Human and Ecosystem Health

The Avis Lab studies both fundamental and applied aspects of food and plant microbiology. More specifically, we are interested in microbial food spoilage and plant pathology. Our main focus is the use of alternatives to synthetic chemicals to control the growth of microorganisms on crops and during food storage. The resulting effects of this research is meant to increase food yield and reduce food loss, which can have a positive impact on food security and environmental sustainability.

We are investigating the use of beneficial microorganisms (biological control agents), as well as microbial and plant extracts and purified natural antimicrobial compounds as potential alternatives to control harmful microorganisms. These novel control measures are meant to mitigate problems associated with some synthetic control measures such as risks to health and the environment as well as to delay or eliminate the onset of resistance development in the targeted microorganisms.

Our laboratory uses a multidisciplinary approach including basic microbiology, biochemistry, bio-analytical and bio-physical chemistry, membrane and lipid chemistry, as well as molecular biology, genetics, and genomics.

Dr. DeRosa’s Lab, the Laboratory for Aptamer Discovery and Development of Emerging Research (LADDER), seeks to develop biosensors and “smart” materials based on DNA aptamers, single stranded DNA or RNA sequences that specifically bind to a diverse variety of targets. Projects in our lab draw on inorganic, organic, materials, and nucleic acids chemistry. Several main research themes are outlined below:

1. Human and Ecosystem Health: We have several projects where we apply our aptamer technology to problems in health. We have developed MRI and CT contrast agents that use aptamers for targeting. Working with colleagues in neuroscience, we have developed an aptamer-based tool to study, and perhaps one day treat, Parkinson’s Disease. We have also discovered aptamers for
2. Molecules and materials for sustainability: Our research on aptamers for controlled release applications is being to “smart” fertilizer technology. Fertilizers play a critical role in increasing agricultural outputs but at high economic and environmental cu_event_costs. The smart fertilizer concept involves the use of aptamers to recognize chemical signals that are exuded from crop roots to trigger the release of nutrients on demand, lowering cu_event_costs for the farmer and lessening environmental impact.
3. Food Safety, Security, and Analytical Methods: The presence of unsafe levels of contaminants in food is a growing public health problem that requires new technology for monitoring the food continuum from production to consumption. Aptamers for food safety targets, such as parasites, bacteria, and mycotoxins, have been discovered and tested in the LADDER. Our main interest is to develop low‐cu_event_cost, sensitive, robust biosensors for the detection of targets, mycotoxins in particular, at early stages in the food production chain (e.g. farm and grain elevator).

For more information, visit the LADDER.

The Environmental Biogeochemistry and Biotechnology (EBB) Lab explores how microbes and the chemical reactions they drive influence the fate of critical materials and environmental contaminants. Our research integrates microbial cultivation, advanced analytical chemistry, and high-resolution imaging to better understand biochemical transformations for metals and organic pollutants. Many research projects also leverage in-demand computational skills to analyze large-scale environmental chemistry, DNA, and RNA data to characterize biogeochemical cycles in diverse habitats.

We foster a collaborative, interdisciplinary environment spanning chemistry, biochemistry, earth science, and engineering. We work closely with partners in government including Environment and Climate Change Canada and Natural Resources Canada to translate our research into effective environmental policies that protect Canadians. We also work closely with partners in the solid waste and biotechnology sectors to develop environmental remediation strategies tailored to their needs. We are committed to inclusive mentorship and work with students to design projects that help them build skills in line with their career goals. Our team’s overarching vision is to develop sustainable, microbe-driven strategies for waste management tailored to real-world applications.

If you want to learn more about projects where you would be a good fit in the EBB lab, check out our website to learn more: https://carleton.ca/envbiotech/

The Hosseinian Group conducts research in the area of phytochemistry/food biochemistry, focusing on:

• The extraction and characterization of novel biomolecules (mainly phenolic lipids and their interaction with dietary fibre) from agri-food by-products/waste;
• Investigating their structure-function relationship (biotransformation) in microemulsions/encapsulations in food and biological membranes (liposomes/artificial cell membranes);
• Enhancing antioxidants and anti-inflammatory activity for human health and well-being;
• Applying techniques (e.g. fermentation and germination) to reduce anti-nutritional factors in foods;
• And developing biomaterails from agri-food by-products/waste.

These novel biomolecules can have considerable potential for food science, agriculture, cosmetic, pharmaceutical, animal science and health science applications. Our lab is now more than 90% solvent free with innovative green techniques (SC-CO2 and Ultrasound) used to extract biomolecules.

Using analytical and bioanalytical chemistry, the Lai Group focuses on the instrumental analysis of biochemical and environmental samples for public health using capillary electrophoresis, dynamic light scattering, fluorescence spectroscopy, gel permeation chromatography, liquid chromatography, mass spectrometry and 3D microfluidics. New photochemical, electrochemical and optical phenomena are developed into analytical methods for enhanced sensitivity and selectivity: (a) molecularly imprinted polymers for the selective determination of therapeutic drugs in serum, ochratoxin A in red wine, and estrogenic compounds in wastewater treatment by solid-phase extraction with differential pulsed elution; (b) self-assembled monolayers and electropolymerized thin films for adsorption of toxic metals (Hg²⁺) and mycotoxins; (c) functionalization of colloidal nanoparticles for removal of endocrine disrupting compounds in environmental water and radioactive nuclides (Pu-238, Sr-90, Y-90,) in urine; (d) detection of nanoparticles in environmental water and air samples; (e) DNA binding with inorganic oxide nanomaterial surfaces; (f) interaction of nanoparticles with graphene quantum dots and simulated lung fluid; (g) surface chemistry/biochemistry of nanoparticles as related to electrochemical analysis by cyclic voltammetry and electrochemical impedance spectroscopy.

Our group is broadly focused on synthetic organic chemistry, particularly on applications in biochemistry and engineering. Our approach to research is highly collaborative with other academic researchers and corporate partners.

In partnership with Prof. Jeff Smith in Chemistry, we developed TrEnDi (Trimethylation Enhancement using Diazomethane, which uses innovative applications of diazomethane to enhance the analysis of certain biological molecules, particularly certain lipids and peptides, via mass spectrometry through the introduction of fixed, permanent positive charge(s). cu_people_phone_ext and expansion of this work is ongoing, with current directions focused on the development of new derivatization reagents, expansion of the scope of substrates suitable for derivatization, and facilitating new fragmentation pathways in tandem mass spectrometry that will facilitate structure identification.

Our group is also currently engaged in a collaboration with Prof. Ron Miller (Carleton University, Department of Mechanical and Aerospace Engineering) to understand the chemical fate of antioxidants in lubricating oils. This work involves the synthesis of various compounds proposed to be the oxidized antioxidants. This work is aimed at improving the understanding of how lubricants are oxidized and their functional lifetimes.

Our group’s expertise and previous work encompasses the total synthesis of natural products, including lipids, polyketides and terpenes; as well as methodologies, including metal-catalyzed organic processes.

For more information, visit the Manthorpe Lab.

The primary research interest of the McMullin Group is studying chemical interactions between microorganisms and their environment through the biosynthesis of natural products. Natural products are ecologically significant as they enable specific species/strains to compete for resources or occupy an ecological niche. While natural products are important socioeconomically, for example as drugs, often unwanted chronic exposures have adverse health effects. These effects are often poorly characterized. To facilitate toxicological experiments and exposure assessments for better hazard characterization, chemical standards are required. This involves evaluating the toxigenic potential of ecologically relevant species/strains, purifying the principle toxins and elucidating their chemical structures. This type of research can have important implications for evidence-based decision making, toxicology and chemical ecology.

Students in the group develop transferable technical skills by (1) growing microorganisms to produce metabolites, (2) purifying and structurally characterizing chemicals, (3) developing analytical or metabolomics methods, and (4) assessing the biological activity of purified compounds. We currently focus on natural products produced by cyanobacteria and fungi.

For more information, visit The McMullin Group.

Research in the Rand Lab is rooted in environmental and analytical chemistry, and crosses with biochemistry and toxicology. These streams of research enable our group to develop analytical and biochemical tools to assess the impact of pollution in North America, and to provide knowledge that leads to safer consumer products. Our research also addresses emerging issues in environmental health, including the interaction between different kinds of environmental stressors (e.g. nutrition and environmental chemicals) that may alter relationships between exposure and effect. We focus on three streams of research:

• Routes of human exposure to organic contaminants
• Contaminant metabolism and biotransformation
• Contaminant effects on lipid signaling and modulators of contaminant action

For more information, visit The Rand Lab.

Dr. Sabatino’s lab focuses on research that spans the areas of nucleic acid, peptide and protein chemical biology. Our research aims to develop synthetically modified biomolecules for applications related to human health, nanotechnology and the material sciences. Specific research applications include:

• RNA Biotechnology. The Sabatino lab has pioneered the design and development of a new class of synthetic branch and hyperbranch (dendrimer-type) RNA. These novel RNA structures template the assembly of discrete, higher-order RNA nanostructures for screening and silencing oncogene expression in cancer cell lines resulting in potent anti-cancer effects. The Sabatino lab continues to innovate novel nucleic acid (supra)molecular structures for enhancing their therapeutic applications.
• Peptide and Protein Chemical Biology. The application of cell-targeting and penetrating peptides in nucleic acid (and drug) delivery is an active area of research in the Sabatino group. These high-precision delivery systems aim to advance new drug delivery formulations into clinical practice. Moreover, the Sabatino lab also applies machine learning tools to design and develop novel peptide binding ligands of important immunological receptors for applications in cancer immunotherapy and vaccine development.

For more info visit, the Sabatino Lab

Overview

Mass spectrometry (MS) has proven to be a powerful analytical tool in many scientific fields for nearly a century. Advances made in soft ionization techniques such as electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) have expanded the use of MS to the biological sciences, allowing biomolecules to be ionized and sampled in the gas phase without fragmentation. These advances have been echoed in an explosion of publications over the past 20 years that have used MS as a tool to illuminate information pertaining to a biological question. The majority of MS-based bioanalytical studies to date have focused on cataloguing the species present in a sample at a static moment in time. Although this is important, measuring the dynamics of a system in response to a stimulus not only aids identification efforts, but offers mechanistic insight into the cellular processes involved. Gaining a better understanding of these dynamics, often expressed through a change in concentration or in the degree of modification, enhances the accuracy of cellular models, assigns functional roles to the identified species, as well as highlights new diagnostic and therapeutic strategies. The research program of the Smith group focuses on developing novel methods to efficiently measure biomolecular dynamics in living systems with the downstream goals of elucidating disease biomarkers and further characterizing biosynthetic and biochemical pathways.

Instrumentation

The Smith Lab uses mass spectrometry as a tool to probe the dynamics of various biomolecules. At present, we mainly conduct research in the area of protein analysis (“proteomics”) and lipid analysis (“lipidomics”). The laboratory is equipped with high-resolution hybrid quadrupole time of flight, triple quadrupole and linear ion trap mass spectrometers. All of these instruments achieve ionization via electrospray ionization and are coupled to high performance liquid chromatographs. The lab additionally houses two gas chromatography-MS systems, one equipped with a headspace sampler.

TrEnDi

Trimethylation Enhancement using Diazomethane (TrEnDi) is a published technique developed by Professors Jeffrey Smith and Jeffrey Manthorpe at Carleton University. The method increases the sensitivity of mass spectrometric detection by assigning a fixed, permanent positive charge to amino groups. It allows for increased and predictable sequence coverage for peptides in proteomic analyses, and increased limits of detection for several important lipid classes in lipidomic analyses.

Wasslen, K.V., Canez, C.R., Lee, H., Manthorpe, J.M., Smith, J.C. (2014) Trimethylation Enhancement using Diazomethane (TrEnDi) II: Rapid In-Solution Concomitant Quaternization of Glycerophospholipid Amino Groups and Methylation of Phosphate Groups via Reaction with Diazomethane Significantly Enhances Sensitivity in Mass Spectrometry Analyses via a Fixed, Permanent Positive Charge. Analytical Chemistry. Oct 7;86(19): 9523-9532. DOI: 10.1021/ac501588y. PMID: 25208053.

Quantitative Proteomics

The Smith Lab uses microfluidic devices to manipulate biological samples in a highly efficient manner to elucidate protein dynamics and post-translational modification patterns using MS in conjunction with TrEnDi. Through studying the dynamics of protein abundances or the modes in which they are modified in cells that are stimulated in some manner (or that are either diseased or healthy), our research will help define how cells communicate with each other, their environment and themselves.

Quantitative Lipidomics

Although lipids have been studied for decades and have been largely regarded as energy storage or structural molecules, recent progress in lipid research has revealed many novel and important roles for lipids in cellular signaling. Many classes of lipids are easily analyzed by mass spectrometry; however, some are more difficult to observe. The Smith Laboratory will focus on developing novel methods to identify lipid species in the context of complicated biological samples. To date, the development of TrEnDi has achieved this goal by increasing the sensitivity of some lipid classes over an order of magnitude. Ultimately, we will apply the novel methods that are developed to investigate lipid dynamics in biological systems to aid our understanding of the roles they play in cellular life.

For more information, visit The Smith Lab.

The Tsopmo Lab is interested in the structures of food molecules and their functionalities. Our research focuses on the hydrodynamic properties of proteins and peptides obtained from by-products of food processing and study how they can be used to improve the texture of foods by performing structural characterization using spectroscopic and microscopic techniques.

We investigate the role of antioxidant molecules on health, lipid, and glucose absorption and metabolism. Oxidative damage to biological molecules increases the risks of developing many chronic diseases, and antioxidants molecules are useful in mitigating the risks. Using cellular models and molecular dynamics, the Lab is involved in the discovery of new antioxidant compounds from foods and human milk that reduce inflammation, inhibit lipid and glucose absorption, or decrease the differentiation of fat cells.

Vitamins and minerals are important for various physiological functions, and the Tsopmo Lab examines how the bioavailability of these nutrients is affected in foods grown in soil-less environments (i.e. vertical farming).

Metals such as hexavalent chromium and arsenic are toxic because of their oxidative stress induced damage to nucleotides and biomolecules. We are interested in finding peptides in foods that can reduce their toxicity by converting them to stable, non-toxic species.

For more information, visit The Tsopmo Lab.

The Willmore Lab examines alteration of protein structure and function by oxygen, in particular, the lack of such alteration under low oxygen (or hypoxic) conditions. Such conditions are commonly encountered by humans at high altitudes, during development, and in clinical conditions such as sleep apnea, hypertension, ischemic (or the cutting off of blood flow) heart disease, acute myocardial infarction, cardiac arrest, cerebrovascular disease (such as stroke), and neurocognitive deficits. Systemic or localized hypoxia affects metabolic pathways, induces angiogenesis (or the formation of new blood vessels), and affects inflammatory responses. Many of the factors that are involved in hypoxia survival are also found to be upregulated in most human tumors. As well as disease, ischemia-associated hypoxia plays a role in tissue damage during organ transplantation as well as preservation. Using mammalian cell lines (human, monkey, rat, etc.) as the model system and a proteomic approach, we examine changes in protein expression, function and stability under varying oxygen conditions.

The Willmore Lab