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• Manel Camps (METX) Use of Random Mutagenesis for Studies of Evolution and for Therapy
• Bin Chen (MCD) Mammalian Brain Development
• Camilla Forsberg (BME) How Stem Cell Fate Is Decided
• David Haussler (BME) Using Stem Cells and Genomics to Study the Evolution and Function of Human Genes
• Lindsay Hinck (MCD) Stem Cells and Self Renewal
• Joel Kubby (EE) Applications of Adaptive Optics for Biological Microscopy
• Susan Strome (MCD) Regulation of Germ Cell Development in C. elegans
• Josh Stuart (BME) Computational Functional Genomics, with Application to Integrative Analysis of Cancer
• John Tamkun (MCD) Regulation of Chromatin Structure and Gene Expression
• Zhu Wang (MCD) Prostate Organ Development and Homeostasis

Prof Manel CampsUse of Random Mutagenesis for Studies of Evolution and for Therapy

Manel Camps, Microbiology and Environmental Toxicology

The Camps laboratory studies how random changes in genetic information (mutations) facilitate the acquisition of new biochemical activities. They couple the generation of random mutant libraries with specific selections or screens to study the functional impact of individual point mutations and to establish how genes evolve in response to selective pressure. As model systems they use extended-spectrum beta-lactamase resistance and the evolution of alterations in the substrate specificity of the demethylase ALKBH2. This work is combined (in a collaboration) with high-end computational approaches aimed at anticipating the effect of individual mutations, alone, or in combination. A separate application of random mutant library generation in vivo is the use of mutation footprints to dissect the role of individual players involved in DNA replication. Finally, the Camps laboratory is applying concepts of directed evolution to whole genomics analysis, with an emphasis on cancer. The goal of these studies is to help understand the contribution of DNA repair genes to resistance to chemotherapy and to oncogenesis. [More]

Camps' Publications Manel Camps' Email

Bin ChenMammalian Brain Development

Bin Chen , Dept. MCD Biology

Proper generation of different neuronal subtypes in the cerebral cortex and their precise wiring into functional neural circuits underlie our most sophisticated cognitive and perceptual abilities. When this process goes awry, neurological disorders, such as schizophrenia, depression, and obsessive compulsive behavior, can arise. Research in the Chen laboratory is focused on the molecular mechanisms that regulate the neural stem cells to generate different types of neurons and determining how they are wired into functional neural circuits. Neurons in the cerebral cortex are organized into 6 layers. Within each layer, neurons ..... [More]

Bin Chen's Publications
Bin Chen's Email

Prof Camilla ForsgergHow Stem Cell Fate Is Decided

Camilla Forsberg, Dept. of Biomolecular Engineering

Camila Forsberg's research group focuses on stem cell fate decisions that give rise to variant blood cell types. Are such decisions made by the stem cell itself, by its descendant multipotent progenitors, or both? To answer such questions, Forsberg's group conducts molecular lineage tracing of HSC differentiation in vivo. In order to elucidate the mechanisms of fate decisions, they employ global analyses, such as genome-wide gene expression analysis and chromatin remodeling assays. The ultimate goal of this research is to facilitate our ability to direct specific fates and improve clinical applications of hematopoietic and non-hematopoietic stem cell therapy. [More]

Forsberg Publications Camilla Forsberg's Email

Prof David HausslerUsing Stem Cells and Genomics to Study the Evolution and Function of Human Genes

David Haussler, Dept. of Biomolecular Engineering

Dr. Haussler's investigative team brings together skills of a computational group and "wet lab" researchers to understand the evolution and function of non-protein coding regions of the human genome. A major focus is on identifying DNA elements and non-coding RNAs that play a role in specifying cortical neuron development. They use embryonic or induced pluripotent stem cell neural differentiation assays with human and primate stem cells followed by genomic characterization of this process using RNA-Seq, ChIP-Seq, etc. This approach allows us to identify both primate- and human-specific features of this important developmental pathway. [More]

Haussler's Publications Haussler's E-Mail

Prof Lindsay HinckStem Cells and Self Renewal

Lindsay Hinck , Dept. MCD Biology

The mammary gland is remarkable in its capacity to self renew since every pregnancy results in prodigious cell growth to prepare for milk production. Stem cells required to maintain this process reside in specialized environments (niches) squeezed between the luminal and myoepithelial cells layers. We are exploring how loss of Slits and Netrins disrupt these niches, and the biological consequences of this disruption. [More]

Hinck Publications Lindsay Hinck's Email

Prof Joel KubbyApplications of Adaptive Optics for Biological Microscopy

Joel Kubby, Dept. of Electrical Engineering

Professor Joel Kubby is collaborating with engineers, physicists and biologists to utilize Adaptive Optics for the improvement of deep tissue imaging of living cells. Current biological microscopy is incapable of obtaining high quality live imaging in samples greater than 30 microns beneath the plasma membrane, where many critical cellular processes occur. Much of the degradation in image quality is the result of local differences in the refractive index, both within the sample and between the sample and the immersion lens. Adaptive optics was first used to correct for image aberrations in astronomical imaging. Kubby and his collaborators have shown that the same principles that improved resolution in telescopes can be adapted to improve wide-field, confocal, two-photon, super-resolution and spinning disk microscopy systems that are crucial for biological research. [More]
Kubby Publications Joel Kubby's Email

Prof Susan StromeRegulation of Germ Cell Development in C. elegans

Susan Strome, MCD Biology

Germ cells (the cells that give rise to eggs and sperm) have special properties. Their immortality allows them to be perpetuated from generation to generation, and their totipotency allows them to generate all of the diverse cell types of the body in each generation. Our lab investigates the molecular mechanisms used by germ cells to establish and maintain their identity, immortality, and totipotency. We study germ cells in the model organism C. elegans using a wide variety of approaches, including genetics, imaging, molecular biology, biochemistry, and whole-genome microarray and sequencing technologies. Our current focus areas are transmission of chromatin states and control of gene expression in germ cells, and regulation of RNA metabolism by germline-specific cytoplasmic "P granules". [More]

Strome Publications Susan Strome's E-Mail

Prof Josh StuartComputational Functional Genomics

Josh Stuart, Dept. of Biomolecular Engineering

Josh Stuart's background is in machine-learning applied to high-throughput datasets and an expertise in developing computational models to integrate multiple sources of molecular biology information. His research focuses on discovering how gene networks program cellular responses and search engines to scan large collections of high-throughput results to predict how genes function. His labrecently developed the PARADIGM pathway-based models to integrate multiple sources of gene activity to predict alterations and clinical outcomes in tumor samples to decipher pathway alterations in many cancer cohorts. Stuart co-leads a Genome Data Analysis Center for the TCGA project, co-chairs the pan-cancer TCGA effort, is a member of the bioinformatics pathway’s group for the International Cancer Genome Consortium, and directs the computational pathway analysis for a Stand Up To Cancer Dream Team to identify therapies for resistant prostate cancer. [More]

Stuart Publications Josh Stuart's Email

Prof John TamkunRegulation of Chromatin Structure and Gene Expression

John Tamkun, Dept. of MCD Biology

The Tamkun lab investigates regulation of chromatin's high order structure and its role in gene expression. Composed of DNA and proteins, chromatin's ability to fold enables the eukaryotic genome to be packaged into an extremely small space inside the nucleus of the cell. Proper transcription and replication of the genome also depend upon precise regulation of these dynamic structures, with defects in these processes believed to underly many human diseases. [More]

Tamkun Publications John Tamkun's E-Mail

Prof Zhu WangProstate Organ Development and Homeostasis

Zhu Wang, Dept. of MCD Biology

The prostate gland is a multiple tubule-like structure in the male reproductive system, and is regulated by androgen. Repeated ablation and administration of testosterone results in cycles of prostate regression and regeneration, implying the existence of tissue stem cells. The two major cell types in the prostate epithelium are basal cells and secretory luminal cells. In vivo genetic lineage-tracing studies have identified luminal cells that express the transcription factor Nkx3.1 and rare basal cells in the regressed prostate in mediating organ regeneration. We are investigating the cellular lineage relationship and the molecular signalings involved in these processes. [More]

Wang Publications Zhu Wang's E-Mail

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