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Current Research

Researchers in CLEE use state of the art techniques to understand how life persists in some of the most extreme habitats on Earth

Physiological adaptation and evolution

The Buckley lab investigates the physiological responses of marine species to elevated temperature and other stressors. We work on fishes from various habitats, comparing responses from eurythermal species such as temperate, estuarine gobies to the cold-adapted stenothermal species endemic to Antarctica. Using genomics-enabled technologies such as cDNA microarrays, we are interested in characterizing broad-scale patterns of environmentally controlled gene expression, with the goal of linking these patterns to phenotypic changes at the cellular and organismal level.


Research in the Podrabsky lab is focused on small cyprinodont fish that live in the desert Southwest of North America  or the coastal deserts of northern South America, who survive in habitats that are unsuitable not only to most other species of fish, but to most vertebrates!  These fish tolerate extremes in temperature, oxygen concentration, pH, salinity, and in some cases even dehydration. We are currently using modern genomic techniques such as cDNA microarrays to search for the genes that may allow these amazing fish to survive in their harsh and often unpredictable desert environments.



Plant mating systems

Research in the Eppley lab focuses on the ecology and evolution of angiosperms and bryophytes.  Current research is centered on investigating the interactions between environmental stress and mating systems in the survival and maintenance of plant populations.  We are particularly interested in understanding the role of extreme environmental stress, such as high temperature stress associated with geothermal areas, in mating system function and the maintenance of sex.




Origins of early life

The Lehman lab is interested in prebiotic chemistry and the origins of life on the Earth. We use catalytic RNA (ribozymes) to reconstruct primitive living processes such as self-assembling systems, cooperative catalytic networks, and simple evolving and/or decision-making molecular constructs.



Post-transcriptional processing

Research in the Iwata-Reuyl lab focuses on problems at the interface of chemistry and biology, and addresses diverse aspects of protein function, mechanism, structure, evolution, and desig

n. We employ a multidisciplinary approach that includes enzymology, kinetics, molecular biology, and organic synthesis, and our close collaborations with other research groups allow us to further broaden the scope of our work to include structural biology, computational genomics, genetics, and physiology.


The start of gene expression

The Bartlett lab focuses on transcription, the first step in gene expression, in microbes from the domain Archaea. DNA-protein interactions are integral to the transcription process, and we study these interactions by cross-linking, using modified versions of transcription factors engineered to contain photochemically reactive unnatural amino acids. By this method the transcription factor surfaces that interact with DNA are being defined, informing new hypotheses for transcription factor function. Because the archaeal transcription machinery is so similar to that of eukaryotes (including humans), our findings help to illustrate the normal process of gene expression in many organisms.


Thermophilic microorganisms

Research in the Reysenbach lab focuses on studying the microbial ecology  of high temperature terrestrial and deep-sea hydrothermal vents. We are interested in global patterns of biodiversity in these ecosystems and use the observations to study the physiological ecology and diversity of key thermophilic populations.  We use a combination of classical cultivation, molecular phylogenetic, metagenomic and transcriptomic approaches to address these fundamental questions about ecosystems that are so tightly connected to the geology and geochemistry of their environment.


Researchers in the Perona lab use genetics, biochemistry, bioinformatics and Xray crystallography to understand unique aspects of metabolism in a variety of methanogenic archaea, including hyperthermophiles that flourish in sea floor sediments under high pressures and in the absence of oxygen.

Recently the Perona lab was awarded a new NASA grant entitled "Biological sulfur metabolism on the anaerobic Earth." Using bioinformatics approaches to exhaustively search all archaeal genomes, John Perona and colleagues have uncovered three conserved protein families, each containing molecular signatures predicting function in sulfur metabolism.  One of these families, classified within clusters of orthologous groups (COG) 1900, possesses two conserved cysteine residues and is often found in genomic contexts together with known sulfur metabolic genes. A second protein family is predicted to bind two 4Fe-4S clusters, while the third family (COG 2122) possesses one conserved Cys and may bind a redox cofactor.  All three genes were also identified in more than 50 strictly anaerobic bacterial genera from nine distinct phyla. Gene-deletion and growth experiments in Methanosarcina acetivorans, using sulfide as the sole sulfur source, demonstrate that two of the proteins (MA1821 and MA1822) are essential to homocysteine biosynthesis in a background lacking an additional gene for sulfur insertion into homocysteine. The third M. acetivorans gene, MA1715, is essential for growth at low concentrations of sulfide.  Together, these findings break open a major unsolved problem in early Earth metabolism relating to the role of microorganisms in the fundamental biogeochemical cycle for sulfur in anaerobic environments.  We are now pursuing additional physiological studies of these proteins as well in vitro biochemistry and biophysics studies to define structures and reaction mechanisms. 


Viral Evolution

The Stedman lab studies viruses from extreme environments, with a focus on high temperature acidic environments, such as those found in Lassen Volcanic National Park.  These viruses have novel genomes and shapes and may provide tools for biotechnology, drug delivery and medical imaging.  We use a combination of metagenomics, genetics, and biochemistry to understand the role that these viruses play in extreme environments.




Open Ocean Microorganisms

Research in the Thompson lab examines the tiny microbial cells that dominate Earth's huge open ocean gyres. These cells, called Prochlorococcus, are a type of phytoplankton that have evolved to thrive on very low concentrations of nutrients and abundant light found in the surface oceans far from land. "Pro", as it is known affectionately, is thought to be the most abundant photosynthetic cell on Earth so is responsible for a large component of global carbon, energy, and nutrient cycles. In addition, these tiny cells form the foundation of oceanic food webs. In order to improve our understanding of the Earth system, we must improve our understanding of ecology of this abundant cell.

To study natural populations of Prochlorococcus, the Thompson lab conducts ship-based research expeditions to the subtropical gyres of the North Pacific. One focus is to determine the importance of genetic diversity to the contributions of Pro to the carbon cycle. Another project examines the influence of surface ocean physical dynamics on Pro diversity and ecology. These projects combine techniques of oceanographic sampling, flow cytometry, stable isotope probing, and sequence-based analysis. The outcomes of these projects will be an improved understanding of the importance of this abundant cell to marine nutrient cycles and food webs.