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Biomedical subjects

Michael L Raymer

Publications and source records attributed to Michael L Raymer.

5 recordsLinked to original sources
PubMed2006

Amino acid cost and codon-usage biases in 6 prokaryotic genomes: a whole-genome analysis.

For most prokaryotic organisms, amino acid biosynthesis represents a significant portion of their overall energy budget. The difference in the cost of synthesis between amino acids can be striking, differing by as much as 7-fold. Two prokaryotic organisms, Escherichia coli and Bacillus subtilis, have been shown to preferentially utilize less costly amino acids in highly expressed genes, indicating that parsimony in amino acid selection may confer a selective advantage for prokaryotes. This study confirms those findings and extends them to 4 additional prokaryotic organisms: Chlamydia trachomatis, Chlamydophila pneumoniae AR39, Synechocystis sp. PCC 6803, and Thermus thermophilus HB27. Adherence to codon-usage biases for each of these 6 organisms is inversely correlated with a coding region's average amino acid biosynthetic cost in a fashion that is independent of chemoheterotrophic, photoautotrophic, or thermophilic lifestyle. The obligate parasites C. trachomatis and C. pneumoniae AR39 are incapable of synthesizing many of the 20 common amino acids. Removing auxotrophic amino acids from consideration in these organisms does not alter the overall trend of preferential use of energetically inexpensive amino acids in highly expressed genes.

Adaptation, Biological↗
PubMed2005

Empirical analysis of the STR profiles resulting from conceptual mixtures.

Samples containing DNA from two or more individuals can be difficult to interpret. Even ascertaining the number of contributors can be challenging and associated uncertainties can have dramatic effects on the interpretation of testing results. Using an FBI genotypes dataset, containing complete genotype information from the 13 Combined DNA Index System (CODIS) loci for 959 individuals, all possible mixtures of three individuals were exhaustively and empirically computed. Allele sharing between pairs of individuals in the original dataset, a randomized dataset and datasets of generated cousins and siblings was evaluated as were the number of loci that were necessary to reliably deduce the number of contributors present in simulated mixtures of four or less contributors. The relatively small number of alleles detectable at most CODIS loci and the fact that some alleles are likely to be shared between individuals within a population can make the maximum number of different alleles observed at any tested loci an unreliable indicator of the maximum number of contributors to a mixed DNA sample. This analysis does not use other data available from the electropherograms (such as peak height or peak area) to estimate the number of contributors to each mixture. As a result, the study represents a worst case analysis of mixture characterization. Within this dataset, approximately 3% of three-person mixtures would be mischaracterized as two-person mixtures and more than 70% of four-person mixtures would be mischaracterized as two- or three-person mixtures using only the maximum number of alleles observed at any tested locus.

Alleles↗
PubMed2004

Systematic differences in electropherogram peak heights reported by different versions of the GeneScan software.

DNA profiling using STRs on the 310 and 3100 Genetic Analyzers routinely generates electropherograms that are analyzed with the GeneScan software available from the instrument's manufacturer, Applied Biosystems. Users have been able to choose from three different smoothing options that have been known to result in significant differences in the peak heights that are reported. Improvements in the underlying algorithm of the most recent version of the software also result in significant and somewhat predictable differences in peak height values. Laboratories that have performed validation studies using older versions of GeneScan should either reanalyze the data generated in those validation studies with the newest version of the software or otherwise take into consideration the systematically higher peak height values obtained as they begin following the recommendation of the manufacturer and use the new algorithm.

Algorithms↗
PubMed2003

Antidiabetic and antimalarial biguanide drugs are metal-interactive antiproteolytic agents.

Various biguanide derivatives are used as antihyperglycemic and antimalarial drugs (e.g., 1,1-dimethyl biguanide (metformin), phenylethyl biguanide (phenformin), N-(4-chlorophenyl)-N'-(isopropyl)-imidodicarbonimidic diamide (proguanil)); however, no common mechanism has been suggested in these controversial therapeutic actions. Biguanides bind endogenous metals that inhibit cysteine proteases independently, e.g., Zn(2+), Cu(2+), Fe(3+). Here, various biguanide derivatives are reported to be metal-interactive inhibitors of cathepsin B from mammals and falcipain-2 from Plasmodium falciparum. Structural homologies were identified among the Phe-Arg protease substrate motif and the metal complexes of phenformin and proguanil. Molecular modeling revealed that the position of the scissile amide substrate bond corresponds to the biguanide-complexed inhibitory metal when the phenyl groups are homologously aligned. Binding of the phenformin-metal complex within the active site of human cathepsin B was modeled with computational docking. A major binding mode involved binding of the drug phenyl group at the protease S2 subsite, and the complexed inhibitory metal shared between the drug and the protease Cys29-His199 catalytic pair. Cysteine protease inhibition was assayed with carbobenzyloxy-PHE-ARG-7-aminomethylcoumarin substrate. In the absence of metal ions, phenformin was a weakly competitive protease inhibitor (apparent K(i) several microM); however, metformin was noninhibitory. In contrast, the metal complexes of both metformin and phenformin were protease inhibitors with potency at therapeutic concentrations. Biguanide-metal complexes were more potent cysteine protease inhibitors than either the biguanide or metal ions alone, i.e., synergistic. Similar to chloroquine, therapeutic extracellular concentrations of metformin, phenformin, and proguanil caused metal-interactive inhibition of lysosomal protein degradation as bioassayed in primary tissue using perfused myocardium. The biguanide moiety is identified as a past and future structural scaffold for synthesis of many protease inhibitors. Results are discussed in relation to Zn(2+)-interactive inhibition of insulin degradation in hormone target tissues, and Fe(3+)-interactive inhibition of hemoglobin degradation in parasite food vacuoles. Previous studies on insulin hypercatabolism and insulin resistance are speculatively reviewed in light of present findings.

Animals↗