Fall 2007 | Fall 2006

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Wednesday, August 29, 2007
12:00 PM
Drena Dobbs
WORK IN PROGRESS: A STRUCTURAL MODEL FOR HUMAN TELOMERASE
Location: 1102 Molecular Biology
Description: I'm volunteering for the 1st spot so Taner won't have to do it. I will introduce a project initiated in our lab this summer -- for which we invite feedback and collaborations: ABSTRACT: Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA repeat sequences to the ends of linear chromosomes. The enzyme plays pivotal roles in cellular senescence and aging, and because it provides a telomere maintenance mechanism for ~90% of human cancers, it is a promising target for cancer therapy. Despite its importance, a high-resolution structure of the telomerase enzyme has been elusive, although a crystal structure of an N-terminal domain of the telomerase reverse transcriptase subunit (TERT), from Tetrahymena has been reported. In this study, we used a comparative strategy in which sequence-based machine learning approaches were integrated with computational structural modeling, to explore the potential conservation of structural and functional features of TERT in phylogenetically diverse species. The structures of N-terminal domains (TEN) from human and yeast TERT generated using threading and homology modeling were strikingly similar in overall architecture to the experimentally determined structure from Tetrahymena. Furthermore, comparative analysis of predicted and experimentally verified DNA and RNA binding sites, in the context of these structures, revealed significant similarities in nucleic acid binding regions of Tetrahymena and human TEN domains. Finally, the combined results of machine learning and structural modeling has led the identification of several specific amino acids that are likely to play a role in binding DNA or RNA, but for which no experimental evidence is currently available. Our results suggest that computational approaches can provide valuable information to guide experimental investigations of "recalcitrant" enzyme complexes, and, potentially, lead to new disease intervention strategies.

Wednesday, September 5, 2007
12:00 PM
Location: 1102 Molecular Biology

Wednesday, September 12, 2007
12:00 PM
Hui-Hsien Chou
INTRODUCTION TO THE NEW PICKY 2.1
Location: 1102 Molecular Biology
Description: I am going to release a new version of my oligo microarray design software Picky. I will talk about its new features and how you may use it for things other than microarray design. People asked me what are those other things, which include genome tiling, splice variant identification, and siRNA design. Maybe audiences can check with me "if I can do this or that" during my informal talk, and then we will learn more about other potential uses of Picky.

Wednesday, September 19, 2007
12:00 PM
Diane Bassham
VESICLE TRAFFICKING TO THE PLANT VACUOLE
Location: 1102 Molecular Biology

Wednesday, September 26, 2007
12:00 PM
Don Sakaguchi
DEVELOPMENT OF EXPERIMENTAL STRATEGIES FOR RETINAL RESCUE AND REPAIR
Location: 1102 Molecular Biology
Description: The field of stem cell biology has much to offer for the study of the mammalian retina. From a developmental perspective, retinal and brain-derived stem cells may serve as ideal models to gain a better understanding of the cellular and molecular basis of retinal specification and differentiation during development, as well as during regeneration. From a pathophysiological perspective, the response of transplanted stem/progenitor cells to various forms of retinal injury and disease provides a powerful means of assaying the status of local cues within the microenvironment. From a clinical perspective, stem/progenitor cell transplantation is a novel and exciting possibility for cell replacement and neuroprotection to the damaged and diseased CNS. While much remains to be demonstrated, stem cell transplantation provides an exciting new strategy for the treatment of retinal disease and offers the hope that effective treatments may be within reach.

Wednesday, October 3, 2007
12:00 PM
Volker Brendel
THE BIOINFORMATICS LANDSCAPE IN 2007
Location: 1102 Molecular Biology
Description: I will discuss my view of where bioinformatics is currently as a field and what the current problems and challenges are. I will then introduce our BioExtract Server project as a potential solution to some of the problems.

Wednesday, October 10, 2007
12:00 PM
Steve Howell
PLANT STRESS SENSOR/TRANSDUCERS
Location: 1102 Molecular Biology
Description: Climate change is one of the most critical issues of our times. Climate change is expected to produce weather extremes, and developing crops to deal with environmental stresses is vital in securing our food and biofuel supplies. One of the most sensitive processes to environmental stress in plants is protein folding. Plants and all other eucaryotic organisms have developed elaborate means to detect and respond to protein misfolding problems. We have found sensor/transducers in plants that respond to environmental stresses and protein misfolding. Efforts to manipulate these sensor/transducers may help in mitigating environmental stresses in plants.

Wednesday, October 17, 2007
12:00 PM
Jo Anne Powell-Coffman
GENETIC ANALYSIS OF HYPOXIA RESPONSE IN C. ELEGANS
Location: 1102 Molecular Biology
Description: During development, homeostasis, tumor growth, or ischemia, cellular oxygen levels are often insufficient to meet physiological demands. The human hypoxia-inducible factor (HIF)-1 implements most of the critical transcriptional changes that mediate adaptation to hypoxia. Cells employ multiple strategies to monitor oxygen levels and keep HIF-1 activity “in check”, including the EGLN / VHL (von Hipple Lindau) pathway for oxygen-dependent degradation of the HIFa subunit. When oxygen is abundant, EGLN enzymes hydroxylate HIFa subunits, allowing HIFa to bind the VHL E3 ligase complex. This results in proteasomal degradation of the HIF alpha subunit. Our research group employs Caenorhabditis elegans, a powerful genetic model system, to identify and characterize the molecules and pathways that control HIF activity. The C. elegans orthologs of HIF alpha, HIF beta, VHL, and the EGLN / PHD / HPH enzymes are termed hif-1, aha-1, vhl-1, and egl-9. Genetic analyses in our lab have demonstrated that, in addition to its role in controlling HIF-1 stabilty, EGL-9 also acts via VHL-1-independent pathway(s) to attenuate HIF-1 function. Using both forward genetic approaches and full-genome RNAi screens, we have identified other genes that inhibit HIF-1 function, and we are working to understand how these genes act in concert with EGL-9 to inhibit expression of HIF-1 target genes.

Wednesday, October 24, 2007
12:00 PM
Taner Sen
MODELING BIOLOGICAL COMPLEXITY AT MULTIPLE STRUCTURAL LEVELS
Location: 1102 Molecular Biology
Description: A multilevel comprehension of molecular interactions is necessary to understand biological complexity; the genome mapping of many organisms has provided a large dictionary of cellular components, but not a full knowledge of how these elements function, interact, and in turn, create a self-sustaining system. To tackle this complexity, we require multiscale, multidisciplinary approaches, covering several temporal and spatial scales. In this talk, I will present my postdoctoral research aimed at understanding biological systems on several levels: sequence, structure, and network. I will give specific examples on protein structure prediction, single protein dynamics, protein-protein binding site predictions, and the organizational characteristics of protein-protein interaction networks. These structural and dynamical analyses of biological systems will lead to an enhanced understanding of cellular machinery.

Wednesday, October 31, 2007
12:00 PM
Mike Muszynski
EFFORTS TO ELABORATE THE MAIZE FLORAL TRANSITION GENE NETWORK
Location: 1102 Molecular Biology
Description: The floral transition is the period in a plant’s life cycle when growth switches from the vegetative to the reproductive phase. The transition is induced by signals that initiate in leaves and translocate to the shoot apex where the shoot apical meristem is reprogrammed to adopt a floral fate. The genetic pathways underlying the floral transition have been largely defined in Arabidopsis but whether these pathways are conserved in all species is not known. In my talk, I will describe my recent efforts aimed to elaborate the floral transition gene network in maize and some new ideas for future studies that I plan to submit in a grant proposal. I look forward to your input and feedback.

Wednesday, November 7, 2007
12:00 PM
Jeffrey Essner
PROGRESS ON A COUPLE OF ZEBRAFISH RESEARCH LAB PROJECTS
Location: 1102 Molecular Biology
Description: First, I will present our recent insights in vascular tube formation and the role of moesin in this process. Moesin functions in other systems to link the actin cytoskeleton to the cortical membrane. We have identified a novel role for this moesin in tube formation and provide a model for its function downstream of VEGF-signaling. Second, I will discuss our attempts at site-specific genome modification in zebrafish. This project utilizes the bacterial protein RecA to perform homology searches and stimulate homologous recombination.

Wednesday, November 14, 2007
12:00 PM
Clark Coffman
Location: 1102 Molecular Biology

Wednesday, November 28, 2007
12:00 PM
Yanhai Yin
NETWORKS AND MECHANISMS OF BRASSINOSTEROID REGULATED GENE EXPRESSION
Location: 1102 Molecular Biology
Description: Plant steroid hormone Brassinosteroids (BRs) promote growth as well as resistance to both biotic and abiotic stresses. BRs function to regulate BES1 and BZR1 family transcription factors, which mediate the expression of many genes. I will present our recent characterization of BES1 partners and target genes that connect BES1 function to different biological processes.

Wednesday, December 12, 2007
12:00 PM
Erik Vollbrecht
TRANSPOSON GENOMICS (THE TRANSPOSOME!) AND BRANCHING ARCHITECTURE IN MAIZE
Location: 1102 Molecular Biology