Biomedical subjects

Mark Reynolds

Publications and source records attributed to Mark Reynolds.

3 recordsLinked to original sources

PubMed2003

Gap mapping: a paradigm for aligning two sequences.

Pairwise sequence alignment is one of the most essential tools in comparative genomic sequence analysis. It is used to compare the sequences of genes and proteins with the aim of inferring structural, functional and evolutionary relationships. However, current 'mainstream' alignment algorithms have optimisation criteria based primarily on computational efficiency using parameters such as gap penalties, which are not biologically motivated. In addition, current alignment algorithms such as the Smith and Waterman technique provide a single alignment that could be sensitive to rather arbitrary choices in parameters such as gap penalties. This paper explores the range of properties resulting from posing the alignment problem more as a 'mapping gaps in sequences' exercise. We argue that this approach is intuitive and provides greater control over the number of gaps placed within an alignment. This type of approach was proposed by Sankoff (1972), but unfortunately has not received much attention. We report and discuss our findings by comparing this approach to other techniques using structurally confirmed aligned sequences from a benchmark alignment database. Interestingly, this approach consistently provides optimal and near optimal alignments and is thus a viable approach to sequence alignment.

Algorithms↗

PubMed2002

The effect of substituents on the phenyl portion of the imido ligand on the structure and properties of molybdenum(VI) imido complexes.

Anilines with alkyl substituents on the phenyl ring (ArNH2 = 2,4,6-trimethylaniline; 2,3-, 2,4-, 2,6-, and 3,4-dimethylaniline; and 2,6-diisopropylaniline) react with MoO(X)2(dtc)2 (X = Cl or Br; dtc = diethyldithiocarbamate) in methanol in the presence of 2 equiv of triethylamine to form ionic imido complexes of the type [MoNAr(dtc)3]2[Mo6O19] or MoNAr(dtc)3]4[Mo8O26]. The same reaction in THF with butyllithium as base yields imido complexes of the type MoNAr(X)2(dtc)2. The structures of three ionic, five chloro, and two bromo complexes have been determined by X-ray crystallography. In all complexes, the molybenum center is a distorted pentagonal bipyramid. While the structures are similar, the angles of the imido linkages differ. The effect of the substituents on the phenyl ring of the imido ligand on the 95Mo NMR chemical shifts was determined. The Mo nucleus becomes more deshielded with the substituents in the following order: 3,4-Me2 < 2,3-Me2 < 2,4-Me2 < 2,6-Me2 < 2,4,6-Me3 < 2,6 isopropyl. Complexes with more deshielded 95Mo centers tend to have angles of the imido linkage that are closer to 180 degrees.

Journal Article↗

PubMed2002

The encapsulation of ribozymes in biodegradable polymeric matrices.

Ribozymes are catalytic RNA that bind and cleave specific regions of target RNA. Therefore, protein synthesis by the target RNA may be specifically inhibited by ribozymes. However, ribozymes are rapidly cleared from plasma so effective treatment of proliferative diseases may rely on the repeated administration of these agents to maintain therapeutic ribozyme concentrations. Therefore, the objective of this study was to encapsulate ribozymes in injectable polymeric paste and microsphere formulations to allow for the controlled release of these agents over extended periods of time. Ribozymes were effectively encapsulated in poly(L-lactic acid) (PLLA) and poly(lactic-co-glycolic) (PLGA) microspheres in various size ranges using a modified water-in-oil-in-water emulsion system and in poly(epsilon-caprolactone) (PCL) pastes by physical blending. These formulations released non-degraded ribozymes, in vitro, in a controlled manner. PLLA microspheres released the ribozymes rapidly whereas PLGA released drugs more slowly. The release rate of ribozymes from PCL pastes could be effectively controlled by altering the loading concentration of ribozymes in the paste. These polymeric injectable formulations of ribozymes may allow for the extended treatment of localized disease sites, such as cancer and arthritis, without the need for repeated dosing.

Biodegradation, Environmental↗