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Biomedical subjects

M J Wise

Publications and source records attributed to M J Wise.

11 recordsLinked to original sources
PubMed2001

0j.py: a software tool for low complexity proteins and protein domains.

Low complexity proteins and protein domains have sequences which appear highly non-random. Over the years, these sequences have been routinely filtered out during sequence similarity searches because interest has been focused on globular proteins, and inclusion of these domains can severely skew search results. However, early work on these proteins and more recent studies of the related area of repeated protein sequences suggests that low complexity protein domains have function and therefore are in need of further investigation. 0j.py is a new tool for demarcating low complexity protein domains more accurately than has been possible to date. The paper describes 0j.py and its use in revealing proteins with repeated and poly-amino-acid peptides. Statistical methods are then employed to to examine the distribution of these proteins across species, while keyword clustering is used to suggest roles performed by proteins through the use of low complexity domains.

Algorithms↗
PubMed1999

Quantitative, scalable discrete-event simulation of metabolic pathways.

DMSS (Discrete Metabolic Simulation System) is a framework for modelling and simulating metabolic pathways. Quantitative simulation of metabolic pathways is achieved using discrete-event techniques. The approach differs from most quantitative simulators of metabolism which employ either time-differentiated functions or mathematical modelling techniques. Instead, models are constructed from biochemical data and biological knowledge, with accessibility and relevance to biologists serving as key features of the system.

Algorithms↗
PubMed1997

Peptide-mass fingerprinting and the ideal covering set for protein characterisation.

The rules that govern the dynamics of protein characterisation by peptide-mass fingerprinting (PMF) were investigated through multiple interrogations of a nonredundant protein database. This was achieved by analysing the efficiency of identifying each entry in the entire database via perfect in silico digestion with a series of 20 pseudo-endoproteinases cutting at the carboxy terminal of each amino acid residue, and the multiple cutters: trypsin, chymotrypsin and Glu-C. The distribution of peptide fragment masses generated by endoproteinase digestion was examined with a view to designing better approaches to protein characterisation by PMF. On average, and for both common and rare cutters, the combination of approximately two fragments was sufficient to identify most database entries. However, the rare cutters left more entries unidentified in the database. Total coverage of the entire database could not be achieved with one enzymatic cutter alone, nor when all 23 cutters were used together. Peptide fragments of > 5000 Da had little effect on the outcome of PMF to correctly characterise database entries, while those with low mass (near to 350 Da in the case of trypsin) were found to be of most utility. The most frequently occurring fragments were also found in this lower mass region. The maximum size of uncut database entries (those not containing a specific amino acid residue) ranged from 52,908 Da to 258,314 Da, while the failure rate for a single cutter in identifying database entries varied from 10,865 (8.4%) to 23,290 (18.1%). PMF is likely to be a mainstay of any high-throughput protein screening strategy for large-scale proteome analysis. A better understanding of the merits and limitations of this technique will allow researchers to optimise their protein characterisation procedures.

Amino Acid Sequence↗
PubMed1997

Better cutters for protein mass fingerprinting: preliminary findings.

Peptide-Mass Fingerprinting (PMF) encompasses a number of techniques for protein characterization which have as a first step the cleaving of target proteins by chemical or enzymatic reagents. Software systems exist which perform similar analyses. However, this is the first study which examines theoretically the effectiveness of the particular reagents for PMF. In this study, the task of PMF was to identify every sequence in a non-redundant protein database, via "in silico" digestion with theoretical proteases. From these experiments, some conclusions are drawn about the characteristics of better reagents and the experimental conditions which are more likely to be useful for PMF. The need for strongly non-redundant databases is also highlighted.

Amino Acid Sequence↗
PubMed1995

Neweyes: a system for comparing biological sequences using the running Karp-Rabin Greedy String-Tiling algorithm.

A system for aligning nucleotide or amino acid biosequences is described. The system, called Neweyes, employs a novel string matching algorithm. Running Karp-Rabin Greedy String Tiling (RKR-GST), which involves tiling one string with matching substrings of a second string. In practice, RKR-GST has a computational complexity that appears close to linear. With RKR-GST, Neweyes is able to detect transposed substrings or substrings of one biosequence that appears rearranged in a second sequence. Repeated substrings can also be detected. Neweyes also supports a form of matching-by-group that gives the effect of different amino acid mutation matrices. Neweyes can be used in a macro mode (searching a database for a list of biosequences that are similar to a given biosequence) or in a micro mode, where two biosequences are compared and more detailed output formats are available.

Algorithms↗
PubMed1982

A view of delayed parenting: some implications of a new trend.

The voluntary postponement of childbearing until after age 30 has become much more common, especially as new opportunities for women have emerged. Little is understood about the psychological impact on parenting and on children of women's reordering of priorities with greater emphasis on work outside the home. The assumption is made and corroborated that older mothers, who have developed competence in the world before childbearing, bring to the mothering experience strengths and shortcomings different from those of their younger counterparts. The same is assumed to be true of fathers. In a study of "on time" and delayed parenting, we found older mothers with established careers to be generally more accepting and less conflicted in the parenting role than were younger professional women. They revealed strengths which were concomitant with their level of maturity and which seemed generally advantageous for their children's development. This study suggests the need for further inquiry into the profound impact on children of parental developmental achievements and indicates that the controversy about working versus nonworking mothers may be of much less importance than an understanding of adult development and its impact on the quality of parenting.

Adult↗
PubMed1977

Contraceptive use and pregnancy planning in the Hutt Valley.

This survey, carried out in an area where there are good family planning services, demonstrates that such surveys can be successfully carried out in New Zealand where so far there is little data on contraceptive practice and pregnancy planning. This article compares failure rates of several contraceptive methods and shows that most women in the survey sample had had some experience in contraception during the previous three years. Pregnancy planning overall is seen as poor, with 29.9 percent of all pregnancies being unwanted at the time of conception.

Adult↗