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Summer 2013 Research Projects

  • Iovine | Berger
  • Itzkowitz / Samollow
  • Rice / Miwa
  • Zhou / Berdichevsky

Identification of the endogenous Sema3d receptors


Iovine Berger Team 2013

Team Leaders:

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

Graduate Students:

Joyita Bhadra
Rachael Barton

Undergraduate Students:

Samuel Flores
Sarah Kayode
Durlav Mudbhari
Francisca Onyiuke

Description of Project:

The vertebrate skeleton is comprised of numerous bones of a variety of sizes and shapes. Flexibility in the skeleton is provided by the correct positioning of joints. Regulatory pathways are coordinated to ensure appropriate bone size, bone shape, and the correct localization of joints.

The Berger-Iovine team is interested in revealing how bone growth (i.e. cell proliferation) and skeletal patterning (i.e. joint placement) are coordinated during development of the skeleton. The zebrafish fin is utilized to study this problem. The fin is comprised of multiple bony fin rays, and each fin ray is comprised of multiple bony segments. Interestingly, mutations in the gap junction gene cx43 have been found to cause defects in the size of bony segments. Therefore, prior studies have focused on identifying the molecular pathways acting downstream of Cx43 function.

For example, our earlier work suggests that Cx43 functions in a common pathway with a semaphorin ligand, Sema3d, to coordinate cell proliferation and joint formation in the zebrafish fin. Sema3d is a secreted signaling molecule that may mediate diverse cellular functions, including cell adhesion, cell migration, tissue patterning, cell proliferation, viability, and changes in the cytoskeleton. Semaphorins utilize different types of membrane receptors, including the Plexins (Plxns) and the Neuropilins (Nrps). Molecular genetics approaches suggest that Sema3d-Nrp2a interactions influence cell division, while Sema3d-PlxnA3 interactions influence joint formation. The main goal of our team’s 2012 BDSI project was to purify large amounts of recombinant Sema3d for continued biochemical studies, which we accomplished.

Our team is now in a position to provide biochemical support for our model that Sema3d protein physically interacts with its putative receptors Nrp2a and PlxnA3. In addition to testing directly for physical interactions with purified Sema3d, we further propose to complete cross-linking analyses to identify Sema3d interacting factors in vivo. The latter studies may reinforce our in vitro findings, providing compelling evidence that Nrp2a and PlxnA3 are the endogenous Sema3d receptors during fin regeneration.

Completion of these aims will reveal the major binding partners for Sema3d and will therefore provide novel insights into the mechanisms underlying Sema3d signal transduction during development of the vertebrate skeleton.

Consequences of habitat restoration and genetic isolation
of a Desert Spring Pupfish (Cyprinodon bovinus)


Team Leaders:

Murray Itzkowitz, Ph.D. (Biological Sciences)
Paul Samollow, Ph.D. (Department of Veterinarian Integrative Biosciences, Texas A&M Univ. )

Itzkowitz Samollow 2013

Graduate Students:

Layla Al-Shaer
Timothy Paciorek

Undergraduate Students:

Zachary Carroll
Lanshi Li
Louise McCallie
Caroline Rago

Description of Project:

This is a conservation project that is currently funded by the Texas Parks and Wildlife Department and is designed to increase the population size of a highly endangered fish, the Leon Springs Pupfish (Cyprinodon bovinus). 

The project consists of two components: 

  • First, is to expand the pupfish’s spawning habitat by removing the bulrush grass that is choking the shallow areas.  Along with this renovation is the dispersal of another endangered fish, Gambusia nobilis, which is a potent egg predator of the pupfish.   Along with these habitat modifications, we will monitor the distribution and reproduction of the pupfish and the subsequent egg predation by G. nobilis.

  • Second, to examine the genetic effects caused by the isolation of the pupfish. 

The BDSI students will perform the field work at the Texas Nature Conservancy property located near Ft. Stockton, Texas, and the genetic analysis at Lehigh University.

Natural variation in genes controlling learning potential

Team Leaders:

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

Rice Miwa Team 2013

Graduate Students:

Kristin Anderson
Michael McQuillan

Undergraduate Students:

Thomas Fox
Chaim Kohen
Jameson Petrochko
Joanna Warren

Description of Project:

Adapting to a complex environment requires the brain to form an accurate internal representation of the external world. The brain refines its connectivity based on early exposure to the environment. The most robust time for rewiring, or plasticity, occurs just after birth and closes down shortly thereafter. In mice, this critical period, as well as learning ability, is regulated by a brain gene called lynx1. Mice expressing very low levels of lynx1 have enhanced learning potential, but also exhibit neurodegeneration. On the other hand, mice expressing intermediate levels of lynx1 still have enhanced learning potential compared to wild-type mice, but do not exhibit neurodegeneration.

For species in which memory and learning influence survival, intermediate levels of lynx1 may be selectively favored. Evolution by natural selection can only occur, however, when heritable variation exists for traits important for fitness. If variation in the lynx1 amino acid sequence has functional consequences, then we might expect natural populations to harbor genetic variation at this locus—especially for species in which learning and memory are important for fitness.

Our goal for this study is to assess the amount of variation in the lynx1 amino acid sequence in a natural population of Black-capped chickadees—a species that relies on memory of food storage locations for survival during the winter. We will capture wild chickadees, collect blood samples, extract DNA from these samples, design primers, amplify and sequence the lynx1 gene, and assess the level of variability in the lynx1 sequence among individuals. Results from this project will provide novel information about lynx1 in natural populations, and will form a foundation for future work linking this variation to learning aptitude in a variety of environments.

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)

Berdichevsky Zhou Team 2013

Graduate Students:

Fengqiang Li
Yu Song

Undergraduate Students:

William Cogguillo
Jonah Kohen
Nicole Pirozzi
Anna Sternberg

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.  We will validate the use of OCM to non-invasively quantify the numbers of neurons in organotypic hippocampal cultures, and then, correlate changes in neural numbers measured with OCM to duration and type of spontaneous seizures.   

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
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