Spring 2014 Seminar
Friday, April 25, 2014
Our laboratory is using label-free expression analysis for relative quantitation. For this work, we are performing LC in combination with mass spectrometry and are using a data independent analysis. A significant advantage of data independent analysis is that no switching of the mass spectrometer is involved, therefore, better quantitation can be obtained. Since reproducibility is very important for quantitation, we analyze both mass error and coefficient of variation of our results. In some cases, we are using two dimensional liquid chromatography prior to mass analysis as it can have several advantages over one dimensional liquid chromatography. We have used this approach to analyze serum from patients who suffer from COPD as well as individuals who suffer from autoimmune disorders. In the case of COPD, our results have been compared to the results obtained from microarray analyses. The abundance of proteins identified spanned a concentration of three orders of magnitude. The significantly changing proteins can hopefully provide insights into the mechanisms of disease.
Friday, April 18, 2014
Land application of livestock manures can lead to the release of zoonotic disease agents into the environment. These disease agents may ultimately infect humans through a variety of pathways including recreational contact with contaminated water, inhalation of bioaerosols generated by agricultural activities, or consumption of contaminated water or produce, often with serious consequences. Complicating these infections are antibiotic-resistant disease agents. The U.S. Food and Drug Administration recently reported that 13.5 million kilograms (29.8 million pounds) of antibiotics were sold for use in domestic animals in 2011, compared to 3.3 million kilograms (7.3 million pounds) for treatment of human illness. These antibiotics are used to increase growth rates in animals and to decrease pathogen load at slaughter; however, their use for growth promotion and prophylaxis create selective pressures favoring the development and proliferation of antibiotic-resistant pathogens. In this seminar, the ecology of pathogenic microorganisms and antibiotic resistant genes in in agroecosystems, animals, and food products will be presented. Challenges and opportunities for their control will be discussed with specific examples from our research projects near concentrated animal feeding operations across the U.S.
Professors Shane Rogers and Costel Darie
Friday, April 11, 2014
Cholesterol is a ubiquitous component of almost all cellular membranes in higher eukaryotes; it drives lipid "raft" formation and modulates membrane fluidity, thereby impacting the spatial organization and activity of membrane-bound receptors, enzymes, transporters, and ion channels. It also covalently modifies the hedgehog family of morphogenic proteins, and is an obligate precursor for bile acids and steroid hormones. Hence, defective cholesterol biosynthesis can lead to disruption of cellular and systemic physiology, resulting in profound pathologies. Merely providing exogenous cholesterol does not effectively ameliorate these pathologies. Dr. Fliesler's lab has shown that inhibiting the last step in cholesterol synthesis in an animal model causes a progressive and irreversible retinal degeneration. However, the molecular mechanism underlying this degeneration is complex, involving marked lipidomic, proteomic, and genomic changes. Lipid and protein oxidation, as well as oxysterol formation, have been implicated in this retinal degeneration. These findings suggest that blocking such oxidation (with antioxidants) may provide a useful adjunct to cholesterol supplementation as a therapeutic intervention for human patients afflicted with diseases involving defective cholesterol biosynthesis.
Professor Steven Fliesler of SUNY Buffalo and Professor Costel Darie of Clarkson University (right).
Friday, April 11, 2014
With increased awareness of nutrition and the advocacy for healthier food choices, there is need for a simple, easy-to-use test that the general population can reliably use to measure the quality and content of foods. Current methods used for analysis are laboratory-confined, expensive and require extensive training for use, highlighting the demand for more accessible technology.
This presentation will discuss fabrication and performance evaluation of a novel paper-based assay, created to address this challenge. This portable assay is intended for field detection, with focus on food-antioxidants. The method introduces a novel concept in the sensing arena that relies on the use of redox active inorganic nanoparticles, primarily cerium oxide, as colorimetric probes to replace commonly used soluble dyes. The sensors have an integrated detection mechanism with all the reagents needed for analysis confined to the sensing platform. We demonstrate the above principles for the construction of sensors for detection of analytes such as hydrogen peroxide, glucose, and polyphenolic antioxidants. The presentation will describe functionality of the assay in real samples including tea infusions, botanical extracts, and human serum.
The results of this work have opened up new opportunities for designing portable easy-to-use sensors for on-site analysis. The developed assays are particularly appealing for remote sensing applications where specialized equipment is not available. Additional advantages of the newly designed system include stability, low production cost, rapid analysis time, and the ability to provide quantitative information without use of advanced instrumentation.
Professor Silvana Andreescu with graduate student Erica Sharpe.
Monday, April 7, 2014
Diversity of engineered nanoparticles (NPs) and their contribution to the development of technology and industry are remarkable. While NPs have enabled important technological advances, they might also have adverse impacts on human health and environment. Current in vitro nanotoxicity studies do not predict the physiological response of intact organisms. Therefore, novel detection techniques are needed in order to provide better understanding on how NPs interact with living organisms.
This presentation will describe fabrication, characterization and in vivo use of electrochemical microsensors for the detection of physiological changes of serotonin (5-HT) and nitric oxide (NO) and the use of these probes for investigating mechanisms related to nanotoxicity in zebrafish embryos. Electrochemical probes, combined with conventional toxicological assays, have been used to obtain mechanistic information on the nanotoxic response including oxidative stress, inflammation and organ dysfunction in intact zebrafish embryos exposed to several types of NPs.
Experimental work demonstrates that electrochemical microsensors have real-time in vivo measurement capabilities of various markers for nanotoxicity assessment with high sensitivity and selectivity while providing high spatial and temporal resolution. Results show evidence that environmental exposure to NPs affect the physiology of the developing intestine in characteristic ways depending on the type, composition, exposure time and concentration of NPs. This method can be used to predict long term physiological effects of NPs on living organisms.
From Left: Professor Kenneth Wallace, graduate student Rıfat Emrah Özel and Professor Silvana Andreescu.
Friday, April 4, 2014
Metal and semiconductor nanoparticles exhibit unique size-dependent optical properties compared to the bulk materials. In assembled metal nanoparticle clusters and metal-quantum dots complexes, the optical interaction between the nanoparticles lead to new phenomenon that are determined by the geometry and spectral overlap of the complexes. For example, the localized surface plasmon resonance (LSPR) of metal nanoparticles is sensitive to molecules/nanoparticles in the proximity. Specifically, plasmonic coupling in random arrays of gold nanoparticles results in blue-shifted and narrower line-width than that of single gold nanoparticles. At the single particle/cluster level, we perform correlated single particle spectroscopy and electron microscopy, in order to understand the relationship between structures of the nanoparticles and the optical properties. For Ag nanosphere dimers and trimers, the LSPR spectra significantly differ from that of the single Ag nanospheres. The additional peaks in the LSPR spectra of Ag nanosphere dimers and trimers are attributed to the coupling between the nanoparticles and they depend on the polarization of the incident light. In the case when quantum dots adsorb onto single metal nanoparticles, the LSPR spectra of the nanocomplexes shifts in wavelength and changes in the lineshape compared to single metal nanoparticles. The strong exciton-plasmon interaction results in dips in the LSPR lineshape of the nanocomplexes.
Professor Jing Zhao of University of Connecticut and Paul Goulet of Clarkson University (right).
Wednesday, April 2, 2014
Prof. Milan N. Stojanovic
Department of Medicine, Columbia University
This presentation will focus on two topics: Oligonucleotide-based devices for analysis of cell surfaces, and oligonucleotide-based sensors for low-epitope targets. For the former, antibody-oligonucleotide conjugates that form reaction cascades on cell surfaces will be presented, and we describe how the outcomes of these cascades depend on types of cells. For the latter topic, an approach to isolate high-affinity aptamers for traditionally challenging targets will be surveyed, and we then describe how this progress may impact clinical chemistry.
Friday, March 28, 2014
Carbon nanotubes, graphene, and other manmade nanoparticles are in the news, but they are costly and hard to produce reproducibly. Biological materials, such as polysaccharides are abundant and cheap. Polysaccharide nanostructures play essential roles in living organisms, where they enable the complex architectures and mechanical performance of plant cell walls, arthropod exoskeletons, and insect wings. They also serve as templates for diverse inorganic-organic composites such as the iridescent inner shell of shellfish.
It is possible to obtain both cellulose, a glucose polymer, and chitin, a 2-acetamido glucose polymer, as nanoparticles for both our own applications as well as to explore the potential for biomimicry of their natural occurring nanocomposites. Finally, we will discuss the possibilities for production, modification, and potential commercial use of these diverse, sustainable materials.
Dr. William Winter, Professor of Chemistry and Director of the Cellulose Research Institute, SUNY College of Environmental Science and Forestry, Syracuse, NY
Friday, March 14, 2014
Poly-3-hydroxyalkanoates (PHAs) are biodegradable polyesters produced by some bacteria as a carbon and energy from renewable resources. PHAs have attracted great interest as environmentally friendly replacements of petroleum-based plastics and have potential applications as bulk-commodity plastics and biomaterials for biomedical use. The physical properties of PHA polymers are dictated by their repeating unit composition and can be divided into three main classes: short-chain-length (SCL) PHA polymers are made up of repeating units of 3-5 carbons and exhibit thermoplastic properties, medium-chain-length (MCL) PHA polymers are made up of repeating units of 6-14 carbons and exhibit elastomeric properties and SCL-MCL PHA copolymers that exhibit a range of physical properties dependent on the mol ratio of SCL to MCL repeating units in the polymer. Our lab is interested in understanding what metabolic pathways in bacteria are used to generate PHA polymers. In this presentation, I will discuss some of the new pathways and methods we have designed to produce PHAs in bacteria.
Professor Christopher T. Nomura from the Department of Chemistry, Center for Applied Microbiology, The State University of New York College of Environmental Science and Forestry (SUNY-ESF).
Friday, March 7, 2014
will speak on“Functional Crystalline Solid-State Materials: Carbon Capture and More”
Metal-organic frameworks (MOFs) are crystalline porous materials built from metal clusters connected by polytopic organic linkers. An important feature of MOFs is that their framework structures, pore environment and functionality can be finely controlled by the choice and connection of inorganic and organic building blocks. Many efforts have been made to tailor their properties to specialized applications, such as carbon capture and hydrogen storage. In our own research we are focused on the synthesis and characterization of new MOF materials based on compact nitrogen-rich ligands as well as zwitterionic ligands. These ligands have been found to be excellent bridging linkers for the formation of coordination compounds exhibiting a great structural diversity and interesting adsorption properties. Upon exposure to external non-ambient stimuli, such as temperature or pressure, some of these compounds show reversible phase transitions which are accompanied by a dramatic change in their physical properties. This presentation will focus on the fundamental understanding in the exciting structure-property relationships of new MOF materials by analyzing their structural changes upon phase transition.
Professor Mario Wriedt
Friday, February 28, 2014
will speak on“Investigating New Methods for Bioconjugation”
A rapidly expanding area of R&D in the biotechnology and pharmaceutical sectors is bioconjugation which encompasses the covalent modification of a protein or other biomolecule. While many protocols exist for these purposes, current methods for the covalent derivatization of proteins lack site selectivity and quantitative control of modifications. Due to the wide variety of applications, advancements in the area of bioconjugation have a significant impact in both academic and industry settings. This seminar will outline two projects investigating new methods for bioconjugation.
The first method examines the use of bioorthogonal click-chemistry as means for protein modification while also offering some unique advantages for product characterization. Tetrazoles undergo a photoinduced 1,3-dipolar cycloaddition reaction with alkenes which can be used as a means of bioconjugation. It is hypothesized that by measuring the fluorescence intensity of the pyrazoline cycloadducts formed during each successful conjugation reaction, the average number of modifications per protein can rapidly be estimated.
The second method utilizes ligands capable of forming a complex with the hexahistidine tag on any recombinant protein. The well-known coordination chemistry of hexahistidine tags is used to form a macrocylic complex serving as a template for subsequent alkylation of one histidine residue of the hexahistidine tag in the protein. These ligands contain Baylis-Hillman esters which are selectively reactive with the imidazole side chains of the hexahistidine tag. The alkylating ligands can then be easily removed through treatment of the solution with EDTA. This system allows for control of modification site and number of modifications.
Professor Artem Melman with graduate student Nicholas Letourneau.
Friday, February 7, 2014
will speak on“Novel oxynitride compounds from cellulose biotemplates”
High energy demands and climate change require alternative sources to fuels. With sunlight in great abundance, most agree that this primary fuel source needs to be harvested and converted into a useful and storable form of energy. Latching onto evolutionary design as an inspiration, the opportunity to mimic nature cannot be disregarded. From novel architectures to energy conversion pathways, nature has found a way to thrive off of sunlight as a primary energy source and serves as a model for the development of synthetic methods towards three-dimensional inorganic architectures using natural materials. These compounds find applications as semiconductor catalysts for water-splitting reactions as well as in the catalysis of dyes and environmental VOCs. Inorganic three-dimensional replicas from cellulose can be produced by infiltration with transition metal-rare earth compounds, leading to an photocatalytic replica structure.
Professor Mario Wriedt of Chemistry and Biomolecular Science (right) and Professor Neal Abrams from the Department of Chemistry, SUNY College of Environmental Science and Forestry (ESF).
will speak on
"Synthesis and Application of Core-shell Structured Particles"
Engineering of particles has attracted a lot of interest because the application of particles greatly depends on their composition, structure and surface chemistry. One of the most popular strategies is fabrication of core-shell structured particles. In this thesis two types of core-shell particles were synthesized and applied in shallow trench isolation (STI) chemical mechanical planarization (CMP) and direct thermal paper for printing.
In STI CMP application commonly used ceria particles were replaced by polymer core-ceria shell particles to achieve tailored properties. Different polymeric core particles e.g. poly(styrene-methyl methacrylate) were synthesized by emulsion polymerization and coated with a layer of ceria particles by self-assembly method. The mechanism of synthesizing polymer core-ceria shell particles was proposed and the CMP results showed the correlation between the composition of particles and the CMP removal rate and surface quality.
In direct thermal paper application core-shell polymeric particles were synthesized using multi-stage emulsion polymerization. Different polymeric core particles e.g. poly(methyl methacrylate-methyl methacrylic acid) were synthesized and coated with a variety of polymeric shell materials such as polystyrene by seeded emulsion polymerization. The mechanism of synthesizing polymeric core-shell particles was proposed and the effect of parameters e.g. feeding rate of emulsion and temperature on the morphology of the resultant particles was discussed. The synthesized core-shell particles were treated (with ammonium hydroxide to form water-filled encapsules), formulated, and coated onto substrates to form an opaque film (thermal paper). The size, morphology, and composition of the core-shell particles were optimized and the fabricated film showed an excellent whiteness and thermal sensitivity resulting in a promising commercializable product.
will speak on“The Hunt for Autism Biomarkers”
Autism spectrum disorders (ASD) have had a dramatic rise in incidence in the United States and Canada in the last several decades, and the causation remains unknown. Especially in the past decade, increased efforts have been dedicated to searching for molecular markers which might prove of diagnostic value for the diagnosis of ASD and furthermore provide insight into the mechanisms which may be at play in the etiology of ASD. This seminar will focus on our efforts over the past decade to detect blood and especially urinary markers of ASD. Early discoveries in our lab shaped the direction of our research today, moving from gluten exorphin peptides as a class of potential biomarkers to the metabolite stercobilin. Since stercobilin is abundant in human waste (urine and feces) it is not only an attractive biomarker target for ASD, but it is also evidence of waste elimination in water, and we will also describe recent efforts to detect stercobilin in public pools. Recent efforts have focused on glutathione as a urinary biomarker of ASD, in particular its interaction with mercury(II) ions. Our studies have used a variety of mass spectrometry platforms in order to take advantage of the high sensitivity and structural elucidation capabilities of modern mass spectrometers.
Professor Costel Darie of Chemistry and Biomolecular Science (left) and Professor Troy Wood from the Department of Chemistry, University at Buffalo.
will speak on“A Systems Biology Approach to Building a Skeletogenic Gene Regulatory Network (GRN)”
Our research is in the novel area of Regenerative Medicine and Stem Cell Biology with a focus on the molecular mechanisms controlling vertebral column development and an emphasis on early embryogenesis and embryonic stem cell commitment to specific differentiation pathways, but from a novel Systems Biology point of view. We are committed to understanding how the vertebral column degenerates with aging, and how this process can be reversed using stem cell based approaches. In particular we are working on understanding the gene regulatory networks (GRNs) that govern normal embryonic development of the vertebral column and intervertebral disc (IVD). We are investigating the role of transcriptional regulators in the restriction of pluripotent embryonic stem cells into specific lineages that in turn comprise functional pre and postnatal vertebral elements with the goal of applying this knowledge in regenerative medicine using patient-specific induced pluripotent stem (iPS) cells and adult mesenchymal stem cells.
Professor Thomas Lufkin, Bayard and Virginia Clarkson Endowed Chair in Biology, Clarkson University.
will speak on“Photoresponsive alginate gels"
Being chemically inert, biocompatible and easy to prepare, calcium alginate hydrogels are widely used as scaffold for tissue engineering, enzyme encapsulation or as responsive materials. The major problem of this type of alginate gel is the fabrication and patterning of calcium alginate for entrapping the cells but also for their release without total degradation of the surface.
In order to do it, iron cross-linked alginate gel can be used. Iron(III) cations strongly bind carboxylate groups and produce highly stable gels. To obtain homogeneous iron alginate gels, Fe2+, a soft cation, is added to a solution of sodium alginate followed by its oxidation by air into “hard” Fe3+ cation thus creating a hydrogel by cross-linking.
We also found that the opposite process of reduction of Fe3+ to Fe2+ can be done photochemically using different α-hydroxycarboxylic as sacrificial photoreductants. This allowed us to use Fe3+ alginate hydrogels as biocompatible photoresist. This method can be further used for production of other ionically cross-linked patterned homogeneous hydrogels through the process of reductive ion exchange.
Professor Artem Melman with graduate student Marion Bruchet.