Current Research Projects
Dr. Brittany Carr
E-mail: bcarr1@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Retinal development and degeneration
Rods and cones are the principal photoreceptor cells of the vertebrate retina. These specialized cells interact with light from our environment and mediate the first steps in vision. I am interested in retinal development and retinal degeneration. The primary methods that my lab uses are genetic modification (CRISPR/transgenesis), PCR, Western blot, live imaging, and fluorescence imaging.
Potential Projects
- Role of Muller glia polysialic acid in retinal regeneration. Tadpoles (like zebrafish) have the ability to regenerate their retina and lost photoreceptors in response to mechanical damage, such as a hole poke. They do this by de-differentiation of Muller glia, which then provide progenitor cells that can migrate to the site of injury and inititate repair. We are interested in whether modulating polysialic acid sugar chains, which regulate the ability of cells to migrate, can impair retinal regeneration.
- Knockdown of ATF6 in frogs. ATF6 is a gene that, in humans, results in no development of cone photoreceptors. Interestingly, in mice, there is no effect of ATF6 knockdown and cones develop normally. We wish to determine whether ATF6 knockdown results in a loss of cones, as it does in humans, or not, as it does in mice. This will allow us to pinpoint more effectively why these species differences arise, and how we can treat ATF6 knockdown in humans.
- Identification of retinal microglia, oxidative stress, lysosome dysfunction in RPE in prom1-null animals. Aging prom1-null animals develop large deposits of cellular debris in the subretinal space. We believe that the origin of these deposits is dead or dying RPE, due to oxidative stress. We are interested in looking at markers of oxidative stress in the RPE of aging PROM1 null animals. Once identified, we can then use pharmaceuticals or genetic modification to try to fix the oxidative stress and prevent cell death.
- Outer segment isolation and imaging with atomic force microscopy. PROM1-null outer segments appear to have less structural integrity than wildtype ones. AFM can use a cantilever to test membrane rigidity. We will need to develop a way to isolate small amount of outer segments, and then prepare them for AFM imaging.
Dr. Jason Dyck
E-Mail: jrbdyck@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: The role of ROMO1 in heart failure
The project will explore the role of ROMO1, a mitochondrial protein, in normal heart function and in the progression into heart failure. Previous reports have shown that ROMO1 is involved in regulating mitochondrial function and integrity, and is required for the generation of oxidative stress from the mitochondria. For these reasons, we have chosen to explore the role of ROMO1 in the cardiac myocyte, with emphasis on its molecular role in the cell and in heart failure pathology. This project has plenty of opportunity to expand to additional diseases, including diabetes, cancer, and stroke, as we have evidence suggesting a role of ROMO1 in these diseases. Student will have the option to learn techniques like western blotting, cell culture, immunofluorescence, and mouse handling.
Dr. Michael Hendzel
E-Mail: michael.hendzel@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: 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)action, we found that histone H1 is rapidly displaced from DNA damage sites as a consequence of poly(ADP-ribosyl)action. 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.
E-Mail: tom.hobman@ualberta.ca
CELL 498/499 Undergraduate Research Projects
Project Title: RNA virus-host interactions
RNA virus infections impose huge economic and social burdens around the globe. Direct-acting antiviral therapeutics and vaccines can be highly effective in controlling epidemic and pandemic viruses, but these drugs/prophylactics take significant time to develop and their efficacy is often limited to specific viral strains. To minimize the impact of future emerging RNA viruses, a stockpile of broad-spectrum antivirals is required to serve as a first line of defense against these pathogens. Identification of host cell-based pathways that are exploited or inhibited by multiple viruses is expected to reveal novel targets for antiviral therapy. Using targeted and unbiased screening approaches, we have identified multiple host cell pathways that can be pharmacologically inhibited or enhanced to reduce infection by multiple RNA viruses including SARS-CoV-2, the causative agent of COVID-19. In addition to SARS-CoV-2 and other coronaviruses, our lab studies HIV and pathogenic mosquito-transmitted viruses such as West Nile virus, Dengue virus, Zika virus, Mayaro virus and Chikungunya virus.
Dr. Maria Ioannou
Email: ioannou@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Lipid trafficking in the brain
Our lab uses a combination of advanced quantitative microscopy techniques to study lipid trafficking in the brain. Specifically, our team studies the mechanisms by which neurons transport lipids to glial lipid droplets, how lipid droplets influence glial physiology, and how the regulation of lipid transport affects the brain in heath and disease. For more information check out: ioannou@ualberta.ca. We typically interview prospective undergraduate students in the fall for the following summer and/or academic year.
Dr. Paul LaPointe
E-Mail: paul.lapointe@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Hsp90 chaperones
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.
E-Mail: rlehner@ualberta.ca
CELL 499 Undergraduate research project
Project Title: Lipid storage dynamics in hepatocytes
Fat [triacylglycerol (TG) and cholesteryl esters CE)] is stored in organelles called lipid droplets (LDs). LDs serve as reservoirs of energy, as well as provide substrates for membrane synthesis and ligands for cellular signaling. While conversion of excess fatty acids (FA) and cholesterol into TG and CE, respectively, protects cells from lipotoxicity, buildup of LDs can lead to various pathological states, including obesity and fatty liver disease. Because of these positive and negative effects of lipid storage, cells have developed homeostatic mechanisms to regulate LD formation and turnover.
Two distinct diacylglycerol acyltransferases (DGAT1 and DGAT2) catalyze the final committed step of TG synthesis in hepatocytes. TG formed through either DGAT1 or DGAT2 can be directed
Dr. Sujata Persad
E-Mail: sujata@ualberta.ca
CELL 398/498/499 Undergraduate research project
Project title: Role of Active β-catenin (ABC) in promoting osteosarcoma metastasis
Osteosarcoma (OS) is a bone cancer that primarily affects children and young adults with prevalence of 2-5 million cases per year. Despite the utilization of various treatment approaches, overall survival rates have remained relatively unchanged. The pathophysiology of OS metastasis involves the Wnt/β-catenin signaling pathway. β-catenin is sequestered in the cytoplasm and targeted for degradation in the absence of Wnt, while its dephosphorylation in the presence of Wnt enables nuclear translocation and gene transcription. Downstream targets of Wnt contribute to OS metastasis. Active β-catenin (ABC), a partially dephosphorylated form of β-catenin, exhibits higher transcriptional activity and is regulated by crosstalk between the PI3K and Wnt/β-catenin pathways. Our prior findings suggest the cellular levels of ABC, as opposed to β-catenin, shows greater association with the aggressiveness of OS.
The present study aims to investigate the correlation between ABC and OS progression by identifying the effects of ABC overexpression on OS invasion and metastasis using 3D cultures of OS cells and an in vivo model, respectively. 3D cultures of OS cells will be used to evaluate larger cellular extensions (invadepodia) and identify potential overexpression of mesenchymal markers. In-vivo models will be used to evaluate the effects of the expression of ABC on metastasis where an orthotic murine model will be used to evaluate primary tumor size and volume and metastasis to the lungs and liver. Our preliminary results show invadepodia in ABC overexpressing 3D cultures as compare to β-catenin overexpressing cultures. However, further studies ongoing in the Persad lab will provide more evidence for the role of ABC in promoting OS metastasis.
Dr. Thomas Simmen
E-Mail: thomas.simmen@ualberta.ca
CELL 398/498/499 Undergraduate Research Project
Project Title: Investigation of Rare Diseases Based on Mitochondria-ER Contact Defects
Mitochondria-ER contacts (MERCs) are the membrane domains where these two organelles exchange lipids, Ca2+ ions and reactive oxygen species (ROS). This crosstalk is a major determinant of cell metabolism, since it allows the ER to control mitochondrial oxidative phosphorylation (OXPHOS) and the Krebs cycle, while conversely, it allows the mitochondria to provide sufficient ATP to control ER proteostasis. MERC metabolic signaling is under the control of tethers and a multitude of regulatory proteins. Many of these proteins have recently been discovered to give rise to rare diseases if their genes are mutated. Surprisingly, these diseases share important hallmarks and give rise to neurological defects, sometimes paired with, or replaced by skeletal muscle deficiency. Typical symptoms include developmental delay, intellectual disability, facial dysmorphism and ophthalmologic defects. Seizures, epilepsy, deafness, ataxia, or peripheral neuropathy can also occur upon mutation of a MERC protein. The undergraduate projects will deal with known and novel mutations of MERC proteins leading to such diseases and the investigation of the mechanistic basis of the pathologic defects. 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
CELL 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. Rineke Steenbergen
E-Mail: rineke@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Intrahepatic cholestasis: developing an organoid model for a rare disease
Organoid models are three-dimensional cell culture systems that mimic the complex structure and function of human organs. Organoids can be used to model diseases, discover new treatments and in the future may play a role in regenerative medicine. My research has led to the development of highly functional liver organoids, and we are currently investigating the molecular pathways that drive the development of these complex structures, from liver stem cells, by using a combination of bioinformatics approaches and cell biology techniques.
We also use of these organoids to study progressive familial intrahepatic cholestasis (PFIC), a group of rare genetic disorders. PFIC is characterized by defects in bile secretion by the liver, and leads to accumulation of bile acids inside liver cells. This causes progressive liver disease and usually leads to liver failure before adulthood is reached.
PFIC3, one of 3 subtypes of PFIC and our main focus, is a rare autosomal recessive disorder that is caused by missense mutations in multi-drug resistant protein 3 (MDR3), resulting in impaired biliary phospholipid secretion. Heterozygosity for the MDR3 mutation may also lead to intrahepatic cholestasis of pregnancy (ICP), a complication of pregnancy with serious consequences for the mother and fetus. We use our organoids to model patient specific mutations of MDR3, investigate the metabolic, structural and molecular consequences of bile accumulation inside cells, and work towards treatments of intrahepatic cholestasis.
Dr. Deniz Top
E-mail: ndtop@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Regulation of behaviour at molecular resolution in the model organism Drosophila melanogaster.
The main goal of the Top Lab is to understand the mechanisms that regulate behaviour at molecular resolution, in the model organism Drosophila melanogaster. Behavioural problems are often caused by mutations or neuronal communication disruption and are closely associated with the inability to consolidate sleep in the nighttime. Thus, circadian rhythms are an opportunity to exploit a known mechanism to explain how behavioural disorders develop. Circadian rhythms are regulated by a transcription negative feedback loop called the circadian clock, which regulates hundreds of genes that influence behaviour and physiology. We have shown that mutations in circadian genes that alter behaviour cause circadian clocks to function differently in different regions in the brain. Thus, mutations have different levels of penetrance in different regions in the brain. We believe that circadian clock misalignments (i.e., clock desynchrony) that arise across different nodes in the brain underlie behavioural disorders. We have developed novel genetically encoded reporters and automated behaviour monitoring systems, accumulating evidence that supports our hypothesis.
When we began our work, the molecular clock was assumed to be a single mechanism that applied to all neurons and tissues. We have shown that the regulatory mechanisms that act on each circadian clock is distinct in different neuronal cluster, and mutations have different efficacy in different parts of the brain for this reason. We are currently (1) mapping the clock interactome across the fly brain, (2) determining the differences in the macromolecular complexes that comprise the molecular clock in different neurons and (3) identifying the signaling cascades that allow neurotransmitters to communicate directly to each clock. We believe that we will continue to demonstrate that (1) mutations associated with various behavioural and neuropsychiatric disorders have different penetrance in the different parts of the brain, and (2) this leads to a loss of transcription synchrony and therefore loss of communication cohesion, which causes the disorder.
Interested students can explore our website (www.top-lab.org) and contact me directly (dtop@ualberta.ca)
Dr. Anastassia Voronova
E-mail: voronova@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project 1. Cell-cell communication between inhibitory neurons and neural stem cells for the generation of oligodendrocytes from neural stem cells.
Proper brain development and function requires neural stem cells (NSCs) to generate a specialized type of cell termed an oligodendrocyte at precise times, locations and in the right numbers. The purpose of oligodendrocytes is to produce myelin, an insulating material that performs vital functions in efficient neural information transmission and constitutes the brain white matter. The formation of oligodendrocytes and/or myelin is perturbed in neurodevelopmental disorders, such as autism spectrum disorder (ASD) and schizophrenia. White matter damage and inefficient remyelination occurs in neurological disorders like multiple sclerosis and white matter stroke. Therefore, it is important to understand how oligodendrocytes are generated from NSCs to not only understand the biology of neurodevelopmental disorders, but also to come up with novel pro-oligodendrogenic therapies for the injured brain. Our work identified a novel paracrine communication between NSCs and a specific type of neurons, inhibitory interneurons. Interneuron-secreted cytokine, fractalkine, promotes oligodendrocyte formation from NSCs in the developing mouse cortex. Several projects are available to study the role of interneuron-secreted molecules, such as fractalkine (FKN) and hepatoma-derived growth factor (HDGF), that drive the genesis of oligodendrocytes from NSCs. We will test how FKN and HDGF signalling in neural stem and/or oligodendrocyte precursor cells affects intracellular signalling pathways critical for oligodendrocyte differentiation from NSCs. This project will involve cultures of primary and/or immortalized precursor cells, shRNA-mediated knockdown analysis, polymerase chain reaction (PCR), immunofluorescent antibody staining and confocal microscopy.
Project 2. Epigenetic regulation of neural stem cell function and brain development.
Autism spectrum disorder (ASD) is highly prevalent in the Canadian population with an incidence of 1 in 66 children and is characterized by brain malformations and intellectual disability. Advancements in next generation sequencing have enabled identification of thousands of individual gene mutations in ASD patients, which cluster into three large groups: synaptic function, transcription and chromatin remodelling. While chromatin regulators constitute the majority of ASD risk genes, there is little understanding of how chromatin remodelling or epigenetic genes regulate the development of brain. Several projects are available to study the role of ASD risk epigenetic genes Ankrd11 (Ankyrin Repeat Domain 11), which affects histone acetylation and Kdm5b, which affects histone methylation. Histone post-translational modification is one of the hallmarks of epigenetic modification that has direct implications on global gene expression and cell behavior. We will test when perturbations of ASD risk epigenetic genes affects neural stem cell function and what is the chromatin-mediated mechanism of neural stem cell regulation by these genes. This project will involve cloning, isolation and cultures of primary mouse embryonic cortical precursor cells, immunofluorescent antibody staining and confocal microscopy. This project has the potential to evolve into a graduate project.
Dr. Richard Wozniak
E-mail: rick.wozniak@ualberta.ca
CELL 398/498/499 Undergraduate Research Projects
Project Title: Function of Flaviviridae viral RNAs in the host cell nucleus
Abstract: Zika, Hepatitis C, Dengue, and West Nile viruses of the Flaviviridae family infect hundreds of millions of people, causing widespread morbidity and mortality. A prominent example is the recently discovered congenital Zika syndrome characterized by severe microcephaly. Except for HCV, there are no approved anti-viral treatments for these viruses, despite decades of research. A central tenant of Flaviviridae biology, and one that defines therapeutic strategies, is that the virus life-cycle occurs within the cytoplasm of host cells. We have now directly challenged this dogma by showing, using highly sensitive and specific detection techniques, that the RNA genomes (vRNAs) of Zika and HCV enter and leave the host cell nucleus (see figure), and travel through the nucleus is required for virus production.
This breakthrough requires a paradigm shift away from a cytoplasm centric view of Flaviviridae biology and a re-evaluation of how we study and combat these viruses. However, before we can leverage this knowledge for societal benefit (e.g. therapeutics), we must understand, at a mechanistic level, why these viruses engage nuclear processes, and how this benefits the virus. Our research will tackle these questions using highly innovative approaches that will allow us to construct dynamic and cell specific systems-level interaction networks between vRNAs and host factors. We expect these high-risk, high-reward endeavors will produce new knowledge and foster novel pan-Flaviviridae therapeutic opportunities.
Proposed student project: The undergraduate student will work with a graduate student and research associate in the lab. Their experiments will first focus on constructing Zika viruses where an RNA tag is inserted into the viral genome. The tagged Zika virus will then be produced in tissue culture cells. The tag in the virus genome, in conjunction with nuclear or cytoplasm proteins that bind the tag, will be used to either increase or decrease the nuclear amounts of the genome in infected cells. The consequences of shifting the cellular distribution of the viral genome on production of the virus will be examined. This work will involve teaching the student basic molecular cloning, cell transfections, fluorescence microscopy, and basic handling and analysis of the Zika viruses. Note, other potential projects are available and can be discussed.
Abstract: The nuclear envelope (NE) provides an environment for the proper regulation and organization of interacting chromatin. In budding yeast, NE-associated chromatin includes telomeres and silenced subtelomeric regions. Multiple mechanisms are employed to tether these chromatin regions to the NE and silence resident genes. Among the factors required for telomere association with the NE is Siz2, a SUMO E3 ligase (Ferreira, et al., 2011. Nature Cell Biology, 13(7), 867-74). We have investigated the role of Siz2 and sumoylation in telomere association with the NE. We found that Siz2 is predominantly distributed throughout the nucleoplasm during interphase, but is recruited to the NE during the early stages of mitosis, when newly replicated telomeres re-associate with the NE. Enrichment of Siz2 at the NE is dependent on its mitotic phosphorylation, a SUMO interacting motif within Siz2, and a nuclear pore complex protein, Nup170, which is known to interact with subtelomeric chromatin (Van De Vosse et al., 2013. Cell, 152(5), 969-983). In all cases, mutant cells which fail to recruit Siz2 to the NE results in telomere tethering defects. We hypothesize that NE recruitment of Siz2, during mitosis, functions to target specific proteins for sumoylation that are required for proper chromatin organization at the NE. Consistent with this model, we show that NE recruitment of Siz2 correlates with the mitotic specific sumoylation of several proteins. This includes Scs2, an integral membrane protein and member of the VAP protein family. Scs2 resides in the endoplasmic reticulum (ER) and the NE where it appears to function in phospholipid metabolism, endoplasmic reticulum/plasma membrane interactions, and telomeric silencing. We have shown that Scs2 is required for telomere association with the NE and our data suggests that Scs2 functions as a receptor for Siz2 on the inner nuclear membrane. Together these data suggests that Scs2 plays an essential role in the spatial and temporal control of sumoylation at the inner nuclear membrane, an important post-translational modification involved in chromatin organization.
Proposed student project: The undergraduate student will work with a graduate student and research associate in the lab. Their experiments will focus on the links between sumoylation, lipid metabolism, and the regulation of nuclear membrane structure. The student will use fluorescence and electron microscopy to examine changes in nuclear membrane structure in yeast mutants that alter the sumoylation of nuclear envelope proteins. Mutations in sumoylation that lead to nuclear membrane proliferation will be tested to examine how they affect lipid metabolism. This work will involve teaching the student basic molecular cloning, yeast molecular genetics, fluorescence microscopy, and basic protein analysis. Note, other potential projects in this area are available and can be discussed.