Current Research Projects

Dr. Joel Dacks
E-Mail: joel.dacks@ualberta.ca
398/498/499 Undergraduate Research Projects

Project 1

Giardia intestinalis is a single-celled intestinal parasite and a leading cause of diarrheal disease in Canada and world-wide. Key to its pathogenic mechanism and transmission is the process of membrane-trafficking, i.e. the import, export and intracellular targeting of material. As a member of the almost exclusively parasitic “Diplomonad” lineage of microbial eukaryotes, Giardia possesses cellular compartments associated with membrane-trafficking that are unlike organelles found in nearly all other eukaryotes. These included an unstacked Golgi apparatus, and several unusual endocytic organelles.  

The divergent nature of Giardia protein sequences has made identification of membrane-trafficking proteins difficult, hampering molecular cell biological efforts to characterize its trafficking system.  To address this problem, and to understand the evolution of parasitism within the diplomonad lineage, we will investigate genomic and transcriptomic data from the free-living relative of Giardia, Carpediemonas membranifera. Importantly, Carpediemonas possesses a relatively canonical set of membrane-trafficking organelles and is known to encode much less diverged protein sequences than Giardia. 

This student project will specifically involve using computer analyses (homology searching and phylogenetics) to look at the Adaptin and related cargo adaptor complexes. Adaptin complexes play vital roles in vesicle formation for trafficking across the eukaryotic cell and will provide important comparative information as to the complexity of the membrane-trafficking system in Carpediemonas and its subsequent reduction in its parasitic relatives. 

Candidates should have completed at least one 200 level cell biology class. No prior programming expertise is necessary. Curiosity and a drive to solve evolutionary puzzles are a major bonus!

Project 2

Membrane-trafficking is a fundamental cellular process that underpins the healthy function of all eukaryotic cells. When disrupted in humans it produces a myriad of disease states including cancer, heart disease, and neurodegenerative disorders. The animal membrane-trafficking system has clearly expanded as compared to that found in single celled ancestors and yet the precise timing and patterns of this diversification have not been well-described.

Membrane-trafficking can be considered as the packaging of material into vesicular carriers at a donor organelle, and the delivery of that material to the accepting or destination organelle. The adaptin complexes serve as cargo recognition and packaging factors for the inclusion of specific proteins into trafficking vesicles. These complexes are composed of four individual subunits and there are five related complexes, each acting at discrete locations within the cell. Additionally, there are tissue-specific isoforms of many of the subunits and the loss of the entire AP4 complex in some lineages. Understanding both the expansions and loss would help to explain the origins of membrane-trafficking tissue-specificity in animals and to enhance experimental work with the proteins in question.

This project will involve using genomic information and molecular evolutionary (computational) techniques to understand the evolutionary dynamic patterns of adaptins in animals. The successful student candidate should have background in 200 level biology courses. Previous programming experience is not required. Curiosity and a strong desire to solve scientific puzzles are essential.

 

Dr. Gary Eitzen
E-Mail: gary.eitzen@ualberta.ca
398/498/499 Undergraduate Research Projects

I have several graduate and undergraduate level research projects available in my lab. My research is focused on studying Rho GTPase signal transduction. I am particularly interested in how Rho, Rac and Cdc42 GTPases control exocytosis and membrane fusion using both a yeast model system for biochemical studies and immune cells (neutrophils and mast cells) for translational studies. Future efforts will be in anti-inflammatory drug discovery using Rho signaling pathways as the target. Three general projects are listed below. Email me to inquire more about these opportunities; please indicate your specific interest.

Undergraduate research projects can be undertaken in my lab for credit in most undergraduate science programs (e.g. Biological Sciences, Cell Biology, Biochemistry, and Immunology).

Functional analysis of Rho signaling using yeast genetics

We will use yeast as a model system to define the function of proteins in the Rho signaling pathway. Regulatory proteins that form complexes with Rho will be used as templates for the development of assays that can be scaled up for high throughput screening of drug libraries. The long term goal is to use this system to study the mode of action (MOA) of drugs identified in high throughput drug screens.

Regulation of immune cell activation and degranulation

We are interested in factors that control immune cell activation and degranulation during inflammation. We will focus on the role of Rho proteins, identifying upstream regulators of Rho signaling and characterization of the downstream processes they control.

Development of high throughput screens to identify anti-inflammatory drugs

Several approaches will be used to develop high throughput assays to identify new drugs with anti-inflammatory effects. Phenotypic screens will use human neutrophils while targeted screens will use biophysical interactions between relevant protein complexes.

 

Dr. Michael Hendzel
E-Mail: michael.hendzel@ualberta.ca
398/498/499 Undergraduate Research Projects

The role of histone H1 in the DNA damage response

DNA double-strand breaks are the most dangerous form of DNA damage. Unless faithfully repaired, double-strand breaks can lead to the gain and loss of genomic material, apoptosis, oncogenic translocations, and genomic instability. Upon formation of a DNA double-strand break, a signaling cascade initiated by the phosphorylation of histone H2AX by the DNA damage activated kinase, ataxia telangiectasia mutated (ATM). A critical part of this signaling cascade is the generation of chains of ubiquitin covalently linked to one or more proteins found at the site of DNA damage. This forms a scaffold that is essential for the recruitment of proteins involved in the error-free repair mechanism, termed homologous recombination repair. The identity of the target protein has long been thought to be histone H2A. Recently, however, histone H1 was identified as the likely substrate for the formation of the K63-linked polyubiquitin scaffold. Our laboratory has a longstanding interest in histone H1. In our studies of another DNA damage-associated post translational modification, poly(ADP-ribosyl)ation, we found that histone H1 is rapidly displaced from DNA damage sites as a consequence of poly(ADP-ribosyl)ation. This result is seemingly inconsistent with a role of histone H1 as a scaffold for the assembly of proteins at sites of DNA double-strand breaks. We want to determine the dynamics of association of histone H1 with DNA double-strand breaks, how the association of histone H1 with sites of DNA damage is altered by the enzymes involved in the assembly of the ubiquitin scaffold, and how this relates to the binding properties of the proteins that bind to this scaffold, such as the breast cancer associated 1 (BRCA1) protein. This will be studied by introducing DNA damage into living cells expressing fluorescently tagged versions of H1 histones, mutant H1 histones, and fluorescently tagged proteins that are recruited to sites of DNA damage by association with the ubiquitin scaffold. Various kinetic techniques such as fluorescence lifetime imaging (FLIM) to detect protein-protein interactions, fluorescence recovery after photo bleaching (FRAP), and fluorescence correlation spectroscopy (FCS) will be used to quantify the dynamic properties of these proteins and their dependence on histone H1 and ubiquitin.

 

Dr. Sarah Hughes
E-Mail: sarah.hughes@ualberta.ca
398/498/499 Undergraduate Research Projects

Project 1

N-acetyl neuraminic acid synthase (NANs) is an enzyme that is important for making glycoproteins and glycolipids. Deficiency of NANs interferes with the glycosylation process – the process by which sugars are chemically attached to proteins to form glycoproteins – which is required proper development. NANs deficiency is a candidate gene identified in a 3 year-old boy with trans-heterozygous mutation and exhibits profound developmental delay, corpus callosum abnormalities, symmetric rhizomelia, osteopenia, and other defects in regards to his brain, nerves, and muscles. NANS deficiency has also been identified in 8 other patients with compound heterozygous mutations. The goal of this project is to generate “humanized” Drosophila containing the patient mutations. We will also create Drosophila with the conserved mutations. We will then analyze the transgenic flies for neural development defects and neural function. This project will involve generation of site directed mutations within human and Drosophila Nans, generating transgenic flies and analysis of the nervous system in flies using immunoflourescent antibody staining and confocal microscopy.

Project 2

Neurofibromatosis Type 2 (NF2) is an autosomal dominant cancer that is identified through the exhibition of large tumours of the nervous system that develop during adolescence. NF2 tumours are either unresponsive or poorly responsive to chemotherapy and radiation. Most patients are treated by repeated surgeries. Similar to other cancers, the presence of other gene mutations are presumably important for the initiation or progression of NF2. The NF2 gene encodes the tumour suppressor protein Merlin. We propose that mutations in Merlin or Merlin-binding proteins interfere with Merlin functions as a tumour suppressor, leading to the formation and/or progression of NF2 tumours. Another important pathway in development that controls animal size is the Hippo signaling pathway. Merlin has been shown to regulate aspects of this pathways but the mechanism is unclear. This project will analyze the potential role of the Merlin interacting protein, Sip1, in regulation of specific members of the Hippo pathway. This work will involve expression of specific protein in Drosophila cell culture combined with co-immunoprecipitation and Western blot assays in addition to antibody immunofluorescence staining and confocal microscopy.

 

Dr. Paul LaPointe
E-Mail: paul.lapointe@ualberta.ca
398/498/499 Undergraduate Research Projects

Research in my laboratory is concerned with elucidating the molecular mechanism of action of the Hsp90 chaperone. Hsp90 is a highly conserved and essential protein in all eukaryotes. It is responsible for the folding and function of numerous signaling kinases, hormone receptors, transcription factors and other proteins. Hsp90 is also emerging as a key target in treatment of cancer, Cystic Fibrosis and other diseases. There are several undergraduate research projects available in my lab ranging from in vivo analysis of Hsp90 interactions with co-chaperones to biochemical/enzymatic analysis of Hsp90-mediated protein folding. Research projects can be tailored to suit the interests or goals of students. More information on my research can be found on my web page.

I can be contacted by email at paul.lapointe@ualberta.ca or by phone at 780-492-1804.

 

Dr. Thomas Simmen
E-Mail: thomas.simmen@ualberta.ca
398/498/499 Undergraduate Research Project

Endoplasmic Reticulum-Associated Rab GTPases and Neuronal Function

The organelles found in eukaryotic cells exhibit a unique protein composition that governs the functions of these organelles. Nevertheless, protein trafficking between organelles is imperative within cells. This is needed to mediate production and maturation of secretory proteins that require organelle-specific, localized modification of nascent proteins. In neurons, this aspect is particularly important, since neuronal cell bodies are extremely distant from their farthest extensions at the synapse. An important group of proteins that regulate secretion and intracellular trafficking are the Rab proteins: the largest subfamily of the Ras-like GTPases with at least 63 members in humans, but many more in several other organisms. Recently, our lab has identified about a dozen Rabs, which localize to the Endoplasmic Reticulum (ER). This is a surprising finding, since the ER is considered the point of origin of vesicular protein trafficking. We hypothesize that ER-associated Rabs perform functions, which are different from other Rabs and include ER-Golgi recycling, ER domain organization, ER structure and autophagosome formation. Independent research has identified some of these Rab proteins in the functioning of neurons, in particular in the maintenance of axons. The undergraduate project will aim to characterize one or more ER-associated Rab in terms of its function and, subsequently, in its significance for the maintenance of axons and neuronal survival.

Interested students should contact me by e-mail at thomas.simmen@ualberta.ca to discuss details.

 

Dr. Andrew Simmonds
E-Mail: andrew.simmonds@ualberta.ca
398/498/499 Undergraduate Research Project

Project Title: Characterizing a transcription factor complex that regulates heart muscle cell specification.

Approximately one percent of newborn infants manifest congenital heart malformation due to inherited mutations in one or more genes required for proper heart formation. We study two proteins (Sd/TEF-1 and Mef-2) that have critical roles in establishing a heart cell fate. There are multiple members of the human Sd/Tef-1 and Mef-2 protein families and it has been extremely difficult to identify co-factors that regulate their activity. However in the animal model system Drosophila melanogaster, there is only a single Sd/Tef-1 and Mef-2 protein family member required during heart formation. We have identified several potential novel co-factors and we are currently testing their role in heart formation and muscle differentiation. Due to the nature of this project, prospective students will need to have completed at least one 300-level course in Biology, Molecular Biology or Genetics.  They will be using a combination of animal studies, visualizing of tissues in whole animals and transfection and culture of isolated cells to study muscle differentiation as it relates to the early events of heart formation.

 

Dr. Andrew Simmonds
E-Mail: andrew.simmonds@ualberta.ca
398/498/499 Undergraduate Research Project

Project Title: Post-transcriptional regulation of cell division by the Gw protein.

In eukaryotic cells, cytoplasmic processing (P-) bodies regulate directly regulate mRNAs. In mammalian cells, a core component of P-bodies is the Gw family of proteins. Using a combination of cultured cells as well as studies in whole animals, we are attempting to dissect the cellular roles and cytoplasmic events that regulate mRNAs. Specifically, we are using Drosophila to establish how Gw function is required for such critical cellular functions as regulating mitosis. With increased understanding of how this protein functions within the cell and how it, in turn, is regulated, our research will help with diagnosis and treatment of several poorly understood diseases that have been linked to the Gw homologues in humans. Due to the nature of this project, prospective students will need to have completed at least one 300-level course in Biology, Molecular Biology or Genetics.  Additionally, preference will be given to academically superior third or fourth year undergraduate students looking to continue on to an MSc or PhD in Cell Biology.  They will be using a combination of live-cell imaging, whole animal genetics, cell culture and molecular biology to study how basic cellular processes like mitosis and cell differentiation controlled by mRNA regulation.