HOWARD BERG
Flagellated bacteria possess a remarkable motility system based on a reversible rotary motor linked by a flexible coupling (the proximal hook) to a thin helical propeller (the flagellar filament). The motor derives its energy from protons driven into the cell by chemical gradients or electrical fields. The direction of the motor rotation depends in part on signals generated by sensory systems, of which the best studied analyzes chemical stimuli. Our research group is trying to learn how the motor works, the nature of the signal that controls the motor's direction of rotation, and how this signal is processed by the chemical sensory system. These questions are being approached by a variety of molecular-genetic and physical techniques. The goal is an understanding of chemiosmotic coupling and sensory transduction at the molecular level.

COLLEEN CAVANAUGH
Symbioses of bacteria in marine invertebrates from deep-sea hydrothermal vents, methane seeps, and coastal reducing sediments. Specific emphasis on characterization of metabolic and genetic capabilities of symbionts, evolutionary relationships with free-living bacteria, and co-evolution of host and symbiont.

KATHLEEN DONOHUE
I conduct research on evolutionary ecology and evolutionary genetics in natural plant populations. My research focuses on adaptations to variable environments, the evolution of phenotypic plasticity and maternal effects, mechanisms of multilevel natural selection, and population demography. I currently focus on the evolution of seed characters such as germination and dispersal using quantitative genetic techniques and ecological manipulations in the field. Ongoing projects investigate the genetic basis and adaptive significance of germination responses to seasonal cues in Arabidopsis thaliana, environment-dependent genetic constraints on the evolution of dispersal, and the functional and developmental basis of variation in fruit morphology in the genus Cakile and its relatives.

JOHN DOWLING
The vertebrate retina is an accessible part of the central nervous system; an understanding of retinal mechanisms should provide clues concerning neural mechanisms throughout the brain. Over the years, our group has been concerned with the cells of the retina, their structure, function and synaptic interactions.

VICTORIA D'SOUZA
Nuclear magnetic resonance (NMR) and other biophysical and biochemical methods are the principal tools used in my laboratory to study relatively large RNA and protein molecules. The structure determination of large protein- RNA complexes by NMR is extremely challenging, but the potential payoff is high and should ultimately lead to detailed models of steps involved in retroviral replication.

CATHERINE DULAC
Our group is exploring the molecular logic of olfactory signaling underlying the coding of odorant- and pheromone-mediated signals and is interested in the developmental processes that ensure appropriate neuronal connections between the olfactory sensory neurons and the brain.

SCOTT EDWARDS
Our laboratory studies the diversity and evolutionary biology of birds and relatives. Students in our group have strong interests in molecular evolution, population genetics, phylogeography, comparative genomics and behavioral ecology of natural populations and non-model species. We study variation in the major histocompatibility complex and other gene families to understand the behavioral and evolutionary consequences of immunogenetic variation; utilize new BAC library, macroarray and robotics approaches to study genome and sex chromosome evolution; and add field and museum work for an organismal perspective.

KEVIN EGGAN
The primary research focus of our group is to understand the mechanisms by which nuclear reprogramming occurs. In particular, we wish to determine the nature of epigenetic information that is reprogrammed (i.e., aspects of DNA methylation and chromatin structure), the times at which reprogramming events occur and the identities of the molecular machinery that accomplish reprogramming.

CASSANDRA EXTAVOUR
Germ cells play a unique role in gamete production, heredity and evolution. Germ cells are likely also the closest wild type in vivo equivalent to laboratory-maintained stem cells. Therefore, to understand the mechanisms that specify germ cells is a central challenge in developmental and evolutionary biology. Data from model organisms show that germ cells can be specified either by maternally inherited determinants (preformation) or by inductive signals (epigenesis). Although preformation is seen in most model organisms, it is actually the less prevalent mode of germ cell specification, and that epigenetic germ cell specification may be ancestral to the Metazoa.

BRIAN FARRELL
Macroevolution of interspecific interactions, particularly between insects and plants. Emphasis is on understanding the conceptual and empirical connections between ecological interactions and long term evolutionary patterns. Main approach applies molecular phylogenetic studies of phytophagous beetles in the enormous, sister superfamilies Chrysomeloidea and Curculionoidea.

NICOLE FRANCIS
My lab aims to understand the nature of epigenetic information and how it is inherited.  We use biochemical methods to study how Drosophila Polycomb Group proteins affect chromatin, and how changes in chromatin can be inherited.

WILLIAM GELBART
Our laboratory focuses on the experimental and computational analysis of the organization, regulation and evolution of the Drosophila genome. Experimental analyses include global approaches to phenotypic dissection of the genome and characterization of non-protein coding segments of the genome. Computational approaches include modeling of anatomical structure, DNA motif analysis, and organization of genetic and genomic information in a robust database tool for the scientific community (FlyBase). Our laboratory focuses on the experimental and computational analysis of the organization, regulation and evolution of the Drosophila genome. Experimental analyses include global approaches to phenotypic dissection of the genome and characterization of non-protein coding segments of the genome. Computational approaches include modeling of anatomical structure, DNA motif analysis, and organization of genetic and genomic information in a robust database tool for the scientific community (FlyBase).

PETER GIRGUIS
With my colleagues, we have been conducting experiments to better understand the potential growth rates of ANME-1 and ANME-2 methanotrophs, and to examine the influence of sediment advective flow rates on the distribution and abundance of these methanotrophs. We are also exploring the role of anaerobic methanotrophs in carbon and nitrogen cycling at hydrothermal vents.

GONZALO GIRIBET
My research focuses on the systematics, evolution, biogeography and biology of arthropods and other metazoans. Within arthropods, my research emphasizes on daddy-long-legs (Arachnida, Opiliones) and centipedes (Myriapoda, Chilopoda) and I am studying these groups at different levels. Higher-level systematics of arthropods is also one of my main research topics. My interest in arthropods has also led me to deepen in their phylogenetic position among metazoans, and naturally to achieve a better understanding of metazoan evolution, emphasizing in those minorgroups and novel body plans. Furthermore, the theory and practice of phylogenetic systematics is a recurrent theme in my research. Current interest focuses on issues related with sensitivity analysis, alignment-related issues and DNA homology, biogeography, and application of parallelism to phylogenetic analyses. These topics are always addressed from an experimental point of view utilizing real data from my empirical studies on arthropods and other metazoans.

DAVID HAIG
Evolutionary theory; intragenomic conflicts; parent-offspring relations; evolution of plant life cycles.

JAMES HANKEN
Evolutionary biology; morphology, development, and systematics. Research focuses on vertebrates, especially amphibians, but otherwise encompasses a broad range of organisms and problems. These include the morphological and developmental correlates and consequences of alternate reproductive modes, such as direct development; life history evolution; mechanisms of cranial pattern formation during embryonic and metamorphic development, including the role of the neural crest and associated patterns of gene expression; and taxonomy and systematics of neotropical salamanders.

DANIEL HARTL
We use molecular genetics and genomics to study how organisms evolve and new species are formed. Our research takes advantage of model organisms (fruit flies, nematodes, yeast, bacteria) or organisms of interest in public health (the malaria parasite, P. falciparum). We also make use of state of the art molecular and statistical approaches, such as gene-expression profiling, bioinformatics, correlations of sequence data with three-dimensional protein structures, and Bayesian analysis of population samples implemented through Markov chain Monte Carlo. The Hartl lab web site gives specific examples and descriptions of ongoing and recently completed projects.

CRAIG HUNTER
RNAi in C. elegans, whether induced by ingestion or injection of double-stranded RNA (dsRNA), spreads throughout the organism and is even transmitted to the progeny. We are using forward genetic screens to identify cellular components required for systemic silencing and then using these gene products to study the process in C. elegans and in heterologous systems. We are using genetics, biochemistry, and genomic approaches to understand the molecular mechanisms that pattern embryonic gene expression in cellular C. elegans embryos.

NANCY KLECKNER
Our laboratory is interested in the basic principles that govern chromosome function. We study three aspects of meiosis, primarily in yeast: pairing of homologs, regulated formation of chiasmata and the nature and role of telomere clustering at the bouquet stage. We also study the mechanism and roles of chromosome-based signal transduction in eukaryotes and the nature and logic of the DNA replication/cell division cycle(s) in the bacterium E.coli. All of this work is carried out from an evolving perspective which emphasizes the mechanical properties of chromosomes. We are testing our hypothesis that an intrinsic tendency for chromatin/chromosome expansion generates stress forces which, in turn, govern diverse basic chromosomal processes.

SAM KUNES
My laboratory studies the development and behavior of Drosophila melanogaster. Current projects include the genetic analysis of axon branching and morphology, the role of tyrosine kinase receptors in learning and neurotransmitter receptor localization, regulation of synapse development and activity, and neuronal migration. We are devising novel methods to examine fruitfly behavior and to resolve neural function in generating these behaviors.

ELENA KRAMER
The focus of my lab can be broadly described as plant evolutionary developmental genetics, but our work touches on many different fields, from systematics to proteonomics. In general, we are interested in the genetic basis of evolutionary change, particularly in relation to flower development. Currently, much of our work is concentrated on the MADS-box genes, a large family of transcription factors which play critical roles in many aspects of plant development. We are studying this family from many perspectives, including patterns of gene duplication, trends in sequence evolution, changes in gene regulation, and evolution of protein dimerization specificity.

JUN LIU
My group develops computational methods for understanding functional and structural genomics data. Selected topics include: regulatory binding motif discoveries; homology modeling and protein sequence analysis; SNP haplotype studies; and microarray analyses. Our general strategy is to build comprehensive probabilistic models to connect specific biological knowledge (e.g., transcription factors’ role in gene regulation and the conservation of their binding sites) with the underlying biological question of interest (e.g., exact location of the sites and their consensus patterns), and use the Bayesian method to make the inference. Computational difficulties are overcome by Markov chain Monte Carlo strategies, e.g., the Gibbs sampler and the Metropolis algorithm. Besides bioinformatics, we are also keenly interested in the general Monte Carlo methods for integration and optimization in complex systems.

RICHARD LOSICK
The laboratory of Richard Losick studies cell fate and development in a simple experimental system, sporulation in the bacterium Bacillus subtilis. Sporulating cells divide asymmetrically, giving rise to dissimilar progeny that express different sets of genes. We study how cells divide asymmetrically, how asymmetric division gives rise to differential gene expression, how progeny cells communicate with each other, and how gene expression is coupled to landmark events in morphogenesis. Underlying the answers to these questions are proteins that localize dynamically to particular sites in the cell. The laboratory also investigates how bacteria segregate their chromosomes absent a conspicuous mitotic apparatus.

TOM MANIATIS
Mechanisms of gene expression.

CHARLES MARSHALL
Use of techniques in paleontology, developmental biology, statistics, molecular and morphological phylogenetics to understand the nature and causes of evolutionary innovation and extinction over geological time scales.

CHRIS MARX
How did the present diversity of physiological capacities arise in bacteria, and how is it maintained? The lab's research approach uses experimental evolution of specialized metabolic capacities as a model to investigate evolutionary dynamics. The current projects in development revolve around three areas: Investigation of fitness tradeoffs associated with specialist vs. generalist lifestyles. Exploration of evolutionary dynamics following acquisition of novel genetic material through horizontal gene transfer. Coevolution of metabolic cpacities in novel, defined microbial consortia.

ANDY MCMAHON
All higher organisms consist of large number of highly specialized cell types which are organized in precise patterns to generate the adult. The basic body plan is laid down early in life, during embryogenesis. Our goal is to elucidate the cellular and molecular mechanisms which regulate growth, differentiation, and patterning of the vertebrate embryo. In particular, we are exploring the role of cell-to-cell signalling in the coordinate regulation of groups of cells during embryonic development of the mouse and chick.

MATTHEW MESELSON
The objective of our research is to understand why nearly all animals and plants reproduce sexually, why the loss of sexual reproduction usually leads to early extinction.

MATT MICHAEL
Work in my laboratory is focused on how cells replicate their chromosomes with high accuracy and fidelity. In particular, we use genetics in the nematode C. elegans together with biochemical approaches in Xenopus egg extracts to explore and define the mechanisms that allow cells to complete DNA replication under stressful conditions, such as when DNA damage is present. The ability to do so is vital not only for the survival of the cell, but also for survival of the organism as genome instability that can result from improper replication during a crisis can cause transformation, tumor formation, and, ultimately, cancer.

ANDREW MURRAY
We work in three areas, chromosome behavior, experimental evolution, and physiology (also known as systems biology). Chromosome work focuses on the spindle checkpoint, the control system that keeps cells from dividing until all their chromosomes are properly attached to the cell division machinery. Evolution experiments deal with general questions like the purpose of sex and the relationship between robustness and evolvability as wells as more specific ones such as speciation, evolving cross talk between pathways and symbiosis. In physiology, we combine theory and experiment in search of an integrated understanding of how yeast cells communicate and mate with each other.

AXEL NOHTURFFT
Our broad goal is to understand the mechanisms and regulation of cellular lipid transport. Specifically, we are studying the process of cholesterol export from lysosomes.Mammalian cells acquire a large fraction of their cholesterol by receptor-mediated endocytosis of serum lipoproteins such as low-density lipoprotein (LDL). LDL particles carry cholesterol predominantly in chemically modified form as cholesteryl esters, i.e. cholesterol covalently attached to a fatty acid molecule. Following endocytosis, cholesteryl esters are transported to late endosomes and lysosomes where they are hydrolyzed to generate cholesterol and fatty acid. Cholesterol is then transported to other destinations in the cell by an as yet unknown process.

MARTIN NOWAK
I am interested in any application of mathematics to biology. At present I am fascinated by somatic evolutionary genetics of cancer. A central question is whether genetic instability is an early event and thus a driving force of tumor progression. I would like to understand how tissue architecture and asymetric cell division and differentiation affects the types of mutations that occur in somatic evolution. There are many fundamental theoretical questions that need to studied. I am also working on the dynamics of viruses and other infectious agents in individual hosts. In particular, I study HIV infection.

ERIN O'SHEA
We study how cells monitor the environment and regulate gene expression, work that has implications for understanding cancer and other diseases. We are also interested in deciphering the logic of signaling and transcriptional networks and in understanding the regulation and mechanism of oscillation of a three-protein circadian clock

NAOMI PIERCE
Behavioral ecology, focusing on species interactions such as insect/host plant associations and symbioses between insects and other organisms. Reconstruction of the phylogeny of the Lycaenidae (Lepidoptera) and other insects using molecular characters; comparative analyses of life history evolution; studies of genetic, behavioral and ecological mechanisms underlying lycaenid/ant associations and other insect/host recognition systems.

ANNE PRINGLE
Ecological genetics uses genetics to explore the ecology and especially evolution of organisms. Ecological geneticists see evolution as a dynamic process that can be observed in nature. Fungi encompass a diverse array of microorganisms with myriad niches. DNA technologies have facilitated an explosion of knowledge related to fungal diversity, biogeography, and the autecology of individual species, including the discovery of cryptic sexuality in ostensibly asexual taxa. The Pringle laboratory is dedicated to both the use of fungi as tools ideal for testing and elucidating general principles of ecological genetics, and the translation of biological paradigms to fungi.

MARYELLEN RUVOLO
A central focus in evolutionary anthropology is to understand the molecular basis for primate adaptations. In particular, we seek to uncover the genetic basis for phenotypic differences between humans and chimpanzees, our closest relatives. Increases in brain size, cognitive ability, and placental invasiveness are some of the more dramatic trends observed in primate evolution that need to be elucidated. We study the molecular evolution of particular genes as well as primate genomic evolution in order to understand selection and adaptation in primates with a particular emphasis on humans.

ALEX SCHIER
Our research focuses on three areas: (i) vertebrate embryogenesis - how do signals influence the fate and movement of cells? (ii) sensory neuron development and function - how does an organism sense potentially harmful stimuli? (iii) sleep and wakefulness - what are the genes and circuits that regulate sleep? We mainly use zebrafish as a model system, because genetic and imaging approaches can be combined to study complex behaviors and developmental processes in a vertebrate.

JOHN WAKELEY
Theoretical population genetics and molecular evolution, with a focus on the analysis of DNA sequence data. Particular interest in models of population subdivision and the divergence of populations and species.

YUN ZHANG
Our laboratory uses C. elegans as a genetic and genomic model system to study the function of neural circuits and regulation of behaviors. We combine molecular genetics, behavioral analyses and calcium imaging to understand the molecular and cellular mechanisms for modification of neural activities and behaviors by experience.