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Fall 2014 Seminar

In this Section

Friday, October 31, 2014

3:30 p.m.
214 B. H. Snell Hall

Dr. Jan Halámek

Department of Chemistry

SUNY, University at Albany

 

will speak on

 

“Newly emerged concept of forensic analysis – bioaffinity-based detection architectures”

 

Abstract:

The field of forensic science has been progressing rather rapidly in the recent years, but the new developments have been largely reliant on studying the contents of common biological samples like the DNA in blood. It is sometimes overlooked, but much more information can be obtained from the samples. For instance, blood is not only a good source of information because of its DNA content, but the composition of proteins and low molecular compounds can also be useful in that it can indicate important personal information about the blood donor. Another often understudied piece of evidence is in the area of latent fingerprints. Currently fingerprints are only good for making a visual comparison, but its potential as evidence is generally overlooked. Latent fingerprints are not just unique patterns; they have a layer of sebum that contains compounds that can be studied and analyzed to acquire personal information about the fingerprint originator.

 By utilizing versatile and re-programmable bioaffinity-based cascades, the evaluation/analysis of blood stains and fingerprints would become a quick and straightforward process that can be easily executed and interpreted by any and all members of law enforcement.  Furthermore, the assays and cascades presented here re merely examples; this approach is in no way limited to only fingerprints and blood or to identifying physical attributes.  This basic concept can be applied to many different markers and can be used for the discernment of many characteristics.

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Friday, October 24, 2014

3:30 p.m.
214 B. H. Snell Hall

Dr. Charles Campana

Senior Scientist
Bruker, Madison, Wisconsin
 
 
will speak on
"An Overview of Single-Crystal X-Ray Diffraction as a Tool for Chemists"
 

Abstract:

Single-crystal X-ray diffraction, commonly referred to as X-ray crystallography, is an analytical technique in which X-ray methods are employed to determine with certainty the actual arrangement of atoms within a crystalline specimen. X-ray crystallographic structure determination can be applied to a wide range of sizes of structures, from very small molecules and simple salts, to complex minerals, synthetically prepared inorganic and organometallic complexes, natural products and biological macromolecules, such as proteins and even viruses. The precise knowledge of the molecular geometry is important in nearly all fields of chemical and biological research.  Many of the most significant advances in structural chemistry and structural biology are based upon results obtained from X-ray crystallographic analyses.  X-ray crystallography is uniquely capable of unambiguously determining the complete three-dimensional molecular structures (including the absolute stereochemistry) of chemical substances.  Modern X-ray crystallographic data permits routine location and refinement of solvent molecules and hydrogen atoms. This seminar is an introductory overview of the theoretical and instrumental aspects of this important technique.

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Friday, October 17, 2014

3:30 p.m.
214 B. H. Snell Hall
 
 

Sapan Patel
Department of Chemistry & Biomolecular Science
Clarkson University
 
 
will speak on
 
"Defective quorum sensing in Ph+ Acute Lymphoblastic Leukemia and identification of diffusible factors secreted by cells growing at high cell density"
 
 

Abstract:

Quorum sensing (QS) is a generic term describing cell-cell communication and collective decision making by bacteria and social insects to regulate expression of specific genes controlling cell density and other properties in response to changes in nutrient supply or environment. QS also has a role in higher organisms in maintaining homeostasis, regulation of the immune system and behavior of cancer cell populations. CML is a classic example of a tumor, which without effective therapy consistently undergoes malignant progression, replacing the chronic phase (CP) cells with undifferentiated blast cells. Like most other types of acute leukemia including Ph+ ALL, the CML blasts proliferate slower than either normal or CP CML stem/progenitor (S/P) cells and individual blasts have greatly reduced proliferative potential and cloning ability suggesting the leukemic blasts achieve dominance by functioning as an aberrant ecosystem subject to different regulatory mechanisms than normal or CP CML S/P cells. To see if QS is involved we selected a p190 bcr-abl driven pre-B cell line (ALL3) derived from the pleural fluid of a patient dying of Ph+ ALL. Unlike other established human or murine Bcr-Abl driven lines, ALL3 cells don't form colonies or grow at low cell densities (LD) but grow progressively faster at increasing densities (HD). ALL3 cells at HD in upper inserts of transwells stimulate growth of LD ALL3 cells in lower wells and LD ALL3 are also stimulated to grow by diffusible factors in the supernate (SN) of HD cells. Our first objective is to identify the stimulatory protein(s) in the secretomes of HD ALL3 and other cells. The HD SN is stable upon storage at 4°C or -80°C with no loss of activity. We are currently working to identify and characterize the stimulatory factors and the novel pathways and regulatory mechanisms involved. Our ultimate goal is to define the aberrant circuitries and find vulnerable targets for specific therapies of leukemias and other cancers.

chem seminar

From Right: Dr. Bayard D. Clarkson, Sapan Patel and Dr. Costel Darie

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Friday, October 10, 2014

3:30 p.m.
214 B. H. Snell Hall

Prof. Danielle Benoit
Research Scientist
Departments of Biomedical Engineering & Chemical Engineering
University of Rochester
 
will speak on
"Nanostructured polymers for targeted and responsive drug delivery"
 

Abstract:

The Therapeutic Biomaterials Laboratory at the University of Rochester focuses on the design of nanostructured polymers for tissue regeneration and drug delivery. In our drug delivery approaches, we are exploiting polymers formed using reversible-addition fragmentation chain transfer polymerizations (RAFT), a controlled, living polymerization strategy, to improve delivery of a variety of therapeutics. We employ bottom-up approaches to design polymer therapeutics to overcome delivery barriers via novel targeting and responsive delivery systems. Polymer therapeutics have numerous advantages for drug delivery, providing higher plasma drug concentrations, longer circulation half-lives, higher (up to 50-fold) concentrations of drug within target tissues than drug alone, enhanced stability of therapeutic molecules, reduced immunogenicity, and improved drug solubility properties. My talk will focus on synthetic methods utilized to develop targeted and responsive polymer therapeutics, as well as demonstration of biological efficacy in vitro and in vivo. Specifically, I will discuss two polymer therapeutic strategies: (1) a novel targeting approach to selectively deliver drugs to actively remodeling bone for the treatment of bone metabolic diseases, and (2) development of pH-responsive nanoparticle carriers (NPC) to treat oral biofilms.

Chemistry Seminar

Professors Danielle Benoit and Devon Shipp (left)

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Friday, October 3, 2014

3:30 p.m.
214 B. H. Snell Hall

Dr. John E. Pearl
Research Scientist
The Trudeau Institute
Saranac Lake, NY
 
will speak on
"The respiratory basis for anoxic growth by Mycobacterium avium"
 

Abstract:

Nontuberculous Lung Disease (NTM) and Tuberculosis (TB) are lung diseases caused by the bacilli Mycobacterium avium and M. tuberculosis. The interplay between pathogenic mycobacteria and their host is characterized by a complex, dynamic escalation of responses in which both bacterium and host co-adapt. This co-adaptation results in chronic lung disease whose hallmark is an inflammatory or granulomatous lesion. These lesions serve to contain the infection, to isolate surrounding tissue from immune-mediated damage and to create a biochemically hostile environment that restricts the growth of the bacilli.

One important aspect of the host response to mycobacterial infection is an attempt to limit the availability of oxygen to the bacteria. Upon close examination of the bacterial response to oxygen limitation, we have discovered that M. avium has the capacity to grow in the complete absence of oxygen, a previously unknown trait for any slow-growing human-pathogenic mycobacteria. This research in progress seminar will discuss the potential mechanism by which this anoxic growth occurs in the context of bacterial respiration.

chemistry seminar

Drs. John Pearl and Silvana Andreescu (left).

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Friday, September 26, 2014

3:30 p.m.
214 B. H. Snell Hall

Professor Kathleen Arcaro
Professor of Environmental Toxicology
University of Massachusetts-Amherst
 
will speak on
Using Breast Milk to Study the Epigenetic Epidemiology of Breast Cancer: Promise and Challenges
 

Abstract:

Human milk provides non-invasive access to breast tissue, as an ounce of milk may contain millions of exfoliated mammary epithelial cells.  The Arcaro lab studies breast milk in an effort to understand the etiology of breast cancer and to develop approaches to reduce breast cancer risk. 

We have detected increased promoter methylation of tumor suppressor genes in cells isolated from breast milk years before the diagnosis of breast cancer, leading us to conclude that breast milk may provide a tool for assessing breast cancer risk as well for early detection of disease.  Ongoing research is aimed at discovering accurate and sensitive biomarkers (DNA modifications and proteins), that can be used clinically.

chemistry seminar

Professors Kathleen Arcaro and Costel Darie (left).

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Friday, September 19, 2014

3:30 p.m.
214 B. H. Snell Hall

Prof. Dr. Christian Näther
Department of Inorganic Chemistry
Kiel University, Germany
 
will speak on
“A Rational Synthetic Route to 1D and 2D Transition Metal Thio- and Selenocyanato Coordination Polymers that show a Slow Relaxation of the Magnetization”
 

Abstract:

Recently, investigations on the synthesis of new magnetic materials like e.g. single chain magnets (SCMs) have become of increasing interest. This behavior was already predicted by Glauber in 1963 but experimentally proven for the first time by Caneschi et al. in 2001. Such compounds show a slow relaxation of the magnetization below the so-called blocking temperature and therefore, are able to store a magnetic moment permanently. Consequently, such materials have some potential for future applications in ultra-high density storage.

In the beginning of this lecture a short historical overview is given on our recent investigations, where a rational solid state route for the selective synthesis of 1D and 2D coordination polymers was developed. Following these ideas a 1D transition metal thiocyanato coordination polymer was prepared that shows single chain magnetic behavior. After a short introduction into the basics of magnetism and the analysis of SCM behavior, investigations on the influence of a chemical and structural modification on those parameters are presented, that describe the performance of such materials. These investigations indicate that a class of compounds was discovered, in which all components - the metal cations, the anionic ligands and the neutral co-ligands - can be exchanged to some extend without losing this behavior. Investigations that allow a deeper insight into this rare magnetic phenomenon and that might be helpful for an optimization of such materials.

chemistry Seminar

 Professors Christian Näther and Mario Wriedt (left).

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Friday, September 12, 2014

3:30 p.m.
214 B. H. Snell Hall

Dr. Eric C. Tyo
Material Science Division
Argonne National Laboratory
Lemont, Illinois
 
will speak on
“Developing Insights into Catalytic Processes Through in-situ Studies: Investigations of Size Selected Clusters and Solution Synthesized Nanoparticles”
 

Abstract:

To develop catalytic processes with higher selectivity and activity, fundamental insights need to be gained into the active site specific mechanisms occurring. The most effective way of gathering such insights is by performing in-situ studies of well-defined systems. Soft-landed, size and composition selected subnanometer Ag clusters are active for the selective partial oxidation of propylene at relatively low temperatures. Temperature programmed reactivity (TPRx) was performed with in-situ synchrotron X-ray characterization, Grazing Incidence Small Angle X-ray Scattering (GISAXS) and X-ray Absorption Spectroscopy (XAS), to determine structural morphology and oxidation state during catalytic activity. Au doped Co3O4 nanoparticles are also investigated, in a similar method, for the oxidative dehydrogenation of cyclohexane. Significant influence in catalytic activity is observed due to the particle size and doping of Au. These investigations illustrate the power of in-situ studies towards developing the fundamental understanding necessary for the directed design of next generation catalysts.

chemistry seminar

 Dr. Eric C. Tyo and Clarkson University Professor Jim Peploski (left).

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Friday, September 5, 2014

3:30 p.m.
214 B. H. Snell Hall

Dinusha Karunaratne
Clarkson University
 
will speak on
"Linear polyamines with variable chain lengths for Cu CMP"
 

Abstract:

Chemical mechanical polishing (CMP) is the most effective wafer planarization method known today in the semiconductor industry. Cu-CMP is one broad and important area in CMP. Significant part of the research on Cu-CMP involves the improvement of slurry composition, a key factor affecting the outcome of the polishing process. The introduction of copper (Cu) as interconnect material has allowed a significant reduction in the dimensions of the conductive tracks and a much improved usage of the real estate on the surface of wafers. Cu-CMP is largely chemically driven and the chemical properties of copper have brought new challenges in optimizing slurry composition. Chelating agents play a significant role in Cu-CMP by controlling material removal rates (MRR). They can act either as complexing that improve the dissolution of the abraded copper and copper oxides (existing or formed in situ) or passivating agents that interact with the surface of copper and stabilizes the zero valent metal. A proper balance between these two compounds/functions is essential for achieving an optimum polishing process that provides an acceptable MRR (in the presence of mechanical abrasion) but lowers the static etch rates (in the absence of mechanical abrasion).

Glycine and Benzotriazole (BTA) are the most commonly used pair of complexing and passivating agents in Cu CMP. In a typical glycine/ peroxide based - slurry, BTA offers an excellent corrosion inhibition, however, this Cu-BTA complexation becomes problematic at extreme pH conditions and during post CMP cleaning steps. This study evaluates the homologous linear polyamines as a potential replacement for the typical Glycine/BTA combination. The research was triggered by the hypothesis that amines with variable chain length form complexes of different stability with copper ions in the liquid phase (a measure of the complexing efficiency) and interact at different extent with the Cu substrate (a measure of the passivating ability). The preliminary experimental findings show that their chelation ability spreads over a wide range and the passivating efficiency increases with the increasing chain length of polyamine. 

Chemistry Seminar

Professor Dan Goia with graduate student Dinusha Karunaratne.

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Friday, August 29, 2014

3:30 p.m.
214 B. H. Snell Hall

Xiaobo Liu
Clarkson University
 
 
will speak on
"Electrochemical investigation of antibiotics-induced oxidative stress and superoxide release in bacteria"
 

Abstract:

Oxidative stress is a redox disequilibrium state. In this physiological state, the generation of reactive oxygen species (ROS) overwhelms the limitation of antioxidant defense in a cell. The presence of excessive ROS is plausible to be used as an indicator of the oxidative stress response and damage. It has been demonstrated in recent studies that oxidative stress and ROS are involved in antibiotics-meditated cell death. However, the kinetic profile and a quantitative relationship between ROS release, bacteria and antibiotic type have not been discussed. Here we report employing an electrochemical biosensor to detect and quantify superoxide radicals, one important species of ROS, in antibiotics-treated bacterial cultures. The results are used to determine the involvement of oxidative stress in the antimicrobial activity of antibiotics against different bacterial strains. Conventional colony forming unit (CFU) and fluorescence-based methods are used to address antibiotic lethality and oxidative stress status, also to further consolidate the electrochemical biosensor results. The study provides a quantitative methodology and fundamental knowledge to further explore the role of oxidative stress in antibiotics-meditated bacterial death and assess physiological changes associated with oxidative stress and bacterial resistance. The strategy also can be used for monitoring the molecular mechanism and physiological status in other biological systems and stress conditions. Examples of such applications will be discussed.

Chemistry Seminar

Professor Silvana Andreescu with graduate student Xiaobo Liu.

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Summer  2014 Seminar

Department of Chemistry & Biomolecular Science & the Center for Advanced Materials Processing 

Joint Seminar

Tuesday, July1, 2014

10:00 AM
214 B.H. Snell Hall

Dr. István Szilágyi
aboratory of Colloid and Surface Chemistry, University of Geneva, Geneva, Switzerland
 
will speak on
" STABILIZATION MECHANISM OF COLLOIDAL PARTICLES IN MOLTEN SALTS "
 

Abstract:

Ionic liquids (ILs) are molten salts and they are composed entirely of ions. Although their synthesis and thermodynamic properties have been extensively studied in the past by several experimental and theoretical methods, these research activities were concentrated on the bulk properties. Despite the predictable importance of ILs in heterogeneous systems, the first studies dealing with interactions between solid surfaces across ILs have been published only recently.  Particle suspensions in ILs represent an important class of systems and they are particularly relevant in sensor development, solar cells, catalysis and electrochemistry. These applications require particle dispersions in ILs with controllable aggregation processes. The present work aims to characterize aggregation of colloidal and nano-sized particles suspended in ILs using light scattering techniques. Polystyrene latex particles were used and ILs contained imidazolium, pyridinium and pyrrolidinium derivatives as cations as well as tetrafluoroborate, dicyanamide and thiocyanate anions.

The particle aggregation can proceed very quickly or slowly, depending on the particle concentration and on the value of the aggregation rate coefficient. In water-IL mixtures, the rate coefficients were found to vary substantially in a characteristic fashion. At low IL concentration, one observes very slow aggregation and the aggregation become fast as the IL content increases.  This behavior is similar to simple salts and can be qualitatively rationalized with the classical theory developed by Derjaguin, Landau, Verwey and Overbeek (DLVO). At very high IL concentration, the aggregation may proceed again very slowly. As a consequence, one can formulate very stable colloidal suspensions in ILs. We identified two generic mechanisms that are responsible for this stabilization. Viscous stabilization mechanism is the most important in highly viscous ILs and originates from the slowdown of the diffusion controlled aggregation rate due to slower diffusion in a viscous liquid. Solvation stabilization mechanism is system specific, but can lead to a dramatic slowdown of the aggregation rate in ILs. This mechanism is probably related to repulsive solvation forces that are operational in ILs due to strong layering close to the surfaces. These two stabilization mechanisms are suspected to be generic, as they were operational in different ILs, for particles differing in surface functionalities and their size. While the present data set is limited and might be influenced by impurities of the ILs, any firm conclusions on specific ion effects are premature. Nevertheless, we suspect that in ILs containing tetrafluoroborate anions the principal mechanism is viscous stabilization and solvation stabilization will be absent, unless the IL is extremely dry. On the other hand, ILs containing dicyanamide or thiocyanate anions tend to stabilize suspensions by both mechanisms. The solvation stabilization can be already operational in ILs containing up to 10% of water by mass.

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Thursday, May 29, 2014

10:00 AM
372 CAMP 

Miao Yang
Clarkson University
 
M.S. Defense
 
will speak on
"Filamentous Supramolecular Peptide-Drug Conjugates as Highly Efficient Drug Delivery Vehicles"
 

Abstract:

Control over drug loading, composition and overall morphology of drug delivery vehicles is crucial for their proper function in chemotherapy. In this thesis, we developed a facile approach to prepare filamentous nanocarriers which have all the desired properties as ideal therapeutics delivery vehicles, such as high drug density and serum stability, precisely controlled drug loading capacity, nearly 100% loading efficiency and well-defined nanostructure. The supramolecular scaffold is based on de novo designed multidomain peptides (MDPs) which form short, soluble nanofibers through the balance of multiple attractive intermolecular forces and electrostatic repulsions. Current work demonstrated that these supramolecular polymers can be used as scaffolds to append hydrophobic anticancer drugs without severely affecting the size and morphology of the nanofibers. Our new design provides an alternative strategy to assemble drugs at more solvent accessible sites on a filamentous supramolecular polymer. Such architecture could allow for rapid release of therapeutics from the delivery vehicles without overcoming significant steric hindrance and diffusion barrier upon the application of specific stimuli. We will demonstrate that the overall nanostructure of the assembly is largely dictated by the peptide-peptide interactions, rather than the physical and chemical property of the therapeutic agents used in the study. To certain extent, this will help alleviate the concern of batch-to-batch structural variation during pharmaceutical formulation where drug-drug interactions are important factors in terms of structural and chemical composition control.

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Spring  2014 Seminar

Friday, May 2, 2014

3:30 p.m.
212 B. H. Snell Hall

Miao Yang
Clarkson University
 
 
will speak on
"Filamentous Supramolecular Peptide-Drug Conjugates as Highly Efficient Drug Delivery Vehicles"
 

Abstract:

Control over drug loading, composition and overall morphology of drug delivery vehicles is crucial for their proper function in chemotherapy. In this seminar, I will present a facile approach to prepare filamentous nanocarriers which have all the desired properties as ideal therapeutics delivery vehicles, such as high drug density and serum stability, precisely controlled drug loading capacity, nearly 100% loading efficiency and well-defined nanostructure. The supramolecular scaffold is based on de novo designed multidomain peptides (MDPs) which form short, soluble nanofibers through the balance of multiple attractive intermolecular forces and electrostatic repulsions. Current work demonstrated that these supramolecular polymers can be used as scaffolds to append hydrophobic anticancer drugs without severely affecting the size and morphology of the nanofibers. Our new design provides an alternative strategy to assemble drugs at more solvent accessible sites on a filamentous supramolecular polymer. Such architecture could allow for rapid release of therapeutics from the delivery vehicles without overcoming significant steric hindrance and diffusion barrier upon the application of specific stimuli. We will demonstrate that the overall nanostructure of the assembly is largely dictated by the peptide-peptide interactions, rather than the physical and chemical property of the therapeutic agents used in the study. To certain extent, this will help alleviate the concern of batch-to-batch structural variation during pharmaceutical formulation where drug-drug interactions are important factors in terms of structural and chemical composition control.

Chemistry Seminar

Professor Dong with graduate student Miao Yang.

__________________

Friday, April 25, 2014

3:30 p.m.
212 B. H. Snell Hall

Dr. Leesa Deterding
Associate Scientist
National Institute of Environmental Health Services
Research Triangle Park, NC
 
will speak on
"Quantitation using Mass-Spectrometry"
 

Abstract:

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.

chemistry seminar

 Dr. Leesa Deterding (Associate Scientist, National Institute of Environmental Health Services) and Clarkson University Professor Costel Darie (right).

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Friday, April 25, 2014

9:30 – 10:30am
213 B. H. Snell Hall

Matt Neal
Clarkson University
 
 
will speak on
"Formation of Thin Latex Films Using Magnetic Nanoparticles as Transport Agents: A Preliminary Study"
 

Abstract:

Latex films can be found in a multitude of applications, from paints and adhesives, to pharmaceuticals and biosensors. As the use of smaller and smaller biosensors continues to grow, it is necessary to provide a stable, chemically inert backbone onto which these sensors can be built. Additionally, the use of on-skin biosensors is becoming more prevalent, meaning that the supporting structure of the biosensors must also have some degree of flexibility. Thin latex films possess these properties, making them excellent candidates for use as supporting structures for on-skin biosensors. This seminar will cover preliminary results in the creation of thin latex films in aqueous environments using magnetic nanoparticles as the transport agents, as well as discuss future directions and applications for these films.

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Friday, April 18, 2014

3:30 p.m.
212 B. H. Snell Hall

Professor Shane Rogers
Departments of Civil & Environmental Engineering
Clarkson University
 
will speak on
"Agricultural Intensification and the Emergence of Water- and Food-borne Infectious Disease: Challenges and Opportunities for Disease Prevention and Mitigation of Antimicrobial Resistance"
 

Abstract:

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.

chemistry seminar

Professors Shane Rogers and Costel Darie

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Friday, April 11, 2014

3:30 p.m.
212 B. H. Snell Hall

Professor Steven Fliesler
Departments of Ophthalmology and Biochemistry
University at Buffalo/State University of New York;
SUNY Eye Institute; and VA Western NY Healthcare System
 
will speak on
"The Ring Trilogy:  Sterols, Membranes, and Retinal Degeneration."
 

Abstract:

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.

Chemistry Seminar

Professor Steven Fliesler of SUNY Buffalo and Professor Costel Darie of Clarkson University (right).

______________________
PhD Defense

Friday, April 11, 2014

10:00 a.m.
New Snell 169

Erica Marie Sharpe
PhD Candidate, Clarkson University
 
 
will speak on
“NANOPARTICLE-BASED PAPER SENSORS FOR FIELD-PORTABLE ANALYSIS OF ANTIOXIDANTS”
 

Abstract:

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.

Chemistry Seminar

Professor Silvana Andreescu with graduate student Erica Sharpe.

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PhD Defense

Monday, April 7, 2014

10:00 a.m.
Petersen Boardroom (Snell 330)

Rıfat Emrah Özel
PhD Candidate, Clarkson University
 
 
will speak on
“ELECTROCHEMICAL ASSESSMENT OF NANOPARTICLE-INDUCED ORGAN DYSFUNCTION AND OXIDATIVE STRESS’”
 

Abstract:

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.

Chemistry Seminar 

From Left: Professor Kenneth Wallace, graduate student Rıfat Emrah Özel and Professor Silvana Andreescu.

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Friday, April 4, 2014

3:30 p.m.
212 B. H. Snell Hall

Dr. Jing Zhao
University of Connecticut
 
 
will speak on
“Optical Interactions in Metal Nanoparticles and Quantum Dot Complexes
 

Abstract:

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.

Chemistry Seminar

Professor Jing Zhao of University of Connecticut and Paul Goulet of Clarkson University (right).

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Department of Chemistry and Biomolecular Science
and
Department of Physics

Clarkson University

Joint Colloquium

Wednesday, April 2, 2014

3:30 p.m.
Science Center (Lecture Wing) 166

 

Prof. Milan N. Stojanovic
Division of Clinical Pharmacology and Experimental Therapeutics
Department of Medicine, Columbia University
 
 
will speak on
“Progress in Oligonucleotide-Based Devices”
 

Abstract:

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.

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Friday, March 28, 2014

3:30 p.m.
212 B. H. Snell Hall

Dr. William T. Winter
Professor of Chemistry and Director of the Cellulose Research Institute
SUNY College of Environmental Science and Forestry, Syracuse, NY
 
will speak on
“Nanoparticles from Nature: Cellulose Nanorods and Nanospheres
 

Abstract:

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.

Chemistry Seminar

Dr. William Winter, Professor of Chemistry and Director of the Cellulose Research Institute, SUNY College of Environmental Science and Forestry, Syracuse, NY

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Friday, March 14, 2014

3:30 p.m.
212 B. H. Snell Hall

Dr. Christopher T. Nomura
Department of Chemistry, Center for Applied Microbiology
The State University of New York College of Environmental Science and Forestry (SUNY-ESF)
 
will speak on
“Polyhydroxyalkanoates: versatile biodegradable plastics
 

Abstract:

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.

Chemistry Seminar

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).

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Friday, March 7, 2014

3:30 p.m.
212 B. H. Snell

Dr. Mario Wriedt
Clarkson University
 

will speak on

Functional Crystalline Solid-State Materials: Carbon Capture and More
 

Abstract:

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.

Chemistry Seminar

Professor Mario Wriedt

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Friday, February 28, 2014

3:30 p.m.
212 B. H. Snell

Nicolas Letourneau
Clarkson University
 

will speak on

Investigating New Methods for Bioconjugation
 

Abstract:

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.

Seminar

Professor Artem Melman with graduate student Nicholas Letourneau.

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Friday, February 7, 2014

3:30 p.m.
212 B. H. Snell

Dr. Neal Abrams
Department of Chemistry
SUNY College of Environmental Science and Forestry (ESF)
 

will speak on

“Novel oxynitride compounds from cellulose biotemplates”
 

Abstract:

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.

seminar

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).

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Department of Chemistry & Biomolecular Science
Clarkson University
PhD Defense
 
Thursday, Feb 4, 2014  
8:45 a.m.
CAMP 372

Lifeng Chen
PhD Candidate, Clarkson University

will speak on

"Synthesis and Application of Core-shell Structured Particles"

Abstract:

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.

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Friday, January 31, 2014
3:30 p.m.
212 B. H. Snell

Dr. Troy Wood
Department of Chemistry
University at Buffalo
 

will speak on

“The Hunt for Autism Biomarkers”
 

Abstract:

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.

Chemistry Seminar

Professor Costel Darie of Chemistry and Biomolecular Science (left) and Professor Troy Wood from the Department of Chemistry, University at Buffalo. 

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Friday, January 24, 2014
3:30 p.m.
212 B. H. Snell

Professor Thomas Lufkin
Bayard and Virginia Clarkson Endowed Chair in Biology
Clarkson University
 

will speak on

“A Systems Biology Approach to Building a Skeletogenic Gene Regulatory Network (GRN)”
 

Abstract:

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.

Chemistry Seminar

Professor Thomas Lufkin, Bayard and Virginia Clarkson Endowed Chair in Biology, Clarkson University.

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Friday, January 17, 2014
3:30 p.m.
212 B. H. Snell

Marion Bruchet
Department of Chemistry & Biomolecular Science
Clarkson University

will speak on

Photoresponsive alginate gels"
 

Abstract:

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.

Chemistry Seminar

Professor Artem Melman with graduate student Marion Bruchet.

 

10:00 a.m.

Oxidative stress is a redox disequilibrium state. In this physiological state, the generation of reactive oxygen species (ROS) overwhelms the limitation of antioxidant defense in a cell. The presence of excessive ROS is plausible to be used as an indicator of the oxidative stress response and damage. It has been demonstrated in recent studies that oxidative stress and ROS are involved in antibiotics-meditated cell death. However, the kinetic profile and a quantitative relationship between ROS release, bacteria and antibiotic type have not been discussed. Here we report employing an electrochemical biosensor to detect and quantify superoxide radicals, one important species of ROS, in antibiotics-treated bacterial cultures. The results are used to determine the involvement of oxidative stress in the antimicrobial activity of antibiotics against different bacterial strains. Conventional colony forming unit (CFU) and fluorescence-based methods are used to address antibiotic lethality and oxidative stress status, also to further consolidate the electrochemical biosensor results. The study provides a quantitative methodology and fundamental knowledge to further explore the role of oxidative stress in antibiotics-meditated bacterial death and assess physiological changes associated with oxidative stress and bacterial resistance. The strategy also can be used for monitoring the molecular mechanism and physiological status in other biological systems and stress conditions. Examples of such applications will be discussed.

Prof. Danielle Benoit