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2008 Research Projects

Bean and Flowers

Selective effects on sperm functions by novel compounds

Bean Flowers team

Team Leaders:

Barry Bean, Ph.D.
Robert Flowers, Ph.D.

Graduate Students:

Rajni Singh

Undergraduate Students:

Melanie Rudnick
Manuel Schubert
Gordon Taylor

Description:

Commonly used spermicides like nonoxynol-9 have some undesirable side effects and detrimental consequences for some infectious processes.  As a result, improved and alternative spermicides are needed.  We are synthesizing and testing novel chemical compounds; these may weaken sperm cells and microbes.   The architecture of human sperm cells includes several distinctive membrane regions that undergo substantial changes during the life history of the sperm cell.  Specific changes must take place within the compartments and membranous surfaces of sperm to make them able to fertilize an egg.  We will examine effects of a number of novel compounds on the functions of human sperm.  Outcomes may lead to new strategies for contraception, or improvements in prevention of disease and pregnancy.

 

Burger, Wu and Zhang

Modeling local synaptic control in neural coincidence detectors

Burger team

Team Leaders:

R. Michael Burger, Ph.D.
Linghai Zhang, Ph.D.
Ping-Shi Wu, Ph.D.

Graduate Students:

Matthew Fischl
Melissa Stoner

Undergraduate Students:

Julie Heidt
Matthew Parks
Harjot Thind
Danielle Trause

Description:

Sensory neurons often process information over a large range of a given stimulus parameter. For example, the auditory system can function over a range of sound intensities corresponding to a 1012 fold increase in sound pressure from detection threshold. Specializations at several levels of the auditory system are in place to maintain low detection sensitivity but at the same time, prevent saturation (overload) of the system. We are exploring one such mechanism at a synaptic site that requires very precisely timed synaptic input to achieve its computational function. Specifically, we propose that a particular receptor system (the GABAB receptor) locally controls the strength of excitatory and inhibitory inputs to this neuron type. Further, we expect that local control of synaptic strength maintains the circuit in an optimal operating range. During last summer’s program we successfully developed the instrumentation necessary to perform these experiments and collected our baseline data. The next phase of the project will be devoted to testing our central hypotheses. Our approach combines computational modeling with advanced experimental techniques to determine the impact of these receptors on circuit function.

 

 

Cassimeris, Marzillier and Wu

Gene expression analysis in Stathmin deficient cancer cell lines

Cassimeris Team

Team Leaders:

Lynne Cassimeris, Ph.D.
Jutta Marzillier, Ph.D.
Ping-Shi Wu, Ph.D.

Graduate Students:

Bruce Carney
Danielle Ringhoff

Undergraduate Students:

Abigail Lefkowitz
Erica Smith

Description:

One of the major ways that cancer develops is through loss of genes encoding tumor suppressor proteins.  One such tumor suppressor is p53, a protein mutated or absent in 50 – 60% of all human cancers.  In a normal cell, p53 is part of a signal relay system which responds to DNA damaging agents or other stresses to halt cell proliferation allowing time for the cell to repair itself, or by activating apoptosis, an active cell death process carried out by the cell itself.  Most chemotherapies act to ultimately activate apoptosis, but cells lacking p53 are resistant to apoptosis, making these cells difficult to destroy.  We are examining a pathway that unexpectedly can lead to the apoptosis of cells lacking p53.  Cells without p53 die when a protein called stathmin is also removed.  Stathmin normally functions to regulate the assembly of the cell’s internal skeleton, so it isn’t clear why cancer cells lacking p53 require stathmin to stay alive, while normal cells are healthy without stathmin.  This summer we will apply genomics methods to compare gene expression changes in cells having or lacking p53, and how these two cell populations respond to loss of stathmin.  Our long term goal is to understand how stathmin contributes to cell survival or cell death.  These studies could uncover new targets for chemotherapy development.

Our summer project is a collaborative effort between Lynne Cassimeris (Biological Sciences; studies stathmin), Ping-Shi Wu (Mathematics; studies statistical analysis of microarray/genomic data) and Jutta Marzillier (Biological Sciences; studies applications of microarray technology).

 

Falk and Jain

Biocompatibility of nano-macro dual-porous
glass bone-replacement scaffolds

Falk Jain team

Team Leaders:

Matthias Falk, Ph.D.
Himanshu Jain, Ph.D.

Graduate Students:

Susan Baker
Shaojie Wang

Undergraduate Students:

Laura Bowen
Regina MacBarb
Andrew Salim
Sean White

Description:

One of the key challenges in today’s medicine is the treatment of organ failure or tissue loss. Advances in cell biology and material sciences have led to tissue engineering where healthy progenitor cells are delivered to the injured site on biocompatible scaffolds to regenerate lost or damaged tissue. This approach has delivered particularly successful results for bone replacement using bone-scaffolds made from CaO-P2O5-SiO2 based glass ceramics. Millions of patients have benefited from implants made from such bioactive glasses.

A macro porous structure of the glass scaffolds is necessary to obtain good implant incorporation through rapid vascularization and bone ingrowth, since such porosity promotes cell growth on the surface as well inside the scaffolds. For additional benefits, the scaffolds should consist of nanopores, which simulate the natural extracellular environment. We have recently developed two novel methods for fabricating such bioactive glasses based on: (a) conventional melt-quench method followed by selective heating and etching, and (b) a sol-gel procedure with polymerization induced phase separation.

In this BDSI Research Project we will fabricate such dual-porous glass bone-replacement scaffolds, and we will test their biocompatibility and bioactivity by monitoring the colonization and growth of bone and bone-precursor cells on the scaffolds. Nano-macro dual porosity glasses with different chemical composition, pore-characteristics, and bioactive coatings will be tested for cell attachment, migration, proliferation, and differentiation. Appropriate fluorescence-based cell detection methods have been established. Thus, this Summer Institute, in combination with our ongoing work supported by NSF and IMI-NFG will elucidate which scaffolds are the most promising ones. It will provide the basis for further testing of our glass scaffolds in vivo by our partners at Tissue Engineering Laboratory, Faculty of Dentistry, Alexandria University, Egypt.

 

Lowe-Krentz and Ghadiali

Multi-scale modeling of cellular mechanics

Lowe-Krentz Ghadiali team

Team Leaders:

Linda Lowe-Krentz, Ph.D.
Samir Ghadiali, Ph.D.

Graduate Students:

Jeffrey Fong
Joshua Slee

Undergraduate Students:

Shannon Alejandro
Jamie Maciaszek

Description:

Scientists have made great strides in understanding organism function at the cellular and molecular level.  Despite all of the disciplinary and cross-disciplinary work, there remains a relatively limited understanding of the physical and biomechanical aspects of cell function.  Yes, we know about the physical chemistry of various biomolecules.  Protein structure and the functions of isolated proteins or protein complexes have also been the subjects of much study.  However, we still know very little about how physical and/or biomechanical forces alter cell function and even less about the physical/biomechanical properties of the cell interior, let alone how changes in the physical structure are controlled and what they mean for the function of tissues and organisms. 

The overarching aim of our proposed study is to determine how physical and biomechanical forces alter the stresses experienced by the cell.  Specifically, we hypothesize that physical forces may alter the cytoskeletal structure of a cell and in turn the shape and elasticity of the cells.  We further hypothesize that correlating experimental measurements with mathematical or computer simulations of cell dynamics will help us to better understand how cells alter their properties in order to minimize damaging physical stresses.  We will initially focus on endothelial cells lining blood vessels which have been documented to experience a variety of physical forces.  In addition, we will also use recent experiments obtained from lung epithelial cells to expand the range of data we incorporate into the computational models of cell dynamics. Features to be included are nuclear staining/morphology, fluorescently tagged proteins that can provide information about the specific attachment sites for the cells and changes in cytoskeletal structure.   Samir Ghadiali provides the expertise in biomechanics, production of specific physical forces on cells, and experience in the computational analysis of physical stress on cells while Linda Lowe-Krentz brings endothelial cell expertise along with experience in studying endothelial cell signaling responses to chemical stress.  Ultimately, the modeling studies will make it possible to predict protective changes and understand how those cell structural changes are normally controlled.

 

Maas and Lopresti

A combined bioinformatics and molecular biological approach
for the identification ofpost-transcriptional recoding events
in the human transcriptome

 

Maas Team

Team Leaders:

Stefan Maas, Ph.D.
Daniel Lopresti, Ph.D.

Graduate Students:

Christina Sie

Undergraduate Students:

Emaan Abdul-Majid
Jessica Latona

Description:

The delineation of whole genome sequences including the human genome have opened up new avenues to study biological phenomena using combined computational and experimental methods. Novel, fundamental questions about diversity and complexity in nature have also arisen from the obtained genomic information. For example, the tremendous complexity of higher organisms, in particular humans, cannot be explained by the number of genetic building blocks present in genomes when comparing primitive species, such as worms and flies, to mammals and primates.

Our interdisciplinary team will apply our substantial experience in computer science, computational biology as well as the molecular biology of RNA editing to mine sequence databases to uncover genes that are subject to modification by RNA editing. RNA editing is a natural phenomenon that allows organisms to produce many more functional molecules than what would be predicted from analyzing the genome.

We are developing a multi-stage software platform that will allow us to mine sequence databases to uncover genes that are subject to modification by RNA editing. The computational work is closely linked to experimental work using mammalian specimen to validate candidate targets and to address how editing regulates gene function.

 

Saldanha and Tatic-Lucic

Ionic sources, gradients and sinks in the control of
gene transcription in glial cells

Saldanha Team

Team Leaders:

Colin Saldanha, Ph.D.
Sveltana Tatic-Lucic, Ph.D.

Graduate Students:

Bradley Walters

Undergraduate Students:

Kevin Naranjo
Katrina Probherbs

Description:

In the vertebrate brain, damage such as a stroke or mechanical injury leads to a pronounced wave of secondary degeneration.  It is this secondary degeneration that is reflected in the symptoms typically associated with stroke.  Understanding what about the primary injury causes the secondary degeneration is a key step towards limiting structural and functional deterioration.  The locus of primary brain damage is a tumultuous environment with dramatically changing concentrations of many biochemicals.  Of these, ionic flux occurs within the first two hours and is most likely responsible for changes in gene transcription associated with apoptotic cell death.  Which ionic species, however, remains a mystery. 

Drs. Saldanha and Tatic-Lucic will combine their expertise to model, manipulate, and measure the induction of apoptosis (qPCR) following rapid introduction and removal of cations (hydronium, calcium, potassium, magnesium) and anions (chloride and bicarbonate) in a flow chamber, in vitro system that contains primary-dissociated cultures of zebra-finch brain (neurons and glia).  Notably, both these projects are anticipated to involve undergraduate students in a team-building, interdisciplinary project that seeks to understand a systems-level problem (cell death and survival) at the bio-electronic (ionic flux) and molecular biology (gene transcription) levels.

 

 

 

 

 
     
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The Biosystems Dynamics Summer Institute is sponsored by a grant from the
Howard Hughes Medical Institute
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