Extensive regulation of metabolism and growth during the cell division cycle

Yeast cells grown in culture can spontaneously synchronize their respiration, metabolism, gene expression and cell division. Such metabolic oscillations in synchronized cultures reflect single-cell oscillations, but the relationship between the oscillations in single cells and synchronized cultures is poorly understood. To understand this relationship and the coordination between metabolism and cell division, we collected and analyzed DNA-content, gene-expression and physiological data, at hundreds of time-points, from cultures metabolically-synchronized at different growth rates, carbon sources and biomass densities. The data enabled us to extend and generalize an ensemble-average-over-phases (EAP) model that connects the population-average gene-expression of asynchronous cultures to the gene-expression dynamics in the single-cells comprising the cultures. The extended model explains the carbon-source specific growth-rate responses of hundreds of genes. Our data demonstrate that for a given growth rate, the frequency of metabolic cycling in synchronized cultures increases with the biomass density. This observation underscores the difference between metabolic cycling in synchronized cultures and in single cells and suggests entraining of the single-cell cycle by a quorum-sensing mechanism. Constant levels of residual glucose during the metabolic cycling of synchronized cultures indicate that storage carbohydrates are required to fuel not only the G1/S transition of the division cycle but also the metabolic cycle. Despite the large variation in profiled conditions and in the time-scale of their dynamics, most genes preserve invariant dynamics of coordination with each other and with the rate of oxygen consumption. Similarly, the G1/S transition always occurs at the beginning, middle or end of the high oxygen consumption phases, analogous to observations in human and drosophila cells.Comment: 34 pages, 7 figure

Cinderella; or Music and the Human Sciences. Unfootnoted Musings from the Margins

It has become fashionable among scholars to wax autobiographical with the reader, presumably to shed any remnant of the illusion (suggested implicitly by the conventional apparatus of a scholarly text and footnotes) that one might be speaking with an objective voice, or with an argument whose merits can be considered and even accepted without reference to personal and therefore circumstantial prejudice. Today's penchant for presumed full disclosure of one's subjective standpoint, however, is more likely either a species of authorial vanity masquerading as methodological scrupulousness or evidence of a greater interest in oneself than the subject one is writing about. In this case, the reader who wishes to distill the prejudices of the author and speculate on their origins must begin with the author's notion that one can talk effectively about the character and value of arguments by using procedures of reading and research that hold up under scrutiny and require no subjective apologetics. Botstein concludes that the definition of future methods of analysis, including the setting of the research agenda, cannot be undertaken from within the current traditions of music history or musicology

Genetic Basis of Ammonium Toxicity Resistance in a Sake Strain of Yeast: A Mendelian Case.

High concentrations of ammonium at physiological concentrations of potassium are toxic for the standard laboratory strain of Saccharomyces cerevisiae In the original description of this metabolic phenotype, we focused on the standard laboratory strains of Saccharomyces In this study, we screened a large collection of S. cerevisiae natural isolates and identified one strain that is resistant to high concentrations of ammonium. This strain, K12, was isolated in sake breweries. When the K12 strain was crossed to the standard laboratory strain (FY4), the resulting tetrads displayed 2:2 segregation of the resistance phenotype, suggesting a single gene trait. Using a bulk segregant analysis strategy, we mapped this trait to a 150-kb region on chromosome X containing the TRK1 gene. This gene encodes a transporter required for high-affinity potassium transport in S. cerevisiae Data from reciprocal hemizygosity experiments with TRK1 deletion strains in K12 and BY backgrounds, as well as analysis of the deletion of this gene in the K12 strain, demonstrate that the K12 allele of TRK1 is responsible for ammonium toxicity resistance. Furthermore, we determined the minimal amount of potassium required for both the K12 and laboratory strain needed for growth. These results demonstrate that the gene encoded by the K12 allele of TRK1 has a greater affinity for potassium than the standard allele of TRK1 found in Saccharomyces strains. We hypothesize that this greater-affinity allele of the potassium transporter reduces the flux of ammonium into the yeast cells under conditions of ammonium toxicity. These findings further refine our understanding of ammonium toxicity in yeast and provide an example of using natural variation to understand cellular processes

Novel integrative genomics strategies to identify genes for complex traits

Forward genetics is a common approach to dissecting complex traits like common human diseases. The ultimate aim of this approach was the identification of genes that are causal for disease or other phenotypes of interest. However, the forward genetics approach is by definition restricted to the identification of genes that have incurred mutations over the course of evolution or that incurred mutations as a result of chemical mutagenesis, and that as a result lead to disease or to variations in other phenotypes of interest. Genes that harbour no such mutations, but that play key roles in parts of the biological network that lead to disease, are systematically missed by this class of approaches. Recently, a class of novel integrative genomics approaches has been devised to elucidate the complexity of common human diseases by intersecting genotypic, molecular profiling, and clinical data in segregating populations. These novel approaches take a more holistic view of biological systems and leverage the vast network of gene–gene interactions, in combination with DNA variation data, to establish causal relationships among molecular profiling traits and Fbetween molecular profiling and disease (or other classic phenotypes). A number of novel genes for disease phenotypes have been identified as a result of these approaches, highlighting the utility of integrating orthogonal sources of data to get at the underlying causes of disease

Genetic Variation and the Fate of Beneficial Mutations in Asexual Populations

The fate of a newly arising beneficial mutation depends on many factors, such as the population size and the availability and fitness effects of other mutations that accumulate in the population. It has proved difficult to understand how these factors influence the trajectories of particular mutations, since experiments have primarily focused on characterizing successful clones emerging from a small number of evolving populations. Here, we present the results of a massively parallel experiment designed to measure the full spectrum of possible fates of new beneficial mutations in hundreds of experimental yeast populations, whether these mutations are ultimately successful or not. Using strains in which a particular class of beneficial mutation is detectable by fluorescence, we followed the trajectories of these beneficial mutations across 592 independent populations for 1000 generations. We find that the fitness advantage provided by individual mutations plays a surprisingly small role. Rather, underlying “background” genetic variation is quickly generated in our initially clonal populations and plays a crucial role in determining the fate of each individual beneficial mutation in the evolving population

Aesthetics and Ideology in the Fin-de-Siecle Mozart Revival

What remains from the fin-de-siecle Mozart revival is, of course, its aesthetic influence on twentieth-century neoclassicism and modernism, particularly within the tradition of the Second Viennese School. Despite the fantastic commercial popularity that Mozart's music now enjoys, from the historian's perpective the turn to Mozart in the early twentieth century constituted an effort to revive the claims among many musicians on behalf of a model of purely musical hearing and listening. A premium on form and procedures of musical development within works of music-on structural devices overtly detached from the sort of extramusical illustration associated with Wagner-became a hallmark of much twentieth-century concert music. The turn away from the associative musical strategies of late Romanticism helped make much of twentieth-century music less accessible and therefore less popular. Wagnerism held the key to the mass audience. Therefore, from the vantage point of the late twentieth century, the rediscovery of Mozart during the early 1900s helped lead, on the one hand, to the most extreme deification and dissemination of Mozart and his music within the museum of music, and, on the other (albeit indirectly, through the medium of modernist advocates of theories of absolute music) to the relative marginalization of contemporary music and musical modernism in our own time

The timing of erf-mediated recombination in replication, lysogenization, and the formation of recombinant progeny by Salmonella phage P22

Following infection, the development of phage P22 by either the lytic or the lysogenic pathways requires recombination, mediated either by the phage erf system or by the bacterial rec system [Botstein, D., and Matz, M. J. (1970) J. Mol. Biol. 54, 417-440]. We have investigated the timing of the essential recombinational processes with temperature-shift experiments using a temperature-sensitive erf mutant. In rec- cells, erf function appears to be required early in the infection to complete some essential step, the timing of which is the same in both the lytic and lysogenic circumstances. Once the step has taken place, subsequent development can occur without further erf function. However, the bulk of recombinant progeny arising in lytic crosses in rec- cells result from nonessential erf action late in the infection, after the time of the required early step.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/23011/1/0000580.pd

Replication in situ and DNA encapsulation following induction of an excision-defective lysogen of Salmonella bacteriophage P22

The induction of an excision-defective bacteriophage P22 lysogen results in the production of particles which carry a DNA molecule of normal length within a normal capsid, but which are nonetheless defective. The DNA content of these particles was characterized physically by a restriction enzyme analysis, and genetically by two marker rescue techniques. The particles carry DNA corresponding to one side of the prophage map as well as additional DNA, apparently derived from the host chromosome to one side of the prophage insertion site. Normally, mature P22 DNA molecules are derived from a concatemer by sequential cleavage of adjacent headful lengths, beginning at a genetically unique site, the encapsulation origin (Tye et al., 1974). The defective particles appear to contain DNA matured by the same sequential mechanisms, operating on the integrated prophage and neighboring bacterial chromosome, rather than on the normal concatemeric substrate. Both the initiation and directional specificities of normal maturation are maintained during the maturation of defective particle DNA. Sequential cleavage begins within the prophage at the encapsulation origin, a site near gene 3, and proceeds into the host chromosome on the proC side of the prophage. The initiation specificity of DNA encapsulation seems to reside in the morphogenetic machinery, rather than in the mechanism of DNA replication. Replication of an induced excision-defective prophage takes place in situ on the host chromosome, apparently without disruption of the linear integrity of the prophage. Further, the entire prophage, as well as adjacent bacterial DNA, is replicated, even though only a portion of this DNA is destined to be encapsulated.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/22678/1/0000231.pd