Archive for the ‘database’ Category

Meeting report: Promoting the international exchange of mouse mutant resources

Monday, May 12th, 2014
Infrafrontier-IMPC workshop: Promoting the international exchange of mouse mutant resources, Munich, Germany, 8-9 May 2014

Infrafrontier-IMPC workshop: Promoting the international exchange of mouse mutant resources, Munich, Germany, 8-9 May 2014

This is a brief meeting report on the INFRAFRONTIER /IMPC workshop: Promoting the international exchange of mouse mutant resources, which was held in Munich, Germany, on 08-09 May 2014.
As indicated in the corresponding Infrafrontier web page: “The main objectives of the workshop were to discuss how to simplify the international exchange of mouse mutant resources and to define the procedural changes to achieve it, to review the key issues facing the mouse community and mouse repositories as well as focus on IP issues and to present best practices in sharing research tools. The workshop was targeted at the directors of major mouse repositories, IP and technology transfer experts, representatives of scientific journals and funders and attracted the attention of 70 participants.” Delegates from major mouse repositories (JAX, MMRRC, EMMA, CMMR, RIKEN BRC, CARD, MARC), mouse international projects and consortia (EUCOMM, EUCOMMTOOLS, KOMP, KOMP2, IKMC, IMPC, KMPC), other related consortia (SGC), scientific journals (Nature, PLOS), funding agencies (NIH), companies (BioDoc, Charles River, AddGene), associations (AMMRA, AMPC, FELASA, EARA), TTOs and lawyers from numerous institutions and end-users gathered to discuss about how to best promote the international exchange of mouse mutant resources.

This workshop was funded by the EC FP7 InfraCoMP project. InfraCoMP’s main objective is to coordinate the collaborative efforts between the Infrafrontier Research Infrastructure and the International Mouse Phenotyping Consortium (IMPC). The scope of this Infrafrontier-IMPC workshop in Munich included various major topics, such as:

  • to discuss about simplified procedures to effectively exchange mouse mutant resources among repositories and between repositories and end-users/customers, trying to review and fix all restrictions preventing from adequately sharing major mouse mutant resources.
  • to review the key issues currently faced by the mouse community and mouse repositories, including emerging new genome editing technologies (ZFNs, TALENs, CRISPRs) and the role of mouse archives in the international exchange of mouse mutant resources
  • to discuss on IP issues and the administrative paperwork usually associated with any transactional international negotiation involving licenses and MTAs
  • to showcase best practices, examples of successful sharing research tools that could be applied on sharing mouse mutant resources

This workshop represented a continuation towards the eventual application of the agreements included in the so-called Rome Agenda, published in 2009 (Schofield et al. 2009, Nature) where the major headlines, best practices and recommendations concerning the deposit and sharing of biological resources, including mice, ES cells and germplasm, under the least restrictive terms possible, had been already discussed and identified but, unfortunately, not sufficiently widespread nor systematically followed, in spite of new initiatives adopted by some funding agencies, enforcing public-access policies for materials associated with projects funded by the NIH or the Wellcome Trust in order to receive the allocated funds.

The impact of the new genome editing technologies on current mouse consortia and mouse archives was discussed at length and in depth, from various angles and by different speakers. It is obvious that a new logic has emerged, the updated mouse genetics toolbox and its widespread among scientists enables them to generate their mouse mutants of interest through alternative, often faster approaches. Instead of considering the new endonuclease-mediated mutations solely a threat for traditional approaches, based on ES cell clones (however using higher genetic and quality-controlled standards), it was finally interpreted as an opportunity for mouse consortia and repositories. For example, the easier and faster generation of new mouse mutations could help finishing the functional annotations of the mouse genome, for all these loci that could not be targeted or, if targeted, did not result in the corresponding mouse strain through IKMC-IMPC current approaches.

The description of innovative shipment methods, for refrigerated biological materials, or using dry-ice, as compared to the standard but more complex liquid-nitrogen dry shippers was also discussed in order to make the distribution of mouse mutant resources cheaper and easier. The new set of sperm and oocyte cryopreservation methods and the optimized associated IVF procedures, as reported by CARD, Kumamoto University, in Japan, have also greatly contributed to promote the international exchange of mouse mutant resources, avoiding the always difficult and expensive shipment of live research laboratory animals.

The legal agreements, such as Material Transfer Agreements (MTAs), governing the access to mouse mutant resources were also discussed extensively. The complexity of some of these MTAs and the often long administrative process involved for executing them, unnecessarily extends the time required to access to a given mouse mutant strain deposited in a major repository for academic use. Interesting analyses of common practices observed within the international mouse community and applied by mouse consortia were presented (Bubela et al. 2012Mishra and Bubela, 2014). The overall recommendation was, whenever possible, avoid using specific MTAs and favor the unrestrictive distribution of mouse resources through simpler “conditions of use”, as regularly applied by The Jackson Laboratory (JAX) to all their mouse strains, and by EMMA-INFRAFRONTIER, for mouse lines non-associated to specific MTAs, in order also to reduce the administrative time to the minimum. In case MTAs should be included, for academic non-commercial use, the recommendations discussed were to simplify, and unify, the document as much as possible, ideally without requesting to disclose the field of use, without imposing reach through on modifications of the received materials and clearly defining third-party use after permission has been obtained. Attribution should also be clearly encouraged. Examples of simplified MTAs, also including useful institutional versions of these agreements, can be found at KOMP. The model deployed by AddGene, a non-profit organization dedicated to efficiently distribute plasmids among the scientific community, using also simple MTA procedures, was also presented as an example of successful solution.

Overall, this intense 2-day Infrafrontier-IMPC workshop fulfilled its aims and expectations. All stakeholders in the field could openly express their opinions, fears, opportunities, problems and solutions. The Organizers should be praised for their selection of speakers, topics and participants. Now it will be the time for the most difficult part: converting the agreements and recommendations into realities, while ensuring that researchers in academia, using mouse mutant resources, have an easier, simpler and faster access to mice and/or their associated products, for the benefit of science, and knowledge advance.

Infrafrontier-IMPC workshop: Promoting the international exchange of mouse mutant resources, Munich, Germany, 8-9 May 2014

Infrafrontier-IMPC workshop: Promoting the international exchange of mouse mutant resources, Munich, Germany, 8-9 May 2014

Submit your abstract(s) to the TT2014 meeting in Edinburgh: 30 June

Sunday, May 11th, 2014
Submit your abstract(s) to the TT2014 meeting in Edinburgh: 30 June

Submit your abstract(s) to the TT2014 meeting in Edinburgh: 30 June

The submission of abstracts for the 12th Transgenic Technology (TT2014) meeting, to be held in Edinburgh (Scotland, UK), on 6-8 October, is OPEN. All TT2014 participants are encouraged to submit their work as an abstract for poster presentation at the TT2014 meeting. Authors are requested to submit an abstract with the following requirements: Title (max. 25 words), Name authors and affiliations (first author is the presenting author), and, Text of the communication (max. 400 words). Abstracts should be submitted no later than June 30, 2014. Accepted abstracts will be published in the scientific journal Transgenic Research (Springer), to which the ISTT is associated.

Posters will be on display in the exhibition area throughout the duration of the meeting. Poster boards are 1.00m wide x 2.00m high and we recommend posters do not exceed 1.50m in length. A supply of Velcro tabs will be available at the venue. No screws or double-sided adhesive tape will be allowed due to the damage they can cause to the boards. All presented Posters at the TT2014 meeting will be entitled to the Best Poster Awards, generously sponsored by Charles River.

Oral Presentations
A limited number of abstract submissions will be selected and invited to present their findings in the form of a short oral presentation within the main meeting program. Should you be interested in being considered to speak at the meeting please select the appropriate option when submitting your abstract.

Abstracts are invited on all aspects of Transgenic Technologies, including the conference themes as listed below:

  • New technologies in animal transgenesis
  • Embryo stem cells
  • Target nucleases or Editing nucleases (ZFNs, TALENs, CRISPRs)
  • Large-scale phenotyping
  • Animal Biotechnology
  • Imaging with transgenic animals
  • Mouse models of human disease
  • Zebrafish models of human disease and transgenesis
  • Animal ethics and welfare

More than 27,000 messages on animal transgenesis available to ISTT members through ISTT_list and tg-l archives

Sunday, February 9th, 2014
More than 27,000 messages on animal transgenesis available through ISTT_list and tg-l archives

More than 27,000 messages on animal transgenesis available through ISTT_list and tg-l archives

One of the most important assets of the International Society for Transgenic Technologies (ISTT), is the amount of information on animal transgenesis accummulated through the archives of the ISTT_list and tg-l email lists. Currently, more than 27,000 messages are fully available to ISTT members, conveniently organized in searchable and dynamic archives. The traditional transgenic-list (tg-l), operative since 1996 and offered from the ISTT web server since the end of 2011, has distributed over 22,000 messages since then, whereas the ISTT_list, associated and born with our Society in 2006, has disseminated some 5,000 messages, discussing both lists on almost each and every topic, issue or situation related directly or indirectly with animal transgenesis. All this endless information resource is fully available to ISTT members, through powerful search engines. Non-ISTT members subscribing to tg-l have access only to the most recent messages distributed through the tg-l, using the simple search engine, which allows simple searches and outputs the 50 most recent messages discussed on the subject of interest. In contrast, ISTT members have access to more sophysticated searching engines and the output always contains all messages archived on the matter investigated.

Obtaining granted access to these rich sources of information is very easy and cheap. Simply apply for ISTT membership! Submit now your application to become a member of the ISTT and you will get immediate and full access to all these messages.

CARD-CNB Cryopreservation Course Report

Monday, October 14th, 2013
Organizers, instructors, lecturers and participants at the CARD-CNB Cryopreservation Course, held at CNB-CSIC in Madrid, Spain, on 7-11 October 2013 and organized by Naomi Nakagata (CARD-University of Kumamoto, Japan) and Lluis Montoliu (CNB-CSIC, Madrid, Spain)

Organizers, instructors, lecturers and participants at the CARD-CNB Cryopreservation Course, held at CNB-CSIC in Madrid, Spain, on 7-11 October 2013 and organized by Naomi Nakagata (CARD-University of Kumamoto, Japan) and Lluis Montoliu (CNB-CSIC, Madrid, Spain)

This past week, 7-11 October 2013, the CARD-CNB Mouse Sperm and Embryo Cryopreservation Course was held at CNB-CSIC, in Madrid, Spain, with great success and accompanied with also great sunny weather. This was the first cryopreservation course of this kind, co-organized by Naomi Nakagata (CARD-University of Kumamoto, Japan) and Lluis Montoliu (CNB-CSIC, Madrid, Spain), were the newest methods developed by CARD, at the Nakagata lab, were demonstrated in Europe, directly by the CARD team. The instructors at this CARD-CNB course were commanded by the CARD-University of Kumamoto team, from Japan (Toru Takeo, Kiyoko Fukumoto, Tomoko Kondo, Yukie Haruguchi, Yumi Takeshita, Yuko Nakamuta and Shuuji Tsuchiyama), and additional help and collaboration was provided from the Mouse Biology Program at UC-Davis, CA, USA (Kristy Kinchen), from INIA, Madrid, Spain (Raúl Fernández), from CIEMAT, Madrid, Spain (Jesús Martínez), from USA (Jorge Sztein), from Paratechs, Lexington, KY, USA (Barbara Stone) and from CNB-CSIC (Julia Fernández, María Jesús del Hierro, Marta Castrillo and Isabel Martín-Dorado), for several of the methods demonstrated. All instructors must to be praised for their deep knowledge, patience and extraordinary dedication and commitment towards the success of this course. Complementary and most interesting lectures were provided on a wide variety of topics related to the course main focus, including: animal welfare and regulations by Belén Pintado and Jorge Guillén; the history, fundaments and comparison of methods by Jorge Sztein; the effects of the in vitro culture of mouse embryos by Alfonso Gutiérrez-Adán; safety and handling issues of liquid nitrogen by Jesús Martínez; shipping frozen and refrigerated materials by Toru Takeo, databases in a cryopreservation lab, by Shuuji Tsuchiyama, about EMMA by Lluis Montoliu and CARD by Naomi Nakagata, as examples of mouse embryo and sperm archives, and, also, on the new editing nucleases for genome modification, by Kai Schönig (Mannheim, Germany), a talk sponsored by Sigma.

As many as 24 participants, coming from research institutions or companies located in 16 countries around the world (UK, Spain, Australia, USA, Canada, Czech Republic, Brazil, Finland, France, Denmark, Israel, Netherlands, Portugal, Sweden, Italy and Taiwan) were presented with the latest advances in mouse sperm and embryo cryopreservation and all associated mouse reproductive biology ancillary techniques.

The topics covered by the course included the following major areas: obtaining sperm from mouse cauda epididymis, obtaining unfertilized mouse oocytes, three different types of in vitro fertilization techniques (using fresh, frozen or refrigerated sperm), vitrification of unfertilized oocytes and 2-cell embryos (freezing and thawing), slow-method for freezing and thawing 2-cell embryos, refrigerated sperm and 2-cell embryos, abdominal and scrotal vasectomies, three types of embryo transfer (oviduct, uterus and non-surgical, with NSET tools), freezing and thawing mouse sperm and ICSI, among many additional common methodologies used to handle mouse embryos and gametes adequately.

The course was very intensive, but the kind atmosphere created by participants and instructors was excellent and, hence, all the tight and carefully devised demonstrations and practices, packed within a very busy schedule, could be run smoothly and successfully without problems. The vast experience in running this type of cryopreservation courses and the remarkable professionality of our colleagues from CARD-University of Kumamoto were key for the accomplished success. All methods followed their three-step learning process. At first, the theory and fundaments were briefly provided and summarized. Then, the method was demonstrated by instructors and, finally, the participants executed the procedures by themselves, with the help of instructors.

The participants left this cryopreservation course to return to their countries and institutions with the most satisfactory results obtained and with plenty of new information to digest, process and reproduce. All participants were given the task to spread the word and disseminate the use of these highly efficient and robust cryopreservation techniques that have boosted the field.

This CARDCNB cryopreservation course was sponsored by the International Society for Transgenic Technologies (ISTT) and received the co-sponsorship and support from a number of companies whose contributions need to be greatly acknowledged as well: Leica, Charles River, Sigma, Labotect, Cosmo-Bio, Kyudo, Harlan and Paratechs.

The new BIOTERIOS.COM web page

Tuesday, July 16th, 2013
The new BIOTERIOS.COM web page

The new BIOTERIOS.COM web page

BIOTERIOS.COM, the reference web portal on animal experimentation and animal welfare in Spanish in Latin America, created and maintained by Juan Manuel Baamonde (Manager of the animal facility at CECs, Valdivia, Chile, and ISTT Member) since 2007, has launched a new web page, a new layout, to show its very interesting and useful contents with a renewed and modern format. Among the new features that have been added, Juan Manuel must be praised for having included a web page translator tool (found at the top-right corner of all pages) which makes now possible to automatically translate the contents of any web page within BIOTERIOS.COM into another language of choice, to be selected among English, German, French or Portughese, hence further expanding the benefits of this wonderful site to all non-Spanish-speaking colleagues that could not read nor benefit from BIOTERIOS.COM before.
The site includes articles, interviews, reports on recent meetings and plenty of information on animal experimentation and animal welfare issues. Really worth visiting and exploring! (and now in English too!).

Structural and Functional Concepts in Current Mouse Phenotyping and Archiving Facilities

Tuesday, September 18th, 2012
Structural and Functional Concepts in Current Mouse Phenotyping and Archiving Facilities

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.

EMMA Cryopreservation Workshop in Madrid: a meeting report

Friday, May 11th, 2012
EMMA Cryopreservation Workshop: a meeting report

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

Genetic differences among C57BL/6 mouse strains available from the Mouse Phenome Database

Monday, April 9th, 2012
Genetic differences among C57BL/6 mouse strains
Genetic differences among C57BL/6 mouse strains

The Mouse Phenome Database (MPD), at the Jackson laboratory web site, has recently updated their list of SNP polymorphisms for closely related strains across the entire mouse genome. The premade lists, genome-wide, ready-to-use, now include three NEW comparisons containing all currently known genetic differences (SNPs) among C57BL/6 strains, particularly between C57BL/6J and C57BL/6N mouse strains, and their related substrains (entire genome occurrences).

  1. (coding and UTR regions only, 4341 SNPs)

  2. C57BL/6J versus C57BL/6NJ (all available SNPs that are polymorphic, 152001 SNPs)
  3. 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!

World Map of Transgenic Core Facilities

Saturday, April 7th, 2012
World Map of Transgenic Core Facilities

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 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.

Course on Genetic Manipulation of ES Cells, Hinxton, Cambridge, UK, 5-18 November 2012

Monday, March 19th, 2012
Course on Genetic Manipulation of ES Cells

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

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