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.
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.
The missing organic molecules on Mars.
- S. Benner, K. G. Devine, L. Matveeva, D. Powell
- PhysicsProceedings of the National Academy of Sciences…
- 14 March 2000
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.
Potential role of sugar (fructose) in the epidemic of hypertension, obesity and the metabolic syndrome, diabetes, kidney disease, and cardiovascular disease.
- Richard J. Johnson, M. Segal, L. Sánchez-Lozada
- Medicine, BiologyAmerican Journal of Clinical Nutrition
- 1 October 2007
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.
Modern metabolism as a palimpsest of the RNA world.
- S. Benner, A. Ellington, A. Tauer
- BiologyProceedings of the National Academy of Sciences…
- 1 September 1989
An approach is developed for constructing models of ancient organisms using data from metabolic pathways, genetic organization, chemical structure, and enzymatic reaction mechanisms found in…
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.
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 ]), catalytic RNA…
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.
Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
This study resurrects candidate sequences for elongation factors of the Tu family found at ancient nodes in the bacterial evolutionary tree, and measures their activities as a function of temperature to suggest that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles.
Is there a common chemical model for life in the universe?
A review of organic chemistry suggests that life, a chemical system capable of Darwinian evolution, may exist in a wide range of environments. These include non-aqueous solvent systems at low…