2014 · Proceedings of the National Academy of Sciences
Michael Lynch, Mark C. Field, Holly V. Goodson, Harmit S. Malik, José B. Pereira‐Leal, David S. Roos, Aaron P. Turkewitz, Sh…
All aspects of biological diversification ultimately trace to evolutionary modifications at the cellular level. This central role of cells frames the basic questions as to how cells work and how cells come to be the way they are. Although these two lines of inquiry lie respectively within the traditional provenance of cell biology and evolutionary biology, a comprehensive synthesis of evolutionary and cell-biological thinking is lacking. We define evolutionary cell biology as the fusion of these two eponymous fields with the theoretical and quantitative branches of biochemistry, biophysics, and population genetics. The key goals are to develop a mechanistic understanding of general evolutionary processes, while specifically infusing cell biology with an evolutionary perspective. The full development of this interdisciplinary field has the potential to solve numerous problems in diverse areas of biology, including the degree to which selection, effectively neutral processes, historical contingencies, and/or constraints at the chemical and biophysical levels dictate patterns of variation for intracellular features. These problems can now be examined at both the within- and among-species levels, with single-cell methodologies even allowing quantification of variation within genotypes. Some results from this emerging field have already had a substantial impact on cell biology, and future findings will significantly influence applications in agriculture, medicine, environmental science, and synthetic biology.
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DOI: 10.1073/pnas.14158611112014 · Proceedings of the National Academy of Sciences
Scott Freeman, Sarah L. Eddy, Miles McDonough, Michelle K. Smith, Nnadozie Okoroafor, Hannah Jordt, Mary Pat Wenderoth
To test the hypothesis that lecturing maximizes learning and course performance, we metaanalyzed 225 studies that reported data on examination scores or failure rates when comparing student performance in undergraduate science, technology, engineering, and mathematics (STEM) courses under traditional lecturing versus active learning. The effect sizes indicate that on average, student performance on examinations and concept inventories increased by 0.47 SDs under active learning (n = 158 studies), and that the odds ratio for failing was 1.95 under traditional lecturing (n = 67 studies). These results indicate that average examination scores improved by about 6% in active learning sections, and that students in classes with traditional lecturing were 1.5 times more likely to fail than were students in classes with active learning. Heterogeneity analyses indicated that both results hold across the STEM disciplines, that active learning increases scores on concept inventories more than on course examinations, and that active learning appears effective across all class sizes--although the greatest effects are in small (n ≤ 50) classes. Trim and fill analyses and fail-safe n calculations suggest that the results are not due to publication bias. The results also appear robust to variation in the methodological rigor of the included studies, based on the quality of controls over student quality and instructor identity. This is the largest and most comprehensive metaanalysis of undergraduate STEM education published to date. The results raise questions about the continued use of traditional lecturing as a control in research studies, and support active learning as the preferred, empirically validated teaching practice in regular classrooms.
9,482 citations3 viewsFull text
DOI: 10.1073/pnas.13190301111999 · Proceedings of the National Academy of Sciences
Justin P. Gallivan, Dennis A. Dougherty
Cation-pi interactions in protein structures are identified and evaluated by using an energy-based criterion for selecting significant sidechain pairs. Cation-pi interactions are found to be common among structures in the Protein Data Bank, and it is clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased toward one that would experience a favorable cation-pi interaction. The sidechain of Arg is more likely than that of Lys to be in a cation-pi interaction. Among the aromatics, a strong bias toward Trp is clear, such that over one-fourth of all tryptophans in the data bank experience an energetically significant cation-pi interaction.
2,024 citations4 viewsFull text
DOI: 10.1073/pnas.96.17.94591994 · Proceedings of the National Academy of Sciences
Emanuel Epstein
Silicon is the second most abundant element in soils, the mineral substrate for most of the world's plant life. The soil water, or the "soil solution," contains silicon, mainly as silicic acid, H4SiO4, at 0.1-0.6 mM--concentrations on the order of those of potassium, calcium, and other major plant nutrients, and well in excess of those of phosphate. Silicon is readily absorbed so that terrestrial plants contain it in appreciable concentrations, ranging from a fraction of 1% of the dry matter to several percent, and in some plants to 10% or even higher. In spite of this prominence of silicon as a mineral constituent of plants, it is not counted among the elements defined as "essential," or nutrients, for any terrestrial higher plants except members of the Equisitaceae. For that reason it is not included in the formulation of any of the commonly used nutrient solutions. The plant physiologist's solution-cultured plants are thus anomalous, containing only what silicon is derived as a contaminant of their environment. Ample evidence is presented that silicon, when readily available to plants, plays a large role in their growth, mineral nutrition, mechanical strength, and resistance to fungal diseases, herbivory, and adverse chemical conditions of the medium. Plants grown in conventional nutrient solutions are thus to an extent experimental artifacts. Omission of silicon from solution cultures may lead to distorted results in experiments on inorganic plant nutrition, growth and development, and responses to environmental stress.
1,741 citations1 viewsFull text
DOI: 10.1073/pnas.91.1.111979 · Proceedings of the National Academy of Sciences
M Nei, Wen‐Hsiung Li
A mathematical model for the evolutionary change of restriction sites in mitochondrial DNA is developed. Formulas based on this model are presented for estimating the number of nucleotide substitutions between two populations or species. To express the degree of polymorphism in a population at the nucleotide level, a measure called "nucleotide diversity" is proposed.
10,658 citations5 viewsFull text
DOI: 10.1073/pnas.76.10.5269