Global landscape of protein complexes in the yeast Saccharomyces cerevisiae

Identification of protein-protein interactions often provides insight into protein function, and many cellular processes are performed by stable protein complexes. We used tandem affinity purification to process 4,562 different tagged proteins of the yeast Saccharomyces cerevisiae. Each preparation was analysed by both matrix-assisted laser desorption/ionization-time of flight mass spectrometry and liquid chromatography tandem mass spectrometry to increase coverage and accuracy. Machine learning was used to integrate the mass spectrometry scores and assign probabilities to the protein-protein interactions. Among 4,087 different proteins identified with high confidence by mass spectrometry from 2,357 successful purifications, our core data set (median precision of 0.69) comprises 7,123 protein-protein interactions involving 2,708 proteins. A Markov clustering algorithm organized these interactions into 547 protein complexes averaging 4.9 subunits per complex, about half of them absent from the MIPS database, as well as 429 additional interactions between pairs of complexes. The data (all of which are available online) will help future studies on individual proteins as well as functional genomics and systems biology.     

‘Conservative prejudice’ in the debate over disjunctively distributed life forms

During the thirties and forties, and early fifties, Wegener's ideas were generally rejected as a fantasy—fascinating but false. ‘Ein Machen, a pipe dream, a beautiful fairy story’ chanted the American bandwagon. During these decades of repudiation, arguments which denied continental dispersion passed without scrutiny or test. They were correct a priori because everybody knew that continental drift was wrong.     

Fate choice of post-natal mesoderm progenitors: skeletal versus cardiac muscle plasticity

Regenerative medicine for skeletal and cardiac muscles still constitutes a fascinating and ambitious frontier. In this perspective, understanding the possibilities of intrinsic cell plasticity, present in post-natal muscles, is vital to define and improve novel therapeutic strategies for acute and chronic diseases. In addition, many somatic stem cells are now crossing the boundaries of basic/translational research to enter the first clinical trials. However, it is still an open question whether a lineage switch between skeletal and cardiac adult myogenesis is possible. Therefore, this review focuses on resident somatic stem cells of post-natal skeletal and cardiac muscles and their plastic potential toward the two lineages. Furthermore, examples of myogenic lineage switch in adult stem cells are also reported and discussed.     

New approaches for sampling and modeling native and exotic plant species richness

We demonstrate new multi-phase, multi-scale approaches for sampling and modeling native and exotic plant species to predict the spread of invasive species and aid in control efforts. Our test site is a 54,000-ha portion of Rocky Mountain National Park, Colorado, USA. This work is based on previous research wherein we developed vegetation sampling techniques to identify hot spots of diversity, important rare habitats, and locations of invasive plant species. Here we demonstrate statistical modeling tools to rapidly assess current patterns of native and exotic plant species to determine which habitats are most vulnerable to invasion by exotic species. We use stepwise multiple regression and modified residual kriging to estimate numbers of native species and exotic species, as well as probability of observing an exotic species in 30 × 30-m cells. Final models accounted for 62% of the variability observed in number of native species, 51% of the variability observed in number of exotic species, and 47% of the variability associated with observing an exotic species. Important independent variables used in developing the models include geographical location, elevation, slope, aspect, and Landsat TM bands 1-7. These models can direct resource managers to areas in need of further inventory, monitoring, and exotic species control efforts.     

Comparison of regression methods for biomass estimation of sagebrush and bunchgrass

Regression analyses for plant biomass estimation from physical measurements of individual plant dimensions that are nonlinear have generally used some form of the allometric equation. Use of this equation has most often involved logarithmic transformation of the variables (power regression). Transformation, however, introduces systematic bias into the analyses. Power regression was compared with a bias correction technique and with nonlinear regression for the prediction of the total foliage biomass (phytomass). Crown volumes of one sagebrush and one perennial grass species were used for these evaluations. The bias correction factor was uniformly applied to all the predicted values from power regression. Nonlinear regression avoided this bias by not requiring logarithmic transformation. It was also consistently less variable than either power regression or the correction factor method in estimating actual total phytomass by the allometric equation and equivalent or better in accuracy. The correction factor technique consistently gave the poorest predictions of the methods evaluated. Standard linear regression worked as well for the bunchgrass as the best method based on the allometric equation. Predictions were generally better when sample sizes used to derive the regression equations represented the range of plant size and variability in the data for which the phytomass was estimated.     

A comparison of the spherical densiometer and ocular methods of estimating canopy cover

Percent tree canopy cover in a ponderosa pine ( Pinus ponderosa ) forest of northeastern California was estimated by the point intercept spherical densiometer and ocular methods. Estimates derived by the two methods were similar (P > .05). The ocular method is recommended when understory vegetation is tall or clumped instead of randomly distributed, or if available field time limits sample size.     

The influence of predator control on two adjacent wintering deer herds

Two mule deer herds were studied on comparable, adjacent winter ranges in Utah. Significant differences in overwinter fawn survival were attributed to intensive predator control.