Evolving a 24-hr oscillator in budding yeast

We asked how a new, complex trait evolves by selecting for diurnal oscillations in the budding yeast, Saccharomyces cerevisiae. We expressed yellow fluorescent protein (YFP) from a yeast promoter and selected for a regular alternation between low and high fluorescence over a 24-hr period. This selection produced changes in cell adhesion rather than YFP expression: clonal populations oscillated between single cells and multicellular clumps. The oscillations are not a response to environmental cues and continue for at least three cycles in a constant environment. We identified eight putative causative mutations in one clone and recreated the evolved phenotype in the ancestral strain. The mutated genes lack obvious relationships to each other, but multiple lineages change from the haploid to the diploid pattern of gene expression. We show that a novel, complex phenotype can evolve by small sets of mutations in genes whose molecular functions appear to be unrelated to each other. DOI: http://dx.doi.org/10.7554/eLife.04875.00

ReCLIP (Reversible Cross-Link Immuno-Precipitation): An Efficient Method for Interrogation of Labile Protein Complexes

The difficulty of maintaining intact protein complexes while minimizing non-specific background remains a significant limitation in proteomic studies. Labile interactions, such as the interaction between p120-catenin and the E-cadherin complex, are particularly challenging. Using the cadherin complex as a model-system, we have developed a procedure for efficient recovery of otherwise labile protein-protein interactions. We have named the procedure “ReCLIP” (Reversible Cross-Link Immuno-Precipitation) to reflect the primary elements of the method. Using cell-permeable, thiol-cleavable crosslinkers, normally labile interactions (i.e. p120 and E-cadherin) are stabilized in situ prior to isolation. After immunoprecipitation, crosslinked binding partners are selectively released and all other components of the procedure (i.e. beads, antibody, and p120 itself) are discarded. The end result is extremely efficient recovery with exceptionally low background. ReCLIP therefore appears to provide an excellent alternative to currently available affinity-purification approaches, particularly for studies of labile complexes

Nagging: A scalable, fault-tolerant, paradigm for distributed search, re-submitted

This paper describes nagging, atechnique for parallelizing search in a heterogeneous distributed computing environment. Nagging exploits the speedup anomaly often observed when parallelizing problems by playing multiple reformulations of the problem or portions of the problem against each other. Nagging is both fault tolerant and robust to long message latencies. In this paper, weshow how nagging can be used to parallelize several different algorithms drawn from the artificial intelligence literature, and describe how nagging can be combined with partitioning, the more traditional search parallelization strategy. Wepresent a theoretical analysis of the advantage of nagging with respect to partitioning, and give empirical results obtained on a cluster of 64 processors that demonstrate nagging’s effectiveness and scalability as applied to A * search, αβ minimax game tree search, and the Davis-Putnam algorithm. 1

Privacy-Preserving Data Set Union

This paper describes a cryptographic protocol for merging two data sets based on identifiers without divulging those identifier records; technically, the protocol computes a blind set-theoretic union. Applications for this protocol arise, for example, in data analysis for biomedical application areas, where identifying fields (e.g., patient names) are protected by governmental privacy regulations or by institutional research board policies