Adaptation and species range

Phase III of Sewall Wright's shifting-balance process involves the spread of a superior genotype throughout a structured population. However, a number of authors have suggested that this sort of adaptive change is unlikely under biologically plausible conditions. We studied relevant mathematical models, and the results suggest that the concerns about phase III of the shifting-balance process are justified, but only if environmental conditions are stable. If environmental conditions change in a way that alters species range, then phase III can be effective, leading to an enhancement of adaptedness throughout a structured population.     

Polarized expression of G protein-coupled receptors and an all-or-none discharge of Ca2+ pools at initiation sites of [Ca2+]i waves in polarized exocrine cells.

In the present work we examined localization and behavior of G protein-coupled receptors (GPCR) in polarized exocrine cells to address the questions of how luminal to basal Ca(2+) waves can be generated in a receptor-specific manner and whether quantal Ca(2+) release reflects partial release from a continuous pool or an all-or-none release from a compartmentalized pool. Immunolocalization revealed that expression of GPCRs in polarized cells is not uniform, with high levels of GPCR expression at or near the tight junctions. Measurement of phospholipase Cbeta activity and receptor-dependent recruitment and trapping of the box domain of RGS4 in GPCRs complexes indicated autonomous functioning of G(q)-coupled receptors in acinar cells. These findings explain the generation of receptor-specific Ca(2+) waves and why the waves are always initiated at the apical pole. The initiation site of Ca(2+) wave at the apical pole and the pattern of wave propagation were independent of inositol 1,4,5-trisphosphate concentration. Furthermore, a second Ca(2+) wave with the same initiation site and pattern was launched by inhibition of sarco/endoplasmic reticulum Ca(2+)-ATPase pumps of cells continuously stimulated with sub-maximal agonist concentration. By contrast, rapid sequential application of sub-maximal and maximal agonist concentrations to the same cell triggered Ca(2+) waves with different initiation sites. These findings indicate that signaling specificity in pancreatic acinar cells is aided by polarized expression and autonomous functioning of GPCRs and that quantal Ca(2+) release is not due to a partial Ca(2+) release from a continuous pool, but rather, it is due to an all-or-none Ca(2+) release from a compartmentalized Ca(2+) pool.     

A de novo protein binding pair by computational design and directed evolution

The de novo design of protein-protein interfaces is a stringent test of our understanding of the principles underlying protein-protein interactions and would enable unique approaches to biological and medical challenges. Here we describe a motif-based method to computationally design protein-protein complexes with native-like interface composition and interaction density. Using this method we designed a pair of proteins, Prb and Pdar, that heterodimerize with a Kd of 130 nM, 1000-fold tighter than any previously designed de novo protein-protein complex. Directed evolution identified two point mutations that improve affinity to 180 pM. Crystal structures of an affinity-matured complex reveal binding is entirely through the designed interface residues. Surprisingly, in the in vitro evolved complex one of the partners is rotated 180° relative to the original design model, yet still maintains the central computationally designed hotspot interaction and preserves the character of many peripheral interactions. This work demonstrates that high-affinity protein interfaces can be created by designing complementary interaction surfaces on two noninteracting partners and underscores remaining challenges.     

Measures of nematode community structure and sources of variability among and within agricultural fields

Whole nematode communities, extracted from soil samples taken from agricultural fields, were enumerated by taxonomic family and trophic group (i.e., bacterivores, fungivores, omnivores, plant-parasites, and predators) to evaluate nematode community structure as an indicator for monitoring ecological condition of soil. No differences were found in mixing treatments or methods of packing or shipping samples. However, extraction using Cobb's sifting and gravity method, followed by sucrose centrifugation, gave greater recovery of free-living nematodes than elutriation followed by sucrose centrifugation. Population means and variance of the sampled area were similar when sampled using different strategies for collecting soil samples within fieds, including several patterns, directions and repetitions of transects. Components of variation associated with ratios among the five trophic groups of nematodes and selected indices of community structure were quantified as variation among regions, among counties, among agricultural fields (2-ha area), among transects within agricultural fields, and within composite soil samples. The variance component for'within composite soil samples' was relatively large compared to the other components of variance. Variation within composite soil samples was less for maturity indices (based on life-history strategy characteristics), ratio of bacterivores to plant-parasites, sum of bacterivores and fungivores, populations of plant-parasites, and populations of bacterivores than for trophic diversity indices, populations of fungivores, populations of omnivores, populations of predators, or the ratio of fungivores to bacterivores. With a single composite sample per field, the ability to differentiate ecological condition of soils among fields within a region improved if the variance among and within fields exceeded the variance within composite samples. Given the variance components, power curves indicated that detection of a 10% change (with 0.8 power) in the ecological condition of soils within a region between two time periods would require sampling a minimum of 25 and 50 fields with one composite soil sample analyzed per field for the maturity and trophic diversity index, respectively. More than 100 fieldsper region would be required to detect temporal change in populations of individual trophic groups. Biplots of maturity indices, but not of trophic diversity or populations of individual trophic groups, identified clear differences among fields. Thus, maturity indices, which differentiated among sampling sites better and more efficiently than trophic diversity indices or measures based on populations of individual trophic groups, may be appropriate for use in a regional and/or national monitoring program.     

A SPATIALLY EXPLICIT STOCHASTIC MODEL DEMONSTRATES THE FEASIBILITY OF WRIGHT'S SHIFTING BALANCE THEORY

Recently there has been a resurgence of theoretical papers exploring Wright's Shifting Balance Theory (SBT) of evolution. The SBT explains how traits which must pass through an adaptive valley may evolve in substructured populations. It has been suggested that Phase III of the SBT (the spread of new advantageous traits through the populations) proceeds only under a very restricted set of conditions. We show that Phase III can proceed under a much broader set of conditions in models that properly incorporate a key feature of Wright's theory: local, random migration of discrete individuals.