SCHOOL OF SCIENCE

View separate schedule for Open House Nights in Astronomy.

St. John's Wort: Take Two Flowers and Call Me in the Morning

November 2, 2007

Hypericum perforatum, commonly known as St. John's Wort, is a popular herbal supplement today in the United States.  This species contains a wide range of compounds of which the biologically active constituent(s) have not been fully elucidated.  Several of the 450 other Hypericum plant species are used a herbal treatments for anti-inflammatory, anti-bacterial, anti-viral, and anti-depressive applications.  The chemical diversity within plants from a single species may explain these multiple medicinal uses.  It has been proposed that biologically active constituents in Hypericum species may be working in concert.

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Secondary Mathematics Education Seminar and Q&A Session

November 28, 2007

The students from Dr. Goodwin's MTHED 411 class will facilitate a high school lesson and then Dr. Goodwin, other faculty and current students will lead a Q&A session about the new Secondary Mathematics Education program here at Behrend.

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Disturbance and Competition:  Forces that Drive Phylloplane Fungal Community Structure and Development

November 30, 2007

The phylloplane, or leaf surface, constitutes a vast terrestrial habitat colonized by numerous (both quantitatively and qualitatively), highly adapted, stress-tolerant microorganisms.  The community structure of these microbes is directly influenced by environmental factors (e.g. temperature, humidity and solar radiation), host factors (e.g. age, leaf position and plant species), competitive and antagonistic interactions, and natural and anthropogenic disturbances.  In this habitat, fungal communities are often challenged by severe fluctuations in nutrient and moisture availability, microclimate and population density, all of which affect competitive interactions and increase vulnerability to disturbance events.  Consequently, disturbance and competition are believed to be primary forces driving fungal community development in the phylloplane.  Therefore, it is the objective of this seminar to profile disturbance and competition as mechanisms that regulate and influence fungal community structure and dynamics. The role that disturbance has in shaping phylloplane fungal communities and the extent inhabitants of the phylloplane influence each other’s ecology will be discussed. 

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Nutrient-cycling Microorganisms from Extreme Environments: from Culturing to Genomics

December 3, 2007

Research describing microbial nutrient cycling in an extreme environment is often a work in progress due to the wide scope of the subject material and the logistical difficulties that often accompany such projects. It is clear from studies using molecular probes that a remarkable degree of microbial diversity exists in virtually all environments, including those once considered inhospitable to life. Molecular techniques have proven especially useful in detecting the presence of microorganisms involved in the cycling of essential nutrients, such as carbon, nitrogen, and sulfur, in a variety of ecosystems. This information can be used to guide primary enrichment culture strategies. The attainment of pure cultures of extremophilic microorganisms involved in nutrient cycling is essential to fully understand the biogeochemical interactions between these microbial communities. Newly isolated strains are traditionally characterized by morphological, physiological, and phylogenetic analyses. In addition to these methods, the advent of complete genome sequencing allows a new level of species characterization to be obtained. Whole genome analyses provide a wealth of information regarding the metabolic capacity and cellular processes of microorganisms based on the genes they contain. Studies integrating both innovative culturing techniques and comparative genomics allow for important distinctions to be made between phylogenetically related microbial species that perform the same ecological function in environments having vastly different physiochemical conditions.

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N-glycosylation-dependent apical trafficking of the sialomucin endolyn in polarized epithelial cells

December 5, 2007

Polarized epithelial cells serve as a protective barrier to infection by microorganisms and also regulate the flow of ions and nutrients between the internal and external environments. To fulfill these functions, polarized epithelial cells must be able to generate and maintain distinct protein populations at the apical and basolateral domains. Cellular mechanisms sustain this polarity by properly sorting apical and basolateral proteins in both the biosynthetic and postendocytic pathways via sorting signals inherent within the protein. N-glycosylation has been specifically implicated as one of several sorting signals responsible for delivery of proteins to the apical surface along the biosynthetic pathway. To examine N-glycan-dependent trafficking along the biosynthetic pathway and explore a possible role for N-glycans in sorting along the postendocytic pathway, I have focused on the sialomucin endolyn. Characterization of the biosynthetic sorting signal revealed that two glycans at amino acid positions 68 and 74 were necessary and sufficient for apical delivery of endolyn. Terminal processing of N-glycans is also necessary for efficient apical delivery as incubation with kifunensine, a drug that inhibits terminal processing of N-glycans, resulted in the nonpolarized delivery of endolyn. A similar N-glycan-dependent sorting signal was also found to be important for apical recycling of endolyn along the postendocytic pathway. The use of the same sorting signal suggested that endolyn may be sorted in a compartment that is common to both the biosynthetic and postendocytic pathway. However, further studies revealed that endolyn is sorted in distinct compartments along these two pathways. These data enhance our understanding of how and where N-glycans mediate apical sorting to maintain the integrity of polarized sorting in epithelial cells.

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December 7, 2007

Cancer encompasses a large number of diseases that are characterized by six hallmarks.  One hallmark is the ability of a cell to survive, or evade apoptosis.  Apoptosis is essential to remove cells that acquire irreparable cellular damage.   Elucidating the mechanism(s) through which cells acquire the ability to evade apoptosis may facilitate development of more effective cancer treatments.  The transcription factor, C/EBPb, is a key mediator of cell survival and tumorigenesis.  C/EBPb-deficient mice treated with carcinogens that produce oncogenic Ras mutations in skin respond with abnormally elevated levels of apoptosis and a complete block in skin tumorigenesis.  This deregulated carcinogen-induced apoptosis results from aberrant up-regulation of the tumor suppressor gene, p53.  However, the signaling event that induces p53 in C/EBPb-/- mice is not known.  Using genetically modified mice, we demonstrated that neither p19Arf nor oncogenic Ras signaling are required for increased p53 and apoptosis in C/EBPb-/- mouse epidermis.  In contrast, when C/EBPb-/- mice were treated with distinct types of DNA damaging agents including alkylating chemotherapeutic agents, these mice displayed deregulated p53 and apoptosis.  These results indicate that C/EBPb represses p53 to promote cell survival downstream of DNA damaging agents independent of oncogenic Ras and p19Arf and suggest inhibition of C/EBPb may be a target for cancer co-therapy to increase the efficacy of chemotherapeutic agents.   Future work will seek to understand the role of putative C/EBPb target genes in the promotion of cell survival and study the role of protein acetylation in response to pesticide exposure using the invertebrate model C. elegans, a free-living bacterivorous soil nematode.

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How cheaply can I travel?

January 30, 2008

This talk will first familiarize the audience with the Traveling Salesperson Problem.  It will then discuss a variant of the problem called the Nested Traveling Salesperson Problem.  Our goal will be to look at an algorithm that will allow someone to visit a set of n cities, using each road at most once, while at the same time using as many cheap roads as possible.

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Reduced Basis Simulation

February 8, 2008

Molecular dynamics (MD) simulation provides a powerful tool to study molecular motion with respect to classical mechanics.  When considering protein dynamics, local motions, such as bond stretching, occur within femtoseconds, while rigid body and large-scale motions, occur within a range of nanoseconds to seconds.  To date, literature reports simulations of solvated proteins on the order of nanoseconds, however, simulations of this length do not provide adequate sampling for the study of large-scale molecular motion.

In this presentation I will describe a method for performing molecular simulations with respect to a reduced coordinate space.  Given a standard MD trajectory I use principal component analysis to identify k dominant characteristics of a trajectory and construct a k-dimensional (k-D) representation of the atomic coordinates with respect to these k characteristics.  Using this model I define equations of motion and perform simulations with respect to the constructed k-D representation. I apply this reduced basis simulation method to test cases and compare the simulations to standard MD simulations of the test cases.  The results indicate that the molecular activity with respect to the reduced basis simulation method is comparable to that observed in the standard MD simulations of test cases.

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Restarting the Lanczos Algorithm for Large Eigenvalue Problems and Linear Equations

February 11, 2008

Large systems of linear equations and large eigenvalue problems require special computer techniques called iterative methods.  This talk focuses on new iterative methods for large symmetric problems.  Specifically, we give a restarted Lanczos algorithm that solves both linear equations and the eigenvalue problem simultaneously.  Also examples are given  and theorems that aide convergence are discussed.  

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Updated February 7, 2008
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