended characterization and typing of organisms and DNAs, for collection management, scientific services and research:
-
laboratories to handle and study cultures of biohazard groups 1, 2 and 3, including quarantine and other pest organisms,
- fully equipped cell culture facility,
- facilities for preservation of cultures by freeze-drying or by cryopreservation at ultra-low temperatures,
- rooms with limited access for storage of the master- and distribution stocks under controlled conditions,
- specific storage rooms at different sites for maintaining back-up collections,
- laboratories for dedicated DNA analyses or biomolecular analyses.
More info on this partner: www.belspo.be/bccm
TRAINING OFFERED
BCCM/LMBP
BCCM/LMG
-
Training on all aspects of bacterial taxonomy, identification, and fine typing. Training is mainly offered on an individual personalized basis, and is mostly integrated in a scientific project of interest to both trainee and BCCM/LMG. In principle, all techniques and methods available are accessible for training purposes. Depending on the context of the training, there can be a bench fee involved. In many cases, a lasting scientific collaboration is the result of a successful training.
BCCM/MUCL
-
General trainings in mycology (morphology, scanning electron microscopy, molecular methods). Besides personalized trainings organized all year long, BCCM/MUCL offers twice a year two international trainings on the in vitro culture of arbuscular mycorrhizal fungi, namely "ROC system training" and "Plant-systems training” (http://emma.agro.ucl.ac.be/formation/).
Some of these abilities are offered under the grant agreement as described below. |
12. Theoretical, practical and regulatory aspects of a plasmid collection management (BCCM/LMBP)
Organisation:
BCCM
Location of work: Zwijnaarde, Belgium
Programme:
Duration: 2 weeks i.e. 10 working days.
Sessions are focusing on a) the theoretical, practical and regulatory aspects related to the management of a plasmid collection and b) the role of plasmids.
Day 1: Welcome, presentation of BCCM/LMBP, visit of the BCCM/LMBP facilities and its host laboratory, explanation of the workplan
Transformation of plasmid DNA: theoretical and practical aspects
Day 2: AM: Presentation of the BCCM/LMBP quality management system
PM: Introduction to VectorNTI: compilation of sequence files
Quality control test: purity
Subcultivation of single colonies
Day 3: Quality control test: viability
Preservation and storage of plasmids: theoretical and practical aspects
Preparation of plasmid DNA: Birnboim, Qiagen miniprep; theoretical and practical aspects
Day 4: AM: Preparation of plasmid DNA: QiaCube; theoretical and practical aspects
PM: Introduction to VectorNTI: continued
Preparation of the authenticity test: theoretical aspects
Day 5: AM: Presentation of the customer database
PM: VectorNTI: practice
Day 6: Presentation of the plasmid database
Authenticity test: analysis of the restriction enzyme pattern; practical aspects
Interpretation of the results
Day 7: Transfection of eukaryotic cells: theoretical aspects and demonstration
Construction of plasmids: importance of the PCR technique (theoretical aspects)
Day 8, 9, 10: A glance at the role of plasmids: presentations and/or internal/external visits to be decided in concert with the trainee; some subjects:
-
the role of plasmids in the analysis of signalling pathways;
-
the role of plasmids in the development of vaccines;
-
the role of plasmids in the production of biopharmaceuticals.
Wrapping up, conclusions.
Type of equipment/service used: laboratories to handle and study cultures of biohazard groups 1 and 2, rooms with limited access for storage of the master- and distribution stocks under controlled conditions, laboratories for dedicated DNA analyses or biomolecular analyses, fully equipped cell culture facility, QiaCube and all the other necessary equipment from the facility
Expected output/deliverables for users: expertise in the management of a plasmid collection according to a quality management system, expertise in basic molecular biological techniques, expertise in compiling sequence files with VectorNTI, knowledge of the role of plasmids
More info on this opportunity: www.belspo.be/bccm
Contact person: Dr Martine Vanhoucke |
|
Location of work: BCCM/LMG: Laboratory for Microbiology, Universiteit Gent, Gent, Belgium
Programme:
Duration: 2 weeks i.e. 10 working days
Day 1: Welcome, visit of the laboratories, introduction of the programme
Day 2: Discussion of the OECD guidelines for the operation of Biological Resource Centres, other regulatory laws, guidelines and recommendations (CBD, IATA, DU)
Day 3: ISO 9001:2000 certification
Day 4-5: Implementation of the different laws, standards, guidelines and recommendations at BCCM/LMG; harmonisation efforts at European level
Day 6-9: Theoretical and practical aspects of the freeze-drying technology and influence of different factors on preservation of bacteria
Day 10: Wrapping up; conclusions
Type of equipment/service used: all expertise of staff will be accessible; for the preservation part: laboratory scale freeze-dryer with monitoring probes, equipment for determination of residual moisture.
Expected output/deliverables for users: good overview of current regulations for the operation of a BRC and how to implement these; extended background on the freeze-drying process.
More info on this opportunity: www.belspo.be/bccm
Contact person: Dr Danielle Janssens |
14. Taxonomy, identification and typing of prokaryotes (BCCM/LMG2)
Organisation:
BCCM
Location of work: BCCM/LMG: Laboratory for Microbiology, Universiteit Gent, Gent, Belgium
Programme:
Duration: 2 weeks i.e. 10 working days
For this option sufficient background in bacteriology is required, and access is provided using selected sets of strains taken from the BCCM/LMG collection
Day 1: Welcome, visit of the laboratories, introduction of the programme, theoretical session on polyphasic taxonomy & classification
Day 2-9: (1) Alternating theoretical and practical sessions on following techniques and their applicability in taxonomy, identification and typing:
-
different methods for DNA preparation (hands on: 2 methods)
-
DNA fingerprinting for dereplication and for identification (hands on: repPCR, AFLP)
-
DNA sequencing and phylogenetic study (hands on: 16S rDNA gene)
-
DNA:DNA hybridisation (hands on: fluorescent microplate technique)
(2) Numerical analysis
(3) Discussion of results
Day 10: Wrapping up; conclusions
Type of equipment/services used: all expertise of staff will be accessible; standard equipment for DNA lab, including spectrophotometer, pipetting robot, PCR equipment, electrophoresis equipment, DNA sequencer, DNA reader and bioNumerics software.
Expected output/deliverables for users: good insight is polyphasic taxonomy and applicability of specific techniques for identification of typing. Sufficient knowhow for start up at own facility. Good overview of services BCCM/LMG can offer to users for identification and typing.
More info on this opportunity: www.belspo.be/bccm
Contact person: Dr Danielle Janssens |
15. In vitro Culture of Arbuscular Mycorrhizal Fungi (BCCM/MUCL)
Organisation:
BCCM
Location of work: Université catholique de Louvain, Louvain-la-Neuve, Belgium
Programme
Duration: 2 weeks i.e. 10 working days. Training concerns similar techniques and know how but on two different basic materials.
In vitro Culture of Arbuscular Mycorrhizal Fungi – Root Organ Culture
Access typically consists of:
Day 1: Session I. Continuous culture and Session II. Seed disinfection (M. truncatula) and basic micro-propagation techniques (S. tuberosum)
Day 2: Session III. HAM-P in vitro culture system preparation & maintenance
Day 3: Session IV. AM-P in vitro culture system preparation & maintenance
Day 4: Session V. Root organ in the HAM-P and AM-P in vitro culture systems
Day 5: Rehearsal of the sessions II to V
In vitro Culture of Arbuscular Mycorrhizal Fungi – Plant System
Access typically consists of:
Day 1: Session I. Continuous culture and Session II. Seed disinfection (M. truncatula) and basic micro-propagation techniques (S. tuberosum)
Day 2: Session III. HAM-P in vitro culture system preparation & maintenance
Day 3: Session IV. AM-P in vitro culture system preparation & maintenance
Day 4: Session V. Plant association in the HAM-P and AM-P in vitro culture systems
Day 5: Rehearsal of the sessions II to V
Type of equipment/service used: mycorrhizal material, benches, equipment and material in use in a collection of mycorrhizal fungi.
Expected output/deliverables for users: know how and ability to preserve and prepare mycorrhizal fungi for research purposes.
More info on this opportunity: www.belspo.be/bccm
Contact person: Dr Stéphane Declerck |
|
|
