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Biomedical subjects

B Shomer

Publications and source records attributed to B Shomer.

10 recordsLinked to original sources
PubMed1999

Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes.

The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% intercoding regions. Subdivision of intercoding regions into divergent (promoting), convergent (terminating) and sequential subregions shows that the excess of W tracts is most concentrated in the promoter regions. A particularly high excess of W tracts is observed in the first 200 bases 5' upstream of coding start sites. The data suggest that W tracts have a role in promoter function. A function as unwinding centers, analogous to the role of R.Y tracts in eukaryotes, is proposed. R.Y and K.M tracts are only modestly over-represented in the two bacteria.

Base Pairing↗
PubMed1998

Expression of allogeneic MHC class I antigens by transgenic mouse trophoblast does not interfere with the normal course of pregnancy.

Mammalian embryos express paternal histocompatibility antigens which make them potential targets for maternal immune responses. Yet, the histoincompatible fetus survives and develops normally. Down regulation of classical MHC antigen expression by trophoblast cells which are in direct contact with maternal circulation has been repeatedly shown. The trophoblast cells are unable to function properly in antigen presentation and do not induce allogeneic rejection reactions. In the present study we have created transgenic mice that express an allogeneic class I transgene whose transcription is controlled by the transferrin receptor promoter. The expression patterns of the transgene product mice from a single transgenic line were studied in each of the typical placental subpopulations. The allogeneic class I antigen was expressed in the allantoic plate region of the trophoblast, and this expression was not restricted to the endothelial region but extended also to the spongiotrophoblast, as well as the major blood vessels and in the endodermal sinuses. In contrast to the normal class I expression, prominent levels of allogeneic H-2 antigens were detected in the labyrinthine trophoblast. The fetal resorption rate in females mated with these transgenic males was not higher then the normal rate, and the embryos survived and developed normally. These data imply that the unusual expression of allogeneic class I antigens in certain trophoblast subpopulations does not affect fetal development.

Animals↗
PubMed1997

Database of p53 gene somatic mutations in human tumors and cell lines: updated compilation and future prospects.

In recent years, there has been an exponential increase in the number of p53 mutations identified in human cancers. The p53 mutation database consists of a list of point mutations in thep53 gene of human tumors and cell lines, compiled from the published literature and made available through electronic media. The database is now maintained at the International Agency for Research on Cancer (IARC) and is updated twice a year. The current version contains records on 5091 published mutations and is expected to surpass the 6000 mark in the January 1997 release. The database is available in various formats through the European Bioinformatics Institute (EBI) ftp server at: ftp://ftp.ebi.ac.uk/pub/databases/p53/ or by request from IARC (p53database@iarc.fr) and will be searchable through the SRS system in the near future. This report provides a description of the criteria for inclusion of data and of the current formats, a summary of the relevance ofp53 mutation analysis to clinical and biological questions, and a brief discussion of the prospects for future developments.

Databases, Factual↗
PubMed1997

EMBL sequence submission system--an object-oriented approach to developing interactive data collection systems through the WWW.

MOTIVATION: To enable a new way of submitting sequence information to the EMBL nucleotide database through the WWW. This process of data submission is long and complex, and calls for efficient and user-friendly mechanisms for collection and validation of information. RESULTS: Described here is a generic, object-oriented data-submission system that is being used for the EMBL database, but can easily, be tailored to serve several data-submission schemes with a relatively short development and implementation time. The program provides the user with a friendly interface that breaks the complex task into smaller, more manageable tasks and, on the other hand, acts as a pre-filter, scanning errors online.

Computer Communication Networks↗
PubMed1997

Seqalert--a daily sequence alertness server for the EMBL and SWISSPROT databases.

MOTIVATION: The aims were to: enable users to deposit complex search profiles against the sequence databases; interface to an independent Sequence Retrieval System (SRS) server through the network to perform these searches on a daily basis through the last day's updates of these databases; mail users the reformatted search results, enabling local usage when loaded by a WWW browser. RESULTS: The deposition of one to many search profiles by the user leads to a daily search of the EMBL and SWISSPROT databases. The search profile is restricted to entries that were deposited during the last 24 h by using the SRS query manager to combine search sets. If the search is successful, the resulting html page is modified from relative URLs to absolute ones, enabling local usage by loading from disk. The results are sent to the user by e-mail.

Algorithms↗
PubMed1996

Somatic point mutations in the p53 gene of human tumors and cell lines: updated compilation.

In 1994 we described a list of approximately 2500 point mutations in the p53 gene of human tumors and cell lines which we had compiled from the published literature and made available electronically through the file server at the EMBL Data Library. This database, updated twice a year, now contains records on 4496 published mutations (July 1995 release) and can be obtained from the EMBL Outstation-the European Bioinformatics Institute (EBI) through the network or on CD-ROM. This report describes the criteria for inclusion of data in this database, a description of the current format and a brief discussion of the current relevance of p53 mutation analysis to clinical and biological questions.

CD-ROM↗
PubMed1996

Information services of the European Bioinformatics Institute.

The scope of the EBI is focused on providing better services to the scientific community. Technological advancements in the hardware area provide EBI with means of producing data much faster than before, and with greater accuracy since there is now a better technical ability to produce more exhaustive searches through larger indices. Hand in hand with the technological developments, research and development work is continuing on better indexing systems and more efficient ways of establishing and maintaining the future databases. The existing links of communication between EBI and the user community are exploited to study the needs of the scientific community, to provide better services, and to enhance the quality of databases by interpreting user feedback and updates. A very important goal is to enhance the awareness of the scientific (and, maybe even more, the nonscientific) public of the importance of the modern field of bioinformatics and to introduce special meetings and courses, in which more specific subjects will be studied in depth. Another aspect of this goal is to help in constructing special bioinformatics programs in university faculties. In such programs, in contrast to the existing layout, students will pursue studies in a combined environment that provides basic training in biology and in computation. Currently, one of the main problems in the field is that scientists are either biologists, who are self-educated in the field of computers and programming, or computer scientists without sufficient knowledge of biology. It is hoped that a combined program will provide a high level of education in both fields of interest at the appropriate ratios. Building an efficient and friendly interface between the EBI and the user community is the basis for any future development. This aim is achieved by using the most modern server systems while continuously researching newer and better systems and interfaces. This task can never be complete without involvement of the user community by providing feedback to any of EBI's services. A better bioinformatics community is a necessity for any future development of the biological research aiming at a better society.

Amino Acid Sequence↗