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Exhaustive matching of the entire protein sequence database.
The alignments made possible by the exhaustive matching are the starting point for successful de novo prediction of the folded structures of proteins, for reconstructing sequences of ancient proteins and metabolisms in ancient organisms, and for obtaining new perspectives in structural biochemistry. Expand
The missing organic molecules on Mars.
Experiments show that one of these, benzenehexacarboxylic acid (mellitic acid), is generated by oxidation of organic matter known to come to Mars, is rather stable to further oxidation, and would not have been easily detected by the Viking experiments. Expand
The potential and challenges of nanopore sequencing
A nanopore-based device provides single-molecule detection and analytical capabilities that are achieved by electrophoretically driving molecules in solution through a nano-scale pore, a unique analytical capability that makes inexpensive, rapid DNA sequencing a possibility. Expand
Potential role of sugar (fructose) in the epidemic of hypertension, obesity and the metabolic syndrome, diabetes, kidney disease, and cardiovascular disease.
It is suggested that high intakes of fructose in African Americans may explain their greater predisposition to develop cardiorenal disease, and a list of testable predictions to evaluate this hypothesis is provided. Expand
Resurrecting ancestral alcohol dehydrogenases from yeast
The resurrection of the last common ancestor of Adh1 and Adh2, called AdhA is reported, which suggests that the ancestor was optimized to make (not consume) ethanol, consistent with the hypothesis that before the Adh 1-Adh2 duplication, yeast did not accumulate ethanol for later consumption but rather used AdHA to recycle NADH generated in the glycolytic pathway. Expand
Modern metabolism as a palimpsest of the RNA world.
An approach is developed for constructing models of ancient organisms using data from metabolic pathways, genetic organization, chemical structure, and enzymatic reaction mechanisms found inExpand
Amino acid substitution during functionally constrained divergent evolution of protein sequences.
The matrices show that the genetic code influences accepted point mutations strongly at early stages of divergence, while the chemical properties of the side chains dominate at more advanced stages. Expand
Empirical and structural models for insertions and deletions in the divergent evolution of proteins.
This model provides theoretical support for using indels as part of "parsing algorithms", important in the de novo prediction of the folded structure of proteins from the sequence data. Expand
Borate Minerals Stabilize Ribose
Evidence for an “RNA world,” an episode of life on Earth during which RNA was the only genetically encoded component of biological catalysts, is found in the ribosome ([ 1 ][1]), catalytic RNAExpand
Predicting functional divergence in protein evolution by site-specific rate shifts.
This work applies the "non-homogeneous gamma model" to multiple gene families to identify sites that are likely to be involved in changing function within the gene family, highlighting the widespread divergence of functional behavior among proteins to generate paralogs and orthologs. Expand