XINE v1 issue 3
Welcome to XINE, a Xenopus newsletter intended to disseminate information to the field at large. Currently, the newsletter is distributed whenever there is news
to report. A monthly or bi-weekly format would be preferable but this depends on contributions of information from Xenopus investigators (not much coming in so
far). If you have anything that you would like the community to be aware of, please e-mail the editor, Bruce Blumberg (email@example.com) who will include it
in the next newsletter.
Xenopus BAC libraries
We now have the details of the process that the Xenopus community can use to request the production of high quality BAC libraries. The process is described
in the attached instructions. Basically, the community needs to write a five-page-long 'White Paper' that addresses the issues requested by the instructions.
NICHD has agreed to provide funds for Xenopus BACs. This will help to ensure that the Xenopus White Paper is received favorably. HOWEVER, it is critical that
the community writes convincing arguments for Xenopus BACs. The fact that Xenopus has not been a genetic organism may be viewed very negatively by the
reviewers. So the Xenopus BAC White Paper will have to be particularly convincing. Applications will be accepted three times each year. The first
receipt date is November 15, 2001.
FIRST RECEIPT DATE - NOVEMBER 15, 2001
Instructions for proposing organisms from which to make new BAC libraries (October 9, 2001)
Over the past several years, the bacterial artificial chromosome (BAC) has emerged as the vector system of choice for the construction of the large-insert
chromosomal DNA libraries that are needed in genomic studies. Because BAC clones are relatively large and appear to faithfully represent an organism's genome,
the BAC system will also be the vehicle of choice for the isolation of targeted regions of genomic DNA from additional organisms being used in specific
biological studies, a variety of mouse strains, and even from individual humans.
With the increasing interest in genomic approaches to biological research, the demand
for new BAC libraries is expected to increase rapidly in the next several
years. To meet the need to increase the number of available BAC libraries, NHGRI, NCRR, NIMH and NICHD plan to award a set of cooperative agreements (by
December 1, 2001) to form the NIH BAC Resource Network and increase the national BAC library-making capacity.
As of November 15, 2001, the following procedure will apply to all requests from investigators who wish to the NIH-supported capacity for constructing BAC
libraries from the genome of any organism for which there is currently no BAC library or for which a new library is needed. This procedure applies to:
Requests for BAC library construction through the BAC Library Resource Network. This procedure applies only to the choice of BAC library construction targets
for the cooperative agreements funded under the NIH BAC Resource Network. Other agencies also support laboratories to construct BAC libraries and inquiries
about having BAC libraries made under that support should be directed to those agencies.
Requests for making BAC libraries from all organisms except eubacteria, archaea, and plants. The Institutes supporting the BAC Resource Network are components of
the National Institutes of Health. Accordingly, their primary missions are to develop and apply techniques of genomics and large-scale biology to the
improvement of human health and to the improved understanding of science that will lead to the improvement of human health. The sequencing of eubacterial,
archaeal, and plant genomes are more appropriate to the missions of other components of the NIH and/or other agencies.
The following is a set of instructions that describe how individuals, groups, or entire research communities can submit requests to gain access to this resource
and how decisions about allocating the capacity will be made.
1. To propose an organism as a candidate for having a BAC library constructed from its genome, a written request must be submitted to NHGRI.
a. The written request should address the following issues:
1) The importance of the organism to biomedical or biological research;
2) Uses to which the BAC library would be put, in addition to genomic sequencing;
3) The size of the research community that could potentially use the BAC library and the community's interest in and support for having a BAC library;
4) Whether the organism will be, or has been, proposed to NHGRI or another publicly funded agency for BAC-based genomic sequencing and the status of that request;
5) Other genomic resources that are available that will complement this resource;
6) The strain of the organism proposed and rationale for its selection
7) The size of the genome;
8) The availability of a source of DNA for construction of the BAC library (evidence of its quality for this purpose);
9) Specifications for the library (e.g., library depth, BAC insert size) and supporting scientific rationale for these specifications. (Note: any request for an unusual vector for a particular application must be thoroughly discussed);
10) The time frame in which the library is needed;
11) Other support that is available or has been requested for the construction of the desired library;
12) The need for an additional BAC library if one or more already exists; and
13) Any other relevant information.
b. Other NIH Institutes or Centers may subsequently decide to contribute funds to this program for the construction of a specific BAC
library using the expanded national BAC library-making capacity. In such cases, the decision about the need for preparing the library will already
have been made. A written request must be still submitted, but can be limited to a discussion of the specifications needed and DNA resources
available, so that the library maker will have the information necessary to develop a plan for making the library.
c. A written request may be submitted by an individual, a research group or a collaborative group, or by an individual(s) on behalf of an entire research community.
d. The written request should not exceed a total of five pages and must address all of the issues under 1a. If one or more issues are not
applicable to the specific request, that should be stated clearly, rather than not addressed. There is no specific form necessary for submission of
a request nor is any specific format required, but all of the issues listed in item 1a should be addressed.
e. The first set of written requests will be accepted on November 15, 2001. Thereafter, written requests will be accepted three times a year, on February 1, June 1, and October 1.
f. The written request should be submitted by e-mail to: BAC_Library_Requests@mail.nih.gov
2. A peer review committee set up by NHGRI program staff will assess
the written requests on the basis of scientific interest and strategic feasibility
based on the responsiveness to the issues described under 1a, and will establish a priority ranking for each request. The membership will be posted at
www.nhgri.nih.gov once the committee is formed. The assessment process will NOT involve the regular NIH peer review system.
a. For each organism proposed, the committee will recommend whether the NIH BAC Resource Network should accept the request and, if so, whether it
should be assigned to a high priority pool or to a standard priority pool. If the written request does not present enough information or a strong enough case to the allow the committee to come to a decision, the request will be declined and the applicant can resubmit the request at the next deadline.
b. Libraries whose construction is specifically being funded by other NIH Institutes participating in this program will automatically be
assigned to the high priority pool, unless there is a serious flaw in the proposed plan.
c. The committee's decisions will be reported yearly, in writing, by NHGRI staff to the National Advisory Council for Human Genome Research.
3. New libraries to be constructed will be chosen from the priority
pools on a schedule to be agreed upon by NHGRI staff and the laboratories participating in
the BAC Library Resource Network.
4. The BAC library Resource Network will be overseen by a BAC Resource Steering Panel of 4-6 scientists, who will regularly evaluate the program's overall progress and make recommendations to the NHGRI and participating Institutes about any adjustments that need to be made to the program. This membership of this Panel will be posted at www.nhgri.nih.gov once the committee is selected.
5. For additional information about the BAC library construction program, please contact:
Dr. Jane Peterson
Program Director, Large-scale Sequencing
National Human Genome Research Institute
Building 31, Room B2B07
National Institutes of Health
9000 Rockville Pike
Bethesda Maryland 20852-2033
Phone: (301) 496-7531
Fax: (301) 480-2770
2002 Cold Spring Harbor Course on Cell and Developmental Biology of
April 6-16, 2002
Course Instructors: Ken Cho and Jan Christian
The frog Xenopus is an important vertebrate model for studies of maternal
factors, regulation and molecular mechanisms of tissue inductions and regulation
of cell fate decisions. In addition, Xenopus oocytes and embryos provide a
powerful system in which to conduct a number of cell biological and gene
regulation assays. This course will provide extensive laboratory exposure to
the biology, manipulation and use of oocytes and embryos of Xenopus. The course
consists of intensive laboratory sessions, supplemented by daily lectures and
demonstrations from experts in cellular, experimental and molecular development.
Areas to be covered include: (i) care of adults; (ii) oocyte isolation and
embryo production; (iii) stages of embryonic development and anatomy; (iv) whole
mount in situ hybridization and immunocytochemistry; (v) microinjection of eggs
and oocytes with lineage tracers, DNA constructs, mRNA and antisense
oligonucleotides; (vi) micromanipulation of embryos, including explant and
transplantation assays; (vii) in vivo time lapse confocal imaging; (viii)
preparation of transgenic embryos; and (ix) use of Xenopus tropicalis for
genetic analyses. This course is suited both for investigators who have had no
experience with Xenopus, as well as those who have worked with Xenopus and wish
to learn new and cutting edge techniques. All applicants should have current
training in molecular biology and some knowledge of developmental biology.
2002 course guest lecturers and assistants will include:
Janet Heasman, Children's Hospital Medical Center
Naoto Ueno, National Institute for Basic Biology
Sally Moody, George Washington University Medical Center
Holly Kline, Cold Spring Harbor Laboratories
Enrique Amaya, Welcome, CRC Institute
Michael Danilchik, Oregon Health and Sciences University
Richard Harland, UC Berkeley
Ken Cho, UC Irvine
Jan Christian, Oregon Health and Sciences University
Ira Blitz, UC Irvine
Catherine Degnin, Oregon Health and Sciences University
Renee Hackenmiller, Oregon Health and Sciences University
Application Deadline is January 15, 2002.
Visit the CSHL web site for details on how to apply and possible scholarship support:
The Cold Spring Harbor Laboratory Meetings Office, 1 Bungtown Road, Cold Spring
Harbor, NY 11724-2213. tel, 516-367-8343, fax 516-367-8845. firstname.lastname@example.org
I have constructed the Xine mailing list from serveral sources. If you are not
on the list and wish to be, want to update your e-mail address or would rather
not receive it at all, please contact Bruce Blumberg (email@example.com).
Until next time.