Spring 2014 Seminar
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.
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.
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.