Edition 8 - November, 2000
Edition 8 - November, 2000 |
A Guided Tour through the BCCM/LMBP On-line Plasmid Database |
|
The circular DNA of a plasmid by Scanning Electron Microscopy |
Ever since its founding in 1977, the BCCM/LMBP Plasmid Collection has, along with its concern for the high-standard safekeeping of plasmid deposits, devoted a great deal of effort to the provision of detailed information about its resources. The collection currently holds over 1,900 plasmids, mainly of the recombinant type. From an operational point of view, they can be arranged into two groups. The "vectors" group contains plasmids intended for primary cloning and high-level expression of coding sequences (derived from a variety of organisms) in bacteria, yeasts, fungi and animal cells. The second group focuses on recombinant constructs that carry cloned genes coding for a variety of proteins from prokaryotic as well as eukaryotic sources. All plasmids are described in full molecular detail, whenever possible at the DNA-sequence level. A standardized database of biological and structural features has been established for this purpose. The database contains a detailed description of the functional elements of the plasmid, such as cloned genes, promoters, transcriptional and translational control elements, as well as full details on the construction of the plasmid, its application areas, the required host strains, selection markers and other instructive details. The BCCM/LMBP database is structured in accordance with the standard recommendations for validated information, as set forth and agreed to by the major European Culture Collections in the CABRI 2 project. The management of the biological resources of the BCCM/LMBP complies with the specifications of the CABRI quality-control guidelines. The management of the related information services complies with the CABRI guidelines for catalogue production.
The 1998 edition of the LMBP Plasmid Catalogue lists some 500 items, grouped in eight functional categories, such as General Purpose Vectors, Expression Vectors, Reporter Genes, and Cytokines. Each entry comes with a descriptive data sheet as well as a size-calibrated circular map showing the location of functional features and all the relevant restriction sites. However instructive a hard-copy catalogue may be, it suffers from two major drawbacks: it is impracticable to provide the potential client with timely additions of new entries, and finding one's way through the mass of information is not always easy. A major breakthrough to resolve both problems came about with the now commonly available capabilities of the World Wide Web. Internet and its related technologies have revolutionized both the timeliness and the format with which an ever more rapidly growing body of information can be accessed. In order to meet the increasing demand for direct user access, BCCM/LMBP has made its plasmid database available world wide through the BCCM Home Page (http://www.belspo.be/bccm). This site introduces the reader to the activities of the Belgian Coordinated Collections of Microorganisms (see also page 1) and guides him or her to the LMBP database.
The plasmid catalogue can be selected out of the four BCCM catalogues by surfing from the BCCM Home page to "Catalogues - Strains/Plasmids". Before describing the actual search procedures, it is useful to clarify the contents of the scrollable windows: FIELDS and LISTS OF VALUES.
Fields:
Each window offers fifteen specific categories of information lines that together
describe a given plasmid. Examples are: (i) Plasmid group: indicating the functional
category in which the plasmid is classified (e.g. Expression Vectors, Reporter
Genes), (ii) Remarks: peculiar features, special functions, queries about fine
structure, (iii) Reference: original publication in which the element is described.
The more important of these fields are further detailed in the lists of values.
Lists of values:
Seven scrollable windows provide a detailed overview of strictly defined features
of any given plasmid. They are particularly useful in a directed search for
a plasmid with a virtually unique combination of properties.
There are several angles from which you may wish to interrogate the database.
Let us first consider the approach in which you know the name of the plasmid.
In this case, the name is clicked on in the box, Name, after which "Run Query"
is activated. A new screen will appear directing you to the description of the
plasmid (see viewing the results of your search). More frequently, however,
you will want to scan the database for plasmids that meet certain functional
requirements. Such is the case, for example, if you are looking for an expression
vector that can be propagated in Escherichia coli and that contains the specific
regulatory elements for expression of a cloned gene in mammalian cells.
This is a kind of query where the search function of the database becomes an
operational tool for identifying those entries that meet the requirements. For
this purpose, the database can be consulted, (i) by a simple search based on
free text, (ii) by an advanced search using the defined descriptions from the
LISTS OF VALUES boxes, or (iii) by a combination of the two.
|
The simple search step-by-step
|
The advanced search step-by-step
|
When this search strategy is used, it should be noted that the phrasing of the query in the text boxes determines the search results.
The Advanced Search is the most certain way of obtaining complete and problem-solving answers.
The search result consists of an alphabetical list of plasmids answering the particular search criteria. Further information can be obtained by clicking on the plasmid name. The following possibilities will be presented.
The presented data sheet contains the more important fields out of the database. The full data sheet together with the reconstructed nucleotide sequence file is supplied to the client with the order.
The circular map of the plasmid is displayed on the screen and shows all its functional features. The start of the nucleotide sequence is always situated at 12 o'clock. The numbering is clockwise. Unique restriction sites are indicated in blue characters, and non-unique restriction sites are indicated in green, which are displayed only when important in the construction or the application of the plasmid. The location of the features and the restriction sites shown on the maps are in most cases approximations. For precise positioning, the sequence file should be consulted. The maps of the plasmids that contain regions of unknown sequence should be interpreted with caution. In these cases, the sites indicated as unique should be read as "unique in the sequenced part of the plasmid".
Circular map of pCAGGS-mCASP-1 (LMBP 4175). The arrows in the circle represent the functional features of the plasmid. Unique restriction sites are indicated in dark characters; non-unique restriction sites are light-coloured. |
When this page is opened, a plasmid map is presented that is not completely
displayed on the screen. However, the print function of your browser will produce
a quality hard copy of the complete circular map with the specifications as
given above. An example is shown in the figure beneath. Black and white prints
will show the non-unique sites in a lighter shade of grey.
The LMBP staff gratefully acknowledges the contributions of the IT team of the
Department of Molecular Biology (LMBP's host laboratory) and the BCCM coordination
team in the realization of the on-line database.
Enjoy searching the BCCM/LMBP catalogue and visit our site regularly as the
database is frequently updated. And, if your search turns up a plasmid that
lacks that one extra feature you desire, please don't hesitate to contact the
LMBP. We will be happy to perform a further in-house search.
Authors:
M. Vanhoucke, M. Beernaert and E. Remaut
Contact
Mr. Martine Vanhoucke
Tel.:+32 9 264 53 47
Fax: +32 9 264.53.48
E-mail: bccm.lmbp@dmb.rug.ac.be
 BCCMHome |
Contents Edition 8 - november, 2000 |
Next Article Edition 8 - november, 2000 |
