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At least 379 records · Page 21Linked to original sources
PubMed1999

Mean free energy topology for nucleotide sequences of varying composition based on secondary structure calculations.

The mean free energy generated from the secondary structure of RNA sequences of varying length and composition has been studied by way of probability theory. The expected boundaries or maximal and minimal values of a given distribution are explored and a method for estimating error as a function of the number of shuffled sequences is also examined. For typical nucleotide sequences found in biologically active organisms, the mean free energy, free energy distributions and errors appear to be scalable in terms of a fixed set of algorithm-dependent parameters and the nucleotide composition of the particular sequence under evaluation. In addition, a general semi-analytical formula for predicting the mean free energy is proposed which, at least to first-order approximation, can be used to rapidly predict the mean free energy of any sequence length and composition of RNA. The general methodology appears to be algorithm independent. The results are expected to provide a reference point for certain types of analysis related to structure of RNA or DNA sequences and to assist in measuring the somewhat related matter of complexity in algorithm development. Some related applications are discussed.

Algorithms↗
PubMed2004

De novo sequencing, peptide composition analysis, and composition-based sequencing: a new strategy employing accurate mass determination by fourier transform ion cyclotron resonance mass spectrometry.

A new strategy is described for the determination of amino acid sequences of unknown peptides. Different from the well-known but often inefficient de novo sequencing approach, the new method is based on a two-step process. In the first step the amino acid composition of an unknown peptide is determined on the basis of accurate mass values of the peptide precursor ion and a small number of accurate fragment ion mass values, and, as in de novo sequencing, without employing protein database information or other pre-information. In the second step the sequence of the found amino acids of the peptide is determined by scoring the agreement between expected and observed fragment ion signals of the permuted sequences. It was found that the new approach is highly efficient if accurate mass values are available and that it easily outstrips common approaches of de novo sequencing being based on lower accuracies and detailed knowledge of fragmentation behavior. Simple permutation and calculation of all possible amino acid sequences, however, is only efficient if the composition is known or if possible compositions are at least reduced to a small list. The latter requires the highest possible instrumental mass accuracy, which is currently provided only by fourier transform ion cyclotron resonance mass spectrometry. The connection between mass accuracy and peptide composition variability is described and an example of peptide compositioning and composition-based sequencing is presented.

Amino Acid Sequence↗
PubMed1996

Biodegradable bone cement compositions based on acrylate and epoxide terminated poly(propylene fumarate) oligomers and calcium salt compositions.

The synthesis of biodegradable bone cement compositions is presented. These bone cement compositions can be applied as a putty-like mixture and harden to a strong material in a bone fracture. They degrade from the site of application to allow the ingrowth of new bone for complete healing of the bone fracture. The bone cement is composed of a solid particulate phase dispersed in an initially liquid polymeric phase, which can be hardened by cross-linking. The polymeric phase is a low-molecular-weight liquid poly(propylene fumarate) (PPF) containing double bonds available for cross-linking. The solid particulate phase consists of calcium carbonate and tricalcium phosphate. PPF oligomers of Mw = 1800 and Mn = 750 were prepared from the condensation of non-volatile bis(2-hydroxypropyl fumarate) and propylene-bis(hydrogen maleate) trimers. PPF terminated divinyl and diepoxide derivatives were obtained from the reactions between PPF diol and acryloyl chloride or epichlorhydrin, respectively. Putty-like cement compositions were prepared from a mixture of 30 wt% polymer phase containing benzoyl peroxide-dimethyl toluidine as polymerization catalyst and 70 wt% calcium salts. The divinyl and diepoxide terminated PPF oligomers provided a high strength composition of between 30 and 129 MPa which is suitable for bone cement applications. In vitro hydrolysis of the composites showed little weight loss with the compressive strength remaining above 20 MPa after 4 weeks in buffer solution. Compositions of the PPF oligomers cross-linked without calcium salts showed a gradual weight loss (10-65 wt% after 4 weeks) when placed in buffer solution followed by high water absorption (18-200 wt% after 4 weeks), with the epoxide terminated PPF being the least to degrade or absorb water.

Acrylates↗