MCDB










BIOCHEMISTRY, MOLECULAR BIOLOGY & CHEMICAL BIOLOGY

Biology is a broad field of study, and its breadth is reflected in the research interests of the faculty members who seek to define biological processes in molecular terms. Individual research topics include the role in vivo of an enzyme with a catalytic RNA subunit (Altman); the roles of structured non-coding RNAs in gene control and catalysis (Breaker); exploration and control of signal transduction pathways using chemical probes (Crews).

Molecular technology from DNA cloning to targeted mutagenesis is being applied and developed in order to elucidate the molecular mechanisms underlying many biological processes. Insight into these processes can be greater when it is gained in the spectrum of diverse experimental approaches that our division employs. Our studies will eventually bring together molecular biology, evolutionary biology, cell and developmental biology, and genetics. Our studies can directly benefit human health and agricultural efficiency.



Faculty having a Primary Affiliation with this Section


Sidney Altman
: post-transcriptional RNA processing as a means of gene regulation

Ronald Breaker : non–coding RNA discovery; ribozyme and riboswitch analysis

Craig Crews : biochemical and molecular analyses of natural products

Mark Hochstrasser : the life and death of proteins: regulation by ubiquitin and the proteasome.

Alanna Schepartz : Development and application of chemical tools to study and manipulate protein–protein and protein–DNA interactions inside cells and whole organisms.

Additional Faculty with Interests in Molecular Biology

Stephen Dellaporta : molecular biology and genetic utility of transposons in plants.

Thierry Emonet: Signal transduction and decision making in bacteria, insects and the immune system.

Christine Jacobs-Wagner : Bacterial cell biology and cell cycle regulation.

Thomas Pollard : the molecular basis of cellular motility and cytokinesis.

Joel Rosenbaum : Studies on the assembly and function of cilia and flagella.

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CELLULAR & DEVELOPMENTAL BIOLOGY

The research interests of the faculty in the area of cell and developmental biology range from studies on nucleotide sequences in RNA and DNA through investigations of subcellular organelles, such as microtubules and chromosomes, through analyses of movement in single cells, to multicellular organization and embryogeny in higher plants and animals.

Despite the diversity of research topics and an equal diversity of experimental approaches, certain general aims are evident. These include the understanding of how macromolecules are organized into the subcellular components of living cells, how the cells themselves become different during development, and how the cellular and developmental processes are controlled.

Faculty having a Primary Affiliation with this Section

Iain Dawson : regulation of cell cycle in Drosophila melanogaster

Xing-Wang Deng : molecular mechanisms involved in light–triggered regulation of growth and development in higher plants.

Thierry Emonet : Signal transduction and decision making in bacteria, insects and the immune system.

Martín García-Castro : the origin of neural crest cells.

Scott Holley : gene networks, pattern formation and morphogenesis in zebrafish.

Valerie Horsley : Mechanisms that control stem cell use during tissue formation, homeostasis and regeneration.

Vivian Irish : mechanisms that govern pattern formation during plant development.

Christine Jacobs-Wagner : Mechanisms underlying cell cycle and developmental regulation in bacteria.

Mark Mooseker : molecular underpinnings of cytoskeletal structure, motility and assembly.

Jon Morrow : understanding the structure and function of the spectrin-ankyrin-actin cytoskeleton.

Kenneth Nelson : genome structure and function.

Timothy Nelson : development of leaves.

Thomas Pollard : the molecular basis of cellular motility and cytokinesis.

Joel Rosenbaum : assembly of cell organelles using the flagella of Chlamydomonas as a model.

Joseph Wolenski : molecular analysis of myosin mechanochemistry.

Additional Faculty with Interests in Cellular and Developmental Biology

John Carlson
: Molecular basis of olfaction and taste in Drosophila.

Craig Crews : molecular mechanisms of amphibian limb regeneration.

Paul Forscher : molecular dynamics of guided axon growth.

Mark Hochstrasser : the life and death of proteins: regulation by ubiquitin and the proteasome.

Douglas Kankel : genetic and molecular analysis of visual system development in Drosophila.

Haig Keshishian : analysis of neuromuscular development in Drosophila.

Frank Slack : microRNAs in development, aging and disease.

Robert Wyman : analysis of genes which control the specificity of neuronal connectivity in Drosophila.

Weimin Zhong : regulation of neural stem cells and development of the mammalian neocortex.

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GENETICS

Research in this fundamental area of biology spans a spectrum of biological organization from the molecular level to the organismal level. The underlying focus of interest is the genetic material: its structure, function, and regulation. A large variety of organisms is being studied using many experimental techniques and approaches. The Department has laboratories active in molecular and biochemical genetics, developmental genetics, molecular and classical cytogenetics, somatic cell genetics, and behavioral genetics.

Faculty having a Primary Affiliation with this Section

John Carlson
: Molecular basis of olfaction and taste in Drosophila.

Stephen Dellaporta : molecular biology and genetic utility of transposons in plants.

Scott Holley : gene networks, pattern formation and morphogenesis in zebrafish.

Douglas Kankel : genetic and molecular analysis of visual system development in Drosophila

Frank Slack : microRNAs in development, aging and disease.

Additional Faculty with Interests in Genetics

Sidney Altman : post-transcriptional RNA processing as a means of gene regulation.

Ronald Breaker : enzymatic DNA and in vitro evolution.

Damon Clark : dissecting neural computations in sensorimotor transformations in Drosophila

Thierry Emonet: Signal transduction and decision making in bacteria, insects and the immune system.

Martín García-Castro : the origin of neural crest cells.

Christine Jacobs-Wagner : Mechanisms underlying cell cycle and developmental coordination in bacteria.

Mark Mooseker : molecular underpinnings of cytoskeletal structure, motility and assembly.

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NEUROBIOLOGY

The faculty of the MCDB neurobiology group examine a wide range of problems in neuroscience, ranging from the molecular and cellular mechanisms that govern the development of the nervous system, to the cell biology of neurons and the functioning of neural systems. The role of asymmetric cell division by neural progenitor stem cells is examined in the Zhong lab to understand how neuronal diversity is regulated in the mammalian neocortex. The mechanisms of axon guidance and growth cone dynamics are studied from a basic cell biological perspective in both the Forscher and Stein labs, with the goal of understanding how external molecular signals are transduced to control neuronal growth cone motility and cytoskeletal structure during axon elongation and pathfinding. The Keshishian, Wells, and Wyman labs examine the establishment and plasticity of synapses, to better understand the molecular factors that govern target recognition, synaptic refinement, and the mechanisms underlying synaptic plasticity and memory formation. Finally, the Carlson lab studies the development and function of insect olfactory and gustatory neurons, to explore the molecular logic through which sensory signals are translated into behavioral outputs. In general, these lines of investigation are relevant not only to understanding the basic biology of the nervous system, but also to problems related to human health.

Faculty having a Primary Affiliation with this Section

Damon Clark : dissecting neural computations in sensorimotor transformations in Drosophila

Thierry Emonet : Signal transduction and decision making in bacteria, insects and the immune system.

Paul Forscher : molecular dynamics of guided axon growth.

Martín García-Castro : the origin of neural crest cells.

Haig Keshishian : analysis of neuromuscular development in Drosophila.

Robert Wyman : analysis of genes which control the specificity of neuronal connectivity in Drosophila.

Weimin Zhong : Regulation of neural stem cells and development of the mammalian neocortex.

Additional Faculty with Interests in Neurobiology

John Carlson : Molecular basis of olfaction and taste in Drosophila.

Douglas Kankel : genetic and molecular analysis of visual system development in Drosophila.

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SPECIAL PROGRAM IN PLANT SCIENCES

Historically, the Molecular, Cellular and Developmental Biology Department has been especially strong in the areas of plant developmental biology, physiology, and systematics. In recent years, these strengths have expanded into the areas of plant molecular biology, genetics, and chemical biology. The Special Program in Plant Sciences reflects ongoing research and training interests of the faculty in the molecular genetics of flowering, the developmental biology of leaves, the physiology of hormone action, the evolution of plants, and a variety of other areas. Colleagues in the Yale School of Forestry and Environmental Studies, at the Cary Arboretum, and at the Connecticut Agricultural Experiment Station contribute as well to the seminars, graduate classes, workshops, and field trips offered through the Program.

Faculty with Interests in Plant Sciences

Nicole K. Clay: plant innate immunity and chemical defenses

Xing-Wang Deng : molecular mechanisms involved in light-triggered regulation of growth and development in higher plants.

Stephen Dellaporta : molecular biology and genetic utility of transposons in plants.

Vivian Irish : mechanisms that govern pattern formation during plant development.

Timothy Nelson : development of leaves.

Joel Rosenbaum : Studies on the assembly and function of cilia and flagella.

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SPECIAL PROGRAM IN BIOTECHNOLOGY

Many recent research breakthroughs in the life sciences are in the areas of biotechnology and genomics. Faculty in the MCDB department is particularly strong in these areas and many are associated with research programs in Biotechnology companies. Research topics encompass the development of nanosensors and controlled nucleic acid enzymes, the generation of transgenic animals and plants, small molecule approaches to the analysis of gene function and therapeutics, functional genomics, and the large scale analysis of genomes and bioinformatics. In addition to advanced topics that are critical for excellence in the life sciences, courses in Biotechnology, Genomics, and Bioinformatics are available to students who wish to explore these emerging areas.

Faculty with Interests in Biotechnology

Sidney Altman
: knockout of gene function and functional genomics using ribonuclease P and external guide sequences

Ronald Breaker : creating new enzymes, molecular switches and genetic sensors using rational and combinatorial approaches for enzyme engineering.

Craig Crews : pharmaceutical target validation and small molecule–based exploration of cell biology.

Xing-Wang Deng : plant heterosis and agribiotechnology.

Douglas Kankel : in collaboration with the Goodrich Corp., the development of new optical instruments for biochip analysis and for image acquisition and analysis.

Perry Miller : biomedical Informatics.

Alanna Schepartz : development of novel pharmaceutical classes and their application as potential therapeutics and synthetic biology tools.

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COMPUTATIONAL BIOLOGY

The combination of mathematical modeling and novel experimental methods that probe the real–time dynamics of biological processes in vivo is emerging as a powerful approach to connect molecular mechanism to behavior in biology. It is now possible to build computational models that relate molecular events inside single cells to the behavior of these cells as they interact with the environment and with each other. Biologists can use dynamical modeling as a new tool to explore the dynamical consequences of a hypothesis before doing an experiment. Models help focusing biological questions and targeting experiments, which in turn impose constraints on the models. Close interaction between experimental studies and modeling is critical to success in this area and leads to the understanding of biological phenomena at the systems level.

Faculty with interests in Modeling

Damon Clark : dissecting neural computations in sensorimotor transformations in Drosophila

Thierry Emonet : Signal transduction and decision making in bacteria, insects and the immune system.

Scott Holley : gene networks, pattern formation and morphogenesis in zebrafish.

Thomas Pollard : the molecular basis of cellular motility and cytokinesis.

Frank Slack : microRNAs in development, aging and disease.

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Updated: March 13, 2013

Biochemistry, Molecular Biology & Chemical Biology
 
Cellular & Developmental Biology
 
Genetics
 
Neurobiology
 
Plant Sciences
 
Biotechnology
 
Dynamical modeling and real-time systems analysis of biological systems
 
 
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