We use biochemical and genetic techniques to understand how conserved RNA binding proteins function in cellular responses to stress and challenges to human health. Much of our work centers around the the La and La-related proteins. Members of this conserved family of RNA chaperones have critical functions in cellular growth. La proteins both enhance the correct maturation of many non-coding RNAs as well as influence the translation of several viral and cellular messenger RNAs implicated in human disease. We aim to understand both the basic mechanisms by which these proteins enhance the correct folding of target RNAs as well as how aberrant La and La-related protein function contribute to human disease states.
I am a Professor in the Department of Biology, in the Faculty of Science and was the Director of York’s Institute for Research and Innovation in Sustainability for 4 terms and a total of 7 years from 2006-14. My group studies plant-animal interactions, from temperate to arctic regions, along with associated research areas, including invasive species, climate change impacts, forest dynamics, and fungal endophytes of grasses. We have done fieldwork in Scotland, England, Scandinavia, Newfoundland, on Hudson Bay, and throughout Ontario. Her research on the effects of deer grazing and browsing in Carolinian forests in southern Ontario has engaged with students, landowners, government and NGOs including Ontario Parks, Parks Canada, Conservation Authorities, Carolinian Canada and First Nations communities.
My research focuses on how the surrounding environment influences the gastrointestinal tract and digestion in fish species. As a comparative physiologist I look at a number of different fish species, both marine and freshwater, and as an integrative physiologist I use a wide variety of techniques in this pursuit — from molecular biology to behavioural studies. Specifically, my research aims to an understanding of how animals cope with challenges associated with, and during, feeding and starvation to ultimately answer the question — why do animals have the digestive physiology they do?
To answer this, my research focuses on two reciprocal questions:
- How does the environment affect the physiology of the gastrointestinal tract and digestion and why have these responses evolved?
- How does the physiology of the gastrointestinal tract and digestion affect an organism’s interaction with its environment and why have these responses evolved?
My research is based on three key biological fields: physiology, behavior, and evolution with an emphasis on physiology. While I investigate questions founded solely within each discipline, I also explore questions that exist in the overlap between the disciplines, using a variety of techniques across numerous biological levels. This work is essential for the protection of natural resources, but also for the development of sustainable industries such as aquaculture.
Below – Listen to Dr. Bucking speak about her research!
Mosquito and midge larvae adapt well to changes in habitat salinity. Our research studies the ion transport mechanisms, and their regulation, in organs of these insects. We utilize both freshwater and brackish water dwelling species to understand the mechanisms that have evolved in response to these two distinct habitats. In addition, results of our research can be used to predict changes in the mosquito and midge species composition by increased environmental salinity from the continued use of road salt. This is important because these insects are vectors of disease but also play important roles in the food chain and ecosystem.
Hydromineral balance is essential to the survival of all animals and is achieved through the actions of ion transporting epithelia that are regulated by neuroendocrine factors. Mosquitoes and midges have specialized organs that permit them to survive a wide range of environmental salinity. Under freshwater conditions, where larvae face dilution of body fluids, the anal papillae of mosquitoes and midges take up salts (e.g. NaCl) from the habitat. Under saline conditions, where larvae face concentration of body fluids a unique specialized salt secreting epithelium in the posterior rectum of some mosquito larvae remove excess salts from the hemolymph. The midgut and Malpighian tubules also play a role in maintaining hydromineral balance. Despite identification of relevant organs responsible for hydromineral balance in mosquito and midge larvae, the molecular and physiological mechanisms at work in these organs are poorly understood, as is their neural and endocrine regulation.
Our research is aimed at filling this void by elucidating the molecular basis of salt (ion) transport and how these mechanisms are regulated by neural and hormonal factors. This fundamental knowledge can permit the development of novel and specific agents to affect control on mosquito and midge populations. These agents can be targeted at the level of the molecular ion transport machinery or at the neural and hormonal level. For example, recent advances have been made in the development of synthetic peptide hormone analogues which disrupt normal hormonal signaling in target insects. Results of our research will also contribute to an understanding of mosquito and midge population distribution related to environmental salinity levels. Continued use of road-salt can ultimately lead to invasion of inland waters by salt-tolerant mosquito and midge species which inhabit coastal areas.
The laboratory uses a combination of molecular and physiological techniques including PCR, qPCR, Western blotting to identify tissue-level expression of genes, intracellular microelectrodes and ion-selective microelectrodes to measure membrane potentials and ion composition in biological fluids and Scanning Ion-selective Electrode Technique (SIET) to measure real-time movement of ions across transporting epithelia.
There are two major areas of interest in Dr. Hilliker’s lab: the molecular and genetic analysis of Drosophila heterochromatin; and the molecular genetic analysis of oxygen defense mechanisms in Drosophila. He also collaborates with other faculty members in the department.
Heterochromatin: constitutive heterochromatin is a ubiquitous feature of higher eukaryotic organisms. It remains condensed throughout the cell cycle, consists largely of highly repeated sequences, and has a low gene density compared to euchromatin. Constitutive heterochromatin is difficult to sequence and many of the genes within these regions of Drosophila were not sequenced by the Drosophila genome project. Dr. Hilliker was the first to demonstrate the existence of otherwise ordinary genes in Drosophila heterochromatin and contributed to the mapping of the repeated sequences that constitute the bulk of heterochromatin in Drosophila. His laboratory is continuing to refine the genetic and molecular map of the heterochromatic regions of the Drosophila genome and to investigate further the dependency of heterochromatic genes for their location in heterochromatin for normal expression.
Molecular Genetic Analysis of Oxygen Defense: reactive oxygen species (ROS), which have been implicated in biological aging, are produced as by-products of normal oxidative metabolism and need to be inactivated by a cell before they cause damage to DNA, proteins, and other molecules. We have studied the mechanisms involved in the defence against ROS. We are currently focusing our efforts on six genes: quiver (qvr), a putative neuropeptide; withered (whd), which encodes carnitine palmitoyltransferase I (CPT1), Cu Zn superoxide dismutase (SOD1); manganese superoxide dismutase (SOD2); aconitase; and the Drosophila frataxin homologue. In addition to looking at the biological effects of the absence of gene activity we are also looking at the effects of tissue-specific expression in otherwise null backgrounds and the biological effects of tissue-specific overexpression in wild type backgrounds. In addition we are investigating the effects of oxidants and putative antioxidants on Drosophila lifespan and on Drosophila strains deficient in oxygen defense. Finally, we are assaying Drosophila homologues to genes identified in yeast as suppressors of SOD deficiency to determine if they can function as SOD deficiency suppressors in Drosophila.
My research is aimed at answering this question: How do living things tell time? I am interested in circadian rhythms, the daily activity cycles driven by internal clocks in almost all organisms, and I work with the fungus Neurospora crassa, a model organism that is at the forefront of circadian rhythm research. My lab uses genetics to identify genes that affect the clock, and biochemistry and molecular biology to discover the functions of those genes. We have recently identified two clock-affecting genes, and we are now carrying out functional analyses to determine where and when the products of these genes are expressed, and what proteins they interact with.
Christopher is an Associate Professor in Biology and co-appointed in graduate research in the Geography Department. He is an integrative scientist with expertise in community theory, sociology, and quantitative methods. The international research team he collaborates with includes graduate students and other community ecologists to globally explore biogeographical contrasts of many forms of community dynamics including invasion, climate change, keystone species, and plant-insect interactions. Christopher is an Editor-in-Chief for Oikos. He is also an Associate Editor for the following journals: PLOSONE, Journal of Ecology, Nature Scientific Data, PeerJ, and Ideas in Ecology and Evolution.
Our research interest concerns the basic regulatory mechanisms involved in cellular differentiation. This work is primarily undertaken using cardiac, skeletal and smooth muscle cells and neurons as model systems and is aimed at understanding the role of transcription factors in orchestrating tissue-specific gene expression and differentiation.
The genesis of this work was in identifying DNA binding proteins that are involved in transcriptional regulation during muscle development. Subsequent work explored the mechanisms by which these factors regulate cellular gene expression and differentiation. A main focus of our work has been the molecular cloning and characterization of a family of transcription factors (four genes, labelled MEF2A-D) that regulate the expression of many cardiac, smooth and skeletal muscle specific genes via the myocyte enhancer factor 2 (MEF2) cis- element. Based on their structural similarity, these genes belong to the MADS superfamily of DNA binding proteins that are involved in cell fate specification in many organisms ranging from yeasts to humans. Since the identification of the MEF2 gene family, further studies have been undertaken to assess the biological role of these genes during cardiac and skeletal muscle differentiation as well as in a variety of post-natal contexts such as cardiac disease (hypertrophy) and muscle regeneration.
It is well known that various intracellular signalling pathways potently regulate cell differentiation by targeting nuclear transcription factors. Moreover, muscle differentiation is extremely sensitive to the action of various growth factors. Therefore, our aim is to delineate the growth factor-activated signalling pathways that specifically converge on and modulate key transcriptional regulators such as MEF2 proteins during myogenesis. We are currently dissecting the effects of kinase mediated phosphorylation of MEF2 protein in order to fully understand how it serves as a nuclear sensor of growth factor -activated signalling pathways. In this regard we have reported a key role of the p38 MAP kinase pathway in targeting MEF2 in the somites during embryogenesis. Included in this post translational analysis of MEF2 function is the identification of MEF2 interacting proteins using state of the art tools in Mass Spectrometry. Studies are also ongoing to determine the contribution of other transcriptional regulators such as the Fra2 subunit of the AP-1 complex and the Smad7 protein to the myogenic program in cardiac and skeletal muscle cells. This work is supported by the Canadian Institutes for Health Research (CIHR), the Natural Sciences and Engineering Research Council (NSERC) of Canada and the Heart and Stroke Foundation of Canada (HSF).
The Paluzzi lab’s research program focuses on the biology of blood-feeding arthropods including ticks and mosquitoes. One main focus is the study of neurohormones that are released from the central nervous system and control most physiological processes (including those related to the gastrointestinal tract and reproductive tissues). Neuroendocrine systems are investigated at the molecular, cellular and tissue level in order to determine their importance and contribution to the biology of whole organism. By examining these systems at multiple levels of complexity, the details are more readily realized and we can then integrate this knowledge from increasing levels of organization. Identifying tissue targets regulated by hormonal factors, which involves determining receptor expression profiles, allows the subsequent application of tissue-specific bioassays (muscle contraction assay, epithelial transport assay, etc.) to determine the roles of these neuroendocrine systems in mosquitoes and ticks. For example, targets of primary interest include the tissues of the alimentary canal (i.e. gut), which play roles in digestion and assimilation of ingested materials, elimination of toxins (including pesticides), immune response and are also chiefly involved in the maintenance of salt and water balance. Similarly, other neurohormones regulate development and reproduction.
Some of the fundamental questions driving our research on mosquitoes and ticks include:
- What neurohormones govern ionic and osmotic balance in these blood-feeding human disease vectors?
- Which hormones control reproductive behavior and related physiological processes?
- Do similar signalling molecules control common activities in diverse blood-feeding arthropod species?
With a putative hormone elucidated, we seek to identify how target cells and tissues interpret the information carried in the form of a chemical message, which ultimately culminates in a physiological response leading to behavior. The information gained from this research can provide fundamental insights for development of lead compounds useful for control or eradication of these disease vectors. This research provides fundamental insight into the functioning of these organisms and furthers our knowledge on these medically-important species that have adapted to gorging on vertebrate blood and act as chief vectors of various human and animal diseases.
Below – Listen to Dr. Paluzzi speak about his research!
The overall goals of my research programs are to study how female reproduction is regulated and to investigate the mechanisms underlying the pathogenesis of diseases related to the female reproductive system.
Currently, three areas of research are being conducted in my lab:
- The role of hormones and growth factors in regulating ovarian follicle growth and oocyte maturation in zebrafish
- The role of growth factors and microRNAs in regulating human placental development and their contribution to the development of preeclampsia
- Involvement of cyclin G2 and its regulators in the development of epithelial ovarian cancer
Freshwater aquatic ecosystems undergo natural environmental changes while they are simultaneously influenced by multiple human-induced (anthropogenic) stressors. These anthropogenic stressors include recent climate change, acid rain, contaminant pollution, nutrient enrichment (eutrophication), land-use change (vegetation clearance for agriculture, urbanization etc), reservoir/impoundment construction and exotic species invasions, to name a few. Environmental monitoring programs of aquatic systems rarely pre-date the onset of human stressors. This lack of long-term ecological data presents difficulties in answering some basic questions that are important to consider when assessing the ecological impacts of stressors: What are ‘natural’ or pre-disturbance conditions of the ecosystem? What is the natural variability of the ecosystem? It is possible to obtain this long-term data through proxy methods, such as through examination of paleoecological data archived in lake and pond sediments. Sediments are natural archives of ecological data, with a host of physical, chemical, and biological variables providing insights into past aquatic ecosystem conditions.
My area of research specialization involves examining the chitinous subfossil remains of midges (Diptera: Chironomidae; “chironomids”) in lake and pond sediments, to generate paleoecological assessments of past aquatic ecosystem changes. However, my research interests are broad, as I am interested in a breadth of paleoecological indicators (including algae (e.g. diatoms) and zooplankton (e.g. Daphnia and Chaoborus) to examine aquatic ecosystem responses to a variety of human-induced stressors. Research projects also include examining the ecological dynamics of present-day aquatic ecosystems, and examining the limnological functioning and structure of aquatic systems. My research interests, and the projects undertaken by my graduate students, encompass numerous types of aquatic systems, predominantly in Canada, ranging from embayments of the Laurentian Great Lakes in southern Canada to shallow ponds in the northern tip of the Canadian High Arctic.
Regulation of Gene Expression in Eukaryotic Cells
Research in the lab aims to understand how cells control expression of genes during normal growth, in response to stress, and in cancer. There are two main research areas in the lab.
Activation and re-initiation of transcription by RNA Polymerase II
In eukaryotic cells, RNA Polymerase II (RNAP II) is responsible for transcribing all protein-coding genes as well as a number of non-coding RNA genes. When a cell requires production of a specific protein or gene product, its gene is “turned on” by the process of transcriptional activation. This involves a step-wise assembly of a number of transcription factors and related complexes on the gene’s promoter, which enables the recruitment of RNAP II. RNAP II then initiates transcription of the gene.
The details of transcriptional activation have been studied for decades and are quite well-understood at many levels. However, not much is known about what happens to the promoter-bound transcription factors and complexes after the first molecule of RNAP II has initiated transcription. Research in the lab addresses this by studying how transcriptional activators, general transcription factors, and other promoter-bound complexes are regulated to make sure that further rounds of transcription can take place (i.e. re-initiation of transcription), and to ensure that the cell can shut down transcription of genes when their gene products are no longer needed.
Regulation of gene expression by SUMO post-translational modifications
Post-translational modifications (PTMs) play important, often essential, roles in practically every cellular process. A relatively newly discovered PTM is protein sumoylation, which involves attachment of the SUMO peptide to specific lysine side chains on target proteins. Sumoylation is an essential and widespread modification that targets hundreds of proteins involved in many cellular processes in all eukaryotes. The effects of protein modification by SUMO vary depending on the target protein, but include changes to localization, stability, and activity of the target.
The lab is interested in sumoylation because several proteins involved in gene expression are known targets of SUMO modification. In particular, numerous transcription and splicing factors are sumoylated, but in most cases, it is not known why they are modified, nor how sumoylation affects their function. Research in the lab aims to characterize how transcription and splicing are regulated by sumoylation of specific proteins, as well as entire protein complexes, involved in each process.
Interestingly, the number of proteins that are sumoylated in cells increases dramatically during exposure to stress, like heat shock. Furthermore, many of the sumoylation enzymes are over-expressed in tumours, presumably resulting in high levels of sumoylated proteins in cancer cells. Therefore, another of the goals of the lab is to determine how changes to sumoylation levels during stress and in cancer affect gene expression. For example, does increased sumoylation due to heat shock facilitate increased transcription specifically of heat shock genes?
Approaches and Techniques Used in the Lab
Both budding yeast and human cell culture systems are used with a combination of molecular biology, biochemistry and yeast genetics approaches. Examples of commonly used procedures include chromatin immunoprecipitation, western blotting, protein immunoprecipitation, and quantitative RT-PCR.
My research and writings have focused on the history of genetics, molecular biology, evolutionary biology, symbiosis and horizontal gene transfer in evolution, tropical ecology and biodiversity.
Human-induced ecological stressors, such as global climate change, pollution, introduction of non-indigenous species, and alterations in land use, water quality and habitat, are impacting our native ecosystems.
We are interested in predicting the effects of a multitude of ecological stressors with a high degree of certainty to develop conservation and management strategies to protect native ecosystems.
Our ability to forecast future biological responses to ecological stressors is limited by the predictive accuracy of current ecological models. We have been evaluating a suite of traditional and non-traditional statistical approaches to determine which are most appropriate for continuous and binary data. This has led to improvements in our ability to effectively predict the effects of environmental variability on habitat availability, species distributions, and community composition.
Spatial and Temporal Dynamics
Understanding changes in ecosystem responses over time to environmental stressors in a diverse set of ecosystems improves our ability to predict the effects of environmental stressors into the future across broad spatial scales.
Below – Listen to Dr. Sharma speak about her research!
Ubiquitination is a post-translational modification in which ubiquitin is covalently attached onto a substrate protein to alter the function and fate of the protein within the cell. It is a highly dynamic and regulatory process that governs nearly every fundamental cellular process, from cell cycle control, cell signaling, and stress response to regulation of protein stability and turnover. As such, deregulation of protein ubiquitination leads to a vast array of human diseases including cancers, immune disorders and neurodegenerative diseases. Understanding the mechanism and regulation of protein ubiquitination is therefore essential for elucidating the role of UPS in pathogenesis of these diseases and for the development of new strategies and therapeutics.
Our research program focus on understanding how proteins are modified by the ubiquitin system and how aberration of this system contributes to pathogenesis of diseases.
Research in my lab focuses on the genetics and evolution of plant breeding systems in a Neotropical group of plants in the genus Turnera. A majority of species in the genus are distylous and strongly self-incompatible, while other species are self-compatible often having anthers and stigmas in close proximity, leading to high rates of self-fertilization. We have been working towards a molecular genetic dissection of the distyly locus in Turnera species which determines both the incompatibility system and the floral dimorphism. We have now cloned, and sequenced a BAC clone corresponding to the recessive haplotype, and have cloned and sequenced a majority of the dominant haplotype. We have developed a transformation system that should allow us to test the functional significance of various candidate genes identified in the BAC clones, as well as those identified through our transcriptomic and proteomic work.
My laboratory has made wide ranging contributions to fundamental mechanisms in animal physiology. We focus on nervous and hormonal control processes because of their central and universal importance to animal organisation. Both these mechanisms show pronounced daily rhythmicities, which are controlled by circadian clocks, located primarily in the brain. Both development and reproduction are analysed, primarily using a model insect system (Rhodnius prolixus), for which the genome has been sequenced. We have published extensive structural and functional parallels with the equivalent, but less readily analysed, mammalian systems and have made extensive contributions to the functional organisation of the nervous, hormonal and circadian systems of higher animals at numerous levels of analysis ranging from molecular and cell biology, to anatomical structure, functional organisation and systems biology.
The main focus of my research is the conservation biology and ecology of migratory songbirds. Dozens of species of North American songbirds have declined significantly over the past four decades, many of which are species that migrate to Central or South America during the northern winter. There are many causes of these declines, and my lab works to discover the key stressors for different species.
My long term research examines the behavioural ecology and conservation of birds. My recent research has used geolocators to map the long distance migration movements of individual songbirds to understand the fitness consequences of different migration strategies, the extent to which breeding populations depend on specific wintering regions, and to forecast how climate change will impact migratory birds. My lab is now beginning studies on the sub-lethal effects of pesticides on bird migration and orientation.
The significant physiological relevance of these studies is highlighted by the fact that obesity has become an epidemic in North America. Associated with this is an alarming increase in the incidence and a decrease in the age of onset of type 2 (insulin-resistant) diabetes. Type 2 diabetes is characterized by insulin resistance, the failure of peripheral tissues, including liver, muscle, and adipose tissue, to respond to physiologic doses of insulin, and a relative insufficiency of insulin production from pancreatic beta-cells in response to blood glucose levels. Obesity is a significant risk factor for the development of insulin resistance (80% of individuals with type 2 diabetes are obese) and it is believed that endocrine effects of hormones released by fat cells (adipokines) play an important role in the pathogenesis of insulin resistance. We are currently studying the role played by adiponectin in glucose uptake and metabolism in skeletal muscle and investigating the signaling mechanisms responsible for effects of these adipokines. These studies are potentially exciting for the development of therapeutic approaches for the treatment of diabetes.
Obesity is also a major risk factor for development of heart failure which occurs when the heart is unable to pump sufficient blood to meet the demands of the body. Progression of heart failure is now commonly believed to result due to a complex interplay of detrimental effects (remodeling). The ability of adiponectin and lipocalin-2 to mediate direct effects on the heart may help explain the strong association between obesity and cardiovascular complications, including heart failure.
Perception means to turn measurements obtained from sensors such as eyes and ears into the coherent, predictable, and more or less reliable experience that we call “reality”. I am studying the sensorimotor processes that make perception possible. In doing so, I am particularly interested in “person perception”, which includes face recognition, biological motion, and other aspects of the appearance and perception of other people.
In my lab, the BioMotion Lab, we are making heavy use of 3D scanning, motion capture technology and virtual realities. Using VR, we are not only studying how we perceive objects and and commuticate with other people, but we are also investigating how we experience and take ownership of our own body, and how we situate ourselves in the space that we seem to occupy.
Our work touches on basic philosophical questions (“What can we possibly know?”). However, it also informs character animation as well as automatic face and gesture recognition, and it has implications for applications of virtual reality for telecommunication, entertainment, training and therapeutic intervention.
The work in the BioMotion Lab is highly interdisciplinary. I am constantly looking for interested graduate students from various backgrounds, including Biology, Psychology, Engineering and Computer Science.
The focus of the research in our laboratory is to understand, at a molecular level, fundamental processes that are utilized by RNA viruses during their infection of host cells. To study these processes we a positive-sensed (i.e. messenger-sensed) single-stranded (ss) RNA virus, Tomato bushy stunt virus (TBSV), as our model pathogen.
The viral processes that we are interested in understanding include:
- 5’ cap-independent translation of viral proteins
- Replication of the viral RNA genome
- Transcription of viral subgenomic (sg) mRNAs
RNA sequences and structures within the ssRNA TBSV genome are involved in each of these processes and we aim to:
- Determine the structure-function relationship of important RNA elements within the genome
- Identify and characterize viral and host proteins that interact with these RNA elements
- Determine the molecular mechanisms by which these RNA elements and protein factors mediate different viral processes
Electrical Synapses in Health and Disease: From Genes to Systems
Communication between cells in the nervous system is mediated by chemical and electrical synapses. Electrical synapses, the gap junctions of the nervous system are far less understood than chemical synapses, but accruing evidence demonstrates that throughout the CNS, gap junction–mediated electrical signals synchronize neural activity on millisecond timescales via cooperative interactions with chemical synapses. Further, gap junction–mediated electrical signals have a significant contribution to synaptic plasticity, learning and memory in health and disease. My research addresses the functional role of electrical communication in the vertebrate nervous system with a particular focus on the visual system. In our studies, we integrate molecular and cellular neurobiology methods with functional imaging, electrophysiology and, most recently, behavioral studies. The overall objective is to develop animal models of human neurological disorders by genetically engineering mutations into zebrafish, evaluating the impacts of these at the molecular and cellular level, and then undertaking behavioral studies to assess the impact of these mutations. This links the molecular machinery of electrical synapses to higher brain functions. The long-term goal of my research is to bridge from biomedical research addressing fundamental neurobiological questions to clinical applications and to inform the translation of important discoveries from molecules to bedside.