Recent advances in Next Generation Sequencing technologies and the subsequent rise in microbiome research has shown that symbiotic microbes are ubiquitous and play vital functions that impact host health; yet we lack a general understanding of how microbes evolve, and what impacts such evolution has on the host. The Batstone Lab combines quantitative genetics, bioinformatics, and mutualism theory to study how mutualistic microbes adapt to hosts, to understand how changing abiotic conditions modulate such adaptation, and to identify the genomic mechanisms underlying symbiosis evolution.

Research in my laboratory is centered on the study of cell proliferation and cell transformation. The control of gene expression in quiescent primary chicken embryo fibroblasts (CEF) is the focus of our current research program. In particular, we recently uncovered a novel response to the conditions of limited oxygen concentrations experienced by contact inhibited CEF and showed that this response is critical for the maintenance of lipid/membrane homeostasis and cell survival. Current investigations have for objective to characterize the cellular processes regulated by the lipid/membrane damage response promoting reversible growth arrest and survival of quiescent cells. To do this work we employ basic techniques of cell and molecular biology as well as genomic, proteomic and lipidomic approaches.

I am a quantitative ecologist and evolutionary biologist. I am interested in the ecology and evolution of host-pathogen interactions, including the evolution of virulence; spatial population dynamics, including plant competition and animal movement; and general statistical methods for ecology and evolution. I have worked with data from historical records and from empirical collaborators from a large variety of biological systems – for example seed dispersal by bluebirds, movement of black bears and panthers in Florida, and evolution of virulence in HIV. I focus on developing theoretical models that can be empirically tested, as well as statistical models that can be interpreted in mechanistic terms.

Plants like animals defend themselves from disease and sometimes succumb to microbial disease. My research group is interested in understanding the molecular genetic and biochemical mechanisms of plant immunity. Our long-term goal is to translate our plant immunity knowledge to reduce crop loss and pesticide use in agriculture. After many years of challenging research, my team demonstrated that DIR1 proteins move via the phloem from an initially infected leaf to distant leaves to participate in alerting/priming distant leaves to respond in a resistant manner to future microbial infections. Knowing that DIR1 is a key protein involved in inter-organ communication to initiate resistance, will allow us to dissect the priming response in distant leaves. We are using this knowledge to find environmentally friendly chemical treatments that initiate natural plant defense to provide pesticide-free methods to protect Ontario greenhouse-grown cucumbers and tomatoes from disease. We also study the Age-Related Resistance response in which plants become highly resistant to normally virulent pathogens as they mature. What molecular changes allow a mature plant to perceive and effectively defend against normally virulent pathogens, is another fascinating question we are investigating. As an instructor my goals include convincing students/future citizens that contrary to popular opinion, plants are fascinating and incredibly important for people and the planet. As a mentor to undergraduate and graduate students, I facilitate their growth as scientists and people. I encourage them to improve in areas they find challenging by reminding them it takes time, but it’s worth it.

The ability to generate genetic variants has greatly aided the study of biochemical and developmental pathways. Given the success of this approach it is not surprising that genetics is being used to address a wide range of neurobiological questions including the generation of behaviour. My laboratory uses the larval visual system of the fruit fly Drosophila melanogaster as a model system to investigate the mechanisms underlying the development and function of the nervous system. To that end, mutations or molecular tools are used to impair specific cell types and/or cellular interactions. Mutations found to disrupt the development of the larval visual system or the larval response to light can be used to identify molecules involved in these processes. Thus, my research programme can be divided in two parts namely the genetic analysis of the larval response to light and the molecular genetic analysis of genes required for the development of the larval visual system. To address these questions a variety of techniques are used such as mutant analysis, molecular and cell biology.

I conduct research on the ecology, conservation and management of aquatic and terrestrial ecosystems in the Great Lakes basin. A primary goal is to develop simple ecological indicators to track impacts of human activities on the long-term health of target ecosystems; these have involved citizen scientists, especially high school students and indigenous youth. Our projects involve extensive sampling in streams, lakes, vernal pools, boreal forests, and coastal marshes throughout Ontario, collecting information on planktonic and benthic algae, zooplankton, macro-invertebrates, aquatic macrophytes, wetland fish and birds, amphibians, and/or turtles. We also use satellite information to assess land-use alterations and shoreline development on wetland connectivity and quality, and to map habitat loss from colonization of invasive Phragmites australis. Working continuously in Georgian Bay (GB) since 2003, we have created one of the largest and most comprehensive databases on coastal wetlands of eastern and northern GB. We have modelled the effect of water level on marsh zonation in GB, and how human activities (particularly associated with agricultural and urban/recreational development) can affect nutrient status in embayments, wetlands and streams. My students also use remote sensing, geographic information systems, and radio-telemetry to determine how at-risk freshwater turtles use their habitats, information that is used to find the best options to protect and conserve connecting corridors and critical habitat. Recently, we have begun to examine how recovery of boreal forests from wildfire outbreaks are affected by proximity to water bodies and human features and activities.

My research program focuses on the effects of anthropogenic stressors on avian wildlife and other predators to monitor broad-scale environmental change. My lab conducts field research in temperate and Arctic ecosystems to examine the impacts of climate change on avian fitness via (1) the indirect effects of environmental variation on (1) prey type, quality, and quantity; and (2) energetics and behaviour; (3) the direct effects of warming temperatures on physiological traits associated with heat stress; and (4) the cumulative effects of multiple stressors including contaminants.

My primary research interests focus on the cellular and molecular mechanisms that regulate various systemic processes within model organisms. Not only is this important to best understand the function of animal physiology, but it also sheds light on analogous regulatory mechanisms that can be translated to human systems. Much of this research has included work on insect model organisms to better understand digestive, cardiac, neural, immune and reproductive processes. In particular, I have identified various regulating proteins and signaling cascades that control cellular machinery and are vital to maximize overall systemic physiology. It is my passion for asking “how” and “why” things happen that I pass on to my students every day. My pedagogical approaches are framed around training students to be leaders in translating interdisciplinary scientific applications to the real world. I have collaboratively established undergraduate research-focused projects (The Stink Bug Project, BioBlend Project, Horizontal Curriculum Integration Project), applied undergraduate laboratory and research facilities (ALLURE lab, Undergraduate Cell Biology Lab, Living Systems Lab) and have engaged students in translating the science they learn beyond the walls of the classroom through the use of social media and emerging technologies including Blended Learning. All of my wet-lab and pedagogical research projects are highly collaborative with teams of students. As a Distinguished MacPherson Institute Leadership in Teaching and Learning (LTL) Fellow, I look forward to continuing to collaborate with other faculty across McMaster University and beyond on additional projects that can ultimately improve the education that students attain in our classrooms.

Cancer Biology, Cadherin-Catenin mediated Cell adhesion and Signaling, POZ Transcription Factors Our research goal is to understand the cellular and molecular basis of E-cadherin-mediated adhesion in normal cell growth, development and tumourigenesis. The primary epithelial cell-cell adhesion system involving E-cadherin and its catenin cofactors a-, b-, g- and p120ctn, is perturbed in ~50% of human metastatic tumours, and this correlates with the invasive phenotype. Interestingly, the catenins also function as transcriptional regulators of genes involved in tumourigenesis. My laboratory focuses on the transcription factor Kaiso that was first identified as a specific binding partner for the catenin p120ctn, which is aberrantly expressed or absent in human breast, colon and skin carcinomas. Kaiso is a novel member of the POZ-zinc finger family of transcription factors implicated as oncoproteins or tumor suppressors, and currently it is the only known POZ protein with bi-modal DNA-binding and transcriptional repression activity; Kaiso recognizes a sequence-specific consensus, TCCTGCNA, or methylated CpG-dinucleotides.

Plant interactions with other plants My current research focuses on plant communication and behaviour, including plant kin recognition. Plants live in highly social environments, and they do behave, though very slowly. Plants sense the presence of other plants, and then respond, usually by producing a more competitive phenotype. Responses to cues of neighbours are thus important in competition. My lab has worked on plant responses to aboveground cues, the presence/absence of belowground neighbours, and the relatedness of belowground neighbours. We collaborate with Dr. Harsh Bais, University of Delaware, on research into the underlying mechanisms for responses to relatives. Adaptation to abiotic stresses My research program on the evolution of plant carbon acquisition traits has included studies that integrate the physiological ecology of drought stress with the natural selection on drought stress traits, and genetic differentiation between populations from environments differing in water availability. A former student, Laura Beaton developed a research program on adaptation of plants to roadside stresses, including salinity and manganese. I collaborate with Dr. Lisa Donovan, University of Georgia, in understanding how plant physiological traits evolve under stress.

I am a theoretical biologist with a wide variety of interests, but my primary focus is the evolution and spread of infectious diseases, with a particular interest in human health. Diseases that the lab works on include HIV, syphilis, canine rabies, and Ebola. We use theoretical, statistical and computational approaches to understanding disease data, with a particular focus on methods that combine dynamical mechanism with statistical inference.

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https://mac-theobio.github.io/dushoff.html

At one level, evolution is remarkably simple, with just a few concepts (mutation, recombination, random drift and natural selection) that underlie the overall process. Yet this description obscures many issues that make evolution a fascinating area for study. Evolution typically involves many genes and often revolves around interactions between individuals and their environments. Moreover, genes interact with one another and with the environment in a nonlinear fashion, resulting in complex phenotypes and evolutionary dynamics. My work aims to describe and analyze such interactions with experimental and quantitative rigor. Specifically work in my lab aims to address the fundamental question about the mechanistic basis of observed phenotypic variation. That is, how genetic (and environmental) variation modulate developmental processes and ultimately influence phenotypic outcomes. My research employs genetic and genomic approaches to address these issues, largely using Drosophila (fruit flies) as a model system. Most labs that work with Drosophila study either individual mutations of large effect (such as those that completely knock out a particular function) or subtle quantitative variation (rarely identifying specific genes). We employ both of these empirical approaches in conjunction with our genomic analyses to help relate our understanding from developmental genetics with the natural variation observed in populations.

Development in multicellular bacteria; Regulation by small RNAs; Antibiotic production The goal of our research is to understand development and regulation in multicellular bacteria, using Streptomyces coelicolor as our model system. The streptomycetes are extremely important to the pharmaceutical industry as they make a large number of secondary metabolites having a profound medical benefit, including anti-cancer agents, immunosuppressants, and the majority of clinically useful antibiotics. They are also unusual in that they have a complex, multicellular life cycle and are capable of differentiating into distinct tissue types. Intriguingly, this differentiation process coincides with the production of secondary metabolites. One aspect of our research is focused on understanding the components necessary for differentiation, and centres on a novel family of proteins, termed the chaplins, that are essential for the transition from one differentiated state to another. We are also interested in the regulatory networks that control differentiation, metabolism, and environmental adaptation in S. coelicolor, and are focussing on a newly emerging, and universally important, class of regulators known as the small RNAs.

Evolutionary Genetics, Genomics, and Sex Chromosomes The Evans lab studies how natural selection, recombination, and demography influence genome evolution. One of the major themes of our work is to study speciation and gene duplication in African clawed frogs. This work aims to further understanding of the extent and mechanisms of biological diversification in this group, and to explore interesting genomic phenomena such as the evolution of sex chromosomes and transposable elements. Another focus of our efforts relates to the role of social systems on genome evolution. This work involves simulations of genome evolution under various social systems, and analysis of molecular polymorphisms from sex chromosomes, autosomal DNA, and mitochondrial DNA of cercopithecine monkeys.

Our research in microbiology is focused on the soil bacterium Sinorhizobium meliloti that forms N2-fixing root nodules on leguminous plants. The genome of S. meliloti consists of a typical chromosome (3.6 Mb) and pSymA (1.35 Mb) and pSymB (1.68 Mb) replicons. We study genes and processes involved in the interaction of the bacteria with the plant and more generally process that are important for survival in a soil environment. A major current project is to define and manipulate the minimal genes that are necessary and sufficient for nodule formation and N2-fixation. In a key step to achieving a minimal symbiotic genome, we constructed a S. meliloti strain lacking 45% of its genome. In other work, we are studying genes and uptake systems that are regulated in response to phosphate limitation, and in a separate project a locus that confers resistance to bacterial viruses.

My group at McMaster University is interested in the area of molecular evolution, bioinformatics, and sequence analysis. Our research attempts to understand how the processes of evolution act to cause the changes observed between molecules, between genes and between genomes. The recent advances in molecular genetics are providing a storm of new data on DNA sequences, on gene structure and higher order genomic structure. However, the implications of these new data are not always clear. This area of scientific inquiry is inter-disciplinary between biology, computer science and mathematics. We make use of computer based analysis, statistical analysis and mathematical models to answer broad questions about the molecular biology of all organisms.

Vulval development in Caenorhabditis elegans, Regulation and function of gene networks, Evolution of developmental mechanisms Specification of cell fate during development involves a large number of genes that interact with each other and are expressed in dynamic patterns. My lab is interested in understanding the function and evolution of gene networks that control cell proliferation and differentiation. Alterations in gene regulation have been shown to give rise to severe developmental abnormalities including hereditary diseases and cancers. Hence, a fundamental understanding of gene regulatory networks is critical for gaining important insights into the pathogenesis of human diseases. Toward this goal, we are studying vulva development in an established model organism, Caenorhabditis elegans and a closely related species, Caenorhabditis briggsae. The hermaphrodite vulva provides a unique opportunity to identify genes and study their regulation and function during development. In C. elegans, vulva is formed by the progeny of three out of six multipotential vulval precursor cells (VPCs) that divide three times to give rise to twenty-two cells. The vulval progeny differentiate during L4 larval stage to generate seven different cell types leading to the formation of an adult vulva. The invariant lineage of the VPCs and stereotypic positions of their progeny offer experimental analyses at single-cell resolution.

Molecular Genetics ofTay-Sachs disease and Sialidosis. My research focuses on the molecular genetics of two diseases, Tay-Sachs and sialidosis, which are lysosomal storage disorders caused by defects in ?-hexosaminidase A and sialidase respectively. The lysosomal storage process begins in the fetus early in pregnancy but most of these diseases become clinically evident within the first 2 years or have a later onset. The majority of patients show a fatal course with progressive involvement of the nervous system. We have focused on identifying disease-causing mutations in order to determine the impact of these mutations on disease phenotype. This provides informative genotype/phenotype correlations and a precise understanding of the structure/function of the enzymes. With the discovery of more mutant alleles, we have utilized this DNA-based technology to complement the enzyme-based prenatal diagnostic procedures. We are also developing mouse models of Tay-Sachs disease and sialidosis which will allow us to study the pathophysiology of the diseases in order to test potential therapeutic strategies in vivo. Finally, we are developing recombinant adenovirus vectors coding for the human sialidase gene for therapeutic applications. Adenoviral vectors represent a new class of biotherapeutics and its development for gene therapy holds much hope for patients.

The heart is the organ most often affected by congenital malformations, as well as diseases associated with aging. Uncovering the molecular and genetic mechanisms that underlie these problems can be accelerated through study with simpler genetic models such as the fruitfly, Drosophila. The Jacobs lab employs the Drosophila genetic model to dissect heart formation and growth of the heart, with particular focus on adhesion signaling, cell polarity, morphogenesis and the formation and remodeling of the heart extra-cellular matrix.

The Jacobs lab is no longer recruiting students for graduate or undergraduate thesis work.

My research program focuses on understanding the impacts of human activities on aquatic ecosystems. More specifically, my students and I study the effects of point (municipal, industrial) and non-point (agriculture, forest harvesting) discharges on the health of aquatic organisms, and the fate of persistent pollutants in freshwater and marine ecosystems. Much of our research is multidisciplinary in nature and an interface between biogeochemistry, chemistry, ecology and toxicology. For example, we use measurements of stable nitrogen, sulfur, hydrogen and carbon isotope ratios in organisms to characterize trophic relationships in diverse aquatic systems and to understand pollutant accumulation from primary producers through to top predators. I have led or been involved in three major whole ecosystem experiments to understand how 1) the estrogen used in the birth control pill affects fish and their prey, 2) wastes from rainbow trout aquaculture affect native organisms, and 3) a commonly-used herbicide and fertilizers affect the health of wetland communities.

I am an ecologist working at the level of species communities and ecosystems. I am primarily interested in the complexity of ecological systems that arises from the richness of species making them up. My group investigates links between the number of species and the stability of community properties, the links crucial to understanding of the functional value of biodiversity as well as indirect and latent threats to it. Specifically, we combine insights from different systems: we use natural model systems such as arrays of miniature aquatic ecosystems as well as we design and test artificial systems. The artificial systems have an extra benefit of being potentially useful in greening of urban living (from supplementing food to enhancing education). Our work blends theoretical and experimental approaches.

The Little Lab explores physiological mechanisms to understand the eco-evolutionary costs of change. Many animals can remodel their physiology within their lifetimes to compensate for changing environments. This plasticity represents the best defense animals have against climate change, but potential costs and trade-offs have been difficult to identify. The Little Lab uses an integrative approach to uncover proximate mechanisms for plasticity, allowing us to make and test predictions about its contextual costs.

My research focuses on the ontogeny, phenotypic plasticity and evolution of muscle metabolism – important for locomotion, thermogenesis, and whole-body metabolic homeostasis. I use mechanistic and evolutionary physiology approaches, and take advantage of “experiments in nature” by studying species that thrive in extreme environments such as high altitude. I do applied research on the impacts of changing temperature, low oxygen, and pollution on the physiology of fishes.

Dr. Carmel Mothersill is a radiobiologist and Canada Research Chair in Environmental Radiobiology. Her interests are in the impacts of low dose and chronic radiation exposures on non-human species and on ecosystems. She is developing biomarkers which can indicate effect (harmful or beneficial) at the level of the population, community or ecosystem. Such biomarkers will hopefully be used to aid decision making about the risks of radioactive releases in environmentally sensitive areas. Many of the system level markers identified so far relate to stress responses and immune responses which can be compromised by low level radiation exposures.

Membrane Physiology of Ion transport and Excretion The primary goal of my research program is to elucidate the cellular and molecular mechanisms of excretion and ion transport, particularly by insect epithelia. We study how such processes are controlled by hormones and intracellular second messengers, and how mechanisms for excretion and ion transport are altered in response to changing environmental conditions. Blood feeding insects such as mosquitoes are of enormous importance as vectors of diseases such as malaria, and our studies of physiological mechanisms of ionoregulation and excretion provide insights that we hope will aid development of novel, environmentally-benign insecticides for pest species. Recently we have become fascinated by the ability of insects to rid themselves of toxins. Co-evolution of insects with flowering plants means that many insects are extraordinarily effective at detoxifying synthetic or natural pesticides, and the excretory system plays an important role in elimination of toxins or their metabolites. My research makes extensive use of electrophysiological methods, including intracellular recording, ion-selective microelectrodes and patch clamping. My students and I develop or adapt specialized micro-techniques for measuring pH or ion concentrations inside or adjacent to epithelial cells, or in nanoliter samples of biological fluids. We have recently developed a method of measuring transport of fluorescent substrates of ion transporters by means of confocal laser scanning microscopy of nanoliter droplets of secreted fluids, and we have used this technique to assess the roles of transporters related to p-glycoproteins and multidrug resistant proteins (MRP) in insect Malpighian (renal) tubules. We are also one of the few labs in Canada to make use of the Automated Scanning Electrode Technique (ASET). Transport of ions into or out of cells perturbs the concentration of ions in the unstirred layer (USL) near the surface of the cell. ASET uses computer-controlled stepper motors to position ion-selective microelectrodes near cells and measure tiny changes ( <0.04% ) in ion concentration between two positions within the USL. The difference in ion concentration is then used to calculate the rate of ion transport using the Fick equation.

Genetic relatedness, parentage and behavioural ecology of colonial and cooperative-breeding birds. My research combines the study of animal behaviour and population biology with the examination of molecular genetic markers. The main areas of research are: the evolution of complex social systems in birds; parental care patterns and mate choice; and genetic effects of environmental mutagen loads as estimated by DNA fingerprint mutation rates. To understand the evolution of communal social system we focus on two communal bird species. In Pukeko, a gallinaceous bird inhabiting New Zealand, groups of one to three males and similar numbers of females raise young at a single nest. Sexual access to laying females is shared among sexually mature males. In contrast, smooth-billed anis, a crotophagid bird of Central and South America, engage in a system of social pairs sharing a single nest and competing for access to the incubated clutch of eggs. Females bury each other’s eggs in the structure of the nest. We have detected mutant fragments of DNA in multi-locus mini-satellite profiles of herring gull families. High levels of polycyclic aromatic compounds (PAC) are associated with steel production facilities and automobile emissions. Rates of genetic mutations are being determined for gull colonies with varying levels of PACs.

We study gene regulation and physiological adaptation in E. coli and other bacteria to better understand how bacteria cause disease and persist in the environment. We also have many collaborative projects with biochemists, engineers, industry and government agencies to develop new tools for monitoring water quality and understanding waste treatment processes from a microbiological perspective. We are using new DNA sequencing technology and bioinformatics analysis tools to track microorganisms, characterize composition of complex microbial communities and conduct comprehensive studies of gene expression.

My lab strives to understand the integrative mechanisms (from molecule to organism) for how vertebrate animals tolerate and perform in challenging physical environments. We are interested in the physiological, cellular, and genomic bases of adaptation and acclimatization, particularly in response to hypoxia and/or temperature change. Physiological systems important for respiration and exercise are emphasized.

I am interested in the biological consequences of low level radiation exposure. The lab uses tissue culture techniques to examine both the direct and indirect effects of radiation, and the transmission of these effects to neighbour and daughter cells. This has implications in both health and environmental fields.

My research area includes population genetics and evolutionary genomics of sexual selection and speciation. Current research includes development of a new theory of male-sex drive or male-driven sexual selection and its effect on rapid evolution of male-biased genes, modification of sex-biased fitness, and maintenance of sex. A special focus of our research involves application of male driven sexual selection theory to the origin of menopause, persistence of maternal mortality, and sex-biased evolution of disease and health in general. Our research work is relevant to all aspects of gender-based controversies in society.

Astro-, Computational, Developmental, and Evolutionary biology (with smattering from Ecology and Physiology); Viruses to elephants, including human menopause and especially gastropods, echinoids, and water bears (oh my).

We study an extremophyte, Eutrema salsugineum, a plant closely related to Arabidopsis thaliana but one far more tolerant of extremes in temperature, water deficits, soil salinity, and nutrient deficiencies. We use comparative genomics, physiology, and biochemical approaches to identify traits that allow E. salsugineum to thrive under extreme environmental conditions. Our approach involves comparing plants collected in the challenging field conditions of its native habitat in the Yukon, Canada, with plants subjected to controlled stress treatments in growth cabinets. Identifying stress tolerance traits will enable us to improve our crop species and help us stabilize yields that are already adversely impacted by climate change.

The Wilson laboratory studies the impacts of environmental stressors on aquatic organisms, with a strong emphasis on aquatic toxicology research. Our research intersects environmental physiology, ecology and evolution, and bioinformatics and functional genomics. Our basic research program focuses on the evolution, regulation and function of cytochrome P450 enzymes; enzymes that are critical for xenobiotic metabolism and steroid production. Cytochrome P450 enzymes are an important superfamily involved in chemical defense. Our environmental physiology research examines the impacts of contaminants (e.g. human drugs, metals, complex effluents), temperature, and low dose radiation. We are particularly interested in the effects on development, growth, and reproduction. The biological approaches used in the lab are quite diverse and include gene expression, histology, protein assays (e.g. enzyme activity, steroid levels), morphometrics, growth, and behaviour. Likewise, our species of interest are diverse. Our primary fish model species are zebrafish and rainbow trout but we include important native species such as lake whitefish, round whitefish, and Arctic charr. For invertebrate systems, we use the brown and green hydra, both freshwater Cnidarian species, and a marine annelid Capitella telata.

According to Canadian Cancer Society, cancer is the leading cause of premature death in Canada and an estimated one out of every four Canadians is expected to die from cancer. An underlying hallmark of cancer is genome instability, which can arise from the disruption of telomere maintenance. The Zhu laboratory is interested in elucidating the molecular mechanism by which human cells maintain their telomere integrity. Knowledge gained from these studies is expected to aid in the design of anti-cancer therapeutics and treatment of cancer patients. Currently the Zhu laboratory focuses on two research areas relevant to telomere maintenance and genome integrity: 1. Elucidating the role of post-translational modifications in telomere maintenance. 2. Elucidating the functional interaction between shelterin proteins and accessary factors.