Intellectual Merit: Genetics is the study of how biological traits are transmitted from parents to offspring. For over 100 years it has been appreciated that owing to biological complexities, a mutations effect may vary with the genetic background in which it occurs. For example, imagine the following biochemical pathway. Here some compound X is converted by Enzyme 1 (coded by one gene) into compound Y and then Y is converted by Enzyme 2 (coded by another gene) into a third compound Z. In this case, a mutation that inactivates Enzyme 2 also inactivates the entire pathway, even in an organism in which Enzyme 1 is functional. On the other hand, the same mutation would have no effect in an organism in which Enzyme 1 was previously inactivated. Such interactions complicate the question, what does this mutation do since the effects of mutations in these cases are context-dependent? But at the same time, such interactions provide opportunities for experimentation to dissect underlying biological mechanisms. In our simple example, the observation that mutations inactivating Enzyme 2 have no effect when Enzyme 1 has been inactivated implies that Enzyme 2 mechanistically acts downstream of Enzyme 1 in some common pathway.
This project formalizes these intuitive notions using two theoretical approaches, one based on a quantitative model of how single enzymes operate and the other based on a quantitative model of whole-organism metabolism. This work will yield an analytic framework to sort pairs of mutations into those that act by a shared mechanism and those that act by distinct mechanisms. In addition it will provide an estimate of the number of distinct mechanisms influencing a biological trait. This research is extremely timely because recent high-throughput technical innovations in genomics are yielding vast datasets on mutational interactions in several microbial model systems (E. coli, S. cerevisiae and S. pombe), and prospects are good for similar datasets in multicellular model organisms such as D. melanogaster and C. elegans. These experimental innovations thus open the door to far more sophisticated mechanistic analyses. Critically, direct experimental attack on specific mechanistic interactions remains prohibitively expensive, further motivating the present theoretical approach. This work also promises to make contributions at several levels of biological organization, from enzymatics to whole organism reproductive success to ecological and biogeochemical resource fluxes. This follows because the theoretical model of single enzymes can also be applied to whole organisms, and because the model of metabolism can be applied to any network of chemical fluxes.
Broader Impacts. Beyond allowing inferences to be made regarding biological mechanisms, mutational interactions have theoretical implications for a diversity of biological processes, including constraints on adaptation, the evolution of sex and speciation. The PI has active research programs in several of these areas and so this research directly complements his ongoing work. Moreover this project directly supports the training of a graduate student at the interface of mathematics and biology, to develop expertise essential in this genomic and post-genomic era. Spin-off projects are planned to engage a number of undergraduate students in research working in the PIs laboratory each term and during the summer. The PI also has an ongoing commitment to the intellectual engagement of Providence public school students and teachers through an existing NSF-funded GK-12 program. This outreach work addresses current cultural barriers to understanding genetics and the implications of evolutionary thinking in the United States.
Intellectual Merit: Mutations introduce changes into an organism’s genome, and thus often change its ability to survive and reproduce, traits that influence its Darwinian fitness. However if the same mutation occurs in two different organisms, it doesn’t necessarily have the same effect on fitness. One reason for this is that mutations interact in determining fitness. For example, consider the following biochemical pathway. X ---------------> Y ---------------> Z Enzyme A Enzyme B Here enzyme A catalyzes the conversion of X into Y, and enzyme B catalyzes the conversion of Y into Z. Suppose compound Z contributes directly to organismal fitness, and enzyme A is a much slower catalyst than is enzyme B. In this case, a mutation in the gene for enzyme B that doubles its rate of catalysis will not yield Z any more quickly, and thus will have a negligible effect on fitness. On the other hand, after a mutation in the gene for A that drastically increases that enzyme’s rate of catalysis, this same mutation in the gene for B will yield a larger effect on the rate of production of Z, and thus will have a much larger effect on fitness. Geneticists use the word ‘epistasis’ to describe these sorts of mutational interactions, when the effect of a mutation depends on what other mutations are already present in the genome. The purpose of this award was to explore two theoretical questions posed by the fact of epistasis. Can data on epistasis among pairs of mutations give insight into the biology responsible for the effect? Building on a model first proposed by RA Fisher in 1930, PI Weinreich and his postdoc Professor Jennifer Knies demonstrated one very promising approach in 2013, described in: Fisher’s Geometric Model of Adaptation Meets the Functional Synthesis: Data on Pairwise Epistasis for Fitness Yields Insights into the Shape and Size of Phenotype Space. Evolution 67:2957 – 2972. Ongoing work seeks to apply methods developed in the context of theoretical immunology to data on enzyme/substrate evolution. How can epistasis among more than two mutations be described, and what are their evolutionary implications? With two students an a colleague at the University of Idaho, PI Weinreich made progress in 2014 by applying methods from computer science to this problem, described: Should Evolutionary Geneticists Worry about Higher-Order Epistasis? Current Opinion in Genetics and Development 23(6):700-707. Ongoing work seeks to extend this work to explicitly identify cases in which a mutation switches from being advantageous to being deleterious to an organism’s fitness. Broader Impacts: The chief broader impact efforts under this award were focused on public outreach, and several accomplishments were realized. Ms. Meghan Hollibaugh Baker, a science teacher at the Providence Career & Technical Academy Public High School spent two summers working in PI Weinreich’s research lab. During this time she made substantive intellectual contributions as well as broadening her understanding of the process of scientific research and specific problems and approaches used in evolutionary biology. This experience will bear dividends in her classroom for years. Approximately a dozen Brown undergraduates have performed independent research projects in PI Weinreich’s lab. This is a productive form ?of training, and Brown undergrads have a strong track record of quickly growing to take intellectual ownership of their projects. On June 5, 2012 PI Weinreich participated in the Science Conference ?at the Vartan Gregorian Elementary School in Providence, RI. He presented a program entitled 'How are people like snowflakes? No two look the same!' to approximately 75 3rd, 4th and 5th grade students. ?In this program he used the game of 'Telephone' to build students' intuition into what Darwin called Descent with Modification. This program was successful in drawing out the students' curiosity, and they asked ?a great number of well-considered questions. A total of four high school students did summer internships in PI Weinreich’s research lab over the period of the award. Two of these four are now pursuing an undergraduate education in biology. While in residence at the Kavli Institute for Theoretical Physics in the summer of 2014, PI Weinreich organized and hosted a public screening of the film Resistance in Santa Barbara, CA. This film explores the scientific and economic drivers of bacterial drug resistance, and the screening drew over 200 locals from Santa Barbara. PI Weinreich participated in a panel discussion entitled The Science Museum of the Future at the Association for ScienceTechnology Centers Annual Conference in Raleigh, NC on October 20, 2014.
