Dr. Terry Hazen, Earth Sciences Division, Lawrence Berkeley National Laboratory

These talks are part of the Thomas Morton Lectureship Series, sponsored through a generous donation by Dr. Jack Hughes, NU '67. They are open to the public.

Talk #1

Bioremediation: the Hope and the Hype of Environmental Cleanup
12:20 pm 126 DePaul Hall, Niagara University
This talk will be immediately followed with an informal meet and greet session in 122 DePaul Hall.

Talk #2

Systems Biology (Omics): the New Frontier in Environmental Biotechnology
8:00 pm at the Grand Niagara Hotel (formerly the Four Points by Sheraton), located at 114 Buffalo Avenue in Niagara Falls, NY.

Mon., Nov. 5, DePaul 126, 12:20- 1:15 PM

William J. Bowers, PhD, Associate Professor of Neurology and of Microbiology and Immunology, Center for Aging and Developmental Biology, University of Rochester School of Medicine and Dentistry

Inflammatory mechanisms underlying early Alzheimer's disease

Alzheimer’s disease (AD) is a complex neurodegenerative disorder that progressively impairs intellectual and emotional functioning in afflicted individuals.  The disease is characterized pathologically by a temporal and spatial advancement of amyloid-beta (Ab) deposition, neurofibrillary tangle formation, and synaptic degeneration.  Inflammatory mediators have been proposed as serving an integral function in initiating and/or propagating AD-associated pathologic processes within the brain. We previously observed significant transcriptional up-regulation of genes encoding pro-inflammatory cytokines and chemokines, which correlated to regionally enhanced microglial activation in brains of triple transgenic mice (3xTg-AD), prior to the onset of overt amyloid pathology.  To further define the role of these factors in AD pathogenesis, viral vector-based gene transfer is being employed to stereotactically modulate the inflammatory environment in pre-pathologic 3xTg-AD mice.  Taking a more reductionist approach to dissecting the function of pro-inflammatory mediators in normal and diseased neuronal physiology, we have also uncovered specific cytokine-mediated effects on intracellular calcium homeostasis that may underlie pre-symptomatic neural transmission deficits observed in early disease.  Elucidating the role of inflammation in “normal” neuronal physiology and in pathogenic cascades associated with neurodegenerative diseases will foster the development of novel diagnostic methodologies and stage-specific therapeutics. 

Wed., Oct. 24, DePaul 126, 12:20- 1:15 PM

Xin Bi, PhD, Associate Professor, Department of Biology, University of Rochester

Chromatin-mediated epigenetic gene regulation

In eukaryotic organisms, chromatin plays a key role in the highly efficient regulation of gene expression. The genome is organized into discrete transcriptionally silent and active domains whose disregulation may lead to diseases such as cancer. Therefore, understanding how these domains are established and maintained are of great importance. We have been studying the structure and function of transcriptionally silent chromatin domains in the model organism Saccharomyces serevisiae (the budding yeast). I will discuss our findings regarding (1) how small regulatory sequences named silencers in the genome act to initiate the formation of a chromatin domain that inhibits gene expression, (2) how special sequences named barriers stops the propagation of the silencing complex along the chromosome, (3) how silent chromatin represses gene transcription, and (4) how enzymes that modify the chromatin overcomes the repressive effect of transcriptionally silent chromatin structure. These findings shed light on the mechanism of chromatin-mediated "epigenetic" gene regulation that is dictated not by the DNA sequence but by the chromatin structure of the genomic locus.

Fri., April 13
Two talks by William Summers, MD., PhD.
Yale Medical School

12:20 pm, in 126 DePaul Hall
and
3:30 pm, 407 St. Vincent’s Hall (preceded by refreshments in the hallway)

These talks are part of Niagara University's 150^th Anniversary celebration.

First talk: "Emerging Infections: Hubris and Horror?"

Second talk: "Marmots, Microbes and Mandarins: The Geopolitical Uses of the Manchurian Plague of 1910-11"

Speaker: Dr. Eugene Madsen, Cornell University Department of Microbiology

Speaker: Mark E. Bier, Ph.D., Assoc. Research Professor & Director, Center for Molecular Analysis, Department of Chemistry, Carnegie Mellon University

In this talk I would start off introducing the basics of mass spectrometry and why and how we do it for small molecule and large ones (MW determinations, structure determinations,.) and then I would discuss my current research activities that will hopefully result in top-down proteomics of biomacromolecular complexes. I will talk about common protein analyses for molecules like apomyoglobin, BSA, IgG and then move into uncommon analyses like ferritin (MW 900 kDa) and the capsid from virus particle HK 97 (13 MegaDa). It is possible to weigh these latter molecules because we have a new MS with a novel cryodetector.

Title B: "Simulated Protein Identification using the Virtual Mass Spectrometry Laboratory"

In this talk I would like to show students and faculty how they can learn about MS and about how one can identify a protein using a simulated mass spectrometer on the Internet: <http://sVMSL.chem.cmu.edu>.

Speaker: Dr. Walter Steiner, NU BIO Dept.

A code for meiotic recombination?

 The cells of humans and other sexually reproducing organisms contain two copies of each chromosome, one from each parent.  These chromosome copies, or homologs, contain similar but not always identical genes.  During meiosis (the process of forming gametes), genetic information is exchanged between maternal and paternal chromosomes through the process of homologous recombination.  Homologous recombination is essential for ensuring that each cell receives the correct number of chromosomes; it is also a major mechanism of repairing DNA damage.  When this process fails, chromosomal rearrangements or other mutations leading to cancer can occur.

            My lab uses the fission yeast S. pombe as model organism for studying homologous recombination.  In most organisms, including S. pombe, meiotic recombination does not occur uniformly along chromosomes, but preferentially at so called recombination hotspots.  Though the factors determining the location of most hotspots are not known, work in my lab has shown that at least some hotspots are determined by a specific nucleotide sequence, 5'-ATGACGTCA-3', known as M26.  Since that sequence accounts for only a small fraction of hotspots in the genome, we are in the process of identifying additional sequence motifs that act as meiotic recombination hotspots.  

Currently, we have identified several hundred 15-30 base-pair sequences that create recombination hotspots.  Analysis of those sequences has revealed at least 14 significantly overrepresented six and seven bp sequence motifs that, like M26, may act as recombination hotspots.  We have confirmed that two of those sequences form recombination hotspots when reconstructed by minimal base changes, and we are in the process of testing the others.  Our results to date support the possibility that many, and perhaps most or all, hotspots of recombination result from defined nucleotide sequence motifs.  Ultimately, we wish to identify the complete set of those motifs.

Monday, September 26, 2005, 12:20 - 1:15 PM - DePaul 126

Speaker: Dr. Eric M. Phizicky, Professor of Biochemistry and Biophysics, University of Rochester

The new world of genomics: genomic analysis of biochemical activity

The flood of genome sequences in the last decade has resulted in an explosion of interest in functional genomics/proteomics, the goal of which is to deduce the role of every gene and protein by parallel analysis methods.  To this end, a number of powerful new approaches have been developed that have in aggregate yielded huge amounts of information, and often precise knowledge, about the functions of large numbers of previously uncharacterized gene products.  In particular, we have developed a method to rapidly map biochemical activities to genes, by construction of a genomic library of yeast strains each expressing a different yeast protein fused at its N-terminus to a purification tag.  This library has been used by us and others to assign activities to genes by assay of pools of purified fusion proteins and subsequent deconvolution of pools, and similar libraries have been used by others to develop protein microarrays for rapid analysis of the proteome.  We will describe these results as well as recent efforts to expedite high throughput cloning and analysis of gene/protein function.

Speaker: Dr. Stacey Sedore Willard, NU '98 (BIO); Postdoctoral Fellow, Department of Cell Biology,
Johns Hopkins University Medical School

Dictyostelium discoideum as a model system: Bioinformatics, developmental genetics, and a little bit of science fiction

Studies in our lab are focused on the process of chemotaxis, or the directed migration of cells toward a chemical stimulus, in the "social amoeba," Dictyostelium discoideum. Chemotaxis is used in a number of biological processes including wound healing, immune response, neural development, and tumor metastasis. Using classical forward genetics, we have isolated many genes involved in the signaling network that governs chemotaxis. The "completion" of the Dictyostelium genome project has revolutionized these studies and new reverse genetic, or candidate, approaches have contributed to our understanding of the regulation of chemotaxis. Despite the obvious advantages of having the genome sequence, I will describe situations where we need to be clever when utilizing this resource: In some cases, annotation errors can result in misleading data interpretations. In addition, I will describe some new approaches provided by bioinformatics to address old problems in our system.

Speaker: Dr. Ronny Priefer, NU Dept. of Chemistry, Biochemistry, and Physics

Bioinformatics: the past, present and future directions from a biologist’s perspective

Abstract: The past forty years has seen an explosion in the knowledge base in the biological sciences, from our initial understanding of DNA as the hereditary material and cracking the code of life to our most recent findings of the sequence of the human genome and ways to monitor the level of expression of the roughly thirty thousand genes that make us human. This talk will survey the rapid successes in biology and why the field of bioinformatics has arisen and its value in future exploration.

The CHS genes in Gesneriads:  A Tool for Deciphering Evolutionary Relationships

Abstract: Chalcone synthase (CHS) is the first enzyme in the biosynthesis of pigments in higher plants.  The CHS genes are a family of closely related sequences found in all plant species and have been cloned and sequenced in over 35 genera.  Most species have three or more members in the CHS family but one branch of the evolutionary tree containing Antirrhinum (snapdragons) and Saintpaulia (African violets) have only one.  The genus Saintpaulia is within the family Gesneriacea which contains 130 genera and over 2,700 species.  The DNA sequence of the CHS gene is being used to analyze the evolution of the Gesneriads.

Cardiac Molecular Imaging

Positron Emission Tomography (PET) provides many advantages for diagnosing and treating conditions such as heart disease. For example, PET diagnoses heart disease non-invasively with 96-98% accuracy in individuals with or without symptoms of heart disease, permitting treatment even before symptoms appear. Since its diagnostic accuracy is much higher than standard tests, PET reduces expense and risk by avoiding unnecessary tests and procedures, thereby providing more efficient diagnoses.

Dr. Merhige is involved in research and clinical practice applying PET imaging technology at The Heart Center of Niagara, located at Niagara Falls Memorial Medical Center. He also heads The Center for Coronary Disease and Reversal, located in two community-based clinics where he provides other cardiac diagnostic and treatment services aimed at stopping the progression of, or reversing coronary artery disease.

Dr. Merhige's approach to using PET imaging instead of the usual methods would allow the cardiologist to identify a significant proportion of patients who could be safely treated with a combination of diet, exercise and medicine without referring them for invasive, risky procedures. Niagara Falls Memorial Medical Center is the only medical facility in this region to use PET imaging for this purpose. Dr. Merhige and his team are seeking to expand the application of this innovative technological approach to address the death and disability caused by heart disease, particularly in Niagara County, where the death rate from cardiovascular disease is 50% higher than the nation as a whole and 60% higher than the New York State average.

The Computational Approach to Microarray Analysis and Pattern Discovery

Progress in mapping the human genome and developments in microarray technologies have provided considerable amount of information for delineating the roles of genes in disease states. Since complex diseases typically involve multiple inter-correlated genetic and environmental factors that interact in a hierarchical fashion and the clinical characteristics of diseases are determined by a network of interrelated biological traits, microarrays hold tremendous latent information but their analysis is still a bottleneck. In this talk, various pattern analysis techniques, clustering and classification tools, and machine learning algorithms will be discussed as part of a unified effort of various disciplines (including computational sciences, artificial intelligence, machine learning, statistics, biological/medical sciences, and pharmaceutical sciences) to deepen our understanding of the factors and the development of certain diseases and pioneer new approaches in their treatment.

Faster Finds From Gallo to Google

Abstract: A core problem in bioinformatics is finding a match for a sequence of DNA or protein in a much larger sequence of DNA (such as a gene or a genome) or protein. In computing theory, this is the same problem, hence is solved by the same algorithms, as are used by word processors and Web search engines to find a word or phrase in a document. Since existing DNA databases have many millions of entries, pattern-matching algorithms must perform efficiently enough to produce their results in an acceptable amount of time. An important strategy for obtaining faster results is the use of parallel (multi-processor) computers, but this often presents new problems of efficient communication of data among processors. Here, we discuss recent solutions of the presenter and Russ Miller (director, Center for Computational Research, UB; and member of the NU Bioinformatics advisory board) to certain data communication problems on parallel computers. These results enable efficient modification of fast algorithms for sequential (single-processor) computers for implementation on parallel supercomputers, achieving an optimal speedup factor, proportional to the number of processors used.