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M E Beck

Publications and source records attributed to M E Beck.

14 recordsLinked to original sources
PubMed1998

The PRINTS protein fingerprint database in its fifth year.

PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 800 fingerprints have been constructed and stored in PRINTS. The current version, 17.0, encodes approximately 4500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via the UCL Bioinformatics World Wide Web (WWW) Server at http://www. biochem.ucl.ac.uk/bsm/dbbrowser/ . We have recently enhanced the usefulness of PRINTS by making available new, intuitive search software. This allows both individual query sequence and bulk data submission, permitting easy analysis of single sequences or complete genomes. Preliminary results indicate that use of the PRINTS system is able to assign additional functions not found by other methods, and hence offers a useful adjunct to current genome analysis protocols.

Animals↗
PubMed1997

Novel developments with the PRINTS protein fingerprint database.

The PRINTS database of protein family 'fingerprints' is a diagnostic resource that complements the PROSITE dictionary of sites and patterns. Unlike regular expressions, fingerprints exploit groups of conserved motifs within sequence alignments to build characteristic signatures of family membership. Thus fingerprints inherently offer improved diagnostic reliability by virtue of the mutual context provided by motif neighbours. To date, 600 fingerprints have been constructed and stored in PRINTS, representing a 50% increase in the size of the database in the last year. The current version, 13.0, encodes approximately 3000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is accessible via UCL's Bioinformatics World Wide Web (WWW) server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser / . We describe here progress with the database, its Web interface, and a recent exciting development: the integration of a novel colour alignment editor (http://www.biochem.ucl.ac.uk/bsm/dbbrowser++ +/CINEMA ), which allows visualisation and interactive manipulation of PRINTS alignments over the Internet.

Amino Acid Sequence↗
PubMed1996

Progress with the PRINTS protein fingerprint database.

PRINTS is a compendium of protein motif 'fingerprints' derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. To date, 400 fingerprints have been constructed and stored in Prints, the size of which has doubled in the last year. The current version, 9.0, encodes approximately 2000 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbours. PRINTS thus provides a useful adjunct to the widely used PROSITE dictionary of patterns. The database is now accessible via the Database Browser on the UCL Bioinformatics server at http://www.biochem.ucl.ac.uk/bsm/dbbrowser .

Amino Acid Sequence↗
PubMed1994

PRINTS--a protein motif fingerprint database.

The PRINTS database of protein 'fingerprints' is described. Fingerprints comprise sets of motifs excised from conserved regions of sequence alignments, their diagnostic power or potency being refined by iterative database scanning (in this case the OWL composite sequence database). Generally, the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3-D space. The use of groups of independent, linearly or spatially separate motifs allows particular protein folds and functionalities to be characterized more flexibly and powerfully than conventional single-component patterns or regular expressions. The current version of the database (4.0) contains 150 entries (encoding > 700 motifs), covering a wide range of globular and membrane proteins, modular polypeptides and so on. The growth of the database is influenced by a number of factors, e.g. the use of multiple motifs, the maximization of sequence information through iterative database scanning and the fact that the database searched is a large composite. The information contained within PRINTS is distinct from but complementary to the single consensus expressions stored in the widely used PROSITE dictionary of patterns.

Amino Acid Sequence↗
PubMed1994

PRINTS--a database of protein motif fingerprints.

PRINTS is a compendium of protein motif 'fingerprints'. A fingerprint is defined as a group of motifs excised from conserved regions of a sequence alignment, whose diagnostic power or potency is refined by iterative databasescanning (in this case the OWL composite sequence database). Generally, the motifs do not overlap, but are separated along a sequence, though they may be contiguous in 3D-space. The use of groups of independent, linearly- or spatially-distinct motifs allows protein folds and functionalities to be characterised more flexibly and powerfully than conventional single-component patterns or regular expressions. The current version of the database contains 200 entries (encoding 950 motifs), covering a wide range of globular and membrane proteins, modular polypeptides, and so on. The growth of the databaseis influenced by a number of factors; e.g. the use of multiple motifs; the maximisation of sequence information through iterative database scanning; and the fact that the database searched is a large composite. The information contained within PRINTS is distinct from, but complementary to the consensus expressions stored in the widely-used PROSITE dictionary of patterns.

Amino Acid Sequence↗
PubMed1984

Cholecystokinin-octapeptide fragments: binding to brain cholecystokinin receptors.

Structural determinants of cholecystokinin octapeptide (CCK-8) binding to central nervous system receptors have been studied to assess the relative importance of the amino and the carboxyl end of the active peptide sequence, CCK-(26-33). The relative ability to inhibit equilibrium binding of [125I]CCK-33 to guinea pig cortical membranes was determined for a series of amino and carboxyl terminal fragments of CCK-8. While N-acetyl CCK-(26-29), N-acetyl CCK-(26-30) amide and N-acetyl CCK-(26-31) amide were inactive, the N-acetyl CCK-(26-32) amide fragment displayed binding to central receptors. Of the carboxyl terminal peptide fragments, both CCK-(29-33) and CCK-(30-33) bound less potently than CCK-8; CCK-(31-33) interacted more weakly than the tetra- and pentapeptide, but with a higher affinity to brain receptors than to peripheral receptors. The heptapeptide, CCK-(26-32) amide, and the tripeptide, CCK-(31-33), are known to antagonize CCK action at peripheral receptors. The heptapeptide bound to central receptors 25 times more potently than a known peripheral antagonist, dibutyryl cyclic GMP. Thus these peptides may act centrally to oppose CCK-8 mediated functions.

Amino Acid Sequence↗
PubMed1978

Potentiation of antibiotic bactericidal activity by normal human serum.

Combinations of certain antibiotics and normal human serum at concentrations at which there was no killing by the agents when used alone were found to be bactericidal for Escherichia coli K-12 cells. This effect was observed with tetracycline, streptomycin (SM), trimethoprim, and ampicillin, but not with chloramphenicol or nalidixic acid. Synergy between SM and human serum was also observed against four of nine smooth strains of E. coli. A plasmid-bearing strain of E. coli K-12 was also killed by combinations of tetracycline or SM plus serum, even though the plasmid conferred resistance to tetracycline and SM. Evidence is presented that the synergy between antibiotics and serum is due to a complement-mediated effect on the bacterial cells that makes the cells more susceptible to the bactericidal effects of the antibiotics.

Anti-Bacterial Agents↗
PubMed1978

Effects of antibiotic resistance plasmids on the bactericidal activity of normal rabbit serum.

The ability of normal rabbit serum to kill Escherichia coli J6-2 was measured. With the concentration of serum adjusted so that approximately 2% of the cells survived after 2 h of incubation, there was no killing of the same strain bearing the F-like plasmid R100. Other F-like plasmids also provided the host strain with resistance to serum bactericidal activity, whereas none of the I-like plasmids used provided the host strain with resistance. When E. coli J6-2 bore both R100 and an I-like plasmid, there was some resistance to serum but less than with R100 alone. The effects of lysozyme on E. coli J6-2, which had been treated with tris(hydroxymethyl)aminomethane and ethylenediaminetetraacetate, were not altered by the presence of R100. The plasmids from 16 clinical E. coli isolates were transferred to J6-2N, a nalidixic acid-resistant mutant of J6-2. Four of the 16 plasmids provided J6-2N with resistance to normal rabbit serum.

Animals↗
PubMed1976

Plasmid-mediated resistance to the bactericidal effects of normal rabbit serum.

An Escherichia coli K-12 strain bearing the plasmids R1 or R100 was more resistant to the bactericidal activity of normal rabbit serum than was the same strain without a plasmid. When the plasmid R100 was transferred to several K-12 strains, the strains acquired resistance to serum bactericidal activity.

Blood Bactericidal Activity↗
PubMed1975

Tetracycline resistance in Escherichia coli isolates from hospital patients.

Hospital isolates of Escherichia coli resistant to tetracycline (TC) were studied to identify mechanisms which regulate TC resistance levels and ability to transfer TC resistance. Antibiotic resistance patterns, resistance levels to TC, and ability to transfer TC resistance were determined for the isolates. Similar data were obtained for the transferable plasmids after transfer to several new host strains of E. coli. Of the 110 isolates, 50% were able to transfer TC resistance by conjugation. There was a nearly linear relationship between the minimum inhibitory concentration (MIC) of TC for the hospital strains and the percentage of strains at a given MIC that could transfer TC resistance. The strains that were simultaneously resistant to tetracycline, streptomycin, and ampicillin had relatively high MICs of TC and high ability to transfer TC resistance. These results and surveys of TC-resistant E. coli by others suggest that TC resistance levels and transmissibility may be influenced by other resistance markers. The isolates which did not transfer TC resistance by conjugation were tested for the presence of TC resistance plasmids by mobilization or by transformation with deoxyribonucleic acid from the isolates. Evidence for plasmid-mediated TC resistance was found in 92 (84%) of the 110 hospital strains.

Colicins↗
PubMed1971

Uptake of 3H-Tetracycline by resistant and sensitive Escherichia coli.

The uptakes of (3)H-tetracycline by 12 tetracycline-sensitive and 24 tetracycline-resistant Escherichia coli hospital cultures were found to be 270 and 75 nmoles of tetracycline per milliliter of cell water per 20 min, respectively. This confirms reports by other investigators who, by using only one or two cultures, suggested a relationship between tetracycline uptake and tetracycline resistance. However, minimum inhibitory concentrations of tetracycline for the cultures bore no relation to the tetracycline uptake values, suggesting that loss of tetracycline uptake may not be the primary cause of resistance. In addition there were three resistant cultures with uptake values greater than 140 and two sensitive cultures with uptakes lower than 180, raising the question of how these tetracycline-resistant cultures could grow with tetracycline at concentrations nearly as high as those found to inhibit growth of sensitive organisms. Of the tetracycline-resistant cultures, 15 were able to transfer tetracycline resistance to a recipient organism and 9 were not. Two of the cultures transferred TC-resistance to a recipient with no modification-restriction system (E. coli C) but did not transfer resistance to a recipient with a known modification-restriction system (E. coli K-12).

Ampicillin↗
PubMedDate not supplied

The PRINTS database of protein fingerprints: a novel information resource for computational molecular biology.

PRINTS is a compendium of protein motif fingerprints derived from the OWL composite sequence database. Fingerprints are groups of motifs within sequence alignments whose conserved nature allows them to be used as signatures of family membership. Fingerprints inherently offer improved diagnostic reliability over single motif methods by virtue of the mutual context provided by motif neighbors. To date, 650 fingerprints have been constructed and stored in PRINTS, the size of which has doubled in the last 2 years. The current version, 14.0, encodes 3500 motifs, covering a range of globular and membrane proteins, modular polypeptides, and so on. The database is now accessible via the UCL Bioinformatics Server on http:@ www.biochem.ucl.ac.uk/bsm/dbbrowser/. We describe here progress with the database, its compilation and interrogation software, and its Web interface.

Amino Acid Sequence↗