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Summer 2014 Research Projects

  • Iovine | Berger
  • Lang / Lopresti
  • Miwa / Rice
  • Zhou / Berdichevsky

Identification of Nrp2a and PlxnA3
signal transduction events


BDSI Iovine Berger Team
front row: M. Kathryn Iovine, Ph.D., Rachael Barton, Joyita Bhadra, Bryan Berger, Ph.D.
back row: Ivan Basurto, Nathanael Sallada, Jasmine Singh, Joshua Parris

Team Leaders:

M. Kathryn Iovione, Ph.D. (Biological Sciences)
Bryan Berger, Ph.D. (Chemical Engineering)

Graduate Students:

Joyita Bhadra
Rachael Barton

Undergraduate Students:

Ivan Basurto
Joshua Parris
Nathanael Sallada
Jasmine Singh

Description of Project:

Signaling pathways are critical for communication between cells during the growth and development of multicellular organisms. These pathways are regulated by a diverse array of ligand-receptor interactions that communicate specific signals throughout development. We are interested in characterizing the role of the ligand Sema3d in influencing cell division via receptor Nrp2a and joint formation via receptor PlxnA3 during skeletal morphogenesis of the zebrafish fin skeleton, with particular emphasis on the cytosolic signaling proteins activated in response to ligand Sema3d binding.

Our strategy for 2014 will be to (1) purify recombinant forms of receptor cytoplasmic domains, (2) isolation of proteins that physically bind to the purified domain and (3) identification of bound components by mass spectrometry. Completion of these Aims will provide novel insights

Identification of driver mutations in
experimental evolutions


Team Leaders:

Gregory Lang, Ph.D. (Biological Sciences)
Dan Lopresti, Ph.D. (Computer Science & Engineering)

BDSI Lang Lopresti Team
front row: Gregory Lang, Ph.D., Daniel MMarad, Matthew Messersmith
back row: Ryan Peace, Thomas Tavolara, Danielle Auth, Kevin Trinh

Graduate Students:

Daniel Marad
Matthew Messersmith

Undergraduate Students:

Danielle Auth
Ryan Peace
Thomas Tavolara
Kevin Trinh

Description of Project:

Laboratory experimental evolution, in combination with next generation sequencing technology, is a powerful tool for pursuing a mechanistic understanding of adaptation.  For a given selection there are a limited number of accessible pathways to substantially higher fitness.  Replicate populations, therefore, tend to find similar adaptive solutions, yet none find the same solution.  This is because, fundamentally, adaptation is driven both by the chance effects of mutation and drift and by the deterministic action of selection on a small number of beneficial “driver” mutations.  

The objective of this proposal is to exploit an experimental system for identifying biological pathways that regularly yield the mutations that drive adaptation in the yeast Saccharomyces cerevisiae.  This work will advance the long-term goal of developing a mechanistic understanding of genome evolution and will provide broad interdisciplinary training in methods spanning molecular biology, evolutionary biology, genetics, genomics, and bioinformatics.

An integrative assessment of a gene family
controlling learning potential

Team Leaders:

Julie Miwa, Ph.D. (Neuroscientist, Biological Sciences)
Amber Rice, Ph.D. (Evolutionary Biologist, Biological Sciences)

BDSI Rice Miwa Team
front row: Amber Rice, Ph.D., Kristin Anderson, Michael McQuillan, Julie Miwa, Ph.D.
back row: Kyra Feuer, Lena Barrett, Leah Gonzalez, Morgan Decker, Kaylynn Genemaras

Graduate Students:

Kristin Anderson
Michael McQuillan

Undergraduate Students:

Lena Barrett
Morgan Decker
Kyra Feuer
Kaylynn Genemaras
Leah Gonzalez

Description of Project:

The potential to learn can be very important to an organism's fitness, and yet we can observe a lot of variation among individuals in their ability to learn--even among humans. In mice, a gene that is expressed in the brain, lynx1, suppresses plasticity when it is upregulated, making it more difficult for individuals to learn.

With our BDSI project, we aim to test whether DNA sequence variation at several lynx1-related genes in birds may lead to variation in learning potential. Previously, we found evidence of sequence variation and a signature of natural selection in the protein-coding region of a lynx1 homologue in wild chickadees.

We will continue this work to

  1. test for variation in the entire lynx1 homologue;
  2. test for sequence variation at two other lynx family members;
  3. test for brain expression of the lynx1 homolog and other lynx family members in birds; and
  4. attempt to link sequence variation in lynx1 to variation in learning potential.

To accomplish this, we will perform both field and laboratory research.

Evaluation of seizure-induced neural injury
using optical coherence microscopy


Team Leaders:

Chao Zhou, Ph.D. (Electrical & Computer Engineering and Bioengineering)
Yevgeny Berdichevsky, Ph.D. (Electrical & Computer Engineering and Bioengineering)

BDSI Berdichevsky Zhou Team
front row: Yevgeny Berdichevsky, Ph.D., Yu Song, Fengqiang Li, Chao Zhou, Ph.D.
back row: Jennifer Finley, Chelsea Serrano, Emma Galarza, Victor Aguero, Marko Chavez

Graduate Students:

Fengqiang Li
Yu Song

Undergraduate Students:

Victor Aguero
Marko Chavez
Jennifer Finley
Emma Galarza
Chelsea Serrano

Description of Project:

Epilepsy affects 2.2 million Americans and 65 million people worldwide.  Seizures have the potential to kill neurons and cause brain injury, leading to reorganization of neural circuits, and progressively more severe epilepsy. Our goal is to quantify neural injury caused by seizures, to provide information to physicians that will assist in selecting optimal treatments for epileptic patients. This quantification is difficult to carry out with current histopathology methods due to inability to compare pre- and post-seizure neural tissue. We plan to overcome these limitations by carrying out Optical Coherence Microscopy (OCM) imaging of an in vitro organotypic hippocampal culture model of epilepsy before, during, and after seizures. 

OCM is an emerging optical imaging technique that enables micron-scale, cross-sectional, and three-dimensional (3D) imaging of biological tissues in situ and in real-time. OCM functions as a type of “optical biopsy,” imaging tissue microstructure with resolutions approaching that of standard histopathology, but without the need to remove and process tissue specimens.  

In the summer of 2013, we designed and constructed a new spectral domain OCM capable of achieving ~2.8 um axial and ~3.2 um transverse resolution in brain tissue, and demonstrated the feasibility of using OCM to non-invasively quantify neuron numbers in organotypic hippocampal cultures.  This summer, we will design a recording chamber and integrate it with the OCM imaging system to enable simultaneous imaging and electrical recording of organotypic hippocampal cultures. We will also determine the relationship between seizure load and neural death in organotypic hippocampal cultures.

Results of this project will lead to a better understanding of the relationship between seizures and death of neurons, potentially leading to improved treatments for patients with epilepsy. 





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

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