Systems Biology and Biological Regulation

Featured Research

Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage
  — Prof. Sabeeha S. Merchant
Iron Deficiency & the Expression of Genes

Prof. Sabeeha Merchant, in cooperation with Prof. Steven Clarke, and Prof. Joseph Loo, surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology
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At least 15 research groups in the UCLA Department of Chemistry & Biochemistry carry out research in the area of Systems Biology and Biological Regulation.

This discipline combines efforts to characterize the structural, biochemical, and in vivo functional properties of individual biomolecules and pathways with the cutting-edge approaches of modern genomics, proteomics, and metabolomics. It combines both experimental and computational approaches to model biological systems and tests the predictions of the models.

Investigators in this focus area are addressing questions concerning such topics as gene regulation at both transcriptional and post-transcriptional levels, metabolic regulation and homeostasis, regulation of cell shape and motility, intracellular transport and compartmentation, phylogenomics, and molecular evolution.


Professor James U. Bowie
Professor James Bowie and his group are fascinated by protein structure, folding and stabilization. This interest has led them into three main areas: (1) learning how membrane proteins fold and how they can be stabilized; (2) the structures and biological functions of a biological polymer they discovered, that is formed by a very common protein module called a SAM domain; (3) developing and stabilizing enzyme pathways for the production of biofuels.
Professor Guillaume F. Chanfreau
Professor Guillaume Chanfreau's laboratory is interested in gene expression regulation in eukaryotic cells, with a particular emphasis on post-transcriptional steps. Within this large field, they are focusing on understanding how cells degrade RNAs that arise from malfunctions in gene expression pathways ("RNA surveillance"). In particular, they are analyzing the functions of the double-stranded RNA endonuclease RNase III and of the nonsense-mediated decay pathway in RNA surveillance, and how these enzymes regulate gene expression.
Professor Catherine F. Clarke
Professor Catherine Clarke and the Clarke lab study the biosynthesis and functional roles of coenzyme Q (ubiquinone or Q). Q functions in mitochondrial respiratory electron transport and as a lipid soluble antioxidant. The group is using the yeast Saccharomyces cerevisiae (bakers yeast) to elucidate the biosynthetic metabolism of Q. Their experimental approach employs a combination of molecular genetics, lipid chemistry and biochemistry to delineate the steps responsible for Q biosynthesis.
Professor Steven G. Clarke
A major interest of Professor Steven Clarke's Laboratory is understanding the biochemistry of the aging process. The group is particularly interested in the generation of age-damaged proteins by spontaneous chemical reactions and the physiological role of cellular enzymes that can reverse at least some portion of the damage. They have focused their efforts on the degradation of aspartic acid and asparagine residues and the subsequent metabolism of their racemized and isomerized derivatives. The group is presently determining the biological role of protein methyltransferases that can initiate the conversion of D-aspartyl residues to the L-configuration as well as the conversion of isopeptide linkages to normal peptide bonds. Such "repair" reactions may greatly increase the useful lifetime of cellular proteins and may help insure organismal survival. View Professor Clarke's YouTube Lecture
Professor Robert T. Clubb
Professor Robert Clubb investigates the molecular basis of bacterial pathogenesis. In particular, they study how microbes display and assemble cell wall attached surface proteins, and how they acquire essential nutrients from their host during infections. The group's study could lead to creating new inhibitors of bacterial infections.
Professor Albert J. Courey
Professor Albert Courey and his group study the molecular basis of cell development. During embryogenesis, a cluster of apparently undifferentiated cells is transformed into an ordered array of differentiated tissues. Using Drosophila as a model system, his research group combines biochemical and genetic approaches to study the molecular basis of this amazing transformation. Essentially all the regulatory circuits they study are conserved throughout the animal kingdom. Therefore, their studies have important implications for human health and development.
Professor Juli Feigon
Professor Juli Feigon and her research group study nucleic acid structure and specific recognition of nucleic acids by proteins. Her group focuses on determining the three-dimensional structures of DNA and RNA, and on investigating their interactions with various proteins and ligands, and to study nucleic acid folding.
Professor James W. Gober
Professor James Gober's group is interested in the mechanisms that couple cellular morphogenesis to gene expression. Early flagellar assembly events are required for the transcription of genes encoding structures that are assembled later in the flagellum. These same events are also required for normal cell division. The group is determining how factors that regulate gene expression and cell division monitor the assembly of the cellular structures.
Professor Carla M. Koehler
Professor Carla Koehler and her research group encompass two major areas: Understanding the mechanism of protein import into mitochondria and determining the process by which defects in mitochondrial protein translocation lead to disease.
Professor Christopher J. Lee
Professor Christopher Lee's main area of research is in bioinformatics. His group studies 1) analysis of alternative splicing and genome evolution, 2) analysis of protein evolutionary pathways, and 3) development of a general framework for working with genomic data as an abstract graph database.
Professor Joseph A. Loo
The research interests of Professor Loo's group include the development and application of bioanalytical methods for the structural characterization of proteins and post-translational modifications, proteomics-based research, and the elucidation of disease. The composition and structure of noncovalently-bound protein-protein and protein-ligand interactions are studied by electrospray ionization mass spectrometry and ion mobility.
Professor Sabeeha S. Merchant
The Merchant research program focuses on trace metal metabolism using Chlamydomonas as a reference organism. The group uses a combination of classical genetics, genomics and biochemistry to discover mechanisms of trace metal homeostasis in Chlamydomonas, especially mechanisms for reducing the quota or for recycling in situations of deficiency.
Professor Margot E. Quinlan
Professor Margot Quinlan and her group use biochemistry, microscopy and genetic approaches to study regulation of the actin cytoskeleton. The group is currently focused on Spire (Spir) and Cappuccino (Capu), two proteins that collaborate to build an actin network essential for early body axis development. Combining an in vitro understanding of the mechanism of Spir and Capu with in vivo studies of polar cells will provide insight into how the actin cytoskeleton is regulated and a broader understanding of cell polarity.
Professor Emil Reisler
Professor Emil Reisler's group investigate cell motility and force generation mechanism of actin, tubulin, and a family of motor proteins. The aim of these studies is to obtain a structural description of the mechanism of motion and force generation. At the cellular level, the group studies the function, interactions, and structural transitions of the assembled protein systems.
Professor Jose Rodriguez
Prof. Rodriguez studies the complex architecture of biological systems - from single biomolecules to cellular assemblies - at high resolution. His work is largely based on diffraction phenomena and combines computational, biochemical and biophysical experiments. The development of new methods is central to this work, particularly using emerging technologies in cryo-electron microscopy, nano and coherent x-ray diffraction, and macromolecular design. Combined, these tools can reveal undiscovered structures that broadly influence chemistry, biology, and medicine.
Professor Alexander Spokoyny
Research in the Spokoyny laboratory is devoted towards establishing new synthetic avenues, structural understanding, and applications for inorganic and organomimetic clusters. These efforts will reveal novel and potentially useful solutions to important problems in the field, including: catalysis, energy storage and selective recognition and labeling of biomolecules.
Professor Jorge Z. Torres
Professor Jorge Torres’ research group is interested in understanding the mechanisms of cell division. Currently they are discovering and characterizing novel enzymatic activities that are critical for cell division (cancer targets) and discovering or designing small molecules that can inhibit their function (anti-cancer agents). To do this, they are taking multidisciplinary approaches that utilize human cancer cell lines and high throughput proteomic and small molecule screening with a combination of disciplines, including biochemistry, cell biology, chemoinformatics, chemical biology and microscopy.
Professor Joan S. Valentine
Professor Joan Valentine's research group focuses on the role of metal ions in biological oxidation, including oxidative stress, and in naturally occurring antioxidant systems. It has three central themes: (1) biological studies of CuZnSOD in vivo, (2) coordination complexes as models for catalysts involved in biological oxidation, and (3) biophysical characterization of isolated copper-zinc and manganese superoxide dismutase ((CuZnSOD and MnSOD). Recent work on CuZnSOD proteins has focused on the role of mutations in CuZnSOD in causing familial amyotrophic lateral sclerosis (ALS, Lou Gehrig’s disease).
Professor Richard L. Weiss
Professor Richard Weiss' research focus is to understand the role of compartmentation of enzymes and metabolites in biological regulation. The organellar localization of metabolic pathways requires considerable expenditure of metabolic energy for protein targeting, organelle assembly, and movement of substrates and products across intracellular membranes. Such expenditures must result in biological efficiencies commensurate with the investment of biological resources. Our hypothesis is that these compartmentation features play a significant role in the biology of the organism.