OoLALA @ UW-Madison
 

Research

Karthik Anantharaman – Bacteriology

Microbial metabolism has the potential to impact the evolutionary ecology of a system across various spatial and temporal scales ranging from the scope of a single cell, ecosystem, to the earth as a whole. Understanding how microbial communities function is critical to unraveling how they underpin human health, and predicting global ecosystem dynamics, especially in the context of environmental perturbations like anthropogenic global change. The broad goal of our research is to unravel how (i) fine-scale genomic diversity impacts microbial community structure and function across various environments, (ii) individual microbes function in a community context, and (iii) microbes impact biogeochemical cycling at various spatial and temporal scales.

 

Annie Bauer – Geoscience

The growth and stabilization of a significant volume of continental crust, the start of plate tectonics, and the development of an oxic atmosphere represent fundamental changes that resulted in a surface environment favorable for the evolution of macroscopic life. Our research group investigates the origin and evolution of the continents and the rise of atmospheric oxygen. We integrate geochronology (e.g. U-Pb) with stable and radiogenic isotope geochemistry to evaluate the coevolution of tectonics and biogeochemical cycling on the early Earth.

 

David Baum – Botany

I take the view that life began as autocatalytic ensembles of chemicals adsorbed onto mineral surfaces. In the presence of a constant flux of food and energy, such systems could collectively propagate (grow) and, through an analog of group selection called neighborhood selection, evolve adaptively. This model suggests that cells arose late, possibly via selection for dispersal among discontinuous mineral surfaces, and allows that a nucleic acid-based genetic system might also have originated long after adaptive evolution kicked-in. More concretely, this hypothesis implies that we might be able to induce the formation of new life-like chemical ensembles in the laboratory and detect them via their capacity to evolve adaptively.

 

Judith Burstyn – Chemistry

In our laboratory, research efforts are directed towards understanding how gas sensing occurs at a metal center, and how changes in the coordination chemistry at the metal center are coupled to allosteric conformational changes in the protein. The interaction of gas molecules with a heme center induces changes in the coordination geometry, and these changes correlate with functional changes in the protein. Our current work aims to elucidate the mechanisms by which the coordination changes are communicated through the protein, resulting in global structural changes. To this end we study several bacterial gas-responsive transcription factors and newly discovered types of heme-containing gas sensors that regulate circadian rhythm in higher organisms.

 

Michael Cox – Biochemistry

Many classes of DNA rearrangements occur in all cells and play important roles in gene regulation, development, carcinogenesis, and evolution. The goal of this laboratory is to understand how these genetic rearrangements come about, and how they are regulated. To this end, we study a range of bacterial enzymes involved in recombinational DNA repair, both in vivo and in vitro. Part of the effort involves screens to identify relevant enzymes with new and sometimes unanticipated functions. In addition to understanding the enzymes themselves, we are increasingly exploring the intersection of recombination with other processes in DNA metabolism, and seeking an understanding of the factors that limit recombination within a cell.

 

Gheorghe Craciun – Mathematics

We are interested in mathematical and computational methods for understanding dynamical properties of biochemical networks, such as gene regulatory networks, signaling pathways, and metabolic networks.  For example, we are working on designing algorithms that allow us to relate the topological structure of a biochemical network to its dynamical properties, such as its capacity to exhibit bistability and oscillations, or its sensitivity to noise and other stochastic properties. Some of these methods can be applied for trying to understand the roles of catalytic reaction networks in the origin of life.

 

Ankur Desai – Atmospheric & Oceanic Sciences
We study the positive, negative, and downright awkward interactions between the land and atmosphere over short (daily) and long (decadal) time scales. We measure how they exchange heat, water, and carbon, using a global network of flux towers organized by a global network of people. We are particularly interested in plants (i.e. vegetation cover) and their unique role in modifying these exchanges, especially how human changes in vegetation cover, via deforestation, hydrologic modification, and land-use change, modify the intensity and outcomes of land-atmosphere interactions. Our long-term experiments have led to greater understanding of how a turbulent atmosphere behaves in response to changes in vegetation cover, across wetland, lake, and forest ecosystems. Our measurements and models directly influence the scientific basis of global change and provide a baseline from which policy makers, land managers, and farmers make decisions about fossil fuel emissions, forest harvest, irrigation practices, and more.

 

Elena D’Onghia – Astronomy

My research combines unique analytic models and high-resolution numerical simulations to get new insights into the dynamical processes that form the stellar skeleton of our Galaxy. While the study of our Solar System is captivating, I am more interested in what happens outside of it. There are 300 billion stars in our Milky Way. Thanks to the GAIA satellite launched in 2013, for the first time in human history, we will know for 1 billion of those stars their location, distance from us, proper motions and in some cases whether they have planets around them. In a future when we might become a space-faring civilization, I believe it is inspiring to have a detailed knowledge of the environment outside of the Solar System.

 

Katrina Forest – Bacteriology

The study of life is the examination of interactions; cooperations of species within ecosystems, adaptation of living organisms to environment stimuli, and partnerships of atoms within the active sites of enzymes. Our lab studies biological interactions at the molecular level. We are particularly interested in the structures, functions, and mechanisms of bacterial proteins with consequences to prokaryotic physiology and symbiosis with eukaryotes. Using X-ray crystallography as our primary tool, we draw on our diverse backgrounds in microbiology, biophysics, biochemistry and chemistry to uniquely approach our two main areas of research: Type IV pili and bacteriophytochromes.

 

Samuel Gellman – Chemistry

Microbial metabolism has the potential to impact the evolutionary ecology of a system across various spatial and temporal scales ranging from the scope of a single cell, ecosystem, to the earth as a whole. Understanding how microbial communities function is critical to unraveling how they underpin human health, and predicting global ecosystem dynamics, especially in the context of environmental perturbations like anthropogenic global change. The broad goal of our research is to unravel how (i) fine-scale genomic diversity impacts microbial community structure and function across various environments, (ii) individual microbes function in a community context, and (iii) microbes impact biogeochemical cycling at various spatial and temporal scales.

 

Simon Gilroy – Botany

We are interested in how plants sense and respond to their environment and how these signals regulate plant development. The research emphasis of the lab is to try and understand these processes at the cellular level. We combine advanced microscopy approaches such as confocal microscopy with biochemistry and molecular biology to address a wide range of biological questions: How do plants sense and respond to abiotic stresses? How do roots and shoots sense and respond to gravity and touch stimuli? How do plants regulate growth? How do plants respond to the spaceflight environment?

 

Chris Hittinger – Genetics

The Hittinger Lab uses yeast carbon metabolism as a model for basic bioenergy, biomedical, and evolutionary research. Our research interests and integrated approaches are at the intersection of biodiversity; biochemistry; biotechnology; and functional, ecological, and evolutionary genomics. Ongoing projects are focused on understanding the origin and evolution of aerobic fermentation, yeast ecology and biodiversity, genetic variation in natural and industrial yeasts, genome engineering and synthetic biology, and the metabolism of alternative carbon sources (e.g. galactose, maltose, xylose) that may have bioenergy and brewing applications.

 

Tristan L’Ecuyer – Atmospheric & Oceanic Sciences

Our research incorporates innovative combinations of satellite observations and numerical models to examine energy and water balance in the Earth-atmosphere system. This requires a coordinated effort to develop and evaluate satellite data products, analyze the resulting datasets to probe relationships between the principal components of the global energy and water cycles, and use this information to evaluate the representation of key physical processes in both mesoscale and climate models. Through this combination of remote sensing, field work, data mining, and numerical modeling we hope to gain a better understanding of the climate system and evaluate our ability to predict its evolution.

 

Sanjay Limaye – Space Science & Engineering Center

Solar system exploration, atmospheres of planets, weather on planets

 

Hiroshi Maeda – Botany

As sessile organisms, plants produce a tremendous array of organic compounds using CO2, underground nutrients, and sunlight energy to survive in challenging ecological niches. These plant-derived metabolites are also widely used as our food, medicine, material, and energy. Although extensive efforts are currently being made to understand plant-specific metabolic pathways, we still have a limited knowledge of how plants allocate available carbon, fixed by photosynthesis, to a variety of downstream metabolic pathways. This fundamental knowledge gap also creates a bottleneck in effective plant breeding and metabolic engineering for the improved production of useful plant-derived compounds. My research program focuses on understanding the organization and regulatory mechanisms of the plant shikimate and aromatic amino acid pathways.

 

Patrick Masson – Genetics

Roots’ primary functions are to take up the water and mineral ions required for plant growth and development, and to anchor the plant to its substratum. Because a plant spends its entire life cycle where it germinated, its roots have to colonize the soil in order to feed the plant without depleting its immediate environment of essential nutrients. They do so by developing specific patterns of growth which are dictated by environmental parameters. Hence, roots are capable of using the directional information provided by the gravity vector, light, touch, gradients in temperature, humidity, ions, chemicals and oxygen to guide their growth. My laboratory is using molecular genetic strategies in Arabidopsis thaliana to study the molecular mechanisms that allows roots to adopt growth behaviors in response to the mechanical parameters present in their environment.

 

Katherine McMahon – Civil and Environmental Engineering

The broad objective of my research program is to improve our capacity to predict and model microbial behavior, while searching for novel biologically mediated transformations that can be harnessed for engineering applications. We study the microbial ecology of both natural and engineered systems. We use molecular tools to investigate microbial community structure and function in lakes and activated sludge. We also use high-frequency environmental sensor networks to measure important variables that we know influence bacterial communities. Sensor data provided through the Global Lake Ecological Observatory Network guides our adaptive sampling efforts and provides rich contextual data for our studies of lake bacterial community ecology. We are particularly interested in phosphorus, nitrogen, and carbon cycling in lakes and how this relates to eutrophication and water quality. We are using highly resolved time series sampling of multiple lakes, combined with metagenomics and meta-transcriptomics to explore how different lineages of freshwater bacteria contribute to this cycling.

 

Nicole Perna – Genetics

Our research is directed at understanding the molecular evolution of complex traits like virulence and host range. Our work focuses on the Enterobacteriaceae, a bacterial family with members occupying diverse environmental niches including plant and animal hosts with lifestyles ranging from mutualism to pathogenesis. We use both computational and experimental approaches to study the rates, patterns, mechanisms and phenotypic consequences of genome-scale evolution. Some of our current areas of research are: 1) Specialization in either plant or animal hosts, 2) Recombination within and between species, populations and strains, 3) Rates and patterns of genome rearrangement, 4) Regulatory evolution and energy metabolism, 5) Evolution of chemotaxis and signaling systems. We also develop tools and resources for genome analysis, including a multiple genome alignment and visualization system, and an interactive web-based genome database and analysis platform.

 

Elliott Sober – Philosophy

Professor Sober’s areas of research are philosophy of science and philosophy of evolutionary biology.  His publications include Ockham’s Razors — A User’s Manual (Cambridge University Press, 2015), Did Darwin write the Origin Backwards? (Prometheus Books, 2011), Evidence and Evolution — the Logic Behind the Science (Cambridge University Press, 2008), Unto Others — The Evolution and Psychology of Unselfish Behavior (with David Sloan Wilson, Harvard University Press, 1998) and Philosophy of Biology (Westview Press, 1993).

 

Michael Sussman – Biochemistry

Plants respond to environmental changes such as drought by a complex network of signaling proteins whose levels of protein phosphorylation are modulated throughout the cell. Our lab is using a mass spectrometric-based quantitative phosphoproteomic pipeline to identify the key components of these signaling networks initiated by hormones and osmosensing receptor proteins at the plant plasma membrane. Arabidopsis thaliana is the model organism under study since it provides facile genetic tests for hypotheses derived from the chemical analyses to ensure that the measured changes play important roles in planta.

 

John Yin – Chemical & Biological Engineering

We are pursuing experimental and theoretical studies to better understand how the de novo synthesis of peptides from amino acids could give rise to novel peptide functions: recording environmental information, collective and cooperative replication, and adaption to new environments. These studies are providing basic insights into the prebiotic origins of information processing. Further, from an applied perspective, this work is suggesting new approaches to drug discovery by target-guided combinatorial chemistries.

 

Tehshik Yoon – Chemistry

The Yoon Research Group is a collaborative team of researchers in synthetic organic chemistry. We specialize in organic photochemistry, radical chemistry, and stereoselective synthesis. We are particularly interested in the development of novel catalytic methodology as a strategy for increasing process efficiency, controlling reaction selectivity, and reducing the environmental impact of chemical synthesis.