The 4th Annual

NC State University

Undergraduate Summer Research Symposium

 

HHMI Science Exploration and

Science House & Biology Outreach

 


Abstracts are listed in alphabetical order by the last name of the corresponding author.

 


 
 
Student Author(s): 

Aggers, Tracy L.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biomedical Engineering

Research Mentor(s)

Glenn Walker/Biomedical Engineering

Title of Presentation:

Shrinking the Lab

 

 

BioMEMS uses techniques from the microelectronics industry to miniaturize and automate procedures and experiments currently performed in biology and chemistry laboratories. BioMEMS also allows new experiments to be conceived that are currently impossible to perform. The objective of this project is to use micromolding, a relatively new procedure in the BioMEMS field, to create a microfluidic device that will perform serial dilutions. First, the device design, or mask pattern, is drawn with the appropriate software and then is printed as a film output by a local printer. This pattern is then transferred to a silicon wafer coated with an ultraviolet sensitive chemical called photoresist. The wafer is then developed, removing all the unexposed photoresist. The remaining positive relief photoresist pattern can now be used as a “master” template for molds. Molds are created by pouring the liquid polymer polydimethylsiloxane (PDMS) over the master wafer inside a Petri dish. The PDMS is allowed to cure and once it has hardened it can be peeled off of the wafer. The resulting mold is then bonded with glass and the experiment performed. The heights of the channels in the molds are generally the size of half the width of a human hair (50 microns). BioMEMS is useful for minimizing reagent use, reducing experiment time, and enabling new experiments; the devices can also be inexpensively mass produced.

 
 



 
 
Student Author(s): 

Ali, Marium A.

Home Institution:

Meredith College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Genetics

Research Mentor(s)

Pat Estes/Genetics

Title of Presentation:

Role of the Sox Gene SoxN and Homeotic Genes Scr and Tsh on CNS Midline of the Drosophila

 

 

How are the fates of cells of the central nervous system determined in various regions of the body during development? Homeotic genes are responsible for specifying the anteroposterior axis of the body by forming the identities of the different segments. These experiments are designed to examine the role of homeotic genes on a specific CNS cell type, the midline cells. Midline cells lie in the center of the CNS and are responsible for guiding the development of axon pathways by sending out ‘signals’ to axons. Sox genes are diverse transcriptional regulators that play an important role in early neural development of midline cells. In the fruit fly, the Sox Neuro (SoxN) gene is necessary for the normal development of midline glia, particularly in the mid section of the embryo. Mutant SoxN flies lack midline glia in the central region of the embryo. The focus of this study is to determine if SoxN has any effect on the expression of the homeotic gene Sex combs reduced (Scr), which determines the identity of the thoracic region. This is to determine if Scr works in conjunction with SoxN in the development of the mid section of the midline. In addition, teashirt (tsh), another homeotic gene expressed in the thorax, abdomen and ventral nerve chord is examined. The role of tsh on the CNS midline is studied, by examining the effect of  tsh mutants on wrapper, a gene that is expressed in midline glia. The results indicate how the Sox gene, SoxN, and the homeotic genes Scr and tsh work with other genes to form cell identities within the CNS of the Drosophila embryo. 

 

 



 
Student Author(s): 

Boyack, Ruth E.

Home Institution:

Peace College

Program:

HHMI Science Exploration and the Science House & Biology Outreach

Department(s):

Microbiology

Research Mentor(s)

Eric S. Miller/Microbiology

Title of Presentation:

Directed Gene Replacement Using λ Red in Escherichia coli and T4

 

 

Recombineering uses the phage λ Red recombination system for directed gene replacement without reliance on cloning. The process can be used to insert a linear DNA fragment into a prokaryotic chromosome anywhere there is homology present between the two. The objectives of the research focused on gaining experience with recombineering through experiments with Escherichia coli, and then advancing to apply the technology to directed gene replacement in the T4 bacteriophage chromosome.

               E. coli strains possessing the pKD46 plasmid were used, a plasmid that carries the lambda Red genes beta, exo and gam. Red expression is induced in these strains by the presence of 0.2% L-arabinose. A Polymerase Chain Reaction (PCR) DNA product, designed to possess 40bp of flanking homology, was introduced into the cells using electroporation, after which the cells were screened for recombinants. The PCR product used in the E. coli experiments was designed to insert a gene for kanamycin resistance into the lacZ gene. This allowed screening for resistance to the antibiotic kanamycin and for the inability to use lactose, both phenotypes that should be present in successfully recombineered cells. When using phage, the PCR product was designed to insert the gene for Green Fluorescent Protein (GFP) into the ac region of the chromosome, disruptions of which result in acriflavin resistance. The electroporated cells were thus allowed to complete the lytic cycle and then the resulting lysates were screened for acriflavin resistance. It was also predicted that the presence of GFP would allow screening for fluorescent plaques by the recombineered phage.

 
 



 
Student Author(s): 

Brumbaugh, Sarah C.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Textile Engineering, Chemistry and

Science

Research Mentor(s)

Bhupender S. Gupta/Textile Engineering,

Chemistry and Science

Title of Presentation:

Morphology and Properties of Electrospun Nanofibrous Webs from PVA and PEO

 

 

In the past several years, electrospinning has become an appealing technique for the production of nanofibers from polymers.  Although many applications are visualized, including the use of the webs as scaffolds for tissue engineering, little is known about the factors affecting the size, the properties, and the uniformity of the fibrous structures produced. Accordingly, the focus of this project was to select two polymers, namely, poly(vinyl alcohol) and poly(ethylene oxide), both considered for tissue engineering, and determine the most effective parameters for electrospinning that would create a uniform web with few broken ends and irregularities.  The three primary variables involved are voltage, pumping rate, and polymer concentration in solvent, i.e. water; these were used at three levels each.  The factorial design gave twenty-seven trials for each polymer.  The webs were examined under SEM for diameter-frequency distribution, the frequency of broken ends, and the nature of irregularities.  The results showed that the 20% PVA solution run at 100μL/hr and 7.5 kV had the least amount of broken ends and irregularities.  These defects increased as the solution concentration decreased or the pumping rate increased.  Several combinations with the lowest concentration of PVA (10%) produced either a matted fiber web or a beaded structure.  The PEO data is currently being evaluated.  When these results are in, conclusions regarding its spinnability into nanofibers will be made.  Immediate future plans are to repeat trials of successful combinations to further vary the processing variables and determine the optimum values, the acceptable ranges, and the properties of the resulting structures.

 
 



 
 
Student Author(s): 

Buerkle, Shawna

Johnson, Emily

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Animal Science

Research Mentor(s)

Sunny Liu/Animal Science

Title of Presentation:

Localization of Eight Unique MDV Proteins

 

 

Marek’s disease, MD, can result in death or severe production loss in commercial chickens.  The causative agent of MD is the α herpes virus Marek’s Disease Virus (MDV).  This is a large double-stranded DNA virus, with a genome size of approximately 175 kb.  Susceptible chickens can develop enlarged nerves and tumors in several organs, which lead to paralysis, blindness, and eventually death.  Vaccines are available, but these do not prevent the replication and spread of the virus.  An open-reading frame (ORF) is a sequence of DNA that encodes for a protein.  There are at least ninety open-reading frames in the MDV, twenty of which are unique.  To better understand the pathogenesis of MDV, eight unique open-reading frames were amplified by PCR and inserted into the GFP vector pGFPC3.  These eight unique open-reading frames were Lorf 6, Lorf 8, Lorf 1, R-Lorf 10, Lorf 3, R-Lorf 13, R-Lorf 11, and R-Lorf 9.  GFP (Green Flourescent Protein) is utilized for its fluorescent characteristic, to allow for visualization of proteins within a host cell.  GFP vector also contains a gene resistant to the antibiotic kanomycin; this allows for selection of transformed bacteria.  The DH5α strain of E. coli bacteria were transformed and plated out on kanomycin LB agar plates to be grown overnight at 37 degrees Celsius.  The colonies grown on the plates would contain the desired ORFs and would produce the MDV proteins.  The final aim of these experiments is to express the viral proteins encoded for by the open-reading frames and determine where they localize and how they function within a host cell.

 

 


 

 
Student Author(s): 

Cone, Laura S.

Finger, Allison R.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Joint Department of Biomedical

Engineering at UNC-Chapel Hill and N.C. State

Research Mentor(s)

Elizabeth G. Loboa/Joint Department of

Biomedical Engineering at UNC-Chapel Hill and N.C. State

Title of Presentation:

Chondrogenic Differentiation of  Osteoarthritic and Normal Human Mesenchymal Stem Cells by Cyclic Hydrostatic Pressure

 

 

Human mesenchymal stem cells (hMSCs) can differentiate into multiple musculoskeletal tissue cells under appropriate mechanical and chemical conditions. The application of cyclic hydrostatic pressure (CHP) to hMSCs may promote chondrogenesis, the formation of cartilage. The purpose of this study was to determine if the application of CHP will induce chondrogenesis in osteoarthritic hMSCs and if the response is different from that of normal hMSCs.  Agarose (2%) constructs were seeded with hMSCs from both normal and osteoarthritic donors.  Constructs were loaded in an oil filled 1L pressure vessel, kept at 37ºC, and placed under CHP for 4 hours a day at 7.5 MPa, 1Hz for 21 days.  The vessel was attached to a hydraulic cylinder powered by a MTS 858 Mini Bionix load frame.  During loading, control constructs remained in static culture in a beaker of oil at 37ºC.  Real time RT-PCR analysis was performed on samples taken at days 0, 7, 14, and will be performed on day 21 samples to determine mRNA expression levels of types I and II collagen, aggrecan, and SOX 9.  Western blots will be performed to detect type II collagen and aggrecan protein levels.  Changes in the pericellular matrix proteins including types II and VI collagen will also be determined by immunohistochemistry. The results of this study will indicate whether osteoarthritic hMSCs undergo chondrogenesis to the same extent as normal hMSCs.

 


 

 

Student Author(s): 

Donnelly, Amanda M.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Chemistry

Research Mentor(s)

Alexander Deiters/Chemistry

Title of Presentation:

Intramolecular [2+2+2] Cyclotrimerization to Form Pyridines on the Solid Phase

 

 

Pyridines are active components in many biological products including a variety of medicines. Developing large libraries of small molecules for pharmaceutical research is useful in the discovery of new therapeutic agents. Performing these reactions on the solid phase allows one to use an excess of reagents, makes purification easier, and is more efficient. Most importantly, it reduces the difficultly associated with regio- and chemoselectivity associated with certain reactions. The goal of this research is to develop novel methodologies to conduct [2+2+2] cyclotrimerizations on the solid phase to yield libraries of pyridines. This will allow for the discovery of new pyridines which could potentially be more helpful in the treatment of various diseases. The research involves the synthesis and immobilization of diynes on the solid phase followed by a cobalt catalyzed cyclotrimerization. The generated pyridines are cleaved from the resin, analyzed by spectroscopic methods, and used in biological screenings.

 




 

Student Author(s): 

Foushee, Kensey L.

Home Institution:

Meredith College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Mathematics

Research Mentor(s)

Ernest Stitzinger/Mathematics

Title of Presentation:

The Use of Cryptography to Develop Secret Code Systems

 

 

Cryptography, the design and implementation of secrecy systems, plays a vital role in everyday life.  Over time, advances in technology have been used to aid in the use of cryptography to protect secret information more efficiently.  Cryptography can be used anytime there is information that needs to be kept confidential, and it is especially used today to secure computer, internet, banking, and military affairs.  The mathematics behind cryptography can be studied by examining all sorts of cryptographic systems ranging from simple ciphers that are easy to break to more complex ciphers that are said to be impossible to break and by using the help of technology, such as the computer software Maple.  After studying many ciphers and the ways in which cryptanalysis has been used to break these ciphers, we chose to pick a relatively simple cipher, the Vigenère cipher, to alter in such a way to make it more difficult to break.  The Vigenère cipher is a private-key cryptosystem that uses a series of shift ciphers based on the letters of a particular secret keyword to encrypt the plaintext message.  The problem with using the Vigenère cipher is that it is easy to break using cryptanalysis by finding the keyword length and then by performing a frequency analysis to determine the keyword.  Once the keyword is found, the ciphertext can easily be deciphered into the original plaintext message.   In order to make the Vigenère cipher more secure, we developed schemes to alter this cryptographic system.  After developing a new form of the Vigenère cipher, we first performed small examples by hand and then with the help of Maple, we were able to develop a program that allowed us to send larger messages back and forth to each other. 

 

 



 
Student Author(s): 

Frankosky, Davin K.

Bradshaw, Troy

Highland, M.

Lee, S.

Walker, M.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Physics

Research Mentor(s)

Jacqueline Krim/Physics

Title of Presentation:

Surface Morphology of Metal Films of Relevance

to Superconductivity-Dependent Friction

 

 

The surface morphology of specific metals evaporated onto a substrate have been found to be linked to certain superconducting characteristics of that metal. These in turn have great impact on the sliding friction of the films.  In order to better understand this, it is important to be able to view the metal film growth modes occurring as a result of deposition.  In this study, we have taken particular interest in niobium and lead thin films due to the fact that lead is a type one superconductor and niobium is a type two.  Also, they have readily accessible transition temperatures, easily achievable in lab for study through the use of a liquid helium cryostat.  To physically view the surface morphology of the respective films, we have employed a scanning tunneling microscope (STM) for imaging.  The films were deposited onto a quartz crystal microbalance (QCM) substrate by way of an electron beam evaporator (Nb), and a thermal evaporator (Pb).  STM images of niobium and lead thin films exhibit different growth modes depending on the deposition method and substrate material.  We present here the morphology of such films.

 
 



 
 
Student Author(s): 

Gass, C. Elizabeth

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biochemistry

Research Mentor(s)

Chris Ashwell/Poultry Science

Title of Presentation:

Targeting Antibiotic-resistant Bacteria with Lytic Viral Phages

 

 

The emergence of antibiotic-resistant pathogens in recent years is of significant concern to the biomedical community. A potential reservoir for these drug-resistant pathogens is locations of intensive animal agriculture where antibiotic use is routine. One approach to reducing this problem is to investigate alternative methods to antibiotic use. Recently, there has been increasing interest in the use of lytic viral phages rather than antibiotics to selectively target and destroy pathogens. This technique has been successfully used to combat bacteria such as E. coli and Salmonella both in vitro and in vivo (particularly in livestock and on produce). The goal of this study is to isolate novel phages capable of killing pathogens that are important to animal and human health. Initial targets of this project include Salmonella and Mycoplasma. Three antibiotic-resistant strains of Salmonella will be targeted: ATCC S. typhimurium 700408, a field isolate of S. kentuck, and a field isolate of S. heidelberg. We will also attempt to isolate a mycophage to target the pathogenic mycobacterium Mycoplasma gallisepticum, which is responsible for substantial economic losses in poultry and has also caused a conjunctivitis epidemic in wild house finches (Carpodacus mexicanus). Phage will be collected from waste waters sampled from animal processing facilities or on farms with prior pathogen exposures. Once lytic phage are isolated in vitro, their effectiveness to kill pathogens in vivo will be examined.

 

 



 
Student Author(s): 

Goins, Brian S.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Electrical & Computer Engineering
Research Mentor(s)

Eric Rotenberg/Electrical & Computer

Engineering
Title of Presentation:

Inside the CPU: What is a Branch

Predictor?

 

 

At the heart of any computer is the central processing unit or the CPU. The CPU reads and executes the instructions given to it by programs. It goes through a certain set of steps to do its job. It retrieves the instruction, decodes it, executes the instruction, and writes the result for use by later instructions. However, instead of completely going through this cycle one instruction at a time, the CPU works more like an assembly line by pipelining, or completing one step and sending it on to the next while retrieving the next instruction. Still, the CPU will occasionally retrieve a conditional branch which may cause different instructions to be executed depending on other conditions. The CPU doesn’t know the next instruction to retrieve until the conditional branch reaches the execute stage, which leaves a gap in the “assembly line”. A branch predictor closes that gap by attempting to predict which instruction to do next. My research includes learning what branch predictors are and how they work, and learning the C programming language so I can write a branch predictor simulator. I have developed and verified a preliminary branch predictor simulator.

 
 



 
Student Author(s): 

Greene, Elizabeth D.

Home Institution:

Meredith College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Zoology

Research Mentor(s)

John Godwin/Zoology

Title of Presentation:

Fish on the Edge of a Nervous Breakdown? Domestication and Anxiety-related Behaviors in Zebrafish

 

 

The zebrafish species, Danio rerio, has recently become a major model in biomedical research and has been designated a model species by the National Institutes of Health. Much of the research with zebrafish has concentrated on genomic mapping and development with little emphasis on behavior. This study compared the anxiety-related behaviors of wild and domestic zebrafish.  The domestic zebrafish were obtained from a commercial supplier while the wild fish were captured in India. There have been relatively few behavioral studies on zebrafish. The tests used in this study were modified from established behavioral paradigms in rodents. Three assays were performed to assess anxiety in domestic and wild zebrafish. These included a shoaling assay, a plus maze assay, and a predator assay. Domestic zebrafish and wild zebrafish showed significant differences in the plus maze as well as the predator assay. Wild zebrafish spent more time in the closed arms and less time in the open arms of the plus maze than the domestic zebrafish. Wild zebrafish also spent less time in close proximity to the barrier separating them from the predator in the predator assay.  In contrast, wild and domestic zebrafish did not show behavioral differences in the shoaling assay. There was evidence of repeatability in the shoaling assay with female domestic zebrafish but not males. The results of this study suggest that domestication is associated with reduced anxiety-related behaviors in zebrafish. However, since the stocks compared here were not raised in the same environment, a ‘common garden’ experiment will be necessary to separate the effects of environment and genotype. More generally these findings indicate that zebrafish may be a valuable model for assessing genetic and neural mechanisms of domestication in relation to anxiety-related behaviors.

 
 



 

Student Author(s): 

Gutierrez, Erika R.

Talwar, Sachin

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Chemical and Biomolecular

Engineering

Research Mentor(s)

Saad A. Khan/Chemical Engineering

Title of Presentation:

Molecular Interactions Between Comb-like Associative Polymer and Nonionic Surfactants: Effects of Surfactant Mixtures and Hydrophilic-lipophilic Balance

 

 

Hydrophobically modified associative polymers are new generation polymers with pendant hydrophobes that form a network of inter- and intramolecular hydrophobic junctions in an aqueous media. These polymers possess unique rheological properties and are found in a variety of industrial applications including anti-icin fluids, oil drills, drug delivery, coatings and personal care products. Their properties can be further tailored by adding nonionic surfactants, which alter the network microstructure. We used rheology, or flow behavior, to examine the molecular interactions and microstructure of these solutions. Previous work in the group on nonylphenol ethoxylate (NPe) nonionic surfactant and associative polymer solutions with varying surfactant concentration and hydrophilic-lipophilic balance (HLB) showed different trends of zero shear viscosity with increasing surfactant concentration. These trends can be related to the structure of the mixed micelles formed in solution.

               In this work, the effect of NPe nonionic surfactant binary mixtures on the rheology of comb-like associative polymers is studied. Steady shear and dynamic experiments are performed on solutions of associative polymers and mixed NPe nonionic surfactants; and the trends of zero shear viscosity, terminal relaxation time, and number of hydrophobic junctions with increasing surfactant concentration are plotted. Insights into the molecular interactions between the binary mixtures of NPe nonionic surfactant and associative polymer are obtained. The mixture of a high and a low HLB nonionic surfactant in associative polymer solution either forms an intermediate structure between those corresponding to the high (spherical micelle) and the low (lamellar) HLB surfactants or maintain the structure of the dominant surfactant. Moreover the molar ratio of the NPe nonionic surfactants in the mixture is expected to significantly affect the microstructure formation and hence, the solution rheology. This study will further facilitate the development of polymeric systems with tailored functional properties for different applications.

 
 



 
 
Student Author(s): 

Iboaya, Aiwane A.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Molecular and Structural Biochemistry
Research Mentor(s)

Linda Hanley-Bowdoin/Molecular and Structural Biochemistry

Trino Ascencio/Molecular and Structural Biochemistry

Mary M. Dallas/Molecular and Structural Biochemistry
Title of Presentation:

Infection of Nicotiana benthamiana through Agrobacterium

 

 

The Geminiviridae are a group of plant viruses with small, circular, single-stranded DNA genomes encapsulated in twinned icosahedral particles. Geminiviruses pose a serious problem to agriculture because they infect many crops in tropical and subtropical areas of the world. We are examining geminivirus gene expression and replication processes to better understand how these important plant pathogens impact their plant hosts and to develop strategies to protect crops from infection. Tomato Golden Mosaic Virus (TGMV) is the model we are using in our laboratory. TGMV is transmitted by whiteflies, infects dicotyledonous plants, and has two DNA components (A and B), both of which are necessary for infection. To produce resistant plants, we transformed Nicotiana benthamiana with an Agrobacterium containing a transgene with a mutant form of one of the viral genes (AL1) and generated several resistant transgenic lines. Kanamycin segregation analysis during germination demonstrated that the transgene is inserted at a single locus of each selected line but the number of copies at the single site is not yet known. In this project, we will determine how many copies of the transgene are inserted into the chromosomes of each transgenic line. This will be accomplished by purifying genomic DNA from plants followed by DNA gel blot hybridization. Another aspect of the project will be to observe a geminivirus infection in wild type Nicotiana benthamiana plants inoculated with TGMV. DNA has already been purified and infection of plants with the virus is underway.

 



 
Student Author(s): 

Law, Pierra

Hanson, Ariel

Walker, Glenn

Home Institution:

Peace College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Joint Department of Biomedical

Engineering at UNC-Chapel Hill & North Carolina State University

Research Mentor(s)

Elizabeth Loboa/Biomedical Engineering

Title of Presentation:

Vaibility and Proliferation of Human Mesenchymal Stem Cells Seeded onto Poly-L-Lactic Acid (PLLA) Scaffolds in a 3D Flow Perfusion Microfluidic Chamber

 

 

Human mesenchymal stem cells (hMSCs) offer the ability to accommodate the need for tissue regeneration and replacement of cartilage, fat, tendon, muscle, and bone. Human mesenchymal stem cells can be promoted down an osteogenic (bone forming) pathway in response to either chemical and/or mechanical stimulation. Two mechanical methods for stimulating hMSCs down an osteogenic pathway are tensile strain and fluid shear stress. Fluid shear stress, as applied via flow perfusion in a three-dimensional culture environment, can be utilized both as a means of applying mechanical load to hMSCs seeded in porous scaffolds and for mass transport.  Proliferation and viability of the cells are influenced by a scaffold’s highly porous architecture, namely the porosity and pore size because of their effects on the availability of nutrients and waste disposal to and from the cells. In our lab, we are utilizing microfluidic technology as a high throughput screening tool to investigate the differential effects of scaffold porosity, pore size and shear stress on cell proliferation and viability. We hypothesize that fluid perfusion will allow cells to remain viable due to the even distribution of nutrients throughout the construct as well as induce proliferation in response to the fluid shear stress.  We have created a microfluidic perfusion bioreactor that incorporates a three-dimensional poly(L-lactic acid) scaffold into which cells are seeded  before being subjected to specific shear stresses. A programmable syringe pump is used to produce constant flow rates of 1.13 ul/hr and 226 ul/hr, inducing shear stresses of 0.05 dynes/cm2 and 10 dynes/cm2 to the hMSCs respectively, for forty-eight hours. A LIVE/DEAD® Viability/ Cytotoxicity Kit (L-3224) (Molecular Probes, Inc, Carlsbad, CA) is then used to evaluate the viability and proliferation of the cells in response to the shear stresses applied.

 


 

 
Student Author(s): 

McIlmoyle, Daniel W.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Chemical Engineering
Research Mentor(s)

Gregory N. Parsons/Chemical

Engineering
Joe C. Spagnola/Chemical Engineering
Title of Presentation:

Transportation and Alignment of

Multi-Walled Carbon Nanotubes

 

 

The objective of this research effort  is to evaluate several methods to transport and align multi-walled carbon nanotubes (MWNTs) onto various substrates, including glass, SiO2, and SiH.  These methods include microfluidics, dip-coating, and accelerated dip-coating.  Each method will be evaluated using an atomic force microscopy (AFM) and scanning electron microscopy (SEM) as well as optical microscopy.

               The MWNTs are dispersed in two solvents, isopropanol and de-ionized water with approximately 0.1 wt % sodium dodecyl sulfate (SDS) surfactant.  Each solution will then be sonicated to ensure uniform distribution of the nanotubes, forming a dispersion.

               In Microfluidics experiments a syringe pump is used to slowly draw the dispersions through a micron-scale channel molded out of Polydimethylsiloxane (PDMS), which can be reversibly sealed onto a substrate.  The high aspect ratio of the nanotubes should cause them to align parallel to the direction of flow, and adsorb on the surface with a small angular distribution.

               In dip-coating experiments, the substrate in submersed in the dispersion, and the nanotubes coat the substrate while the solvent evaporates.  Due to the nature of the liquid-substrate-air interface, the nanotubes should align perpendicular to the direction of flow.  A thin film of nanotubes forms over a long period of time, usually several hours to days.

               In accelerated dip-coating experiments, a small volume of the nanotube dispersion is slowly pulled across a substrate.  The nanotube dispersion is pipetted beneath a piece of glass placed at an angle of 35 degrees to the substrate.  As it moves at a constant speed across the substrate, the dispersion evaporates and nanotubes are uniformly deposited.

               Simple transport and alignment methods must be identified and refined before carbon nanotubes and their extraordinary electronic properties can be integrated into electronic devices.

 



 
Student Author(s): 

Merrell, Bonnie F.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biochemistry

Research Mentor(s)

Dennis Brown/Biochemistry

Raquel Hernandez/Biochemistry

Title of Presentation:

The Effect of Arginine Mutations in the Transmembrane/Endodomain Region of  the E2 Glycoprotein on Sindbis Virus Growth and Infectivity

 

 

Sindbis virus is an alphavirus that is capable of growth in the dissimilar biochemical environments of mammalian and insect cells.  The lipid bilayer of mammalian cells is thicker in comparison to the lipid bilayer of insect cells.  Since wild type Sindbis virus can grow in both environments, the thickness of the host cell’s lipid bilayer is irrelevant to the development of the virus.  This is significant because Sindbis virus is closely related to other viruses such as Yellow Fever and West Nile Virus, which pose a great health risks.  If a variation of Sindbis virus can be found which is able to grow in insect cells but not mammalian cells, this could lead to the development of vaccines for Sindbis and other related viruses.  In this experiment, two mutants of Sindbis virus were generated.  The first mutant, Arg1, consisted of a single Arginine deletion in the transmembrane region of the E2 protein.  The second mutant, Arg2, was a double Arginine deletion in the same region.  The objective of this project is to analyze the effects of deleting these amino acids on Sindbis virus growth and infectivity.  To characterize these mutants, mammalian cells and insect cells were transfected with the Arginine mutants.  A plaque assay was conducted on the virus harvested to determine its infectivity, or titer.  The infected cells were then radioactively labeled and an immunoprecipitation was performed to determine the viral protein profile.  When the Arginine mutants were grown in mammalian cells, the mutant virus grew to a lower titer in comparison to wild type virus.  Analysis of the proteins produced by these mutant viruses from BHK cells showed that the resulting virus contained all normal proteins.  This indicates that the decreased titer was not due to incorporation of other, aberrant, proteins, but most likely due to lower amounts of infectious virus being produced. 

 
 



 
Student Author(s): 

Morrow, Joseph M.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Mechanical and Aerospace Engineering

Research Mentor(s)

Stearns B. Heinzen/Mechanical and

Aerospace Engineering

Title of Presentation:

Aeroelastic Tailoring of a Forward-Swept Wing and Pressure Port Analysis

 

 

Modern aircraft are often designed with swept wings to improve high subsonic and supersonic performance.  Though aft swept wings are, by far, the most common planform design, it has been long recognized that forward swept wings yield many of the same benefits with the added advantage of increased aerodynamic efficiency.  The main drawback to these wings has been the potential for aerodynamic and structural instabilities at high angles.  This is most commonly manifested in the high loading at the wing tips which causes an unstable load case for the wing.  This load case has the potential to lead to flutter and structural failure.  Recently, the use of select composite materials has made it feasible to consider forward-sweep as a viable option if sufficient aeroelastic tailoring is used in the design process to overcome the wing tip divergence.  The purpose of this work is to aeroelastically tailor a forward-swept wing with a wing-loading ratio that exceeds 50:1.  Wind tunnel testing will be used to verify the aerodynamic computations of CMARC, and inviscid irrotational panel code, which outputs the pressure distribution used in the ANSYS structural finite element model.  Initial work will include the structural analysis of the forward-swept wing, verification of the CMARC pressure distribution, and a calibration to obtain the lift coefficient slope across the span of the wing using sets of two pressure ports located on the same vertical plane.  This research will facilitate more extensive future research by verifying the ANSYS and CMARC analysis through physical loading in the NCSU wind tunnel.  Future work could include more detailed wind tunnel testing, refining of the tailored structural design and flight testing of an aeroelastically tailored wing on an NCSU unmanned aerial flight vehicle.

 

 



 
Student Author(s): 

Nifong, Elisabeth

Smith, Arianna

O’Nan, Audrey

Cassady, Joe

Ashwell, Melissa

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Animal Science

Research Mentor(s)

Melissa Ashwell/Animal Science

Title of Presentation:

Effects of CLA on the Expression of Genes Involved in Apoptosis

 

 

Trans-10, cis-12-conjugated linoleic acid (t10c12-CLA) is a protein that has gained much attention in recent years, due to its potential delipidative abilities.  CLA may obtain its delipidative effects by increasing energy expenditure, apoptosis, fatty acid oxidation, and lipolysis.  In a previous study (House et al., Physiol. Genomics, v. 21, p. 351, 2005), oligo microarrays were used to investigate differential gene expression in epididymal fat tissue when CLA was fed to a line of obese mice.  On days 5 and 14, epididymal fat tissues were collected from 185 mice and RNA was extracted.  Results indicated that over 100 genes were differentially expressed in adipose tissue.  In particular, expression of the apoptosis gene, Bcl-2, was found to decrease when mice were fed CLA.  In this study real-time PCR is being used to verify these microarray findings. Real-time PCR primers were designed for Bcl-2 using Beacon Designer 4 software.  Amplification was optimized using the Bio-Rad iCycler and the iQ SYBR Green Supermix kit.  Bcl-2 expression levels are being evaluated in 38 tissue samples and will be normalized using beta-actin as the reference housekeeping gene.

 
 



 

Student Author(s): 

Park, Ji-Seon

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biochemistry

Research Mentor(s)

Robert B. Rose/Biochemistry

Title of Presentation:

The Use of DCoH/HNF-1 Fusion Protein as a Tool to Analyze the Activities of a Bifunctional Protein DCoH

 

 

DCoH (dimerization cofactor of HNF-1) is a bifunctional protein which functions as a metabolic enzyme in the cytoplasm and a transcriptional coactivator in the nucleus.  In the nucleus, DCoH interacts with the transcription factor HNF-1 and stabilizes HNF-1 dimers. Significantly, the mutations in HNF-1-alpha (hepatocyte nuclear factor-1-alpha) are the most common causing factor of Maturity-onset diabetes of the young (MODY). We have generated a DCoH/HNF-1 fusion protein to determine: 1) whether the two functions of DCoH are independent and 2) how DCoH increases the transcriptional activity of HNF-1. The fusion protein of DCoH and HNF-1 was produced by Polymerase Chain Reaction (PCR) using a primer overlap strategy. The DCoH/HNF-1 fusion protein will be tested for enzymatic activity in order to test whether formation of the interaction with HNF-1 might regulate the enzymatic activity of DCoH. One study has concluded that DCoH does not lose its enzymatic activity when it is bound to HNF-1. However, this study did not determine whether the CoH/HNF-1 complex was stable throughout the study. Structural studies of the DCoH/HNF-1-alpha complex indicate an active site residue of DCoH, which is necessary to perform enzymatic activity of DCoH, is involved with interaction with HNF-1, suggesting the DCoH/HNF-1 complex should be enzymatically inactive. The fusion protein will prevent dissociation of the complex during enzymatic measurements. The fusion protein will also allow us to test the effect of DCoH on transcriptional activity of HNF-1. In future, we will analyze the transcriptional activity of the fusion protein. Our current hypothesis is that DCoH increases the half-life of HNF-1, therefore enhancing transcriptional activity of HNF-1.    

              

 


 

 
Student Author(s): 

Ribeill, Guilhem J.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Physical and Mathematical Sciences
Research Mentor(s)
Keith Weninger/Physics
Title of Presentation:

Quantitative Analysis of Non-specific

Protein Adsorption on PEGylated Glass and Nanocrystalline Diamond Film

Surfaces

 

 

Protein adsorption by materials is a crucial factor in determining the biocompatibility of materials. Qualitative studies have shown that polyethylene glycol (PEG) coated glass surfaces as well as CVD nanocrystalline diamond films are resistant to adsorption. The aim of this study is to quantify non-specific protein adsorption on these surfaces through fluorescence microscopy. Quartz surfaces silated with 3-aminopropyl triethoxysilane and 3-mercaptopropyl trimethoxysilane were then coated with a self-assembled monolayer of mPEG-succinimidyl propionate and mPEG-maleimide, respectively. Some of the surfaces also had 1% of their mPEG molecules terminated with biotin. The CVD diamond film was tested in both hydrogen-terminated and oxidized (through a nitric acid etch) forms. The PEG surfaces as well as the diamond film were then coated with varying concentrations of Cy3 labeled streptavidin protein and Cy5 labeled straptavidin protein. A fluorescence microscope was then used to quantify the amount of protein adsorption on the surface by counting the number of immobilized fluorophores found at various sample areas on the surfaces. These were then compared to the amount of adsorption on unprepared quartz surfaces as a control. It is hoped that this data will allow a precise determination to be made of the biocompatibility of PEGylated and CVD diamond film surfaces to be made, as they are promising candidates for the creation of biologically inert medical implants and for other applications which require low protein adsorption.

 


 

 

Student Author(s): 

Scott, Kimberly

Home Institution:

NC Wesleyan College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Statistics, Biostatistics

Research Mentor(s)

Pam Arroway/Statistics

Title of Presentation:

Health Characteristics Associated with

Ischemic Heart Events

 

 

Aspirin is known to lower the risk of death and myocardial infarction (MI) in patients suffering from acute coronary syndromes (ACS).  Sibrafibin, along with other intravenous glycoprotein 11b/111a receptor antagonists, also reduces the rates of ischemic events in patients suffering from ACS.  However, the long term effectiveness of such receptors has not been recognized.  Sibrafibin, a so-called “super aspirin” drug was the main focus of the Sibrafiban Versus Aspirin to Yield Maximum Protection from Ischemic Heart Events Post Acute Coronary Syndromes (SYMPHONY) study.  This randomized study was designed to determine if sibrafibin is more effective than traditional aspirin in treating patients suffering from acute coronary syndromes.  An analysis of health characteristics associated with death or myocardial infarction within 90 days will be presented.  This data was analyzed by a group of three undergraduate students.

 




 
Student Author(s): 

Shrestha, Ritu

Home Institution:
Salem College
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Chemistry
Research Mentor(s)

Jonathan S. Lindsey/Chemistry

Masahiko Taniguchi/Chemistry

Title of Presentation:

Probing the Formation of Peptides Under

Primordial Earth Conditions

 

 

The chemical evolution of bioorganic compounds on earth prior to the origin of life remains an unsolved problem in chemical and evolutionary sciences. In this study, a series of experiments was carried out to understand the mechanism of peptide formation under primordial conditions. A wide variety of amino acids were treated under diverse conditions (pH, temperature, time and concentration of amino acids) with condensing reagents assumed to be present under prebiotic conditions. Mineral additives (e.g., clay, metal oxides) were also used to facilitate peptide formation. Peptide formation was analyzed by using 1H and 13C NMR spectroscopy, HPLC and mass spectrometry. The results provide insights concerning possible pathways for the formation of biopolymers, which led to the origin of life on early earth.

 



 
Student Author(s): 

Sommerville, Elizabeth R.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biochemistry

Research Mentor(s)

Clay Clark/Biochemistry

Title of Presentation:

Contributions of the Salt Bridge Between Lysine-242 and Glutamate-246 to Stability of Procaspase-3

 

   

Caspases are cysteinyl proteases that are members of a protease family involved in apoptosis (programmed cell death) and the inflammatory response.  Caspases exist in normal cells as zymogens (quiescent precursors to proteins), and are activated through a protolytic cascade when the apoptotic pathways are initiated.  The final commitment step to apoptosis is activation of procaspase-3. Previous studies have demonstrated that a salt bridge between lysine 242 and glutamate 246 in loop L4 of (pro)caspase-3 is vital for the fidelity of the enzyme.  The following study focuses on two mutants of an inactive procaspase-3 model, procaspase-3 (C163S,E246A) and procaspase-3 (C163S,K242A). 

               Mutants were made via site directed mutagenesis using Deep Vent polymerase. Glu246 and Lys242 were mutated to alanine residues, thus prohibiting their interaction. Equilibrium studies were done using varying urea concentrations from zero to nine molar. To study the folding process, fluorescence emission data and circular dichroism spectra were obtained at multiple protein concentrations.  The data will be fit to a folding model to determine how the conformational free energy differs from that of wild-type procaspase-3.  The results will be used to help correlate how this salt bridge contributes to the stability and folding procaspase-3.  Procaspase-3 mutants could be used as a novel therapeutic approach to treating cancer and inflammation.

 



 
Student Author(s): 

Tingen, Andrew S.

Home Institution:
North Carolina State University
Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):
Electrical and Computer Engineering
Research Mentor(s)
Wenye Wang/Electrical and Computer Engineering
Title of Presentation:

Securing Mobile Wireless Networks

 

 

This research is aimed at creating and securing mobile, infrastructureless wireless networks.  There are many advantages of this type of wireless network over a traditional network; they can be set up instantly, without having to establish any access points or base stations, and they can be moved effortlessly, simply by moving the nodes around.   The main goal of this research is to examine a method of securing mobile ad-hoc networks (MANETs) using Secure Ad-Hoc On-demand Distance Vector (Secure AODV) routing protocol.  We examine the installation methods on various devices, primarily Red Hat Linux 9, kernel 2.4.20, on the x86 architecture.  We also analyze the performance and security of the protocol under various conditions and situations.

 




 
Student Author(s): 

Vadlamudi, Charita

Home Institution:

Salem College

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Biomedical Engineering

Research Mentor(s)

Peter L. Mente/Biomedical Engineering

Title of Presentation:

Effect of Mechanical Damage on Apoptosis

in Porcine Patellar Cartilage

 

 

Osteoarthritis is characterized by a significant deterioration in articular cartilage covering a synovial joint.  It is believed that mechanical damage to cartilage is a key factor in the development of osteoarthritis.  This study intends to determine if indeed, mechanical damage induces apoptosis (programmed cell death).  We hypothesize that there would be significantly higher numbers of apoptotic cells in impacted patellae and also that there are significantly greater numbers of apoptotic cells tissue that was cultured for 0 days than in tissue cultured for 14 days.  Porcine patellae were used in this study for their convenient size and structure.  A high impact load of 2000 N was applied to patellae that were then cultured for 0 or 14 days.  Controls for this study were un-impacted patellae that were 0 or 14 days in culture.  TUNEL staining using Apotag detection kit of tissues from the impacted and non-impacted patellae resulted in staining of apoptotic cells.  The apoptotic cells were counted using Meta Morph and analyzed for significant differences in apoptotic cells between control and impacted tissues.  The average percent of apoptotic cells for the control tissue cultured for 0 and 14 days was 1.2% and 0.42% respectively.  The average percent of apoptotic cells for the high impacted tissue cultured for 0 and 14 days was 1.8% and 12.5% respectively.  There is a significant difference in the number of apoptotic cells between tissue that was un-impacted and tissue that was impacted with a high load.

 
 



 
 
Student Author(s): 

Whited, Rachel M.

Home Institution:

North Carolina State University

Program:

HHMI Science Exploration and the

Science House & Biology Outreach

Department(s):

Molecular and Structural Biochemistry

Research Mentor(s)

Paul Wollenzien/Molecular and Structural Biochemistry

Tatjana Shapkina/Molecular and Structural Biochemistry

Title of Presentation:

Structural Analysis of the 16S Ribosomal RNA

in the Escherichia coli 30S Subunit

 

 

The 30S ribosomal subunit of the bacterial ribosome carries out the functions of messenger RNA (mRNA) binding and is also largely responsible for transfer RNA (tRNA) binding and movement.  It is likely that the 30S subunit undergoes different types of conformational changes during its function, but the determination of these is experimentally difficult.  The patterns of 4-thiouridine-induced cross-linking in 16S ribosomal RNA (rRNA) should reveal structural changes in the 16S rRNA in the E. coli 30S subunit.  An E. coli strain deficient in pyrimidine synthesis has been used to incorporate 4-thiouridine during normal synthesis and assembly of ribosomes.  However, 4-thiouridine strongly inhibits cell growth in this strain, so concentrations of uridine and 4-thiouridine were found to obtain maximum cell growth.  UVA irradiations of 4-thiouridine-containing ribosomes were used to create cross-links at different temperatures to determine the conformational response to temperature.  The frequency of the formation of these cross-links was determined by gel electrophoresis.  This provides a measure of the intrinsic conformational flexibility in the 30S subunit.  This flexibility may be linked to the conformational changes that occur during protein synthesis.

 

 

 

 

 

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