Archive for the ‘database’ Category
Tuesday, September 18th, 2012
Structural and Functional Concepts in Current Mouse Phenotyping and Archiving Facilities
Anyone interested in building, modifying or renewing an animal (mouse) facility, with the aim of using it eventually for archiving (cryopreservation) and/or phenotyping purposes might find interesting reading the following article, which we prepared through the execution of the European Project INFRAFRONTIER.
Structural and Functional Concepts in Current Mouse Phenotyping and Archiving Facilities. Kollmus, Heike; Post, Rainer; Brielmeier, Markus; Fernández, Julia; Fuchs, Helmut; McKerlie, Colin; Montoliu, Lluis; Otaegui, Pedro J.; Rebelo, Manuel; Riedesel, Hermann; Ruberte, Jesús; Sedlacek, Radislav; de Angelis, Martin Hrabé; Schughart, Klaus . Journal of the American Association for Laboratory Animal Science, Volume 51, Number 4, July 2012 , pp. 418-435(18).
Abstract from JAALAS journal web page:
Collecting and analyzing available information on the building plans, concepts, and workflow from existing animal facilities is an essential prerequisite for most centers that are planning and designing the construction of a new animal experimental research unit. Here, we have collected and analyzed such information in the context of the European project Infrafrontier, which aims to develop a common European infrastructure for high-throughput systemic phenotyping, archiving, and dissemination of mouse models. A team of experts visited 9 research facilities and 3 commercial breeders in Europe, Canada, the United States, and Singapore. During the visits, detailed data of each facility were collected and subsequently represented in standardized floor plans and descriptive tables. These data showed that because the local needs of scientists and their projects, property issues, and national and regional laws require very specific solutions, a common strategy for the construction of such facilities does not exist. However, several basic concepts were apparent that can be described by standardized floor plans showing the principle functional units and their interconnection. Here, we provide detailed information of how individual facilities addressed their specific needs by using different concepts of connecting the principle units. Our analysis likely will be valuable to research centers that are planning to design new mouse phenotyping and archiving facilities.
Tags: animal facility, building, construction, cryopreservation, phenotyping
Posted in animal experimentation, cryopreservation, database, embryos, ES cells, facility, information, phenotyping, publication, web site | No Comments »
Friday, May 11th, 2012
EMMA Cryopreservation Workshop: a meeting report
The EMMA (European Mouse Mutant Archive) Cryopreservation Workshop took place earlier this week in Madrid, May 7-8, at the main campus of CSIC, with an excellent success, organized by EMMA, supported by the EC-7th Framework Programme and co-sponsored by the International Society for Transgenic Technologies (ISTT). Sixty participants from many countries around the world gathered to present and discuss, in depth, the latest approaches, methodologies and techniques available for the efficient cryopreservation of mouse strains, through embryo, sperm and ovary cryopreservation. In addition to invited speakers and invited participants, the workshop was attended by delegates from EMMA nodes and 12 ISTT members. As many as 21 talks were delivered, by selected invited speakers, representing the different major archiving iniatives currently existing (EMMA, MMRRC, The Jackson Laboratory, RIKEN, APN, CMMR, AMMRA) and the research and development initiatives, as well as state-of-art protocols in the field. Presentations, abstracts and pictures from this EMMA Cryopreservation Workshop are freely available to anyone interested, from the meeting web site, and can be also accessed from ISTT and EMMA web sites. The remaining presentations will be progressively added upon receiving the approval from the corresponding guest speakers.
At EMMA, we envisaged this cryopreservation workshop as a forum to brainstorm and discuss in depth the latest technological advances in cryopreservation, including sperm and embryo cryopreservation, updated IVF methods and related techniques as ovary cryopreservation, laser-assisted and piezo-driven ICSI, transportation of frozen material and other technical and logistic challenges relevant to the operation of current mouse embryo/sperm archives. We believed we entirely fulfilled the expectations and all participants went back home, to their research institutions, loaded with new ideas, updated solutions and suggested improvements that can be explored and applied for a most efficient management of a mouse embryo/sperm cryopreservation bank. All participants agreed to continue organizing this type of focused workshops in the near future. The ISTT will be always there, ready to support these very interesting initiatives.
Lluis Montoliu, EMMA Spanish node
Tags: cryopreservation, database, embryo cryopreservation, EMMA, sperm cryopreservation
Posted in co-sponsorhip, cryopreservation, database, embryos, ES cells, facility, ISTT, knock-outs, knockout, Meeting report, rodent genetics, service, sperm, transgenic research, web site, workshop | No Comments »
Monday, April 9th, 2012
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(coding and UTR regions only, 4341 SNPs)
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13 C57BL/6 mouse related strains,
J and N, including: C57BL/6J, C57BL/6ByJ, C57BL/6JArc, C57BL/6JBomTac, C57BL/6JCrl, C57BL/6JEiJ, C57BL/6JOlaHsd, C57BL/6JRccHsd, C57BL/6NCrl, C57BL/6NHsd, C57BL/6NJ, C57BL/6NNIH, C57BL/6NTac
The entire community of researchers in biomedicine using mouse genetics greatly appreciates the most useful service and helpful web resources provided by the MPD team. Thanks a lot colleagues!
Tags: C57BL/6 mice, genetic background, genetic differences, mouse genetics, Mouse Phenome Database, polymorphisms, rodents genetics, SNP
Posted in database, genes, information, rodent genetics, web site | No Comments »
Saturday, April 7th, 2012
World Map of Transgenic Core Facilities
At the International Society for Transgenic Technologies (ISTT) web site, according to the aims of our Society. we care to provide the entire scientific community with as much information as possible regarding how and where to generate genetically modified animals, particularly transgenic and knockout mice, as useful animal models for research projects in biology, biotechnology and biomedicine. One of these resources of information is the World Map of Transgenic Core Facilities, currently holding more than 125 links to web sites of transgenic core facilities located in 27 countries, world wide. The transgenic core facilities can be easily found in a list, arranged per country, or using a useful Google Maps built-in feature depicting the geographic location of each transgenic facility.
Is your transgenic core facility not yet listed in the World Map of Transgenic Core Facilities offered from the ISTT web site? No problem. Whether public or private, whether based on an academic environment or associated with a company, all transgenic core facilities, all initiatives meant to produce transgenic animals (mice, rats, other mammals, other vertebrates,…) on demand, for research purposes, are welcome and we, at the ISTT, will be pleased to include all these links in our web site. Please contact us at istt@transtechsociety.org and send us your web link and contact details of your transgenic core facility and we will be more than happy to add your transgenic core facility to the list of World Map of Transgenic Core Facilities.
Thanks for submitting the web site of your Transgenic Core Facility to the ISTT.
Tags: core facilities, link to your transgenic facility, Transgenic links, transgenic mice
Posted in database, embryos, ES cells, facility, general, genes, information, knock-outs, knockout, list, rodent genetics, transgenic, transgenic research, web site | No Comments »
Monday, March 19th, 2012
Course on Genetic Manipulation of ES Cells
Course on Genetic Manipulation of ES Cells, 5-18 November 2012
Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Deadline for applications: 6 July 2012
Course summary
This laboratory-based training course will provide a comprehensive overview and practical laboratory experience of the genetic manipulation of mouse ES cells for a broad range of applications. Recent advances in genome informatics, recombineering, transposon technology and uses of conditional gene targeting will be covered in lectures by both instructors and invited expert speakers and through interactive demonstrations.Laboratory work will focus on the culture and transfection of ES cells, design and construction of gene targeting vectors from BACs by recombineering, genotyping of gene targeting events and the practical use of transposon technology. Participants will also be trained in the informatics and practical use of public gene targeting resources being produced by the IKMC (International Knockout Mouse Consortium).
Course instructors
Professor Francis Stewart (Dresden University of Technology, Dresden, Germany)
Dr William Skarnes (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Pentao Liu (Wellcome Trust Sanger Institute, Cambridge, UK)
Dr Barry Rosen (Wellcome Trust Sanger Institute, Cambridge, UK)
The Course programme includes the following topics:
1. Informatics
The informatics underlying the visualization of gene structures and the design of gene targeting vectors, recombineering oligos and genotyping primers will be demonstrated. Students will also run their own gene targeting designs using web-based tools.The informatics of locating existing public IKMC gene targeting resources will also be covered.
2. Recombineering of Gene Targeting Vectors
Students will build a variety of targeting constructs from BACs using recombineering technology. The theoretical principles underlying both recombineering and rational targeting vector design will be emphasized by both lectures and practical exercises.
3. ES Cell Culture
Students will learn feeder-dependent and feeder-free culture of ES cells derived from 129 and C57BL/6 mouse strains.ES cell colonies will be picked, expanded and frozen and subsequently thawed to test their integrity.
4. Gene Targeting in ES Cells
Students will electroporate conditional gene targeting constructs into ES cells and learn to genotype cells by LR-PCR and qPCR-based methods.
5. Transposon Technology
Students will be introduced to the uses of the highly efficient piggyBac transposon system for expression, mutagenesis and mouse induced pluripotent stem cell (iPS) cell generation.
6. Modular Targeting Resources
Students will assemble a variety of modular knock-in targeting vectors from IKMC resources and analyse their integrity.Recombination Mediated Cassette Exchange (RMCE) using Flp and Cre recombinases will be used to modify IKMC conditional alleles directly in ES cells.
Additional information and instructions to apply are available from the web site of this course
Tags: IKMC, mouse ES cells, practical course
Posted in course, database, ES cells, general, information, knock-outs, knockout, practical course, transgenic research, web site | No Comments »
Friday, February 24th, 2012
- Project Offer: Website design/update, maintenance and technical support for the ISTT
The International Society for Transgenic Technologies (ISTT) plans to update its website and is seeking individuals/companies capable of developing a new concept for the site, modern, professional, appealing and adapted to the projects, events and activities associated with the ISTT.
Layout should be based on a CMS (Drupal, Joomla, Concrete or similar), for ease of update and modification of web content by identified individuals with publishing permissions. The new concept may include defining new letter types, sizes and colours, to be used consistently throughout the website.
Additional details for this PROJECT OFFER can be obtained from this detailed document.
Interested candidates should contact ISTT by email (istt@transtechsociety.org) and include a CV, list of projects developed/portfolio of previous work, proposed budget and references, as well as any additional information that could be relevant for this project. Applications are requested by March 31st, 2012.
Ideally, the website design proposals should be prepared for review on a test web server, although alternative methods are available if needed (please contact the ISTT for details). A basic layout for the new website proposal, showing the concept of the new design and including illustrative examples of functionality are required for evaluation purposes. Thereafter, upon selection and agreement on conditions, the selected candidate will develop the entire new website for the ISTT.
Projects will be assessed by quality, functionality, ease in modifying web contents, integration with server and associated costs. Candidates can be based anywhere in the world. Selected candidates for this project and technical support may be invited for an interview through Skype.
Tags: ISTT, ISTT website
Posted in database, general, information, ISTT, membership, online boks, publication, transgenic research, TT meeting, web site | No Comments »
Thursday, January 12th, 2012
ISTT co-sponsors Course on Managing Mouse Colonies: Genetics, Breeding & Welfare (6-8 June 2012, WTGC, Hinxton, UK)
The International Society for Transgenic Technology (ISTT) is most pleased to announce the co-sponsorship of the 2012 Edition of the popular training Course on Managing Mouse Colonies: Genetics, Breeding & Welfare, organized as a collaborative effort by four institutions: MRC Harwell, the Leeds Institute of Molecular Medicine, the RSPCA Transgenic Training Working Group (TTWG) and the Wellcome Trust Sanger Institute. The course will be held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, on June 6-8 June 2012. Registration deadline: 29 February 2012. ISTT members are entitled to a reduced registration fee.
This training Course aims to introduce experienced technicians and scientific staff involved with the management of genetically-modified mouse colonies to best practice with respect to the 3Rs and animal welfare. The programme covers historical and current best practice in the maintenance of genetically-modified mouse colonies for scientific research and the differing disciplines involved in production, phenotyping and archiving. Topics covered will include: Topics covered will include: nomenclature, basic colony management, maintaining transgenic and gene-targeted lines, breeding for experimental purposes and maintenance of high health status colonies.
Scientific organisers
James Bussell Wellcome Trust Sanger Institute, UK, ISTT member
Neil Dear Leeds Institute of Molecular Medicine, UK
Nikki Osborne RSPCA, UK
Sara Wells Medical Research Council, Harwell, UK
Keynote speakers
Karen Steel Wellcome Trust Sanger Institute, UK
Ian Jackson Medical Research Council Human Genetics Unit, UK
Confirmed tutors
James Bussell Wellcome Trust Sanger Institute, UK, ISTT member
Neil Dear Leeds Institute of Molecular Medicine, UK
Adrian Deeny University College London, UK
Martin Fray Medical Research Council, Harwell, UK, ISTT member
Richard Houghton Wellcome Trust Sanger Institute, UK, ISTT Member
Natasha Karp Wellcome Trust Sanger Institute, UK
Nikki Osborne RSPCA, UK
Sara Wells Medical Research Council, Harwell, UK
Jacqui White Wellcome Trust Sanger Institute, UK
Ben Woodman Leeds Institute of Molecular Medicine, UK
Tags: animal experimentation, animal welfare, Managing Mouse Colonies Course, practical course, Welfare
Posted in animal experimentation, animal welfare, bioethics, coat color, course, cryopreservation, database, embryos, ES cells, facility, general, genes, information, ISTT Members, knock-outs, legislation, phenotyping, pigmentation, practical course, rodent genetics, rules, sperm, transgenic research, web site, workshop | No Comments »
Thursday, June 16th, 2011
Targeting strategies and constructs used by KOMP-CSD and EUCOMM
Today’s issue of Nature includes the article reporting the great initiative, efforts and results achieved so far by the International KnockOut Mouse Consortium (IKMC) towards the systematic gene-targeting of the mouse genome, aiming to functionally annotate and thus deciphering the precise role of all genes encoded by a mammalian genome (mouse), most similar to the human genome. The authors are members of the KOMP (the National Institutes of Health Knockout Mouse Program) and EUCOMM (the European Conditional Mouse Mutagenesis) international projects.
In this work, the authors report the establishment of a high-throughput gene-targeting efficient strategies and a successful pipeline to produce reporter-tagged, conditional alleles on an unprecedent scale. As they report, “more than 12,000 vectors and 9,000 conditional targeted alleles“ have been produced so far. Targeted ES cells and targeting vectors are available from KOMP and EUMMCR. Mice derived from EUCOMM ES cells are available as live animals or cryopreserved embryos from EMMA.
A conditional knockout resource for the genome-wide study of mouse gene function
William C. Skarnes, Barry Rosen, Anthony P. West, Manousos Koutsourakis, Wendy Bushell, Vivek Iyer, Alejandro O. Mujica, Mark Thomas, Jennifer Harrow, Tony Cox, David Jackson, Jessica Severin, Patrick Biggs, Jun Fu, Michael Nefedov, Pieter J. de Jong, A. Francis Stewart & Allan Bradley. Nature 474 (337-342) Date published: 16 June 2011 DOI: doi:10.1038/nature10163
Additional comments available here.
Tags: functional genomics, high-throughput, knockout mice, mouse ES cells
Posted in database, embryos, ES cells, gene trap, general, genes, information, knock-outs, knockout, mouse strains, web site | No Comments »
Monday, May 30th, 2011
TT2011 Meeting: 24-26 October 2011, Trade Winds Island Grand Resort, St Pete Beach, Florida, USA
The 10th Transgenic Technology meeting (TT2011) will be held at the Trade Winds Island Grand Resort, in St Pete Beach, Florida, USA, on 24-26 October 2011, organized by the International Society for Transgenic Technologies (ISTT). The first deadline for submitting abstracts and applying for the various awards (Registration and Young Investigator Awards) will be due in about one month, on 30th June 2011. Accepted abstracts will be published in the scientific journal Transgenic Research, associated with the ISTT. Results from the various awards will be communicated by 16th July 2011.
Please, mark the TT2011 meeting in your agendas and don’t miss this opportunity to discuss the latest developments on Transgenic Technologies, at the International Level, with the world experts in the field. Looking froward to receive your latest work, experiments, designs, developments, your hottest research achievements using genetically modified animals.
Tags: ISTT, ISTT Members, registration awards, Transgenesis, transgenic mice, transgenic research, TT2011 Meeting
Posted in animal experimentation, animal welfare, cryopreservation, database, embryos, ES cells, genes, information, iPS cells, ISTT, ISTT booth, ISTT Prize, knock-outs, knockout, meetings, phenotyping, rat, rodent genetics, sperm, Springer, transgenic, transgenic research, travel awards, TT meeting, web site, Young Investigator Award | No Comments »
Tuesday, February 22nd, 2011
Course on Managing Mouse Colonies: Best Practices, Genetics, Breeding and Welfare, June 13-16, 2011, WTCC, Hinxton, UK
The International Society for Transgenic Technologies (ISTT) is happy to support the second edition of the Course on Managing Mouse Colonies: Best Practices, Genetics, Breeding and Welfare, organized as a collaboration between MRC Harwell, the Leeds Institute of Molecular Medicine and the Wellcome Trust Sanger Institute, and aiming to introduce experienced technicians and scientific staff involved with the management of genetically-modified mouse colonies. The Course will be held at the Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK, on June 13-16, 2011, and is organized by James Bussell (WTSI), ISTT Member; Neil Dear (LIMM) and Sara Wells (MRC). Application deadline is April 1, 2011.
The course looks at historical and current best practice in the maintenance of genetically-modified mouse colonies for scientific research and the differing disciplines involved in production phenotyping and archiving. All of these are presented with particular attention to the 3Rs and animal welfare. Confirmed tutors attending this course include:
James Bussell, Wellcome Trust Sanger Institute, UK
Michael Cheeseman, Medical Research Council, Harwell, UK
Neil Dear, Leeds Institute of Molecular Medicine, UK
Adrian Deeny, University College London, UK
Martin Fray, Medical Research Council, Harwell, UK
Ian Jackson, Medical Research Council Human Genetics Unit, UK
Sarah Johnson, Medical Research Council, NIMR, UK
Natasha Karp, Wellcome Trust Sanger Institute, UK
Raffaele Matteoni, European Mouse Mutant Archive DataBase, Italy
Karen Steel, Wellcome Trust Sanger Institute, UK
Sara Wells, Medical Research Council, Harwell, UK
Jacqui White, Wellcome Trust Sanger Institute, UK
Ben Woodman, Leeds Institute of Molecular Medicine, UK
The Organizers of this 2nd Edition of the Course hope again to attract a very diverse group of participants from a Scientific, Veterinary and Animal Technology background. This in itself provided a great dynamic when discussing the various routines and concepts involved with genetically-modified mouse production, maintenance, utilisation and cryopreservation. Underpinning this are the good practices associated with animal welfare and the 3R’s.
Tags: animal experimentation, animal welfare, course
Posted in animal experimentation, animal welfare, course, cryopreservation, database, facility, general, information, practical course, transgenic research, web site | No Comments »
